Liang Z, Xue Z, Rajaraman S, Antani SK. Automated quantification of SARS-CoV-2 pneumonia with large vision model knowledge adaptation. New Microbes and New Infections, Volume 62, 2024, 101457, ISSN 2052-2975, https://doi.org/10.1016/j.nmni.2024.101457.
Liang Z, Xue Z, Rajaraman S, Antani S. Automated quantification of SARS-CoV-2 pneumonia with large vision model knowledge adaptation. New Microbes and New Infections. New Microbes and New Infections, Volume 62, 2024, 101457, ISSN 2052-2975, https://doi.org/10.1016/j.nmni.2024.101457.
Mayer CS, Fontelo P. Semaglutide use in people with obesity and type 2 diabetes from real-world utilization data: An analysis of the All of US Program. Diabetes Obes Metab. 2024 Sep 9. doi: 10.1111/dom.15911. Online ahead of print. PMID: 39248157.
Rajaraman S, Xue Z, Antani S. Editorial on Special Issue “Artificial Intelligence in Image-Based Screening, Diagnostics, and Clinical Care”. Diagnostics. 2024; 14(17):1984. https://doi.org/10.3390/diagnostics14171984.
Rajaraman S, Liang Z, Xue Z, Antani S. Noise-Induced Modality-Specific Pretext Learning for Pediatric Chest X-ray Image Classification. Frontiers in Artificial Intelligence, vol. 7, 2024, doi: 10.3389/frai.2024.1419638, ISSN: 2624-8212.
Rajaraman S, Zamzmi G, Yang F, Liang Z, Xue Z, Antani SK. Semantically redundant training data removal and deep model classification performance: A study with chest X-rays. Computerized Medical Imaging and Graphics. Volume 115, 2024, 102379, ISSN 0895-6111, https://doi.org/10.1016/j.compmedimag.2024.102379.
Angara S, Kim J. Deep Ensemble Learning for Classification of Glaucoma from Smartphon Fundus Images. IEEE-CBMS 2024, pp. 412-417, Guadalajara, Mexico, June 2024. DOI Bookmark: 10.1109/CBMS61543.2024.00074.
Mayer CS, Fontelo P. Alcohol consumption and its correlation with medical conditions: a UK Biobank study. Front Public Health. 2024 May 22;12:1294492. doi: 10.3389/fpubh.2024.1294492. eCollection 2024.PMID: 38841662 Free PMC article.
Liang Z, Xue Z, Rajaraman S, Antani SK. Covid-19 Pneumonia Chest X-Ray Pattern Synthesis by Stable Diffusion. 2024 IEEE Southwest Symposium on Image Analysis and Interpretation (SSIAI), Santa Fe, NM, USA, 2024, pp. 21-24, doi: 10.1109/SSIAI59505.2024.10508671.
Williams N. Modifiable Areal Unit Problems for Infectious Disease Cases Described in Medicare and Medicaid Claims, 2016-2019. 10.21203/rs.3.rs-4004950/v2.
Rajaraman S, Zamzmi G, Yang F, Liang Z, Xue Z, Antani SK. Uncovering the effects of model initialization on deep model generalization: A study with adult and pediatric chest X-ray images. PLOS Digital Health 3(1): e0000286. https://doi.org/10.1371/journal.pdig.0000286.
Liang Z, Xue Z, Feng Y, Rajaraman S, Huang JX, Antani SK. Emergency Department Wait Time Forecast based on Semantic and Time Series Patterns in COVID-19 Pandemic. 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Istanbul, Turkiye, 2023, pp. 3067-3072, doi: 10.1109/BIBM58861.2023.10385758.
Mahmoodi E, Xue Z, Rajaraman S, Antani SK. A Study on Reducing Big Data Image Annotation Burden Through Iterative Expert-In-The-Loop Strategy. 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Istanbul, Turkiye, 2023, pp. 3097-3102, doi: 10.1109/BIBM58861.2023.10385356.
Gartrell K, Warren JI, Fontelo P. PubMed4Hh: A Point-of-Care Mobile App for Evidence-Based Clinical Decision Support for Nurse Residents in Maryland. Comput Inform Nurs. 2023 Dec 1;41(12):983-992. doi: 10.1097/CIN.0000000000001063.PMID: 38062547.
Manzo G, Celi LA, Shabazz Y, Mulcahey R, Flores JL, Demner-Fushman D. Caregivers Attitude Detection From Clinical Notes. American Medical Informatics Association (AMIA), Nov 2023.
Rajaraman S, Yang F, Zamzmi G, Xue Z, Antani S. Can deep adult lung segmentation models generalize to the pediatric population? Expert Systems with Applications, Volume 229, Part A, 2023, 120531, ISSN 0957-4174, https://doi.org/10.1016/j.eswa.2023.120531.
Williams N. Covid-19, Diagnostic History and Mortality from Medicare 1999-2021, In an All-Cause Mortality Approach. Archives of Internal Medicine Research. 6 (2023):74-85.
Fung KW, Baye F, Baik SH, McDonald CJ . Nirmatrelvir and Molnupiravir and Post–COVID-19 Condition in Older Patients. JAMA Internal Medicine. https://doi.org/10.1001/JAMAINTERNMED.2023.5099.
Liang Z, Xue Z, Rajaraman S, Feng Y, Antani SK. Automatic Quantification of COVID-19 Pulmonary Edema by Self-supervised Contrastive Learning. In: Xue Z, et al. Medical Image Learning with Limited and Noisy Data. MILLanD 2023. Lecture Notes in Computer Science, vol 14307. Springer, Cham. https://doi.org/10.1007/978-3-031-44917-8_12.
Janakiram C, Okunev I, Tranby EP, Fontelo P, Iafolla TJ, Dye BA. Opioids for acute and chronic pain when receiving psychiatric medications. PLoS One. 2023 Sep 26;18(9):e0286179. doi: 10.1371/journal.pone.0286179. eCollection 2023.PMID: 37751410 Free PMC article.
Zamzmi G, Hsu LY, Rajaraman S, Li W, Sachdev V, Antani S. Evaluation of an artificial intelligence-based system for echocardiographic estimation of right atrial pressure. Int J Cardiovasc Imaging. 2023 Sep 8. doi: 10.1007/s10554-023-02941-8. Epub ahead of print. PMID: 37682418.
Cheng, C, Weiss JC. Typed Markers and Context for Clinical Temporal Relation Extraction. To appear in the Conference on Machine Learning for Health, Proceedings of Machine Learning Research (PMLR), 2023.
Zolnour A, Eldredge CE, Faiola A, Yaghoobzadeh Y, Khani M, Foy D, Topaz M, Kharrazi H, Fung KW, Fontelo P, Davoudi A, Tabaie A, Breitinger SA, Oesterle TS, Rouhizadeh M, Zonnor Z, Moen H, Patrick TB, Zolnoori M. Front . A risk identification model for detection of patients at risk of antidepressant discontinuation. Artif Intell. 2023 Aug 24;6:1229609. doi: 10.3389/frai.2023.1229609. eCollection 2023.PMID: 37693012 Free PMC article.
Bui VCB, Yaniv Z, Harris M, Yang F, Kantipudi K, Hurt D, Rosenthal A, Jaeger S. Combining Radiological and Genomic TB Portals Data for Drug Resistance Analysis. IEEE Access. 2023;11:84228-84240. doi: 10.1109/access.2023.3298750. Epub 2023 Jul 25. PMID: 37663145; PMCID: PMC10473876.
Kim J, Tran L. Ensemble Convolutional Neural Networks for the Classification and Visualization of Retinal Diseases in Optical Coherence Tomography Images. IEEE-CBMS 2023, pp. 123-28, L'Aquila, Italy, June 2023.
Williams N. Building the observational medical outcomes partnership's T-MSIS Analytic File common data model. Inform Med Unlocked. 2023;39:101259. doi: 10.1016/j.imu.2023.101259. Epub 2023 May 5. PMID: 37305615; PMCID: PMC10249773.
Le D, Mork J. Check Tags MeSH Terms Indexing Research Project. A report to the Applied Clinical Informatics Branch.
Williams N. Too sick for surveillance: Can federal HIV service data improve federal HIV surveillance efforts? arXiv preprint arXiv:2304.10023 (2023).
Oguguo T, Zamzmi G, Rajaraman S, Yang F, Xue Z, Antani S. A Comparative Study of Fairness in Medical Machine Learning. 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI), Cartagena, Colombia, 2023, pp. 1-5, doi: 10.1109/ISBI53787.2023.10230368.
Fung KW, Baye F, Baik SH, Zheng Z, McDonald CJ . Prevalence and characteristics of long COVID in elderly patients: An observational cohort study of over 2 million adults in the US. PLoS Medicine, 20(4). https://doi.org/10.1371/JOURNAL.PMED.1004194.
Ondov B, Samet H. An efficient region expansion algorithm for regular triangulated meshes. Pattern Recognition Letters, Volume 168, 2023, Pages 1-7, ISSN 0167-8655, https://doi.org/10.1016/j.patrec.2023.02.014.
Xue Z, Yang F, Rajaraman S, Zamzmi G, Antani S. Cross Dataset Analysis of Domain Shift in CXR Lung Region Detection. Diagnostics. 2023; 13(6):1068. https://doi.org/10.3390/diagnostics13061068.
Bonilla H, Peluso MJ, Rodgers K, Aberg JA, Patterson TF, Tamburro R, Baizer L, Goldman JD, Rouphael N, Deitchman A, Fine J, Fontelo P, Kim AY, Shaw G, Stratford J, Ceger P, Costantine MM, Fisher L, O'Brien L, Maughan C, Quigley JG, Gabbay V, Mohandas S, Williams D, McComsey GA. Therapeutic trials for long COVID-19: A call to action from the interventions taskforce of the RECOVER initiative. Front Immunol. 2023 Mar 9;14:1129459. doi: 10.3389/fimmu.2023.1129459. eCollection 2023.PMID: 36969241 Free PMC.
Karki M, Kantipudi K, Haghighi B, Bui V, Yang F,Yu H, Harris M, Kassim YM, Hurt DE, Rosenthal A, Yaniv Z, Jaeger S. Training Data for Machine Learning to Enhance Patient-Centered Outcomes Research (PCOR) Data Infrastructure — A Case Study in Tuberculosis Drug Resistance.
Yang F, Zamzmi G, Angara S, Rajaraman S, Aquilina A, Xue Z, Jaeger S, Papagiannakis E, Antani SK. Assessing Inter-Annotator Agreement for Medical Image Segmentation. IEEE Access, doi: 10.1109/ACCESS.2023.3249759.
Ahmed SR, Befano B, Lemay A, Egemen D, Rodriguez AC, Angara S, Desai K, Jeronimo J, Antani S, Campos N, Inturrisi F, Perkins R, Kreimer A, Wentzensen N, Herrero R, Del Pino M, Quint W, de Sanjose S, Schiffman M, Kalpathy-Cramer J. Reproducible and Clinically Translatable Deep Neural Networks for Cancer Screening. Res Sq. 2023 Mar 3;. doi: 10.21203/rs.3.rs-2526701/v1. PubMed PMID: 36909463; PubMed Central PMCID: PMC10002800.
Williams N. Prehospital Cardiac Arrest should be considered when evaluating Covid-19 mortality in the United States. Methods Inf Med. 2023 Jan 18. doi: 10.1055/a-2015-1244. Epub ahead of print. PMID: 36652957.
Rajaraman S, Yang F, Zamzmi G, Xue Z, Antani SK. Assessing the Impact of Image Resolution on Deep Learning for TB Lesion Segmentation on Frontal Chest X-rays. Diagnostics. 2023; 13(4):747. https://doi.org/10.3390/diagnostics13040747.
Yu H, Mohammed FO, Hamid MA, Yang F, Kassim YM, Mohamed AO, Maude RJ, Ding XC, Owusu ED, Yerlikaya S, Dittrich S, Jaeger S . Patient-level performance evaluation of a smartphone-based malaria diagnostic application. Malar J 22, 33 (2023). https://doi.org/10.1186/s12936-023-04446-0.
Rajaraman S, Zamzmi G, Yang F, Xue Z, Antani SK. Data Characterization for Reliable AI in Medicine. Recent Trends Image Process Pattern Recogn (2022). 2023;1704:3-11. doi: 10.1007/978-3-031-23599-3_1. Epub 2023 Jan 11. PMID: 36780238; PMCID: PMC9912175.
Attal K, Ondov B, Demner-Fushman D. A dataset for plain language adaptation of biomedical abstracts. Scientific Data. 2023;10(1):8.
Sorbello A, Haque S, Hasan R, Jermyn R, Hussein A, Vega A, Zembrzuski K, Ripple A, Ahadpour M. Artificial Intelligence–Enabled Software Prototype to Inform Opioid Pharmacovigilance From Electronic Health Records: Development and Usability Study. JMIR AI 2023;2:e45000 URL: https://ai.jmir.org/2023/1/e45000 DOI: 10.2196/45000.
Liang Z, Huang JX, Antani SK. Image Translation by Ad CycleGAN for COVID-19 X-Ray Images: A New Approach for Controllable GAN. Sensors (Basel). 2022 Dec 8;22(24):9628. DOI: 10.3390/s22249628.
Williams N. Considering non-hospital data in clinical informatics use cases, a review of the National Emergency Medical Services Information System (NEMSIS). Inform Med Unlocked. 2022;35:101129. doi: 10.1016/j.imu.2022.101129. Epub 2022 Nov 9. PMID: 36532947; PMCID: PMC9757756.
McDonald CJ, Baik SH, Zheng Z, Amos L, Luan X, Marsolo K, Qualls L. Mis-mappings between a producer’s quantitative test codes and LOINC codes and an algorithm for correcting them. Journal of the American Medical Informatics Association, 2022;, ocac215, https://doi.org/10.1093/jamia/ocac215.
Lu CJ, Payne A, Mork J. Enhancing The SPECIALIST Lexicon with WordNet. AMIA 2022 Annual Symposium, Nov. 5-9, 2022.
Rajaraman S, Antani SK. Editorial on Special Issue “Artificial Intelligence in Image-Based Screening, Diagnostics, and Clinical Care of Cardiopulmonary Diseases”. Diagnostics. 2022; 12(11):2615. https://doi.org/10.3390/diagnostics12112615.
Chen Q, Wang L, Guo S, Xia H, Yang F, Zhu Y. Glioma grade prediction using a cross-fusion network based on unsegmented multi-sequence magnetic resonance images. 2022 16th IEEE International Conference on Signal Processing (ICSP), 2022, pp. 447-451. doi: 10.1109/ICSP56322.2022.9965327. (Best paper award)
He Y, Wang L, Yang F, Clarysse P, Robini M, Zhu Y. Effect of different configurations of diffusion gradient direction on accuracy of diffusion tensor estimation in cardiac DTI. 2022 16th IEEE International Conference on Signal Processing (ICSP), 2022, pp. 437-441. (Best paper award)
Santosh K, Allu S, Rajaraman S, Antani SK. Advances in Deep Learning for Tuberculosis Screening using Chest X-rays: The Last 5 Years Review. J Med Syst 46, 82 (2022). https://doi.org/10.1007/s10916-022-01870-8.
Ondov B, Attal K, Demner-Fushman D. A survey of automated methods for biomedical text simplification. J Am Med Inform Assoc. 2022 Oct 7;29(11):1976-1988. doi: 10.1093/jamia/ocac149. PMID: 36083212.
Xue Z, Angara S, Guo P, Rajaraman S, Jeronimo J, Rodriguez AC, Alfaro K, Charoenkwan K, Mungo C, Fokom‐Domgue J, Wentzensen N, Desai K, Ajenifuja K, Wikström E, Befano BS, Antani S. Image Quality Classification for Automated Visual Evaluation of Cervical Precancer. Zamzmi, G., Antani, S., Bagci, U., Linguraru, M.G., Rajaraman, S., Xue, Z. (eds) Medical Image Learning with Limited and Noisy Data. MILLanD 2022. Lecture Notes in Computer Science, vol 13559. Springer, Cham. https://doi.org/10.1007/978-3-031-16760-7_20.
Rajaraman S, Yang F, Zamzmi G, Xue Z, Antani SK. A Systematic Evaluation of Ensemble Learning Methods for Fine-Grained Semantic Segmentation of Tuberculosis-Consistent Lesions in Chest Radiographs. Bioengineering. 2022; 9(9):413. https://doi.org/10.3390/bioengineering9090413.
Zamzmi G, Rajaraman S, Hsu LY, Sachdev V, Antani S. Real-time echocardiography image analysis and quantification of cardiac indices. Med Image Anal. 2022 Aug;80:102438. doi: 10.1016/j.media.2022.102438. Epub 2022 Jun 9. PMID: 35868819; PMCID: PMC9310146.
Xue Z, Yu K, Pearlman PC, Chen TC, Hua CH, Kang CJ, Chien CY, Tsai MH, Wang CP, Chaturvedi AK, Antani S. Extraction of Ruler Markings For Estimating Physical Size of Oral Lesions. 2022 26th International Conference on Pattern Recognition (ICPR), Montreal, QC, Canada, 2022 pp. 4241-4247. doi: 10.1109/ICPR56361.2022.9956251.
Kim J, Tran L, Peto T, Chew EY, HN. Deep Learning and Ensemble Method for Optic Disc and Cup Segmentation. IEEE CIBCB 2022, August 15-17, 2022. https://doi.org/10.1109/CIBCB55180.2022.9863022.
Yang F, Lu PX, Deng M, Wáng YXJ, Rajaraman S, Xue Z, Folio LR, Antani SK, Jaeger S. Annotations of Lung Abnormalities in the Shenzhen Chest X-ray Dataset for Computer-Aided Screening of Pulmonary Diseases. Data 2022, 7, 95. https://doi.org/10.3390/data7070095.
Young L, Kim J, Yakin M, Lin H, Dao D, Kodati S, Sharma S, Lee A, Lee C, Sen, HN. Automated Detection of Vascular Leakage in Fluorescein Angiography – A Proof of Concept. TVST, 2022, Vol. 11, No. 7, Article 19; https://tvst.arvojournals.org/article.aspx?articleid=2783507.
Xue Z, Yu K, Pearlman PC, Pal A, Chen TC, Hua CH, Kang CJ, Chien CY, Tsai MH, Wang CP, Chaturvedi AK, Antani S. Automatic Detection of Oral Lesion Measurement Ruler Toward Computer-Aided Image-Based Oral Cancer Screening. Annu Int Conf IEEE Eng Med Biol Soc. 2022 Jul;2022:3218-3221. doi: 10.1109/EMBC48229.2022.9871610.
Rajaraman S, Guo P, Xue Z, Antani SK. A Deep Modality-Specific Ensemble for Improving Pneumonia Detection in Chest X-rays. Diagnostics (Basel). 2022 Jun 11;12(6). doi: 10.3390/diagnostics12061442. PubMed PMID: 35741252; PubMed Central PMCID: PMC9221627.
Rajaraman S, Zamzmi G, Yang F, Xue Z, Jaeger S, Antani SK. Uncertainty Quantification in Segmenting Tuberculosis-Consistent Findings in Frontal Chest X-rays. Biomedicines 2022, 10, 1323. https://doi.org/10.3390/biomedicines10061323.
Liang Z, Huang JX. Emergency Department Wait Time Prediction based on Cyclical Features by Deep Neural Networks. AMIA 2022 Clinical Informatics Conference. 2022, May 24-26, Houston, USA, Poster.
Liang Z, Huang JX. CycleGAN with Dynamic Criterion for Malaria Blood Cell Image Synthetization. AMIA 2022 Informatics Summit. 2022, Mar 21-24, Chicago. USA.
Angara S, Guo P, Xue Z, Antani S. An Empirical Study of Vision Transformers for Cervical Precancer Detection. In: Santosh, K., Hegadi, R., Pal, U. (eds) Recent Trends in Image Processing and Pattern Recognition. RTIP2R 2021. Communications in Computer and Information Science, vol 1576. Springer, Cham. https://doi.org/10.1007/978-3-031-07005-1_3.
Guo P, Xue Z, Angara S, Antani SK . Unsupervised Deep Learning Registration of Uterine Cervix Sequence Images. Cancers, 14(10), 2401. https://doi.org/10.3390/cancers14102401.
Kim J, Tran L, Peto T, Chew EY. Identifying Those at Risk of Glaucoma: A Deep Learning Approach for Optic Disc and Cup Segmentation and Their Boundary Analysis. Diagnostics 2022, 12(5), 1063; https://doi.org/10.3390/diagnostics12051063.
Fung KW, Baik SH, Baye F, Zheng Z, Huser V, McDonald CJ. Effect of common maintenance drugs on the risk and severity of COVID-19 in elderly patients. PLoS ONE 17(4): e0266922. https://doi.org/10.1371/journal.pone.0266922.
London SD, Chamut S, Fontelo P, Iafolla T, Dye BA. Assessment of the Quality of Current American Dental Association Clinical Practice Guidelines. JDR Clin Trans Res. 2022 Apr 2:23800844221083563. doi: 10.1177/23800844221083563.
Wijesiriwardene T, Nguyen V, Bajaj GK, Yip HY, Javangula V, Mao Y, Fung KW, Sheth A, Parthasarathy S, Bodenreider O. UBERT: A Novel Language Model for Synonymy Prediction at Scale in the UMLS Metathesaurus. arXiv:2204.12716 https://doi.org/10.48550/arXiv.2204.12716.
Rajaraman S, Cohen G, Spear L, Folio L, Antani S. DeBoNet: A deep bone suppression model ensemble to improve disease detection in chest radiographs. PLOS ONE 17(3): e0265691. https://doi.org/10.1371/journal.pone.0265691
Pal A, Xue Z, Antani S. Deep Cervix Model Development from Heterogeneous and Partially Labeled Image Datasets. 7th INTERNATIONAL CONFERENCE ON EMERGING APPLICATIONS OF INFORMATION TECHNOLOGY (EAIT 2022), Kolkata, India, March 30-31, 2022.
Levitz D, Angara S, Jeronimo J., Rodriguez AC, Sanjose S, Antani S, Schiffman MW. "A survey of image quality defects and their effect on the performance of an automated visual evaluation classifier". Proc. SPIE PC11950, Optics and Biophotonics in Low-Resource Settings VIII, PC1195003 (7 March 2022); https://doi.org/10.1117/12.2610213.
Rajaraman S, Zamzmi G, Folio LR, Antani S. Detecting Tuberculosis-Consistent Findings in Lateral Chest X-Rays Using an Ensemble of CNNs and Vision Transformers. Front Genet. 2022;13:864724. doi: 10.3389/fgene.2022.864724. eCollection 2022. PubMed PMID: 35281798; PubMed Central PMCID: PMC8907925.
Xue Z, Pearlman PC, Yu K, Pal A, Chen TC, Hua CH, Kang CJ, Chien CY, Tsai MH, Wang CP, Chaturvedi AK, Antani S. Oral Cavity Anatomical Site Image Classification and Analysis. Proceedings of SPIE Medical Imaging 2022.
Oguguo T, Zamzmi G, Rajaraman S, Antani S. Open-world active learning for echocardiography view classification. SPIE Medical Imaging, (February 2022).
Wang L, Hong Y, Qin YB, Cheng XY, Yang F, Yang J, Zhu YM. Connecting macroscopic diffusion metrics of cardiac diffusion tensor imaging and microscopic myocardial structures based on simulation. Med Image Anal. 2022 Apr;77:102325. doi: 10.1016/j.media.2021.102325. Epub 2022 Feb 5.
Rajaraman S, Ganesan P, Antani S. Deep learning model calibration for improving performance in class-imbalanced medical image classification tasks. PLoS ONE 17(1): e0262838. https://doi.org/10.1371/journal.pone.0262838.
Xue Z, Angara S, Levitz D, Antani S. Analysis of Digital Noise And Reduction Methods On Classifiers Used In Automated Visual Evaluation In Cervical Cancer Screening. Proceedings of SPIE Photonics West 2022.
Karki M, Kantipudi K, Yang F, Yu H, Wang xY, Yaniv Z, Jaeger S. Generalization Challenges in Drug-Resistant Tuberculosis Detection from Chest X-rays. Diagnostics (Basel). 2022 Jan 13;12(1):188. doi: 10.3390/diagnostics12010188. PMID: 35054355; PMCID: PMC8775073.
Rajaraman S, Zamzmi G, Antani SK. Novel loss functions for ensemble-based medical image classification. PLoS ONE 16(12): e0261307.
Xie B, Zhu Y, Niu P, Su T, Yang F, Wang L, Rodesch PA, Boussel L, Douek P, Duvauchelle P. Super-Energy-Resolution Material Decomposition for Spectral Photon-Counting CT Using Pixel-Wise Learning. IEEE Access, vol. 9, pp. 168485-168495, 2021, doi: 10.1109/ACCESS.2021.3134636.
Xue Z, Guo P, Angara S, Pal A, Jeronimo J, Dasai KT, Ajenifuja KO, Adepiti CA, Schiffman M, Antani S. Cleaning Highly Unbalanced Multisource Image Dataset for Quality Control in Cervical Precancer Screening. Proceedings of the 4th International Conference on Recent Trends in Image Processing & Pattern Recognition (RTIP2R) 2021.
London SD, Fontelo P, Boroumand S, Dye BA. COVID-19 provides an opportunity for integration of dentistry into the health informatics system. J Am Dent Assoc. 2022 Jan;153(1):3-8. doi: 10.1016/j.adaj.2021.11.003. Epub 2021 Nov 18.PMID: 34996533 Free PMC article. No abstract available.
London SD, Fontelo P, Boroumand S, Dye BA. COVID-19 provides an opportunity for integration of dentistry into the health informatics system. J Am Dent Assoc. 2022 Jan;153(1):3-8. doi: 10.1016/j.adaj.2021.11.003. Epub 2021 Nov 18.
Pal A, Xue Z, Desai K, Banjo AAF, Adepiti CA, Long LR, Schiffman M, Antani S. Deep Multiple-Instance Learning for Abnormal Cell Detection in Cervical Histopathology Images. Computer in Biology and Medicine, 2021, vol. 138.
Karki M, Kantipudi K, Yu H, Yang F, Kassim Y, Yaniv Z,Jaeger S. Identifying Drug-Resistant Tuberculosis in Chest Radiographs: Evaluation of CNN Architectures and Training Strategies. 43rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, accepted on July 15th, 2021, will be held virtually October 31 – November 4, 2021.
Lu CJ, Payne A, Mork J. Identifying Criteria for Antonym Generation from Corpora. AMIA 2021 Annual Symposium, Oct. 30 - Nov. 3, 2021, p.1734.
Kassim YM, Yang F, Yu H, Maude RJ, Jaeger S. Diagnosing Malaria Patients with Plasmodium falciparum and vivax Using Deep Learning for Thick Smear Images. Diagnostics (Basel). 2021 Oct 27;11(11):1994. doi: 10.3390/diagnostics11111994. PMID: 34829341; PMCID: PMC8621537.
Le DX, Mork JG, Antani S. Hybrid Ensemble-Rule Algorithm for Improved MEDLINE® Sentence Boundary Detection. AMIA Annual Symposium Proceeding 2021;2021:677-686.
Liang Z, Huang JX. Adaptive Cycle-consistent Adversarial Network for Malaria Blood Cell Image Synthetization. IEEE Applied Imagery Pattern Recognition Workshop (AIPR), 2021, Oct 12 -14, Washington DC, USA, pp.1-7. DOI: 10.1109/AIPR52630.2021.9762068.
Jaeger S. The Golden Ratio in Machine Learning. 50th IEEE Applied Imagery Pattern Recognition Workshop (AIPR), October 2021.
Ufuktepe DK, Yang F, Kassim YM, Yu H, Maude RJ, Palaniappan K, Jaeger S. Deep Learning-Based Cell Detection and Extraction in Thin Blood Smears for Malaria Diagnosis. 50th Annual IEEE AIPR 2021, held virtually October 12-14, 2021.
Yang F, Yu H, Kantipudi K, Rosenthal A, Hurt DE, Yaniv Z, Jaeger S. Automated Drug-Resistant TB Screening: Importance of Demographic Features and Radiological Findings in Chest X-Ray. 50th Annual IEEE AIPR 2021, held virtually October 12-14, 2021.
Kim J, Tran L. Retinal Disease Classification from OCT Images Using Deep Learning Algorithms. IEEE-CIBCB 2021, pp. 42-47, Melbourne, Australia, October 2021
Ben-Omran MO, Livinski AA, Kopycka-Kedzierawski DT, Boroumand S, Williams D, Weatherspoon DJ, Iafolla TJ, Fontelo P, Dye BA. The use of teledentistry in facilitating oral health for older adults: A scoping review. J Am Dent Assoc. 2021 Dec;152(12):998-1011.e17. doi: 10.1016/j.adaj.2021.06.005. Epub 2021 Sep 11.
Duarte-Salles T, Vizcaya D, Pistillo A, Casajust P, Sena AG, Lai LYH, Prats-Uribe A, Ahmed W-U-R, Alshammari TM, Alghoul H, Alser O, Burn E, You SC, Areia C, Blacketer C, DuVall S, Falconer T, Fernandez-Bertolin S, Fortin S, Golozar A, Gong M, Tan EH, Huser V, Iveli P, Morales DR, Nyberg F, Posada J. 30-Day Outcomes of Children and Adolescents With COVID-19: An International Experience. Pediatrics September 2021, 148 (3) e2020042929; DOI: https://doi.org/10.1542/peds.2020-042929.
Zamzmi G, Rajaraman S, Sachdev V, Antani S. Trilateral Attention Network for Real-Time Cardiac Region Segmentation. IEEE Access, vol. 9, pp. 118205-118214, 2021, doi: 10.1109/ACCESS.2021.3107303.
McCall T, Ali MO, Yu F, Fontelo P, Khairat S. Development of a Mobile App to Support Self-management of Anxiety and Depression in African American Women: Usability Study. JMIR Form Res. 2021 Aug 17;5(8):e24393. doi: 10.2196/24393.
Huser V, Williams ND, Mayer CS. Linking provider specialty and outpatient diagnoses in Medicare claims data: Data quality implications. Appl Clin Inform. 2021 Aug;12(4):729-736. doi: 10.1055/s-0041-1732404.
Yang F, Yu H, Kantipudi K, Rosenthal A, Hurt D, Antani S, Yaniv ZR, Jaeger S. Differentiating between Drug-Sensitive and Drug-Resistant Tuberculosis with Machine Learning for Clinical and Radiological Features. Quantitative Imaging in Medicine and Surgery, 0(0): 1–16, 2021.
Angara S, Guo P, Xue Z, Antani S. Semi-Supervised Learning for Cervical Precancer Detection. 2021 IEEE 34th International Symposium on Computer-Based Medical Systems (CBMS), 2021, pp. 202-206, doi: 10.1109/CBMS52027.2021.00072.
Xue Z, Guo P, Desai K, Pal A, Ajenifuja KO, Adepiti CA, Long LR, Schiffman M, Antani S. A Deep Clustering Method for Analyzing Uterine Cervix Images Across Imaging Devices. 34th IEEE International Symposium on Computer-Based Medical Systems (CBMS), June 2021, pp. 527-532, doi: 10.1109/CBMS52027.2021.00085.
Yadav S, Gupta D, Ben Abacha A, Demner-Fushman D. Reinforcement Learning for Abstractive Question Summarization with Question-aware Semantic Rewards. The 59th Annual Meeting of the Association for Computational Linguistics (ACL 2021).
Fontelo P, Bastola MM, Zheng Z, Baik SH. A review of thromboembolic events in hospitalized COVID-19 patients. Thromb J 2021;19:47. https://doi.org/10.1186/s12959-021-00298-3.
He Y, Wang L, Yang F, Xia Y, Clarysse P, Zhu Y. Systematic Study of Joint Influence of Angular Resolution and Noise in Cardiac Diffusion Tensor Imaging. Ennis D.B., Perotti L.E., Wang V.Y. (eds) Functional Imaging and Modeling of the Heart. FIMH 2021. Lecture Notes in Computer Science, vol 12738. Springer, Cham. https://doi.org/10.1007/978-3-030-78710-3_20.
Young L, Kim J, Yakin M, Lin H, Dao D, Kodati S, Sharma S, Lee A, Lee C, Sen, HN. Automated detection of vascular leakage on fluorescein angiography [Poster]. The Association for Research in Vision and Ophthalmology (ARVO) 2021, May 2021.
Niu P, Wang L, Xie B, Robini M, Boussel, L Douek P, Zhu Y, Yang F. Improved Image Reconstruction Using Multi-Energy Information in Spectral Photon-Counting CT. IEEE Access, vol. 9, pp. 97981-97989, 2021, doi: 10.1109/ACCESS.2021.3083505.
Kassim YM, Palaniappan K, Yang F, Poostchi M, Palaniappan N, Maude RJ, Antani S, Jaeger S. Clustering-Based Dual Deep Learning Architecture for Detecting Red Blood Cells in Malaria Diagnostic Smears. IEEE J Biomed Health Inform. 2021 May;25(5):1735-1746. doi: 10.1109/JBHI.2020.3034863. Epub 2021 May 11.
Mayer CS, Williams N, Huser V. CONSIDER Statement: Consolidated Recommendations for Sharing Individual Participant Data from Human Clinical Studies. AMIA Annu Symp Proc. 2021;2021:438-444.
Williams N, Mayer CS, Huser V. Data Characterization of Medicaid: Legacy and New Data Formats in the CMS Virtual Research Data Center. AMIA Annu Symp Proc. 2021;2021:644-652.
Rajaraman S, Zamzmi G, Folio L, Alderson P, Antani S. Chest X-ray bone suppression for improving classification of tuberculosis-consistent findings. Diagnostics. 2021; 11(5):840. https://doi.org/10.3390/diagnostics11050840.
Zamzmi G, Rajaraman S, Antani S. UMS-Rep: Unified Modality-Specific Representation for Efficient Medical Image Analysis. Informatics in Medicine Unlocked, 24, art. no. 100571. http://www.journals.elsevier.com/informatics-in-medicine-unlocked doi: 10.1016/j.imu.2021.100571
Williams ND, Huser V, Rhame F, Mayer CS, Fung KW. The changing patterns of comorbidities associated with human immunodeficiency virus infection, a longitudinal retrospective cohort study of Medicare patients. Medicine (Baltimore). 2021;100(16):e25428. doi:10.1097/MD.0000000000025428.
Rajaraman S, Zamzmi G, Folio L, Alderson P, Antani S. Improved TB classification using bone-suppressed chest radiographs. arXiv preprint arXiv:2104.04518 [eess.IV].
Wilson P, Huser V. Discoverability of Information on Clinical Trial Data Sharing Platforms. J Med Libr Assoc. 2021 Apr 1;109(2):240-247. doi: 10.5195/jmla.2021.992.
Rajaraman S, Folio LR, Dimperio J, Alderson PO, Antani SK. Improved Semantic Segmentation of Tuberculosis-Consistent Findings in Chest X-rays Using Augmented Training of Modality-Specific U-Net Models with Weak Localizations. Diagnostics (Basel). 2021 Mar 30;11(4):616. doi: 10.3390/diagnostics11040616.
Pal A, Xue Z, Befano B, Rodriguez AC, Long L, Schiffman M, Antani SK. Deep Metric Learning for Cervical Image Classification. IEEE Access, vol. 9, pp. 53266-53275, 2021, doi: 10.1109/ACCESS.2021.3069346.
Moldwin A, Demner-Fushman D, Goodwin TR. Empirical Findings on the Role of Structured Data, Unstructured Data, and their Combination for Automatic Clinical Phenotyping. AMIA Summit 2021.
Bastola M, Locatis C, Fontelo P. Diagnostic Reliability of In-Person Versus Remote Dermatology: A Meta-Analysis. Telemed J E Health, 2021 Mar; 27(3): 247-250.
Guo P, Xue Z, Jeronimo J, Gage JC, Desai KT, Befano B, García F, Long LR, Schiffman M, Antani S. Network Visualization and Pyramidal Feature Comparison for Ablative Treatability Classification Using Digitized Cervix Images. J Clin Med. 2021 Mar 1;10(5):953. doi: 10.3390/jcm10050953.
Rajaraman S, Folio L, Dimperio J, Alderson P, Antani S. Training custom modality-specific U-Net models with weak localizations for improved Tuberculosis segmentation and localization. arXiv preprint arXiv:2102.10607 [cs.CV].
Sen N, Young L, Kim J, Sharma S, Lee A, Lee C. Fully Automated Algorithm to Detect Vascular Leakage in Uveitis. The 44th Virtual Annual Macula Society Meeting, ID 141, February, 2021.
Baik SH, Fung K-W, McDonald CJ. The mortality risk of Proton Pump Inhibitors in 1.9 Million US Seniors: an extended Cox survival analysis. Clin Gastroenterol Hepatol 2021. https://doi.org/10.1016/j.cgh.2021.01.014.
McDonald CJ, Baik SH, Zheng Z, Amos L. A method for prioritizing risk groups for early SARS-CoV-2 vaccination, by the numbers. MedRxiv 2020:2020.12.18.20248504. https://doi.org/10.1101/2020.12.18.20248504.
Lu CJ, Payne A, Mork J. Proper filter usage to retrieve multiwords from the MEDLINE n-gram set: Reply to the Turki et al commentary "Enhancing filter-based parenthetic abbreviation extraction methods" [Letter]. Journal of the American Medical Informatics Association, Volume 28, Issue 3, March 2021, Page 670, https://doi.org/10.1093/jamia/ocaa313.
Liang Z, Huang JX, Li J, Chan S. Enhancing automated COVID-19 chest X-ray diagnosis by image-to-image GAN translation. 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2020, Dec 16-19, Seoul, Korea (South), pp. 1068-1071. DOI: 10.1109/BIBM49941.2020.9313466.
Li Z, Wang X, Wang L, Ji W, Zhang M, Zhu Y, Yang F. UNet-ESPC-Cascaded Super-Resolution Reconstruction in Spectral CT. 2020 15th IEEE International Conference on Signal Processing (ICSP).
Baik S, Lau J, Huser V, McDonald CJ. Association between tendon ruptures and use of fluoroquinolone, and other oral antibiotics: A 10-year retrospective study of 1 million US senior Medicare beneficiaries. BMJ Open 2020;10:34844. https://doi.org/10.1136/bmjopen-2019-034844.
Lu CJ, Payne A, Mork JG. Enhanced Features in the SPECIALIST Lexicon - Antonyms. AMIA 2020 Virtual Annual Symposium, November 14-18, 2020.
Rajaraman S, Sornapudi S, Alderson PO, Folio LR, Antani SK. Analyzing inter-reader variability affecting deep ensemble learning for COVID-19 detection in chest radiographs. PLoS ONE 15(11): e0242301.
Yu H, Yang F, Rajaraman S, Ersoy I, Moallem G, Poostchi M, Palaniappan K, Antani S, Maude RJ, Jaeger S. Malaria Screener: a smartphone application for automated malaria screening. BMC Infect Dis. 2020 Nov 11;20(1):825. doi: 10.1186/s12879-020-05453-1.
Mayer CS, Huser V. Computerized monitoring of COVID-19 trials, studies and registries in ClinicalTrials.gov registry. PeerJ. 2020 Oct 23;8:e10261. doi: 10.7717/peerj.10261.
Desai KT, Ajenifuja KO, Banjo A, Adepiti CA, Novetsky A, Sebag C, Einstein MH, Oyinloye T, Litwin TR, Horning M, Olanrewaju FO, Oripelaye MM, Afolabi E, Odujoko OO, Castle PE, Antani S, Wilson B, Hu L, Mehanian C, Demarco M, Gage JC, Xue Z, Long LR, Cheung L, Egemen D, Wentzensen N, Schiffman M. Design and feasibility of a novel program of cervical screening in Nigeria: self-sampled HPV testing paired with visual triage. Infect Agent Cancer 2020 Oct 14;15:60. doi: 10.1186/s13027-020-00324-5.
Mao Y, Fung KW. Use of Word and Graph Embedding to Measure Semantic Relatedness between UMLS Concepts. Journal of the American Medical Informatics Association, 27(10), 1538-1546.
Mayer CS, Williams N, Huser V. Analysis of data dictionary formats of HIV clinical trials. PLoS One. 2020 Oct 5;15(10):e0240047. doi: 10.1371/journal.pone.0240047.
Ye J, Xue Y, Long LR, Antani S, Xue Z, Cheng K, Huang X. Synthetic Sample Selection via Reinforcement Learning. In: Martel A.L. et al. (eds) Medical Image Computing and Computer Assisted Intervention – MICCAI 2020. MICCAI 2020. Lecture Notes in Computer Science, vol 12261. Springer, Cham. https://doi.org/10.1007/978-3-030-59710-8_6.
Bastola MM, Locatis C, Fontelo P. Thromboprophylaxis, Delta SOFA and Main Outcomes in Ventilated Patients: An Analysis of the MIMIC-III Clinical Database. Clinical Database, 22 September 2020, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-78878/v1]
Ben Abacha A, Datla V, Hasan S, Demner-Fuschman D, Muller H. Overview of the VQA-Med Task at ImageCLEF 2020: Visual Question Answering and Generation in the Medical Domain. CLEF 2020.
Misra D, Gill M, Lee JS, Antani S. Segmentation of Anterior Tissues in Craniofacial Cone-Beam CT Images. 2020 IEEE 33rd International Symposium on Computer-Based Medical Systems (CBMS), Rochester, MN, USA, 2020, pp. 71-76, doi: 10.1109/CBMS49503.2020.00021.
Kim I, Misra D, Rodriguez L, Gill M, Liberton D, Almpani K, Lee JS, Antani S. Malocclusion Classification on 3D Cone-Beam CT Craniofacial Images Using Multi-Channel Deep Learning Models. 2020 42nd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Montreal, QC, Canada, 2020, pp. 1294-1298, doi: 10.1109/EMBC44109.2020.9176672.
Kim J, Tran L. Ensemble Learning Based on Convolutional Neural Networks for the Classification of Retinal Diseases from Optical Coherence Tomography Images. 2020 IEEE 33rd International Symposium on Computer-Based Medical Systems (IEEE CBMS 2020), pp 535-540, Rochester, USA, July 2020. DOI Bookmark: 10.1109/CBMS49503.2020.00106.
Demner-Fushman D, Cohen KB, Ananiadou S, Tsujii J. Proceedings of the 19th SIGBioMed Workshop on Biomedical Language Processing, 2020. Journal of the American Medical Informatics Association, 2020: 27 (2), 194-201.
Demner-Fushman D, Mrabet Y, Ben Abacha A. Consumer
health information and question answering: helping consumers find
answers to their health-related information needs. Journal of the
American Medical Informatics Association. Journal of the American Medical Informatics Association, 2020: 27 (2), 194-201.
Goodwin T, Demner-Fushman D. A
customizable deep learning model for nosocomial risk prediction from
critical care notes with indirect supervision. Journal of the American Medical Informatics Association, 2020: 27 (4), 567-576.
Voorhees EM, Alam T, Bedrick S, Demner-Fushman D, Hersh WR, Lo K, Roberts K, Soboroff I, Wang LL. TREC-COVID: Constructing a Pandemic Information Retrieval Test Collection. CoRR abs/2005.04474 (2020)
Savery M, Ben Abacha A, Gayen S, Demner-Fushman D. Question-Driven Summarization of Answers to Consumer Health Questions. arXiv preprint arXiv:2005.09067.
Datta S, Rodriguez L, Shooshan SE, Demner-Fushman D, Roberts K. Understanding
Spatial Language in Radiology: Representation Framework, Annotation,
and Spatial Relation Extraction from Chest X-ray Reports using Deep
Learning. Journal of Biomedical Informatics, 103473.
Sarrouti M, Ben Abacha A, Demner-Fushman D. Visual Question Generation from Radiology Images. Proceedings of the First Workshop on Advances in Language and Vision Research.
Bastola MM, Locatis C, Fontelo P. Diagnostic Laboratory Tests for COVID-19 in US: Methodology and Performance. Res Sq [Preprint]. 2020 Jul 20:rs.3.rs-43374. doi: 10.21203/rs.3.rs-43374/v1.
Rajaraman S, Siegelman J, Alderson PO, Folio LS, Folio LR, Antani SK. Iteratively Pruned Deep Learning Ensembles for COVID-19 Detection in Chest X-Rays. IEEE Access, vol. 8, pp. 115041-115050, 2020, doi: 10.1109/ACCESS.2020.3003810.
Zheng Q, Lu Y, Lure F, Jaeger S, Lu P. Clinical and radiological features of novel coronavirus pneumonia. Journal of X-Ray Science and Technology, vol. 28, no. 3, pp. 391-404, 2020.
Jaeger S. The Golden Ratio of Learning and Momentum. arXiv:2006.04751 [cs.LG], 2020.
Rajaraman S, Sornapudi S, Alderson PO, Folio LR, Antani SK. Interpreting Deep Ensemble Learning through Radiologist Annotations for COVID-19 Detection in Chest Radiographs. medRxiv 2020.07.15.20154385; doi: https://doi.org/10.1101/2020.07.15.20154385.
Roberts K, Alam T, Bedrick S, Demner-Fushman D, Lo K, Soboroff I, Voorhees E, Wang LL, Hersh WR. TREC-COVID: Rationale and Structure of an Information Retrieval Shared Task for COVID-19. Journal of the American Medical Informatics Association, 2020.
Guo P, Xue Z, Mtema Z, Yeates K, Ginsburg O, Demarco M, Long LR, Schiffman M, Antani SK. 2.
Ensemble Deep Learning for Cervix Image Selection toward Improving
Reliability in Automated Cervical Precancer Screening. Diagnostics (Basel) 2020 jul3;10(7):451.
Zamzmi G, Hsu L, Li W, Sachdev V, Antani SK. Harnessing Machine Intelligence in Automatic Echocardiogram Analysis: Current Status, Limitations, and Future Directions. IEEE Reviews in Biomedical Engineering, doi: 10.1109/RBME.2020.2988295
Zamzmi G, Hsu L, Li W, Sachdev V, Antani SK. Fully automated spectral envelope and peak velocity detection from Doppler echocardiography images. Proc. SPIE 11314, Medical Imaging 2020: Computer-Aided Diagnosis, 113144G (16 March 2020); https://doi.org/10.1117/12.2551183
Zamzmi G, Hsu L, Li W, Sachdev V, Antani SK. Echo Doppler Flow Classification and Goodness Assessment with Convolutional Neural Networks. 2019 18th IEEE International Conference On Machine Learning And Applications (ICMLA), Boca Raton, FL, USA, 2019, pp. 1744-1749, doi: 10.1109/ICMLA.2019.00283
Salekin S, Zamzmi G, Paul R, Goldgof D, Kasturi R, Ho T, Sun Y. Harnessing the Power of Deep Learning Methods in Healthcare: Neonatal Pain Assessment from Crying Sound.
Jain
SK, Andronikou S, Goussard P, Antani SK, Gomez-Pastrana D, Delacour C,
Starke JR, Ordonez AA, Jean-Philippe P, Browning RS, Perez-Velez
C. Advanced imaging tools for childhood tuberculosis: potential applications and research needs. The Lancet Infectious Diseases. DOI:https://doi.org/10.1016/S1473-3099(20)30177-8
Zamzmi G, Rajaraman S, Antani SK. Unified Representation Learning for Efficient Medical Image Analysis. arXiv:2006.11223 [cs.CV] Under Review
Zamzmi G, Rajaraman S, Antani SK. Accelerating Super-Resolution and Visual Task Analysis in Medical Images. Appl. Sci. 2020, 10, 4282.
Rajaraman S, Antani SK. Weakly Labeled Data Augmentation for Deep Learning: A Study on COVID-19 Detection in Chest X-Rays. Diagnostics 2020, 10, 358.
Lu CJ, Payne A, Mork JG. The Unified Medical Language System SPECIALIST Lexicon and Lexical Tools: Development and applications. J Am Med Inform Assoc. 2020 May 29;27(10):1600-1605. doi: 10.1093/jamia/ocaa056.
Fung KW, Xu J, Bodenreider O. The new International Classification of Diseases 11th edition – A comparative analysis with ICD-10 and ICD-10-CM. J Am Med Inform Assoc. 2020 May 1;27(5):738-746. doi: 10.1093/jamia/ocaa030.
Xue Z, Novetsky A, Einstein M, Marcus J, Befano B, Guo P, Demarco M, Wenzenten N, Long LR, Schiffman M, Antani SK. A demonstration of automated visual evaluation of cervical images taken with a smartphone camera. Int J Cancer. 2020 Apr 30.
Savery M, Rogers W, Pillai M, Mork JG, Demner-Fushman D. Chemical Entity Recognition for MEDLINE Indexing. AMIA 2020 Virtual Informatics Summit, 2020.
Rajaraman S, Siegelman J, Alderson PO, Folio LS, Folio LR, Antani SK. Iteratively Pruned Deep Learning Ensembles for COVID-19 Detection in Chest X-rays. 2020, [Online].
Ionescu B, Müller H, Péteri R, Dang-Nguyen DT, Zhou L, Piras L, Riegler M, Halvorsen P, Tran MT, Lux M, Gurrin C, Chamberlain J, Clark A, Campello A, de Herrera AGS, Ben Abacha A, Datla VV, Hasan SA, Liu J, Demner-Fushman D, Pelka O, Friedrich CM, Cid YD, Kozlovski S, Liauchuk V, Kovalev V, Berari P, Brie P, Fichou D, Dogariu M, Stefan L, Constantin M. ImageCLEF 2020: Multimedia Retrieval in Lifelogging, Medical, Nature, and Internet Applications. ImageCLEF 2020:
Multimedia Retrieval in Lifelogging, Medical, Nature, and Internet
Applications. ECIR (2) 2020: 533-541.
Bastola MM, Locatis C, Maisiak R, Fontelo P.. The Effectiveness of Mobile Phone-Based Text Messaging to Intervene with Problem Drinking in Youth and Younger Adult Populations: A Meta-Analysis. Telemed J E Health. 2020 Mar; 26(3): 270-277.
Robini MC, Yang F, Zhu Y. A stochastic approach to full inverse treatment planning for charged-particle therapy. J Glob Optim 77, 853–893 (2020). https://doi.org/10.1007/s10898-020-00902-2.
Rajaraman S, Kim I, Antani SK. Detection
and visualization of abnormality in chest radiographs using
modality-specific convolutional neural network ensembles. PeerJ 8:e8693 https://doi.org/10.7717/peerj.8693
Sornapudi S, Brown G, Xue Z, Long LR, Allen L, Antani SK. Comparing
Deep Learning Models for Multi-cell Classification in Liquid- based
Cervical Cytology Image. AMIA Annu Symp Proc. 2019; 2019: 820–827.
Guo P, Xue Z, Long LR, Antani SK. Anatomical landmark segmentation in uterine cervix images using deep learning. Proc. SPIE 11318, Medical Imaging 2020: Imaging Informatics for Healthcare, Research, and Applications, 1131810 (2 March 2020)
Zou J, Xue Z, Brown G, Long LR, Antani SK. Deep learning for nuclei segmentation and cell classification in cervical liquid based cytology.
Proc. SPIE 11318, Medical Imaging 2020: Imaging Informatics for
Healthcare, Research, and Applications, 1131811 (2 March 2020); doi:
10.1117/12.2549547
Yang F, Quizon N, Silamut K, Maude RJ, Jaeger S, Antani SK. Cascading YOLO: Automated Malaria Parasite Detection for Plasmodium Vivax in Thin Blood Smears. Proc. SPIE 11314, Medical Imaging 2020: Computer-Aided Diagnosis, 113141Q (16 March 2020); https://doi.org/10.1117/12.2549701.
Janakiram C, Venkitachalam R, Fontelo P, Iafolla TJ, Dye BA. Effectiveness of herbal oral care products in reducing dental plaque & gingivitis - a systematic review and meta-analysis. BMC Complement Med Ther; 2020 Feb 11; 20(1):43.
Rajaraman S, Antani SK. Modality-Specific Deep Learning Model Ensembles Toward Improving TB Detection in Chest Radiographs. IEEE Access, vol. 8, pp. 27318-27326, 2020.
Baik SH, McDonald CJ. Independent effects of 15 commonly prescribed drugs on all-cause mortality among US elderly patients with type 2 diabetes mellitus. BMJ Open Diabetes Res Care 2020;8:e000940. https://doi.org/10.1136/bmjdrc-2019-000940.
Bastola MM, Locatis C, Maisiak R, Fontelo P. Selenium, copper, zinc and hypertension: an analysis of the National Health and Nutrition Examination Survey (2011-2016). BMC Cardiovasc Disord. 2020 Jan 31;20(1):45. doi: 10.1186/s12872-020-01355-x. PMID: 32005161; PMCID: PMC6995060.
Guo P, Xue Z, Long LR, Antani SK. Cross-Dataset Evaluation of Deep Learning Networks for Uterine Cervix Segmentation. Diagnostics (Basel). 2020 Jan 14;10(1). pii: E44. doi: 10.3390/diagnostics10010044.
Sarrouti M, Quatik EL, Alaoui S. SemBioNLQA: A semantic biomedical question answering system for retrieving exact and ideal answers to natural language questions. Artif Intell Med. 2020 Jan;102:101767. doi: 10.1016/j.artmed.2019.101767. Epub 2019 Nov 28.
Zeiss CJ, Donwook S, Vander Wyk B, Beck AP, Zatz N, Sneiderman CA, Kilicoglu H. Menagerie: A text-mining tool to support animal-human translation in neurodegeneration research. PLoS One. 2019 Dec 17;14(12):e0226176. doi: 10.1371/journal.pone.0226176. eCollection 2019.
Goodwin T, Demner-Fushman D. Deep Learning from Incomplete Data: Detecting Imminent Risk of Hospital-acquired Pneumonia in ICU Patients. Proceedings of the AMIA 2019 Annual Symposium, Washington, DC, USA, November 17-20, 2019.
Ben Abacha A, Demner-Fushman D. A Question-Entailment Approach to Question Answering. arXiv:1901.08079.
Ben Abacha A, Hasan SA, Datls W, Liu J, Demner-Fushman D, Muller H. VQA-Med: Overview of the medical visual question answering task at imageclef 2019. CEUR Workshop Proceedings, 9-12, 2019.
Goodwin T, Demner-Fushman D, Fung K, Do P. Overview of the TAC 2019 Track on Drug-Drug Interaction Extraction from Drug Label. Proceedings of the Text Analysis Conference (TAC) 20 19, Gathersburg, MD, USA, November 12-13, 2019.
Mrabet Y, Demner-Fushman D. On Agreements in Visual Understanding. 2019 Conference on Neural Information Processing Systems.
2019 Conference on Neural Information Processing Systems, December
8-14, 2019. Vancouver, Canada.
Cheng P, Lu P, Wang P, Zhou W, Yu W, Jaeger S, Li J, Wu T, Ke X, Zheng B, Antani SK, Candemir S, Quan S, Lure F, Li H, Guo L. Applying
Deep Learning and Radiomics to Determine Biological Lung and Heart Age
from Chest Radiographs. Chinese Congress of Radiology.
Wang X, Guan Y, Lu P, Cheng G, Zhou W, Jaeger S, Zhen B, Antani SK, Yin X, Yu W, Guo L, Quan S, Lure F, Hurt D, Gabrielian A, Li H, Ke X. Screening of Tuberculosis in a TB High-burden Large Rural Region in China with Deep Learning Multi-modality Artificial Intelligence. Chinese Congress of Radiology.
Yu H, Yang F, Silamut R, Maude S, Jaeger S, Antani SK. Automatic Blood Smear Analysis with Artificial Intelligence and Smartphones [Poster]. ASTMH 68th Annual Meeting, Washington DC, Nov. 20-24, 2019.
Rae A, Savery M, Mork JG, Demner-Fushman D. A High Recall Classifier for Selecting Articles for MEDLINE Indexing. AMIA Fall Symposium, 2019.
Savery M, Huston M, Mork JG, Printseva O, Rae A, Schmidt S, Demner-Fushman D. Evaluation of System for Selective Indexing Classification [Poster]. AMIA Fall Symposium, 2019.
Lu CJ, Payne A, Demner-Fushman D. Classification Types: A New Feature in the SPECIALIST Lexicon [Poster]. MIA 2019 Annual Symposium, Washington, DC, November 16-20, 2019.
Mao Y, Fung K, Demner-Fushman D. Drug-drug Interaction Extraction via Transfer Learning [Poster]. AMIA Fall Symposium, 2019.
Lu C, Aronson AR, Shooshan SE, Demner-Fushman D. Spell checker for consumer language (CSpell). Journal of the American Medical Informatics Association, Volume 26, Issue 3, 1 March 2019, Pages 211-218, https://doi.org/10.1093/jamia/ocy171 21 January 2019 (Editor's Choice).
Rajaraman S, Jaeger S, Antani SK. Performance
evaluation of deep neural ensembles toward malaria parasite detection
in thin-blood smear images. PeerJ. doi: 10.7717/peerj.6977.
Mayer CS, Williams N, Fung KW, Huser V. Evaluation of Research Accessibility and Data Elements of HIV Registries. Curr HIV Res. 2019;17(4):258-265. doi: 10.2174/1570162X17666190924195439.
Lure F, Jaeger S, Cheng G, Li H, Lu P, Yu W, Kung J, Guan Y. Applying Multi-modality Artificial Intelligence for Screening of Tuberculosis in a TB High-burden Large Rural Region in China [Poster]. TBScience, 50th Union World Conference on Lung Health, Hyderabad, India.
Yang F, Poostchi M, Silamut K, Maude RJ, Jaeger S, Thoma G. Automated Parasite Classification of Malaria on Thick Blood Smears [Poster]. ASTMH 67th Annual Meeting, New Orleans, LA, Oct. 28 – Nov. 1, 2018.
Goodwin T, Demner-Fushman D. Bridging the Knowledge Gap: Enhancing Question Answering with World and Domain Knowledge. arXiv preprint arXiv:1910.07429
Yang F, Yu H, Silamut K, Maude RJ, Jaeger S, Antani SK. Parasite Detection in Thick Blood Smears Based on Customized Faster-RCNN. Proceedings of AIPR2019, Washington DC, USA, Oct 15-17, 2019.
Yang F, Yu H, Silamut K, Maude R, Jaeger S, Antani SK. Smartphone-Supported Malaria Diagnosis Based on Deep Learning. Proceedings of 10th Workshop on Machine Learning in Medical Imaging (MLMI 2019) in conjunction with MICCAI, Shenzhen, China, Oct 13-17, 2019.
Zou J, Antani SK, Thoma G. Unified Deep Neural Network for Segmentation and Labeling of Multi-Panel Biomedical Figures. Journal of the Association for Information Science and Technology (JASIST), 2019
Zou J. Unified Deep Neural Network for Segmentation and Labeling of Multi-Panel Biomedical Figures. Journal of the Association for Information Science and Technology (JASIST), 2019
Demner-Fushman D, Mrabet Y, Ben Abacha A. Consumer
health information and question answering: helping consumers find
answers to their health-related information needs. JAMIA, 2019.
Yang F, Poostchi M, Yu H, Zhou Z, Silamut K, Yu J, Maude RJ, Jaeger S, Antani S. . Deep learning for smartphone-based malaria parasite detection in thick blood smears. IEEE J Biomed Health Inform. 2020 May;24(5):1427-1438. doi: 10.1109/JBHI.2019.2939121. Epub 2019 Sep 23.
Janakiram C, Fontelo P, Huser V, Chalmers NI, Lopez Mitnik G, Brow AR, Iafolla TJ, Dye BA. Opioid Prescriptions for Acute and Chronic Pain Management Among Medicaid Beneficiaries. Am J Prev Med; 2019 09 31; 57(3):365-373. PubMed ID: 31377093.
Rosemblat G, Fiszman, M, Shin D, Kilicoglu H. Towards a characterization of apparent contradictions in the biomedical literature using context analysis. Journal of Biomedical Informatics. 2019. In Press. https://doi.org/10.1016/j.jbi.2019.103275.
Vasilakes J, Fan Y, Rizvi R, Bompelli A, Bodenreider O, Zhang R. Normalizing Dietary Supplement Product Names Using the RxNorm Model. Stud Health Technol Inform. 2019 Aug 21;264:408-412. doi: 10.3233/SHTI190253.
Ben Abacha A, Mrabet Y, Sharp M, Goodwin T, Shooshan S, Demner-Fushman D. Bridging the Gap Between Consumers’ Medication Questions and Trusted Answers. Stud Health Technol Inform. 2019 Aug 21;264:25-29. doi: 10.3233/SHTI190176.
Kho SU, Sheth A, Bodenreider O. Automatic Identification of Individual Drugs in Death Certificates. Stud Health Technol Inform. 2019 Aug 21;264:183-187. doi: 10.3233/SHTI190208.
Rajaraman S, Candemir S, Xue Z, Alderson P, Thoma G, Antani SK. A Novel Stacked Model Ensemble for Improved TB Detection in Chest Radiographs. In Santosh KC et al. (Eds.). Medical Imaging: Artificial Intelligence, Image Recognition, and Machine Learning Techniques. (pp. 1-26). New York, NY: CRC Press, Taylor & Francis Group.
Datta S, Si Y, Rodriguez L, Shooshan S, Demner-Fushman D, roberts K. Understanding
Spatial Language in Radiology: Representation Framework, Annotation,
and Spatial Relation Extraction from Chest X-ray Reports using Deep
Learning. arXiv preprint arXiv:1908.04485, 2019.
Divita G, Rosemblat G, Browne AC. Building a medical Spanish lexicon. AMIA Annu Symp Proc. 2007 Oct 11:941.
Ben Abacha A, Shivade C, Demner-Fushman D. Overview
of the MEDIQA 2019 Shared Task on Textual Inference, Question
Entailment and Question Answering. Proceedings of the 18th BioNLP Workshop and Shared Task, Florence, Italy, August 1, 2019.
Demner-Fushman D, Cohen KB, Ananiadou S, Tsujii J. Sesame Street at BioNLP 2019. Proceedings of the BioNLP 2019 workshop.
Ben Abacha A, Shivade C, Demner-Fushman D. Overview
of the MEDIQA 2019 Shared Task on Textual Inference, Question
Entailment and Question Answering. . Proceedings of the BioNLP 2019 workshop.
Ben Abacha A, Demner-Fushman D. On the Summarization of Consumer Health Questions. ACL 2019, Florence, Italy.
Xue Y, Zhou Q, Ye J, Long LR, Antani SK, Cornwell C, Xue Z, Huang X. Synthetic
Augmentation and Feature-based Filtering for Improved Cervical
Histopathology Image Classification. ArXiv, abs/1907.10655.
Ganesan P, Xue Z, Singh S, Long LR, Ghoraani B, Antani SK. Performance
Evaluation of a Generative Adversarial Network for Deblurring
Mobile-phone Cervical Images.
Proc. IEEE Engineering in Medicine and Biology Conference (EMBC),
Berlin, Germany, 23 – 27 July 2019. pp. 4487 – 4490.
Rajaraman S, Sornapudi S, Kohli M, Antani SK. Assessment
of an ensemble of machine learning models toward abnormality detection
in chest radiographs.
Proc. IEEE Engineering in Medicine and Biology Conference (EMBC),
Berlin, Germany, 23 – 27 July 2019. pp. 3689 – 3692.
Ganesan P, Rajaraman S, Long LR, Ghoraani B, Antani SK. Assessment
of Data Augmentation Strategies Toward Performance Improvement of
Abnormality Classification in Chest Radiographs.
Proc. IEEE Engineering in Medicine and Biology Conference (EMBC),
Berlin, Germany, 23 – 27 July 2019. pp. 841 – 844.
Rajaraman S, Antani SK. Visualizing
Salient Network Activations in Convolutional Neural Networks for
Medical Image Modality Classification. . Santosh K., Hegadi R. (eds) Recent Trends in Image Processing and Pattern Recognition. RTIP2R 2018. Communications in Computer and Information Science, vol 1036. Springer, Singapore
Kim J, Tran L, Chew E, Antani SK. Optic Disc and Cup Segmentation for Glaucoma Characterization Using Deep Learning. 2019 IEEE 32th International Symposium on Computer-Based Medical Systems (CBMS), pp 489-494, Cordoba, Spain, June 2019.
Ben Abacha A, Demner-Fushman D. On the Summarization of Consumer Health Questions. Proceedings of the 57th Annual Meeting of the Association for Computational Linguistics, Florence, Italy 2019.
Allam A, Magy M, Thoma G, Krauthammer M. Neural networks versus Logistic regression for 30 days all-cause readmission prediction. . Sci Rep. 2019 Jun 26;9(1):9277. doi: 10.1038/s41598-019-45685-z.
Janakiram C, Chalmers NI, Fontelo P, Huser V, Mitnik GL, Iafolla TJ, Brow AR, Dye BA. Sex and race or ethnicity disparities in opioid prescriptions for dental diagnoses among patients receiving Medicaid. J Am Dent Assoc; 2019 Oct; 150(10):e135-e144. PMID 31561765.
Rajaraman S, Jaeger S, Antani SK. Performance
evaluation of deep neural ensembles toward malaria parasite detection
in thin-blood smear images. PeerJ 7:e6977
Ben Abacha A, Demner-Fushman D. On
the Role of Question Summarization and Information Source Restriction
in Consumer Health Question Answering. AMIA Informatics Summit, March 2019.
Chowdhuri S, McCrea S, Demner-Fushman D, Overby TC. Extracting Biomedical Terms from Postpartum Depression Online Health Communities. AMIA Jt Summits Transl Sci Proc. 2019 May 6;2019:592-601.
Zhang
XA, Yates A, Vasilevsky N, Gourdine JP, Callahan TJ, Carmody LC, Danis
D, Joachimiak MP, Ravanmehr V, Pfaff ER, Champion J, Robasky K, Xu H,
Fecho K, Walton NA, Zhu RL, Ramsdill J, Mungall CJ, Kohler S, Haendel
MA, McDonald CJ, Vreeman DJ, Peden DB, Bennett TD, Feinstein JA, Martin
B, Stefanski AL, Hunter LE, Chute CG, Robinson PN. Semantic
integration of clinical laboratory tests from electronic health records
for deep phenotyping and biomarker discovery. NPJ Digit Med. 2019;2. pii: 32. doi: 10.1038/s41746-019-0110-4. Epub 2019 May 2.
Kesav N, Yang Q, Losert W, Kim J, Jaeger S, Sen HN. Novel automated processing techniques of fluorescein angiography (FA) images in patients with Uveitis [Poster]. Annual Meeting of the Association for Research in Vision and Ophthalmology (ARVO).
Bastola MM, Locatis C, Maisiak R, Fontelo P. The Effectiveness of Mobile Phone-Based Text Messaging to Intervene with Problem Drinking in Youth and Younger Adult Population: A Meta-Analysis. Telemed J E Health; 2020 03 31; 26(3):270-277. PubMed ID: 30985258.
Ionescu B, Muller H, Peteri R, Dang-Nguyen DT, Piras L, Riegler M, Tran MT, Lux M, Gurrin C, Cid YD, Liauchuk V, Kovalev V, Ben Abacha A, Hasan SA, Datla V, Liu J, Demner-Fushman D, Pelka O, Friedrich CM, Chamberlain J, Clark C, de Herrera AGS, Garcia N, Kavallieratou E, del Blanco CR, Rodriguez CC, Vasillopoulos N, Karampidis K. Multimedia retrieval in medicine, lifelogging, security and nature.
International Conference of the Cross-Language Evaluation Forum for
European Languages, Springer, Cham, 358-386, 2019
Kim I, Rajaraman S, Antani SK. Visual Interpretation of Convolutional Neural Network Predictions in Classifying Medical Image Modalities. Diagnostics (Basel). 2019 Apr 3;9(2). pii: E38. doi: 10.3390/diagnostics9020038.
Guo P, Singh S, Xue Z, Long LR, Antani SK. Deep Learning for Assessing Image Focus for Automated Cervical Cancer Screening. 2019 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI) DOI: 10.1109/BHI.2019.8834495.
Kim J, Tran L, Chew E, Antani SK, Thoma GR. Optic Disc Segmentation in Fundus Images Using Deep Learning.
SPIE Medical Imaging 2019: Imaging Informatics for Healthcare,
Research, and Applications, Vol. 10954, San Diego, USA, February
2019.
Ben Abacha A, Demner-Fushman D. On
the Role of Question Summarization and Information Source Restriction
in Consumer Health Question Answering. Proceedings of the AMIA 2019 Informatics Summit, San Francisco, CA, USA, March 25-28, 2019.
Goodwin T, Harabagiu S. The Impact of Inferring Treatments on Information Retrieval for Precision Medicine. Proceedings of the AMIA 2019 Informatics Summit, San Francisco, CA, USA, March 25-28, 2019.
Zolnoori M, Fung K, Patrick DB,
Fontelo P, Kharrazi H, Faiola A, Shah ND, Shirley WYS, Eldredge CE, Luo
J, Conway M, Zhu J, Park SK, Xu K, Moayyed H. The PsyTAR dataset: From patients generated narratives to a corpus of adverse drug events and effectiveness of psychiatric medications. Data Brief. 2019 Mar 15;24:103838. doi: 10.1016/j.dib.2019.103838. eCollection 2019 Jun.
Rajaraman S, Candemir S, Thoma G, Antani SK. Visualizing and explaining deep learning predictions for pneumonia detection in pediatric chest radiographs.
Proc. SPIE 10950, Medical Imaging 2019: Computer-Aided Diagnosis,
109500S (13 March 2019); doi: 10.1117/12.2512752.
Mayer CS, Williams N, Gold S, Fung KW, Huser V. Sharing of Individual Participant Data from Clinical Trials: General Comparison and HIV Use Case. AMIA Annu Symp Proc. 2020 Mar 4;2019:647-654.
Rodriguez L, Demner-Fushman D. Finding Understudied Disorders Potentially Associated with Maternal Morbidity and Mortality. AMIA Informatics Summit, March 2019.
Kilicoglu H, Peng Z, Tafreshi S, Tran T, Rosemblat G, Schneider J. Confirm
or Refute?: A Comparative Study on Citation Sentiment Classification in
Clinical Research Publications. J Biomed Inform. 2019 Feb 9:103123. doi: 10.1016/j.jbi.2019.103123.
Demner-Fushman D. Clinical, Consumer Health, and Visual Question Answering.
Springer Nature Switzerland AG 2019. J. A. Lossio-Ventura et al.
(Eds.): SIMBig 2018, CCIS 898, pp. 1–6, 2019.
Candemir S, Antani SK. A review on lung boundary detection in chest X-rays. Int J Comput Assist Radiol Surg. 2019 Feb 7. doi: 10.1007/s11548-019-01917-1.
Rodriguez L, Demner-Fushman D. Finding Understudied Disorders Potentially Associated with Maternal Morbidity and Mortality. AJP Rep. 2019 Jan;9(1):e36-e43. doi: 10.1055/s-0039-1683363. Epub 2019 Mar 4.
Ben Abacha A, Demner-Fushman D. On
the role of question summarization and information source restriction
in consumer health question answering. . In Proceedings of the AMIA 2019 Informatics Summit, San Francisco, CA, USA, 2019.
Zolnoori
M, Fung K, Patrick TB, Fontelo P, Kharrazi H, Faiola A, Wu YSS,
Eldredge CE, Luo J, Conway M, Zhu J, Park SK, Xu K, Moayyed H,
Goudarzvand S. A systematic approach for developing a corpus of patient reported adverse drug events: A case study for SSRI and SNRI medications. J Biomed Inform. 2019 Feb;90:103091. doi: 10.1016/j.jbi.2018.12.005. Epub 2019 Jan 4.
Hu
L, Bell D, Antani SK, Xue Z, Yu K, Horning MP, Gachuhi N, Wilson B,
Jaiswal MS, Befano B, Long LR, Herrero R, Einstein MH, Burk RD, Demarco
M, Gage JC, Wentzensen N, Schiffman M. An
Observational Study of Deep Learning and Automated Evaluation of
Cervical Images for Cancer Screening. J Natl Cancer Inst. 2019 Jan 10. doi: 10.1093/jnci/djy225
Scarton LA, Wang L, Kilicoglu H, Jahries M, Del Fiol M. Expanding vocabularies for complementary and alternative medicine therapies. Int J Med Inform. 2019 Jan;121:64-74. doi: 10.1016/j.ijmedinf.2018.11.009. Epub 2018 Nov 22.
Rindflesch TC, Blake CL, Cairelli MJ, Fiszman M, Zeiss CJ, Kilicoglu H. Investigating
the role of interleukin-1 beta and glutamate in inflammatory bowel
disease and epilepsy using discovery browsing. J Biomed Semantics. 2018 Dec 27;9(1):25. doi: 10.1186/s13326-018-0192-y.
Ben-Zikri Y, Yaniv Z, Baum K, Linte C. A Marker-Free Registration Method for Standing X-ray Panorama Reconstruction for Hip-Knee-Ankle Axis Deformity Assessment. Comput Methods Biomech Biomed Eng Imaging Vis. 2019;7(4):464-478. doi: 10.1080/21681163.2018.1537859. Epub 2018
Jaeger
S, Juarez-Espinosa OH, Candemir S, Poostchi M, Yang F, Kim L, Ding M,
Folio LR, Antani SK, Gabrielian A, Hurt D, Rosenthal A, Thoma
GR. Detecting drug-resistant tuberculosis in chest radiographs. Int J Comput Assist Radiol Surg. 2018 Dec;13(12):1915-1925. doi: 10.1007/s11548-018-1857-9. Epub 2018 Oct 3.
Thoma, GR. Where we’ve been.. And where we’re going. Talk given by George Thoma at his retirement.
Lau JJ, Gayen S, Ben Abacha A, Demner-Fushman D. A dataset of clinically generated visual questions and answers about radiology images. Sci Data. 2018 Nov 20;5:180251. doi: 10.1038/sdata.2018.251.
Demner-Fushman D, Fung K, Do P, Boyce R, Goodwin T. Overview of the TAC 2018 Drug-Drug Interaction Extraction from Drug Labels Track.
Proceedings of the Text Analysis Conference (TAC) 2018, Gaithersburg,
MD, USA, November 13-14, 2018.
Peters TM, Linte CA, Yaniv Z, Williams J. Mixed and Augmented Reality in Medicine. CRC Press.
Lu C, Demner-Fushman D. Improving
Spelling Correction with Consumer Health Terminology Improving Spelling
Correction with Consumer Health Terminology. AMIA 2018 Annual Symposium, San Francisco, CA, November 3-7, 2018, p. 2053.
Lu C, Demner-Fushman D. Improving Spelling Correction with Consumer Health Terminology . AMIA 2018 Annual Symposium, San Francisco, CA, November 3-7, 2018, p. 2053.
Candemir S, Rajaraman S, Thoma GR, Antani SK. Deep Learning for Grading Cardiomegaly Severity in Chest X-rays: An Investigation.
Proc. IEEE Life Sciences Conference (LSC 2018), Montreal, Quebec,
Canada, 28 – 30 October 2018. pp. 109-113.
Yaniv Z, Güler Ö, Gong RH. Cost Effective Simulation; A Mixed Reality Approach. Ch. 10 in Mixed and Augmented Reality in Medicine.
Dhoot R, Humphrey JM, O'Meara P, Gardner A, McDonald CJ, Ogot K, Antani SK, Abuya J, Kohli M. Implementing
a mobile diagnostic unit to increase access to imaging and laboratory
services in western Kenya. BMJ Glob Health. 2018 Oct 8;3(5):e000947. doi: 10.1136/bmjgh-2018-000947. eCollection 2018.
Poostchi
M, Ilker E, McMenamin K, Gordon E, Palaniappan N, Pierce S, Maude RJ,
Bansal A, Srinivasan P, Miller L, Palaniappan K, Thoma GR, Jaeger
S. Malaria parasite detection and cell counting for human and mouse using thin blood smear microscopy. J Med Imaging (Bellingham). 2018 Oct;5(4):044506. doi: 10.1117/1.JMI.5.4.044506. Epub 2018 Dec 12.
Zolnoori M, Fung K, Fontelo P, Kharrazi H, Faiola A, Wu YSS, Stoffel V, Patrick T. Identifying the Underlying Factors Associated With Patients' Attitudes Toward Antidepressants: Qualitative and Quantitative Analysis of Patient Drug Reviews. JMIR Ment Health. 2018 Sep 30;5(4):e10726. doi: 10.2196/10726.
Fontelo P, Liu F. A review of recent publication trends from top publishing countries. Syst Rev. 2018 Sep 27;7(1):147. doi: 10.1186/s13643-018-0819-1.
Rajaraman S, Candemir S, Kim I, Thoma GR, Antani SK. Visualization and Interpretation of Convolutional Neural Network Predictions in Detecting Pneumonia in Pediatric Chest Radiographs. Appl. Sci. 2018, 8, 1715.
Sylim P, Liu F, Marcelo A, Fontelo P. Blockchain Technology for Detecting Falsified and Substandard Drugs in Distribution: Pharmaceutical Supply Chain Intervention. JMIR Res Protoc. 2018 Sep 13;7(9):e10163. doi: 10.2196/10163.
Yang F, Yu H, Poostchi M, Silamut K, Maude RJ, Jaeger S. Smartphone-Supported Automated Malaria Parasite Detection. SIIM conference on Machine Intelligence in Medical Imaging, 2018.
Ben Abacha A, Gayen S, Lau JJ, Rajaraman S, Demner-Fushman D. NLM at ImageCLEF 2018 Visual Question Answering in the Medical Domain. CLEF2018 Working Notes. CEUR Workshop Proceedings, Avignon, France, CEUR-WS.org (September 10-14 2018).
Jaeger S, Antani SK, Rajaraman S, Yang F, Yu H. Malaria Screening: Research into Image Analysis and Deep Learning. Report to the Board of Scientific Counselors September 2018.
Beare R, Lowekamp B, Yaniv Z. Image Segmentation, Registration and Characterization in R with SimpleITK. J Stat Softw. 2018 Aug;86. pii: 8. doi: 10.18637/jss.v086.i08. Epub 2018 Sep 4.
McDonald CJ, Maglott D, Abhyankar S, Goodwin RM, Kanduru A, Lu S, Lynch P, Vreeman D, Wang Y, Wood G. US Realm, Chapter 5, Use Case – Clinical Genomics Results Reporting. in HL7 Version 2.5.1 Implementation Guide: Lab Results Interface (LRI), DTSU3. HL7 International (Ann Arbor).
McDonald CJ, Maglott D, Abhyankar S, Goodwin RM, Kanduru A, Lu S, Lynch P, Vreeman D, Wang Y, Wood G. US Realm, Chapter 14, Use Case – Clinical Genomics Code Systems. in HL7 Version 2.5.1 Implementation Guide: Lab Results Interface (LRI), DTSU3. HL7 International (Ann Arbor).
Rae A, Kim J, Le DX, Thoma GR. Main Content Detection in HTML Journal Articles.
DocEng ’18: ACM Symposium on Document Engineering 2018, August 28–31,
2018, Halifax, NS, Canada. ACM, New York, NY, USA, 4 pages.
https://doi.org/10.1145/3209280.3229115
Vajda S, Karargyris A, Jaeger S, Santosh KC, Candemir S, Xue Z, Antani SK, Thoma GR. Feature Selection for Automatic Tuberculosis Screening in Frontal Chest Radiographs. J Med Syst. 2018 Jun 29;42(8):146. doi: 10.1007/s10916-018-0991-9.
Bodenreider O, Cornet R, Vreeman DJ. Recent Developments in Clinical Terminologies - SNOMED CT, LOINC, and RxNorm. Yearb Med Inform. 2018 Aug;27(1):129-139. doi: 10.1055/s-0038-1667077. Epub 2018 Aug 29.
Huser V, Shmueli-Blumberg D. Data sharing platforms for de-identified data from human clinical trials. Clin Trials. 2018 Aug;15(4):413-423. doi: 10.1177/1740774518769655.
Rajaraman S, Silamut K, Hossain MA, Ersoy I, Maude RJ, Jaeger S, Thoma GR, Antani SK. Understanding
the learned behavior of customized convolutional neural networks toward
malaria parasite detection in thin blood smear images. J Med Imaging (Bellingham). 2018 Jul;5(3):034501. doi: 10.1117/1.JMI.5.3.034501. Epub 2018 Jul 18.
Xue Z, Long LR, Jaeger S, Folio L, Thoma GR. Extraction of Aortic Knuckle Contour in Chest Radiographs Using Deep Learning. EMBC 2018.
Rajaraman S, Candemir S, Xue Z, Alderson P, Kohli M, Abuya J, Thoma GR, Antani SK. A novel stacked generalization of models for improved TB detection in chest radiographs.
Proc. IEEE Engineering in Medicine and Biology Conference (EMBC 2018),
Honolulu, Hawaii, 2018. pp. 718-721.
Kim I, Thoma GR. Automated
Identification of Potential Conflict-of-Interest in Biomedical Articles
Using Hybrid Deep Neural Network.
Proc. 14th Int’l Conf. Machine Learning and Data Mining (MLDM 2018),
LNAI 10934, pp. 99-112, Newark, NJ, July 2018.
Thamizhvani TR, Lakshmanan S, Rajaraman S. Mobile application-based computer-aided diagnosis of skin tumours from dermal images. The Imaging Science Journal, 66:6, 382-391, 2018, DOI: 10.1080/13682199.2018.1492682
Xue Z, Rajaraman S, Long LR, Antani SK, Thoma GR. Gender Detection from Spine X-ray Images Using Deep Learning.
Proc. IEEE International Symposium on Computer-Based Medical Systems
(CBMS), Karlstad, Sweden, 2018. pp. 54-58,
DOI:10.1109/CBMS.2018.00017.
Kim I, Thoma GR. Automated
Identification of Potential Conflict-of-Interest in Biomedical Articles
Using Hybrid Deep Neural Network.
Proc. 14th Int’l Conf. Machine Learning and Data Mining (MLDM 2018),
LNAI 10934, pp. 99-112, Newark, NJ, July 2018.
Kilicoglu H, Rosemblat G, Malicki M, Ter Riet G. Automatic recognition of self-acknowledged limitations in clinical research literature. J Am Med Inform Assoc. 2018 Jul 1;25(7):855-861. doi: 10.1093/jamia/ocy038.
Kim J, Candemir S, Chew E, Thoma GR. Region
of Interest Detection in Fundus Images Using Deep Learning and Blood
Vessel Information. The 31th IEEE International Symposium on
Computer-Based Medical Systems. (IEEE CBMS 2018), pp. 357-362, Karlstad, Sweden, June 2018.
McDonald CJ. Logical
Observation Identifiers Names and Codes for In Vitro Diagnostic Test;
Guidance for Industry and Food and Drug Administration Staff.
. Silver Spring, Md: Center for Devices and Radiological Health, FDA, 2018.
Yao S, Yu H, AliAkbarpour H, Seetharaman G, Palaniappan K. EpiX: A 3D Measurement Tool for Heritage, Archeology, and Aerial Photogrammetry. Heritage Preservation, pp. 47-66, 2018.
Yaniv Z, Lowekamp B, Johnson HJ, Beare R. SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research. J Digit Imaging. 2018 Jun;31(3):290-303. doi: 10.1007/s10278-017-0037-8.
Goss
FR, Lai KH, Topaz M, Acker WW, Kowalski L, Plasek JM, Blumenthal KG,
Seger DL, Slight SP, Fung KW, Chang FY, Bates DW, Zhou L. A value set for documenting adverse reactions in electronic health records. J Am Med Inform Assoc. 2018 Jun 1;25(6):661-669. doi: 10.1093/jamia/ocx139.
Gartrell K, Brennan CW, Wallen GR, Liu F, Smith KG, Fontelo P. Clinicians' perceptions of usefulness of the PubMed4Hh mobile device application for clinical decision making at the point of care: a pilot study. BMC Med Inform Decis Mak. 2018 May 8;18(1):27. doi: 10.1186/s12911-018-0607-9.
Sornapudi
S, Stanley RJ, Stoecker WV, Almubarak H, Long LR, Antani SK, Thoma GR,
Zuna R, Frazier SR. Deep Learning Nuclei Detection in Digitized Histology Images by Superpixels. J Pathol Inform. 2018 Mar 5;9:5. doi: 10.4103/jpi.jpi_74_17. eCollection 2018.
Fernandez-Repollet E, Locatis CN, De Jesus-Monge WE, Maisiak R, Lie WL. Effects
of summer internship and follow-up distance mentoring programs on
middle and high school student perceptions and interest in health
careers. BMC Med Educ. 2018 May 2;18(1):84. doi: 10.1186/s12909-018-1205-3.
Santosh KC, Antani SK. Automated chest x-ray screening: Can lung region symmetry help detect pulmonary abnormalities?. doi: 10.1109/TMI.2017.2775636 vol. 37, no. 5, 1168-1177.
Vreeman DJ, Abhyankar S, McDonald CJ. Re: Unit conversions between LOINC codes Published June 19, 2017 [Letter]. J Am Med Inform Assoc. 2018 May 1;25(5):614-615. doi: 10.1093/jamia/ocx087.
Misra D, Gill MJ. FaceMatch: A System for Dynamic Search and Retrieval of Faces. Proc. Archiving 2018. Washington DC. pp. 53-57. DOI: 10.2352/issn.2168-3204.2018.1.0.12.
Edinger T, Demner-Fushman D, Cohen AM, Bedrick S, Hersh W. Evaluation of Clinical Text Segmentation to Facilitate Cohort Retrieval. AMIA Annu Symp Proc. 2018 Apr 16;2017:660-669. eCollection 2017.
Fung K, Xue Z, Ameye F, Gutierrez AR, D'Have A. Achieving Logical Equivalence between SNOMED CT and ICD-10-PCS Surgical Procedures. AMIA Annu Symp Proc. 2018 Apr 16;2017:724-733. eCollection 2017.
Kayaalp M. Modes of De-identification. AMIA Annu Symp Proc. 2018 Apr 16;2017:1044-1050. eCollection 2017.
Rajaraman
S, Antani SK, Poostchi Mohammadabadi M, Silamut K, Hossain MA, Maude
RJ, Jaeger S, Thoma GR. Pre-trained
convolutional neural networks as feature extractors toward improved
malaria parasite detection in thin blood smear images. PeerJ. 2018 Apr 16;6:e4568. doi: 10.7717/peerj.4568. eCollection 2018.
Rodriguez L, Morrison SM, Greenberg K, Demner-Fushman D. Mining the literature for genes associated with placenta-mediated maternal diseases. AMIA Annu Symp Proc. 2018 Apr 16;2017:1498-1506. eCollection 2017.
Rajaraman S, Antani SK, Poostchi M, Silamut K, Hossain MA, Maude RJ, Jaeger S, Thoma GR. Pre-trained convolutional neural networks as feature extractors toward improved malaria parasite detection in thin blood smear images. PeerJ. 2018 Apr 16;6:e4568. doi: 10.7717/peerj.4568. PMID: 29682411; PMCID: PMC5907772.
Bodenreider O. Evaluating the Quality and Interoperability of Biomedical Terminologies. Technical Report to the LHNCBC Board of Scientific Counselors April 2018.
Rodriguez L, Demner-Fushman D. Extracting Diseases Co-occurring with Past Medical History of Lyme Disease. AMIA 2018 Informatics Summit
Gimbel RW, Pirrallo RG, Lowe SC, Wright DW, Zhang L, Woo MJ, Fontelo P, Liu F, Connor Z. Effect of clinical decision rules, patient cost and malpractice information on clinician brain CT image ordering: a randomized controlled trial. BMC Med Inform Decis Mak. 2018 Mar 12;18(1):20. doi: 10.1186/s12911-018-0602-1.
Xue Z, Antani SK, Long LR, Thoma GR. Using deep learning for detecting gender in adult chest radiographs.
Proc SPIE 10579, Medical Imaging 2018: Imaging Informatics for
Healthcare, Research, and Applications, 105790D (6 March 2018) pp. doi:
10.1117/12.2293027.
Moallem
G, Sari-Sarraf H, Poostchi M, Maude RJ, Silamut K, Hossain MA, Antani
SK, Jaeger S, Thoma G. Detecting and segmenting overlapping red blood cells in microscopic images of thin blood smears. Proc. SPIE 10581, Medical Imaging 2018:Digital Pathology, 105811F (6 March 2018); doi: 10.1117/12.2293762.
Xue Z, Jaeger S, Antani SK, Long LR, Karargyris A, Siegelman J, Folio L, Thoma GR. Localizing tuberculosis in chest radiographs with deep learning. Proc SPIE 10579, Medical Imaging 2018: Imaging Informatics for Healthcare, Research, and Applications, 105790U (6 March 2018) pp. doi: 10.1117/12.2293022.
Zohora FT, Antani SK, Santosh KC. Circle-like
foreign element detection in chest x-rays using normalized
cross-correlation and unsupervised clustering.
Proc. SPIE 10574, Medical Imaging 2018: Image Processing, 105741V (2
March 2018); doi: 10.1117/12.2293739;
doi.org/10.1117/12.2293739.
Almubarak H, Guo P, Stanley RJ, Long LR, Antani SK, Thoma GR. Algorithm
Enhancements for Improvement of Localized Classification of Uterine
Cervical Cancer Digital Histology Images.
in Handbook of Research on Emerging Perspectives on Healthcare
Information Systems and Informatics,. IGI Global (Hershey, PA).
Tang P, McDonald CJ. Computer-Based Patient-Record Systems - Chapter 9.
In Shortliffe E, Perreault L, eds. Medical Informatics. New York:
springer. 2001:327-358. DOI:
10.1007/978-0-387-21721-5_9.
Rajaraman S, Antani SK, Candemir S, Xue Z, Abuya J, Kohli M, Alderson P, Thoma GR. Comparing deep learning models for population screening using chest radiography. Proc. SPIE 10575, Medical Imaging 2018: Computer-Aided Diagnosis, 105751E (27 February 2018).
Thamizhvani TR, Lakshmanan S, Rajaraman S. Computer Aided Diagnosis of Skin Tumours from Dermal Images. .
Hemanth D., Smys S. (eds) Computational Vision and Bio Inspired
Computing. Lecture Notes in Computational Vision and Biomechanics, vol
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Zhang Y, Baik SH, Zuvekas SH. Simulating Variation in Families' Spending across Marketplace Plans. Health Serv Res. 2018 Feb 14. doi: 10.1111/1475-6773.12831.
Ghosh A, Brown GT, Fontelo P. Telepathology at the Armed Forces Institute of Pathology: A Retrospective Review of Consultations From 1996 to 1997. Arch Pathol Lab Med. 2018 Feb;142(2):248-252. doi: 10.5858/arpa.2017-0055-OA. Epub 2017 Oct 2.
Xue Z, Antani SK, Long LR, Thoma GR. Using deep learning for detecting gender in adult chest radiographs. SPIE Medical Imaging 2018
Kilicoglu H, Ben Abacha A, Mrabet Y, Shooshan SE, Rodriguez L, Masterton K, Demner-Fushman D. Semantic annotation of consumer health questions. BMC Bioinformatics. 2018 Feb 6;19(1):34. doi: 10.1186/s12859-018-2045-1.
Cui L, Bodenreider O, Shi J, Zhang GQ. Auditing
SNOMED CT hierarchical relations based on lexical features of concepts
in non-lattice subgraphs. Biomed Inform. 2018 Feb;78:177-184. doi: 10.1016/j.jbi.2017.12.010. Epub 2017 Dec 20.
McDonald CJ. FHIR Overview. Presentation by Clement J. McDonald, MD.
Lynch P, Wang Y, Kanduru A, Luan X, Mericle L, Lu S, McDonald CJ. On-the-Fly Data Capture Tooling for FHIR/HL7 V2. HL7 January 2018 Working Group Meeting, New Orleans, LA.
Zweigenbaum P, Demner-Fushman D. Advanced Literature-Mining Tools. .
In Edwards D, Stajich J, and Hansen D. (Editors). Bioinformatics: Tools
and Applications. Springer 2009.
Janakiram C, Chalmers NI, Fontelo P, Huser V, Lopez Mitnik GL, Iafolla TJ, Brow AR, Dye BA. Gender and Race/ethnic Disparities in Opioid Prescriptions for Dental Diagnoses among Patients with Medicaid. J Am Dent Assoc, 2018. 149(4): p. 246-255.
Dangi S, Linte C, Yaniv Z. Cine cardiac MRI slice misalignment correction towards full 3D left ventricle segmentation.
SPIE Medical Imaging: Image-Guided Procedures, Robotic Interventions,
and Modeling, Houston, Texas, in press.
Demner-Fushman D. A dataset of 200 structured product labels annotated for adverse drug reactions. . Sci Data. 2018 Jan 30;5:180001. doi: 10.1038/sdata.2018.1.
Poostchi M, Silamut K, Maude RJ, Jaeger S, Thoma GR. Image analysis and machine learning for detecting malaria. Transl Res. 2018 Apr;194:36-55. doi: 10.1016/j.trsl.2017.12.004. Epub 2018 Jan 12.
Kayaalp M. Patient Privacy in the Era of Big Data. Balkan Med J. 2018 Jan 20;35(1):8-17. doi: 10.4274/balkanmedj.2017.0966. Epub 2017 Sep 13.
Huser V, Kahn MG, Brown JS, Gouripeddi R. Methods for examining data quality in healthcare integrated data repositories. Pac Symp Biocomput. 2018;23:628-633.
Bryant B, Sari-Sarraf H, Long LR, Antani SK. A Kernel Support Vector Machine Trained Using Approximate Global and Exhaustive Local Sampling.
Proceedings of the 4th IEEE/ACM International Conference on Big Data
Computing, Applications and Technologies (BDCAT) 2017, Austin, Texas,
USA, December 2017. Pp. 267-8 DOI:
https://doi.org/10.1145/3148055.3149206
de Herrera G, Long LR, Antani SK. Graph Representation for Content–based fMRI Activation Map Retrieval.
Proceedings of 1st Life Sciences Conference, Sydney, Australia,
December 2017 pp. 129-32 DOI:
https://doi.org/10.1109/LSC.2017.8268160.
Rajaraman S, Antani SK, Xue Z, Candemir S, Jaeger S, Thoma GR. Visualizing abnormalities in chest radiographs through salient network activations in Deep Learning.
Proc. IEEE Life Sciences Conference (LSC), Sydney, Australia, 2017. pp.
71-74, DOI:10.1109/LSC.2017.8268146.
Harpaz
R, DuMouchel W, Schuemie M, Bodenreider O, Friedman C, Horvitz E,
Ripple A, Sorbello A, White RW, Winnenburg R, Shah NH. Toward multimodal signal detection of adverse drug reactions. . J Biomed Inform. 2017 Dec;76:41-49. doi: 10.1016/j.jbi.2017.10.013. Epub 2017 Nov 1.
Ben Abacha A, Long LR, Seco de Herrera AG, Antani SK, Wang K, Demner-Fushman D. Named Entity Recognition in Functional Neuroimaging Literature. BIBM 2017
Zou J, Antani SK, Thoma GR. Localizing and Recognizing Labels for Multi-Panel Figures in Biomedical Journals. Proceedings of International Conference on Document Analysis and Recognition, November 13, 2017
Gavino AI, Sarmiento RFR, Santos ADF, Sylim P, Magtubo KMP, Umali MJP, Pasco PM, Fontelo P, Fernandez-Marcelo P, Marcelo AB. Use of Text Messaging and Email for Telemedicine Consultations by Remote Rural Doctors. In “eHealth: A Step Towards the Universal Health Coverage in Developing Countries”. EDUFMA: 195-201. ISBN 978-85-7862-711-9.
Zolnoori M, Patrick TB, Fung KW, Fontelo P, Faiola A, Wu YSS, Xu K, Zhu J, Eldredge CE. Development of an Adverse Drug Reaction Corpus from Consumer Health Posts. Workshop: American Medical Informatics Association, Annual Symposium, 2017.
Moallem
G, Poostchi M, Yu H, Palaniappan N, Silamut K, Maude RJ, Hossain Md
Amir, Jaeger S, Antani SK, Thoma GR. Detecting and Segmenting White Blood Cells in Microscopy Images of Thin Blood Smears [Poster]. Annual Meeting of the American Society of Tropical Medicine & Hygiene (ASTMH), Poster, 2017.
Lu C, Tormey D, McCreedy L, Browne AC. Enhancing LexSynonym Features in the Lexical Tools . AMIA 2017 Annual Symposium, Washington, DC, November 04-08, 2017, p. 2090
Raje S, Bhupatiraju R, Abdelrahman H, Busby B. MeSHgram: An Open Source Tool to Visually Browse Co-occurrence of MeSH Terms in PubMed [Poster]. AMIA 2017 Symposium Proceedings.
Abhyankar S, Schluter P, Bennett K, Vreeman D, McDonald CJ. Enabling Interoperability between Healthcare Devices and EHR Systems. In 2017 AMIA Symposium. Wasington DC: IEEE.
McDonald CJ, Vreeman D, Wang K, Carr C, Colins B, Abhyankar S, Deckard J, Rubin D, Langlotz C. The LOINC/RSNA Radiology Playbook: A unified terminology for radiology procedures. . In 2017 AMIA Symposium. Washington DC.
Almubarak HA, Stanley RJ, Long LR, Antani SK, Thoma GR, Zuna R, Frazier SR. Convolutional
Neural Network Based Localized Classification of Uterine Cervical
Cancer Digital Histology Images.
Procedia Computer Science, Volume 114, 2017, Pages 281-287, ISSN
1877-0509, https://doi.org/10.1016/j.procs.2017.09.044.
Kury F, Baik SH, McDonald CJ. Cardioprotective Drugs and Incident Dementias in Medicare's Big Data. AMIA 2017.
Fallavollita P, Kersten M, Linte CA, Pratt P, Yaniv Z. Guest
Editors' Foreword: Special Issue on Augmented Environments for
Computer-Assisted Interventions CAI systems enable more precise, safer,
and less invasive interventional treatments [Letter]. Healthc Technol Lett. 2017 Oct 27;4(5):149. doi: 10.1049/htl.2017.0078. eCollection 2017 Oct.
Baik SH, Kury F, McDonald CJ. Risk
of Alzheimer's Disease Among Senior Medicare Beneficiaries Treated With
Androgen Deprivation Therapy for Prostate Cancer. J Clin Oncol. 2017 Oct 20;35(30):3401-3409. doi: 10.1200/JCO.2017.72.6109. Epub 2017 Aug 25.
Ekong DU, Fontelo P. Prototype telepathology solutions that use the Raspberry Pi and mobile devices. 2017 IEEE Global Humanitarian Technology Conference (GHTC), San Jose CA, 2017: 1-4.
Chatain
GP, Patronas N, Smirniotopoulos J, James G, Piazza M, Benzo S,
Ray-Chaudrury A, Sharma S, Lodish M, Nieman L, Stratakis CA, Chittiboina
P. Potential utility of FLAIR in MRI-negative Cushing's disease. J Neurosurg. 2017 Oct 13:1-9. doi: 10.3171/2017.4.JNS17234.
Fung K, Gutierrez A, Ameye F, D’Have A, Ariel B. Demonstrating the Benefits of Mapping SNOMED CT to ICD-10-PCS through a Prototype Application for End User Implementation. SNOMED Expo Oct 2017, Bratislava, Slovakia pp. 0
Guan
Y, Li M, Jaeger S, Lure F, Raptopoulos V, Lu P, Folio LR, Candemir S,
Antani SK, Siegelman J, Li J, Wu T, Thoma GR, Qu S. Applying
Artificial Intelligence and Radiomics for Computer Aided Diagnosis and
Risk Assessment in Chest Radiographs.
2nd Conference on Machine Intelligence in Medical Imaging (CMIMI) of
the Society for Imaging Informatics in Medicine (SIIM), Poster,
2017.
Moallem G, Jaeger S, Poostchi M, Palaniappan N, Yu H, Silamut K, Maude RJ, Antani SK, Thoma GR. White Blood Cell Detection and Segmentation in Microscopy Images of Thin Blood Smears [Poster]. NIH Research Festival, Poster, 2017.
Bhupatiraju R, Huser V, Fung K. Phenotype modelling tools utilizing standardized EHR data in a Common Data Model format [Poster]. NIH Research Festival 2017.
Fung K. Medical Terminologies in Action. Technical Report to the LHNCBC Board of Scientific Counselors September 2017.
Ben Abacha A, De Herrera A, Gayen S, Demner-Fushman D, Antani SK. NLM at ImageCLEF 2017 Caption Task. International Conference of the Cross-Language Evaluation Forum for European Languages 2017 Sep 11 (pp. 358-360). Springer, Cham.
Roberts K, Gururaj A, Chen X, Pournejati S, Cohen T, Hersh WR, Demner-Fushman D. Information Retrieval for Biomedical Datasets. 2016 bioCADDIE Challenge. AMIA 2017.
Sun H, Li J, Wu Y, Wang L, Fung K. Using
an Ontology-Based Approach to Handle Author Affiliations in a Large
Biomedical Citation Database. Stud Health Technol Inform. 2017;245:1338.
Coakley
M, Hurt D, Weder N, Mtingwa M, Fincher EC, Alekseyev V, Chen D, Yun A,
Gizaw M, Swan J, Yoo TS, Huyen Y. The NIH 3D Print Exchange: A Public Resource for Bioscientific and Biomedical 3D Prints. 3D Print Additive Manufacturing, Sep. 1, 2014, 1(3):137-140.
Abhyankar S, Vreeman DJ, Westra BL, Delaney CW. Comments on the Use of LOINC and SNOMED CT for Representing Nursing Data [Letter]. Int J Nurs Knowl. 2017 Aug 30. doi: 10.1111/2047-3095.12183.
Raje S, Bodenreider O. Interoperability
of disease concepts in clinical and research ontologies – Contrasting
coverage and structure in the Disease Ontology and SNOMED
CT. Stud Health Technol Inform. 2017;245:925-929.
Bhupatiraju R, Fung K, Bodenreider O. MetaMapLite in Excel: Biomedical named-entity recognition for non-technical users. Stud Health Technol Inform (Proc Medinfo): 1252.
Rajaraman S, Antani SK, Jaeger S. Visualizing Deep Learning Activations for Improved Malaria Cell Classification.
Proceedings of The First Workshop in Medical Informatics and Healthcare
(MIH 2017), Proceedings of Machine Learning Research (PMLR), v. 69, p.
40-47.
Marchell R, Locatis CN, Brgess G, Maisiak R, Liu WL, Ackerman M. Patient and Provider Satisfaction with Teledermatology. Telemed J E Health. 2017 Aug;23(8):684-690. doi: 10.1089/tmj.2016.0192. Epub 2017 Apr 4.
Mundkur ML, Callaghan FM, Abhyankar S, McDonald CJ. Use
of Electronic Health Record Data to Evaluate the Impact of Race on
30-Day Mortality in Patients Admitted to the Intensive Care
Unit. J Racial Ethn Health Disparities. 2017 Aug;4(4):539-548. doi: 10.1007/s40615-016-0256-6. Epub 2016 Jun 20.
Blake C, Rindflesch TC. Leveraging syntax to better capture the semantics of elliptical coordinated compound noun phrases. J Biomed Inform. 2017 Aug;72:120-131. doi: 10.1016/j.jbi.2017.07.001. Epub 2017 Jul 4.
Mrabet Y, Kilicoglu H, Demner-Fushman D. TextFlow: A Text Similarity Measure based on Continuous Sequences. Proceedings of the 55th Annual Meeting of the Association for Computational Linguistics, 2017, Vancouver, Canada, July 30 - August 4, Volume
Kim I, Thoma GR. Machine
Learning with Selective Word Statistics for Automated Classification of
Citation Subjectivity in Online Biomedical Articles. Proc. Int’l Conf. Artificial Intelligence (ICAI’17), pp. 201-207, Las Vegas, July 2017.
Kim J, Hong S, Thoma GR. Labeling Author Affiliations in Biomedical Articles Using Markov Model Classifiers.
The 13th International Conference on Data Mining (DMIN2017), pp.
105-110, Las Vegas, USA, July 2017.
Kilicoglu H, Rosemblat G, Rindflesch TC. Assigning factuality values to semantic relations extracted from biomedical research literature. PLoS One. 2017 Jul 5;12(7):e0179926. doi: 10.1371/journal.pone.0179926. eCollection 2017.
Bongiorno MA, Nathan N, Oyerinde O, Wang JA, Lee CR, Brown G, Moss J, Darling TN. Clinical
Characteristics of Connective Tissue Nevi in Tuberous Sclerosis Complex
With Special Emphasis on Shagreen Patches. JAMA Dermatol. 2017 Jul 1;153(7):660-665. doi: 10.1001/jamadermatol.2017.0298.
Fung K, Kapusnik-Uner J, Cunningham J, Higby-Baker S, Bodenreider O. Comparison
of three commercial knowledge bases for detection of drug-drug
interactions in clinical decision support. J Am Med Inform Assoc. 2017 Jul 1;24(4):806-812. doi: 10.1093/jamia/ocx010.
Cui L, Zhu W, Tao S, Case JT, Bodenreider O, Zhang GQ. Mining non-lattice subgraphs for detecting missing hierarchical relations and concepts in SNOMED CT. J Am Med Inform Assoc. 2017 Jul 1;24(4):788-798. doi: 10.1093/jamia/ocw175.
Rindflesch TC, Blake CL, Fiszman M, Kilicoglu H, Rosemblat G, Schneider J, Zeiss CJ. Informatics Support for Basic Research in Biomedicine. ILAR J. 2017 Jul 1;58(1):80-89. doi: 10.1093/ilar/ilx004.
Zhang, K, Demner-Fushman D. Automated
classification of eligibility criteria in clinical trials to facilitate
patient-trial matching for specific patient populations.
. J Am Med Inform Assoc. 2017 Jul 1;24(4):781-787. doi: 10.1093/jamia/ocw176.
Candemir S, Antani SK, Xue Z, Thoma GR. Novel Method for Storyboarding Biomedical Videos for Medical Informatics. 30th IEEE International Symposium on Computer-Based Medical Systems
Vreeman DJ, Abhyankar S, McDonald CJ. Unit conversions between LOINC codes Published June 19, 2017 [Letter].
Journal of the American Medical Informatics Association, 1–3.
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Kilicoglu H. Biomedical text mining for research rigor and integrity: tasks, challenges, directions. Brief Bioinform. 2017 Jun 13. doi: 10.1093/bib/bbx057.
Guo P, Stanley RJ, Cole JG, Hagerty JR, Stoecker WV. Color Feature-based Pillbox Image Color Recognition. Published 2017 in VISIGRAPP DOI:10.5220/0006136001880194.
Bush R, Heierman E, Knafel A, Lardin L, McDonald CJ. LIVD – Digital Format for Publication of LOINC to Vendor IVD Test Results. IVD Industry Connectivity Consortium. http://ivdconnectivity.org/livd/. Published June 1, 2017. Accessed August 9, 2017.
Chakrabarti S, Sen A, Huser V, Hruby GW, Rusanova A, Albers DJ, Weng C. An
Interoperable Similarity-based Cohort Identification Method Using the
OMOP Common Data Model version 5.0. J Healthc Inform Res. 2017 Jun;1(1):1-18. doi: 10.1007/s41666-017-0005-6. Epub 2017 Jun 8.
Ben Abacha A, Agichtein E, Pinter Y, Demner-Fushman D. Overview of the Medical QA Task @ TREC 2017 LiveQA Track. TREC, Gaithersburg, MD, 2017.
Ames NJ, Powers JH, Ranucci A, Gartrell K, Yang L, VanRaden M, Leidy NK, Wallen GR. A
systematic approach for studying the signs and symptoms of fever in
adult patients: the fever assessment tool (FAST). Health Qual Life Outcomes. 2017 Apr 27;15(1):84. doi: 10.1186/s12955-017-0644-6.
Ash J, Sittig D. Everything Electronic Medical Records: Systems, Standards and Studies. Conversations with Medical Informatics Pioneers: An oral history project.
Gardner C, Liu F, Fontelo P, Flanagan MC, Hoang A, Burke HB. Assessing the usability by clinicians of VISION: A hierarchical display of patient-collected physiological information to clinicians. BMC Med Inform Decis Mak. 2017 Apr 14;17(1):41. doi: 10.1186/s12911-017-0435-3.
Ekong D, Liu F, Brown G, Ghosh A, Fontelo P. Evaluation of Android Smartphones for Telepathology. J Pathol Inform. 2017 Apr 10;8:16. doi: 10.4103/jpi.jpi_93_16. eCollection 2017.
Huser V. Clinical Data Science. Technical Report to the LHNCBC Board of Scientific Counselors April 2017.
Mayer JE, Fontelo P. Meta-analysis on the effect of text message reminders for HIV-related compliance. AIDS Care. 2017 Apr;29(4):409-417. doi: 10.1080/09540121.2016.1214674. Epub 2016 Aug 1.
Borovikov E, Vajda S, Gill MJ. Face Match for Family Reunification: Real-World Face Image Retrieval. International Journal of Computer Vision and Image Processing. DOI: 10.4018/IJCVIP.2017040102.
Roberts
K, Boland MR, Pruinelli L, Dcruz J, Berry A, Georgsson M, Hazen R,
Sarmiento RF, Backonja U, Yu K-H, Jiang Y, Brennan PF. Biomedical
informatics advancing the national health agenda: the AMIA 2015
year-in-review in clinical and consumer informatics. J Am Med Inform Assoc. 2017 Apr 1;24(e1):e185-e190. doi: 10.1093/jamia/ocw103.
Raje S, Bodenreider O. Investigating the coverage of diseases across biomedical research and clinical ontologies. Proceedings of the AMIA Joint Summits on Translational Science CRI: 384-385.
Sorbello A, Ripple AM, Tonning J, Munoz M, Hasan R, Ly T, Francis H, Bodenreider O. Harnessing
scientific literature reports for pharmacovigilance. Prototype software
analytical tool development and usability testing. Appl Clin Inform. 2017 Mar 22;8(1):291-305. doi: 10.4338/ACI-2016-11-RA-0188.
Collins H, Calvo SC, Greenberg K, Forman NL, Morrison SM. Using Genetics Home Reference to Reinforce Patient Education [Poster]. American College of Medical Genetics Annual Meeting, Phoenix, AZ, March 21-25, 2017.
Xue Z, Antani SK, Long LR, Thoma GR. Automatic multi-label annotation of abdominal CT images using CBIR.
Proc. SPIE 10138, Medical Imaging 2017: Imaging Informatics for
Healthcare, Research, and Applications, 1013807 (March 13, 2017);
doi:10.1117/12.2254368.
Ding M, Antani SK, Jaeger S, Xue Z, Candemir S, Kohli M, Thoma GR. Local-Global Classifier Fusion for Screening Chest Radiographs.
Proc. SPIE 10138, Medical Imaging 2017: Imaging Informatics for
Healthcare, Research, and Applications, 101380A (March 13, 2017);
doi:10.1117/12.2252459
Marchell R, Locatis C, Burges G, Maisiak R, Liu WL, Ackerman M. Comparing
High Definition Live Interactive and Store-and-Forward Consultations to
In-Person Examinations. Telemed J E Health. 2017 Mar;23(3):213-218. doi: 10.1089/tmj.2016.0093. Epub 2016 Oct 5.
Mork JG, Aronson A, Demner-Fushman D. 12 years on - Is the NLM medical text indexer still useful and relevant?. J Biomed Semantics. 2017 Feb 23;8(1):8. doi: 10.1186/s13326-017-0113-5.
Lu C, Tormey D, McCreedy L, Browne AC. Generating A Distilled N-Gram Set: Effective Lexical Multiword Building in the SPECIALIST Lexicon.
The 10th International Joint Conference on Biomedical Engineering
Systems and Technologies (BIOSTEC 2017), Vol(5): HEALTHINF, PORTO,
Portugal, February 21-23, 2017, p. 77-87.
Lure F, Jaeger S, Antani SK. Automated Systems for microscopic and radiographic tuberculosis screening.
Electronic Journal of Emerging Infectious Diseases, Vol. 2, No. 1, pp.
5-9, February 2017. [In Chinese]
Workman E, Weir, C, Rindflesch TC. Differentiating Sense through Semantic Interaction Data. AMIA Annu Symp Proc. 2017 Feb 10;2016:1238-1247. eCollection 2016.
Ben Abacha A, Demner-Fushman D. Recognizing Question Entailment for Medical Question Answering. AMIA Annu Symp Proc. 2017 Feb 10;2016:310-318. eCollection 2016.
Fung K, Xu J, Amey F, Gutierrez AR, D'Have A. Leveraging
Lexical Matching and Ontological Alignment to Map SNOMED CT Surgical
Procedures to ICD-10-PCS. AMIA Annu Symp Proc. 2017 Feb 10;2016:570-579. eCollection 2016.
Kury F, Baik SH, McDonald CJ. Analysis
of Healthcare Cost and Utilization in the First Two Years of the
Medicare Shared Savings Program Using Big Data from the CMS
Enclave. AMIA Annu Symp Proc. 2017 Feb 10;2016:724-733. eCollection 2016.
Mrabet Y, Kilicoglu H, Roberts K, Demner-Fushman D. Combining Open-domain and Biomedical Knowledge for Topic Recognition in Consumer Health Questions. AMIA Annu Symp Proc. 2017 Feb 10;2016:914-923. eCollection 2016.
Roberts K, Rodriguez L, Shooshan SE, Demner-Fushman D. Resource Classification for Medical Questions. . AMIA Annu Symp Proc. 2017 Feb 10;2016:1040-1049. eCollection 2016.
Cahan A, Cimino JJ. Improving precision medicine using individual patient data from trials. CMAJ. 2017 Feb 6;189(5):E204-E207. doi: 10.1503/cmaj.160267. Epub 2016 Aug 29.
Peters L, Nguyen T, Bodenreider O. Terminology Status APIs - Mapping Obsolete Codes to Current RxNorm, SNOMED CT, and LOINC Concepts. Stud Health Technol Inform. 2017;245:1333.
Demner-Fushman D, Rogers W, Aronson A. MetaMap Lite: an evaluation of a new Java implementation of MetaMap. J Am Med Inform Assoc. 2017 Jul 1;24(4):841-844. doi: 10.1093/jamia/ocw177.
KC S, Aafaque A, Antani SK, Thoma GR. Line Segment-Based Stitched Multipanel Figure Separation for Effective Biomedical CBIR.
Int. J. Patt. Recogn. Artif. Intelligence 31, 1757003 (2017)
https://doi.org/10.1142/S0218001417570038.
KC S, Antani SK. Automated chest X-ray screening: Can lung region symmetry help detect pulmonary abnormalities? . IEEE Transactions on Medical Imaging. doi: https://doi.org/10.1109/TMI.2017.2775636.
Lu C, Tormey D, McCreedy L, Browne AC. Enhanced LexSynonym Acquisition for Effective UMLS Concept Mapping. Stud Health Technol Inform. 2017;245:501-505.
Bahr NJ, Nelson SD, Winnenburg R, Bodenreider O. Eliciting the Intension of Drug Value Sets - Principles and Quality Assurance Applications. Stud Health Technol Inform. 2017;245:843-847.
Topaz
M, Goss F, Blumenthal K, Lai K, Seger DL, Slight SP, Wickner PG,
Robinson GA, Fung KW, McClure RC, Spiro S, Acker WW, Bates DW, Zhou
L. Towards improved drug allergy alerts: Multidisciplinary expert recommendations. Int J Med Inform. 2017 Jan;97:353-355. doi: 10.1016/j.ijmedinf.2016.10.006. Epub 2016 Oct 6.
Dhombres F, Bodenreider O. Trends in Fetal Medicine: A 10-Year Bibliometric Analysis of Prenatal Diagnosis. Stud Health Technol Inform. 2017;245:853-857.
Deardorff A, Masterton K, Roberts K, Kilicoglu H, Demner-Fushman D. A
protocol-driven approach to automatically finding authoritative answers
to consumer health questions in online resources. JASIST, 68(7): 1724-1736. doi: 10.1002/asi.23806.
Nelsonn SD, Parker J, Lario R, Winnenburg R, Erlbaum MS, Lincoln MJ, Bodenreider O. Interoperability
of medication classification systems: Lessons learned mapping
estab-lished pharmacologic classes (EPCs) to SNOMED CT. Stud Health Technol Inform. 2017;245:920-924.
Yu Z, Nguyen T, Dhombres F, Johnson T, Bodenreider O. "Hybrid Topics" - Facilitating the Interpretation of Topics Through the Addition of MeSH Descriptors to Bags of Words. Stud Health Technol Inform. 2017;245:662-666.
Cohen T, Roberts K, Gururaj AE, Chen X, Pournejati S, Alter G, Hersh WR, Demner-Fushman D, Ohno-Machado L, Xu H. A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge. Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax061.
Guo P,
Almubarak H, Banerjee K, Stanley RJ, Long LR, Antani SK, Thoma GR, Zuna
R, Frazier S, Moss R, Stoecker W. Enhancements
in localized classification for uterine cervical cancer digital
histology image assessment. J Pathol Inform. 2016 Dec 30;7:51. doi: 10.4103/2153-3539.197193. eCollection 2016.
Borovikov E, Vajda S. FaceMatch: real-world face image retrieval.
In: Santosh K., Hangarge M., Bevilacqua V., Negi A. (eds) Recent Trends
in Image Processing and Pattern Recognition. RTIP2R 2016.
Communications in Computer and Information Science, vol 709. Springer,
Singapore. 405-419.
Chachra S, Ben Abacha A, Shooshan SE, Rodriguez L, Demner-Fushman D. A Hybrid Approach to Generation of Missing Abstracts in Biomedical Literature. Proceedings of COLING 2016, the 26th International Conference on Computational Linguistics: Technical Papers: 1093-1100.
Kilicoglu H. Inferring Implicit Causal Relationships in Biomedical Literature. Proc 15th Workshop on Biomedical Natural Language Processing. Pages 46-55. 2016.
Huser
V, DeFalco FJ, Schuemie M, Ryan PB, Shang N, Velez M, Park RW, Boyce
RD, Duke J, Khare R, Utidjian L, Bailey L. Multisite Evaluation of a Data Quality Tool for Patient-Level Clinical Data Sets. EGEMS (Wash DC). 2016 Nov 30;4(1):1239. doi: 10.13063/2327-9214.1239. eCollection 2016.
Greenberg K, Calvo SC, Collins H, Foreman NL, Morrison SM. Genetics Home Reference: A point of care resource in the genomic medicine era [Poster].
American Society of Human Genetics Annual Meeting, Vancouver, British
Columbia, Canada, November 18-22, 2016.
Narum R, Zou J, Antani SK. Semi-Automated Ground-Truth Data Collection and Annotation for Journal Figure Analysis [Poster]. 2016 NIH Research Festival
De Herrera A, Long LR, Antani SK. Content-Based fMRI Brain Maps Retrieval. International Conference on Brain and Health Informatics, Omaha, NE, USA, October 13-16, 2016.
De Herrera A, Schaer R, Antani SK, Müller H. Using Crowdsourcing for Multi-label Biomedical Compound Figure Annotation.
In: Carneiro G. et al. (eds) Deep Learning and Data Labeling for
Medical Applications. LABELS 2016, DLMIA 2016. Lecture Notes in Computer
Science, vol 10008. Springer, Cham
Ben Abacha A. NLM_NIH at TREC 2016 Clinical Decision Support Track.
Proceedings of TREC 2016, the 25th Text Retrieval Conference,
Gaithersburg, MD, USA, November 2016.
Wang Y, Lynch P, Kanduru A, Hook J, Mericle L, Ludet C, Vreeman D, McDonald CJ. LHC-Forms and Related Widgets for Capturing and Tuning Health Data [Poster]. AMIA Annual Symposium, Chicago IL
Ben Abacha A, Demner-Fushman D. NLM_NIH
at SemEval-2017 Task 3: from Question Entailment to Question Similarity
for Community Question Answering.
In Proceedings of the 11th International Workshop on Semantic
Evaluation (SemEval@ACL) 2017: 349-352.
Liang Z, Powell A, Ersoy I, Poostchi M, Silamut K, Palaniappan K, Guo P, Hossain M, Antani SK, Maude R, Huang J, Jaeger S, Thoma GR. CNN-Based Image Analysis for Malaria Diagnosis. IEEE International Conference on Bioinformatics & Biomedicine (BIBM), Shenzhen, China, 2016.
Borovikov E, Yershov S. On Virtual Characters that Can See.
7th Annual International Conference on Biologically Inspired Cognitive
Architectures, BICA 2016, held July 16 to July 19, 2016 in New York
City, NY, USA
Ben Abacha A, de Herrera A, Wang Ke, Long LR, Antani SK, Demner-Fushman D. Named entity recognition in functional neuroimaging literature.
2017 IEEE International Conference on Bioinformatics and Biomedicine
(BIBM), Kansas City, MO, 2017, pp. 2218-2220.
Jaeger
S, Silamut K, Yu H, Poostchi Mohammadabadi M, Ersoy I, Powell A, Liang
Z, Hossain M, Antani SK, Palaniappan K, Maude R, Thoma
GR. Reducing
the Diagnostic Burden of Malaria Using Microscopy Image Analysis and
Machine Learning in the Field [Poster]. Annual Meeting of the American Society of Tropical Medicine & Hygiene (ASTMH), Atlanta, USA, 2016.
Madani S, Henderson J, Fung K. Development of an oncology subset of SNOMED CT based on patient notes. AMIA Annu Symp Proc 2016: 91-92.
Rodriguez L, Morrison SM, Greenberg K, Demner-Fushman D. Towards Automatic Discovery of Genes Related to Human Placenta [Poster]. Poster Fall AMIA 2016.
Guo P, Stanley RJ, De S, Long LR, Antani SK, Thoma GR, Demner-Fushman D, Sornapudia S. Features Advances to Automatically Find Images for Application to Clinical Decision Support. Medical Research Archives. 4(7) 2016. DOI: 10.18103/mra.v4i7.761.
Linte CA, Yaniv Z. Image-Guided Interventions: We've come a long way, but are we there?. IEEE Pulse. 2016 Nov-Dec;7(6):46-50.
Shih RY, Smirniotopoulos J. Posterior Fossa Tumors inAdult Patients. Neuroimaging Clin N Am. 2016 Nov;26(4):493-510. doi: 10.1016/j.nic.2016.06.003. Epub 2016 Sep 2.
Drake-Perez M, Smirniotopoulos J. Extraparenchymal Lesions in Adults. Neuroimaging Clin N Am. 2016 Nov;26(4):621-646. doi: 10.1016/j.nic.2016.06.009.
Kochmann M, Locatis CN. Telemedicine in the Apple App Store: An exploratory study of teledermatology apps. . In Smari, W. & Natarian, J. (Eds.), Proc 2016 Int Conf Collaboration Technologies and Systems, Orlando, Florida, October 31-November 4, Institute for Electrical and Electronic Engineers & Association for Computing Machinery, 534-537.
Marchell R, Locatis CN, Ackerman MA. High
definition live interactive and store and forward teledermatology: A
comparison of concordance, confidence, and satisfaction with in-person
exams. In Smari, W. & Natarian, J. (Eds.), Proceedings of the 2016 International Conference on Collaboration Technologies and Systems, Orlando, Florida, October 31. Institute for Electrical and Electronic Engineers & Association for Computing Machinery, 520-523.
McDonald CJ, Wang Y, Lynch P, Kanduru A. Feeding FHIR with LHC-Forms. HL7 Partners in Interoperability Mt. Washington Conference Center, Baltimore, MD
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Z, Faruque J, Howe S, Dunn K, Sharlip D, Bond A, Perillan P,
Bodenreider O, Ackerman M, Yoo TS. The national library of medicine pill image recognition challenge: An initial report. Z.
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Recognition Workshop (AIPR), Washington, DC, 2016, pp. 1-9. doi:
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De Herrera A, Long LR, Antani SK. Content–based fMRI activation maps retrieval [Poster]. BIH 2016: Brain Informatics and Health pp 173-180, October 13-16, 2016.
Demner-Fushman D, Elhadad N. Aspiring to Unintended Consequences of Natural Language Processing: A Review of Recent Developments in Clinical and Consumer-Generated Text Processing. . IMIA Yearbook of Medical Informatics 2016.
Kastrin A, Rindflesch TC, Hristovski D. Link prediction on a network of co-occurring MeSH terms: Towards literature-based discovery. . Methods of Information in Medicine 55(4):340-6.
Xue Z, Rahman M, Antani SK, Long LR, Demner-Fushman D, Thoma GR. Modality Classification for Searching Figures in Biomedical Literature.
Proceedings of the IEEE 29th International Symposium on Computer-Based
Medical Systems, pp. 152-157, 2016.
doi:10.1109/CBMS.2016.29.
De Herrera A, Schaer R, Bromuri S, Müller H. Overview of the ImageCLEF 2016 Medical Task. CLEF working notes 2016, CEUR, 2016.
Villegas M, Müller R, De Herrera A, Schaer R, Bromuri S, Gilbert A, Piras L, Wang J, Yan F, Ramisa A, Dellandrea E, Gaizauskas R, Mikolajczyk K, Puigcerver J, Toselli A, Sánchez J, Vidal E. General Overview of ImageCLEF at the CLEF 2016 Labs. CLEF Proceedings, Springer, 2016
Borovikov E, Vajda S, Lingappa G, Bonifant MC. Parallel Computing in Face Image Retrieval: Practical Approach to the Real-World Image Search. Multi-Core Computer Vision and Image Processing for Intelligent Applications. IGI Global, 2017. 155-189. Web. 12 Sep. 2016. doi:10.4018/978-1-5225-0889-2.ch006
Kim J, Thoma GR. Named Entity Recognition in Affiliations of Biomedical Articles Using Statistics and HMM Classifiers.
The 2016 International Conference on Data Mining (DMIN2016), Las Vegas,
USA, pp. 236-241, July, 2016.
Mrabet Y, Vougiouklis P, Kilicoglu H, Gardent C, Demner-Fushman D, Hare J, Simperl E. Aligning Texts and Knowledge Bases with Semantic Sentence Simplification. WebNLG 2016.
Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Borlan MR, Georgiev I, Liu H, Livingston K, Luna A, Mallon AM, Manda P, Robinson PM, Rustici G, Simonn M, Wang L, Winnenburg R, Dumontier M. The digital revolution in phenotyping. Brief Bioinform. 2016 Sep;17(5):819-30. doi: 10.1093/bib/bbv083. Epub 2015 Sep 29.
Xu T, Zhang H, Xin C, Kim E, Long LR, Xue Z, Antani SK, Huang Z. Multi-feature based Benchmark for Cervical Dysplasia Classification Evaluation. Pattern Recognition. ISSN 0031-3203, DOI: 10.1016/j.patcog.2016.09.027.
KC S, Vajda S, Antani S, Thoma GR. Edge map analysis in chest X-rays for automatic pulmonary abnormality screening. Int J Comput Assist Radiol Surg. 2016 Sep;11(9):1637-46. doi: 10.1007/s11548-016-1359-6. Epub 2016 Mar 19.
Jarlenski M, Baik SH, Zhang Y. Trends in Use of Medications for Smoking Cessation in Medicare, 2007-2012. Am J Prev Med. 2016 Sep;51(3):301-8. doi: 10.1016/j.amepre.2016.02.018. Epub 2016 Mar 30.
Borovikov E, Bonifant MC, Lingappa G, Gill MJ, Thoma GR. FaceMatch: a visual search system for family reunification during disasters [Poster]. NIH Research Festival, September 2016
Mrabet Y, Kilicoglu H, Demner-Fushman D. Unsupervised Ranking of Knowledge Bases for Named Entity Recognition. ECAI 2016, The Hague, The Netherlands, 1248-1255.
Demner-Fushman D, Antani SK, Chachra S, Kushnir M, Gayen S. Open-i Imaging informatics, natural language processing and multi-modal information retrieval - research and development. Technical Report to the LHNCBC Board of Scientific Counselors September 2016.
Hristovski D, Kastrin A, Dinevski D, Burgun A, Ziberna L, Rindflesch TC. Using Literature-Based Discovery to Explain Adverse Drug Effects. J Med Syst. 2016 Aug;40(8):185. doi: 10.1007/s10916-016-0544-z. Epub 2016 Jun 18.
Boyce RD,
Voss EA, Huser V, Evans L, Reich C, Duke JD, Tatonetti NP, Lorberbaum T,
Dumontier M, Hauben M, Wallberg M. LAERTES:
An open scalable architecture for linking pharmacovigilance evidence
sources with clinical data.
Proc International Conference on Biomedical Ontology and BioCreative
(ICBO BioCreative 2016).
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Kochmann M, Locatis C. Direct to Consumer Mobile Teledermatology Apps: An Exploratory Study. Telemed J E Health. 2016 Aug;22(8):689-93. doi: 10.1089/tmj.2015.0189. Epub 2016 Mar 9.
Driessen J, Baik SH, Zhang Y. Trends
in Off-Label Use of Second-Generation Antipsychotics in the Medicare
Population From 2006 to 2012. Psychiatr Serv. 2016 Aug 1;67(8):898-903. doi: 10.1176/appi.ps.201500316. Epub 2016 Apr 15.
Wei W, Marmor R, Singh S, Wang S, Demner-Fushman D, Kuo TT, Hsu CN, Ohno-Machado L. Finding Related Publications: Extending the Set of Terms Used to Assess Article Similarity. AMIA Jt Summits Transl Sci Proc. 2016 Jul 20;2016:225-34. eCollection 2016.
Homer ML, Palmer NP, Bodenreider O, Cami A, Chadwick L, Mandl KD. The
Drug Data to Knowledge Pipeline: Large-Scale Claims Data Classification
for Pharmacologic Insight. AMIA Jt Summits Transl Sci Proc. 2016 Jul 20;2016:105-11. eCollection 2016.
Shin HC, Roberts K, Lu L, Demner-Fushman D. Learning to Read Chest X-Rays: Recurrent Neural Cascade Model for Automated Image Annotation. IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 2016.
Roberts K, Demner-Fushman D. Annotating Logical Forms for EHR Questions. Proceedings of the Language Resources and Evaluation Conference, LREC,23-28 May 2016, Portorož.
Kim J, Lobuglio PS, Thoma GR. Visualization of Statistics from MEDLINE.
2016 IEEE 29th International Symposium on Computer-Based Medical
Systems (CBMS 2016), Dublin and Belfast, Ireland, pp. 290-291, June,
2016.
Ben Abacha A, Demner-Fushman D. Meta-Learning with Selective Data Augmentation for Medical Entity Recognition. International Journal of Computational Linguistics and Applications (IJCLA) 7(2): 167-182 (2016)
Hripcsak
G, Ryan PB, Duke JD, Shah NH, Park RW, Huser V, Suchard MA, Schuemie
MJ, DeFalco FJ, Perotte A, Banda JM, Reich CG, Schilling LM, Matheny ME,
Meeker D, Pratt N, Madigan D. Characterizing treatment pathways at scale using the OHDSI network. Proc Natl Acad Sci U S A. 2016 Jul 5;113(27):7329-36. doi: 10.1073/pnas.1510502113. Epub 2016 Jun 6.
Kwon J, Wang A, Burke DJ, Boudreau HE, Lekstrom KJ, Korzeniowska A, Sugamata R, Kim YS, Yi L, Ersoy I, Jaeger S, Palaniappan K, Ambruso DR, Jackson SH, Leto TL. Peroxiredoxin
6 (Prdx6) supports NADPH oxidase1 (Nox1)-based superoxide generation
and cell migration. Free Radic Biol Med. 2016 Jul;96:99-115. doi: 10.1016/j.freeradbiomed.2016.04.009. Epub 2016 Apr 14.
Roberts K, Demner-Fushman D. Interactive use of online health resources: a comparison of consumer and professional questions. J Am Med Inform Assoc. 2016 Jul;23(4):802-11. doi: 10.1093/jamia/ocw024. Epub 2016 May 4.
Candemir S, Jaeger S, Antani S, Bagci U, Folio LR, Xu Z, Thoma G. Atlas-based rib-bone detection in chest X-rays. Comput Med Imaging Graph. 2016 Jul;51:32-9. doi: 10.1016/j.compmedimag.2016.04.002. Epub 2016 Apr 13.
Huser V, Cimino JJ. Impending Challenges for the Use of Big Data. Int J Radiat Oncol Biol Phys. 2016 Jul 1;95(3):890-894. doi: 10.1016/j.ijrobp.2015.10.060. Epub 2015 Nov 5.
Benedict SH, Hoffman K, Martel MK, Abernethy AP, Asher AL, Capala J, Chen RC, Chera B, Couch J, Deye J, Efstathiou JA, Ford E, Fraass BA, Gabriel PE, Huser V, Kavanagh BD, Khuntia D, Marks LB, Mayo C, McNutt T, Miller RS, Moore KL, Prior F, Roelofs E, Rosenstein BS, Sloan J, Theriault A, Vikram B. Overview
of the American Society for Radiation Oncology-National Institutes of
Health-American Association of Physicists in Medicine Workshop 2015:
Exploring Opportunities for Radiation Oncology in the Era of Big
Data. Int J Radiat Oncol Biol Phys. 2016 Jul 1;95(3):873-879. doi: 10.1016/j.ijrobp.2016.03.006.
James E. McDonald, MD, Ron Fishman, MD (Editor), McDonald CJ (Editor). FOCUS Eye Care in Haiti and Nigeria from 1961-1996. E-book (1st edition 2010, 2nd edition 2014).
KC S, Alam M, Roy P, Wendling L, Antani SK, Thoma GR. A simple and efficient arrowhead detection in biomedical images.
International J Pattern Recognition and Artificial Intelligence
(IJPRAI), 30(5), 1657002, 2016, DOI:
10.1142/S0218001416570020.
Kilicoglu H, Ben Abacha A, Mrabet Y, Roberts K, Rodriguez L, Shooshan SE, Demner-Fushman D. Annotating named entities in consumer health questions. LREC,23-28 May 2016, Portorož.
Lu C, Tormey D, McDreedy L, Browne AC. Multiword frequency analysis based on MEDLINE N - gram set [Poster]. AMIA 2016 Annual Symposium, Chicago, IL, November 12-16, 2016.
KC S, Wendling L, Antani SK, Thoma GR. Overlaid arrow detection for labeling biomedical image regions.
IEEE Intelligent Systems, Special Issue on Pattern Recognition,
31(3):66-75, May-June 2016.DOI: 10.1109/MIS.2016.24.
Xue Z, Antani SK, Long LR, Demner-Fushman D, Thoma GR. Improving face image extraction by using deep learning technique.
Proc. SPIE 9789, Medical Imaging 2016: PACS and Imaging Informatics:
Next Generation and Innovations, 97890J (March 25, 2016);
doi:10.1117/12.2216278.
Collins H, Calvo SC, Greenberg K, Forman, NL, Morrison SM. Information Needs in the Precision Medicine Era: How Genetics Home Reference Can Help. Interact J Med Res 2016;5(2):e13 DOI: 10.2196/ijmr.5199
Kilicoglu H, Rosemblat G, Fiszman M, Rindflesch TC. Sortal anaphora resolution to enhance relation extraction from biomedical literature. BMC Bioinformatics. 2016 Apr 14;17:163. doi: 10.1186/s12859-016-1009-6.
Moyer E, Hagenauer M, Lesko M, Francis F, Rodriguez O, Nagarajan V, Huser V, Busby B. MetaNetVar: Pipeline for applying network analysis tools for genomic variants analysis. F1000Res. 2016 Apr 13;5:674. doi: 10.12688/f1000research.8288.1. eCollection 2016.
Fung KW, Richesson R, Smerek M, Pereira KC, Green BB, Patkar A, Clowse M, Bauck A, Bodenreider O. Preparing
for the ICD-10-CM Transition: Automated Methods for Translating ICD
Codes in Clinical Phenotype Definitions. EGEMS (Wash DC). 2016 Apr 12;4(1):1211. doi: 10.13063/2327-9214.1211. eCollection 2016.
Demner-Fushman D, Mork JG. NLM Medical Text Indexer. Technical Report to the LHNCBC Board of Scientific Counselors April 2016.
Workman TE, Fiszman M, Cairelli MJ, Nahl D, Rindflesch TC. Spark, an application based on Serendipitous Knowledge Discovery. J Biomed Inform. 2016 Apr;60:23-37. doi: 10.1016/j.jbi.2015.12.014. Epub 2015 Dec 28.
Morid MA, Fiszman M, Raja K, Jonnalagadda SR, Del Fiol G. Classification of clinically useful sentences in clinical evidence resources. J Biomed Inform. 2016 Apr;60:14-22. doi: 10.1016/j.jbi.2016.01.003. Epub 2016 Jan 13.
Hume S, Aerts J, Sarnikar S, Huser V. Current
applications and future directions for the CDISC Operational Data Model
standard: A methodological review. J Biomed Inform. 2016 Apr;60:352-62. doi: 10.1016/j.jbi.2016.02.016. Epub 2016 Mar 2.
Potter M, Yaniv Z. Cost-effective surgical registration using consumer depth cameras .
Proc. SPIE 9786, Medical Imaging 2016: Image-Guided Procedures, Robotic
Interventions, and Modeling, 97861W (March 24, 2016);
doi:10.1117/12.2217515
Faruque J, Antani SK, Long LR, Kim L, Thoma GR. Image similarity ranking of focal computed tomography liver lesions using a 2AFC technique.
Proc. SPIE. 9787, Medical Imaging 2016: Image Perception, Observer
Performance, and Technology Assessment, 97870N. DOI:
10.1117/12.2217364.
Candemir S, Jaeger S, Lin W, Xue Z, Antani SK, Thoma GR. Automatic heart localization and radiographic index computation in chest x-rays.
Proc. SPIE. 9785, Medical Imaging 2016: Computer-Aided Diagnosis,
978517. DOI: 10.1117/12.2217209.
Kilicoglu H, Demner-Fushman D. Bio-SCoRes: A Smorgasbord Architecture for Coreference Resolution in Biomedical Text. PLoS One. 2016 Mar 2;11(3):e0148538. doi: 10.1371/journal.pone.0148538. eCollection 2016.
Driessen J, Baik SH, Zhang Y. Explaining Improved Use of High-Risk Medications in Medicare Between 2007 and 2011. J Am Geriatr Soc. 2016 Mar;64(3):674-6. doi: 10.1111/jgs.14000.
Baik SH, Hernandez I, Zhang Y. Evaluating the Initiation of Novel Oral Anticoagulants in Medicare Beneficiaries. J Manag Care Spec Pharm. 2016 Mar;22(3):281-92. doi: 10.18553/jmcp.2016.22.3.281.
Demner-Fushman
D, Kohli MD, Rosenman MB, Shooshan SE, Rodriguez L, Antani S, Thoma GR,
McDonald CJ. Preparing a collection of radiology examinations for distribution and retrieval. J Am Med Inform Assoc. 2016 Mar;23(2):304-10. doi: 10.1093/jamia/ocv080. Epub 2015 Jul 1.
Lu C, Tormey D, McDreedy L, Browne AC. Generating
SD-Rules in the SPECISLIST Lexical Tools - Optimization for suffix
derivation rule set [Poster].
BIOSTEC 2016), Vol(5): HEALTHINF, Rome, Italy, February 21-23, 2016, p.
353-358 (9th International Conference on Health Informatics,
HEALTHINF/BIOSTEC, 2016 Best Poster Award
KC S, Naved A, Roy PP, Wendling L, Antani SK, Thoma GR. Arrowhead detection in biomedical images.
Proceedings IS&T Electronic Imaging, Document Recognition and
Retrieval XXIII, 2016, pp. 1-7.
Dhombres F, Bodenreider O. Interoperability
between phenotypes in research and healthcare
terminologies--Investigating partial mappings between HPO and SNOMED
CT. J Biomed Semantics. 2016 Feb 9;7:3. doi: 10.1186/s13326-016-0047-3. eCollection 2016.
Yaniv Z. Registration for Orthopaedic Interventions.
Chapter 3 in: Zheng G, Li S, editors. Computational Radiology for
Orthopaedic Interventions: Lecture Notes in Computational Vision and
Biomechanics. Springer International Publishing; c2016. p.
41-70.
Mundkur ML, McDonald CJ. Utilizing Medicare claims for the assessment of influenza vaccination coverage in the US elderly. . J Gen Intern Med, 2016. 31: p. S463.
Guo P, Banerjee K, Stanley RJ, Long LR, Antani SK, Thoma GR, Frazier SR, Moss RH, Stoecker WV. Nuclei-Based Features for Uterine Cervical Cancer Histology Image Analysis with Fusion-based Classification. DOI 10.1109/JBHI.2015.2483318. IEEE Journal of Biomedical and Health Informatics.
Karargyris
A, Siegelman J, Tzortzis D, Jaeger S, Candemir S, Xue Z, KC S, Vajda S,
Antani SK, Folio L, Thoma GR. Combination of texture and shape features to detect pulmonary abnormalities in digital chest X-rays. Int J Comput Assist Radiol Surg. 2016 Jan;11(1):99-106. doi: 10.1007/s11548-015-1242-x. Epub 2015 Jun 20.
Zhang K, Liu WL, Locatis CN, Ackerman MJ. Mobile Videoconferencing Apps for Telemedicine. Telemed J E Health. 2016 Jan;22(1):56-62. doi: 10.1089/tmj.2015.0027. Epub 2015 Jul 23.
Bodenreider O. Identifying
missing hierarchical relations in SNOMED CT from logical definitions
based on the lexical features of concept names.
Proceedings of the 6th International Conference on Biomedical Ontology
(ICBO 2016), 2016: p. (electronic proceedings:
http://ceur-ws.org/Vol-1747/IT601_ICBO2016.pdf).
Kury F, Bodenreider O. Desiderata
for drug classification systems for their use in analyzing large drug
prescription datasets. Proceedings of the 3rd Workshop on Data Mining for Medical Informatics (DMMI 2016), 2016.
Webster RJ, Yaniv Z. Image-Guided Procedures, Robotic Interventions, and Modeling. Proc. SPIE 9786. (ISBN: 9781510600218 ).
McDonald CJ. Lister Hill National Center for Biomedical Communications Annual Report FY2015. Lister Hill National Center for Biomedical Communications Annual Report FY2015.
Roberts K, Shooshan SE, Rodriguez L, Abhyankar S, Kilicoglu H, Demner-Fushman D. The
role of fine-grained annotations in supervised recognition of risk
factors for heart disease from EHRs. J Biomed Inform. 2015 Dec;58 Suppl:S111-9. doi: 10.1016/j.jbi.2015.06.010. Epub 2015 Jun 26.
Lu C, Tormey D, MCreedy L, Browne AC. Generating the MEDLINE N-Gram Set [Poster]. AMIA 2015 Annual Symposium, San Francisco, CA, November 14-18, 2015, p. 1569.
Peters LB, Bodenreider O. Approaches to Supporting the Analysis of Historical Medication Datasets with RxNorm. AMIA Annu Symp Proc. 2015 Nov 5;2015:1034-41. eCollection 2015.
Roberts K, Rodriguez L, Shooshan SE, Demner-Fushman D. Automatic Extraction and Post-coordination of Spatial Relations in Consumer Language. AMIA Annu Symp Proc. 2015 Nov 5;2015:1083-92. eCollection 2015.
Rodriguez LM, Fushman DD. Automatic
Classification of Structured Product Labels for Pregnancy Risk Drug
Categories, a Machine Learning Approach. AMIA Annu Symp Proc. 2015 Nov 5;2015:1093-102. eCollection 2015.
Uy RC, Kury FP, Fontelo PA. The
State and Trends of Barcode, RFID, Biometric and Pharmacy Automation
Technologies in US Hospitals. AMIA Annu Symp Proc. 2015 Nov 5;2015:1242-51. eCollection 2015.
Morid MA, Jonnalagadda S, Fiszman M, Raja K, Del Fiol G. Classification of Clinically Useful Sentences in MEDLINE. AMIA Annu Symp Proc. 2015 Nov 5;2015:2015-24. eCollection 2015.
Cimino JJ, Huser V. Characterization of the Context of Drug Concepts in Research Protocols: An Empiric Study to Guide Ontology Development. AMIA Annu Symp Proc. 2015 Nov 5;2015:441-7. eCollection 2015.
Demner-Fushman D, Mork JG. Extracting Characteristics of the Study Subjects from Full-Text Articles. AMIA Annu Symp Proc. 2015 Nov 5;2015:484-91. eCollection 2015.
Kayaalp M, Browne AC, Sagan P, McGee T, McDonald CJ. Challenges and Insights in Using HIPAA Privacy Rule for Clinical Text Annotation. AMIA Annu Symp Proc. 2015 Nov 5;2015:707-16. eCollection 2015.
Kilicoglu H, Fiszman M, Roberts K, Demner-Fushman D. An Ensemble Method for Spelling Correction in Consumer Health Questions. AMIA Annu Symp Proc. 2015 Nov 5;2015:727-36. eCollection 2015.
Kury F, Huser V, Cimino JJ. Reproducing a Prospective Clinical Study as a Computational Retrospective Study in MIMIC-II. AMIA Annu Symp Proc. 2015 Nov 5;2015:804-13. eCollection 2015.
Pan X, Cimino JJ. Identifying the Clinical Laboratory Tests from Unspecified "Other Lab Test" Data for Secondary Use. AMIA Annu Symp Proc. 2015 Nov 5;2015:1018-23. eCollection 2015.
Xue Z, Candemir S, Antani SK, Long LR, Jaeger S, Demner-Fushman D, Thoma GR. Foreign Object Detection in Chest X-rays. Proc IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2015, International Workshop on Biomedical and Health Informatics, Bethesda, Maryland, Nov. 9-12, 2015, pp: 56-61.
Kayaalp M, Browne AC, Dodd ZA, Sagan P, McDonald CJ. An Easy-to-Use Clinical Text De-identification Tool for Clinical Scientists: NLM Scrubber [Poster]. Proceedings of the Annual American Medical Informatics Association Fall Symposium: 1522.
Szolovits P, Aberdeen J, Meystre S, Kayaalp M. Panel on: State of the Art of Clinical Narrative Report De-Identification and Its Future [Poster]. . Proceedings of the Annual American Medical Informatics Association Fall Symposium: 240–242.
Sorbello A, Ripple AM, Bodenreider O. A pilot study to support prospective detection of emerging adverse drug events [Poster]. AMIA Annu Symp Proc 2015:1699.
Rossi E, Fontelo P, Ackerman M, Pozzi G, Marceglia S. A Prototype of Mobile app/EHR Communication through Standards for Home Treatment of Transcranial Direct Current Stimulation. International Conference on Healthcare Informatics (ICHI), Dallas TX, 2015. 310-315.
Xu T, Xin C, Long LR, Antani SK, Xue Z, Kim E, Huang X. A New Image Data Set and Benchmark for Cervical Dysplasia Classification Evaluation.
Machine Learning in Medical Imaging: 6th International Workshop, MLMI
2015, LNCS 9352, pp. 26–35, 2015. DOI: 10.1007/978-3-319-24888-2
4.
Rahman MM, Antani SK, Demner-Fushman D, Thoma GR. Biomedical
image representation approach using visualness and spatial information
in a concept feature space for interactive region-of-interest-based
retrieval. J Med Imaging (Bellingham). 2015 Oct;2(4):046502. doi: 10.1117/1.JMI.2.4.046502. Epub 2015 Dec 30.
Winnenburg R, Sorbello A, Ripple AM, Harpaz R, Tonning J, Szarfman A, Francis H, Bodenreider O. Leveraging MEDLINE indexing for pharmacovigilance - Inherent limitations and mitigation strategies. J Biomed Inform. 2015 Oct;57:425-35. doi: 10.1016/j.jbi.2015.08.022. Epub 2015 Sep 2.
Fontelo P, Liu F, Uy RC. How does evidence affect clinical decision-making? Evid Based Med. 2015 Oct;20(5):156-61. doi: 10.1136/ebmed-2015-110250. Epub 2015 Sep 2.
Antani SK. Automatic x-ray screening for tuberculosis. SPIE Newsroom. October 2015. DOI: 10.1117/2.1201509.006128
Huser V, Sastry C, Breymaier M, Idriss A, Cimino JJ. Standardizing
data exchange for clinical research protocols and case report forms: An
assessment of the suitability of the Clinical Data Interchange
Standards Consortium (CDISC) Operational Data Model (ODM). J Biomed Inform. 2015 Oct;57:88-99. doi: 10.1016/j.jbi.2015.06.023. Epub 2015 Jul 15.
Kim I, Thoma GR. Automated
Classification of Author’s Sentiments in Citation Using Machine
Learning Techniques: A Preliminary Study. Proc. the 2015 IEEE Conf. Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2015), Niagara Falls, Canada, Aug. 12-15, 2015.
Demner-Fushman D, Kilicoglu H, Roberts K, Masterton K, Deardorff A. Consumer Health Question Answering to Automatically Support NLM Customer Services. September2015 Technical Report to the LHNCBC Board of Scientific Counselors.
Folio L, Sigelman J, Wang xY, Lu P, Antani SK, Jaeger S. Automatic Identification and Classification of Tuberculosis Findings on Chest Radiographs for Global Surveillance Programs [Abstract]. Annual Meeting of the American Roentgen Ray Society (ARRS)
Payne
TH, Corley S, Cullen TA, Gandhi TK, Harrington L, Kuperman GJ, Makar E,
Mattison JE, McCallie DP, McDonald CJ, Tang PC, Tierney WM, Weaver C,
Weir CR, Zaroukian MH. Report of the AMIA EHR-2020 Task Force on the status and future direction of EHRs. J Am Med Inform Assoc. 2015 Sep;22(5):1102-10. doi: 10.1093/jamia/ocv066. Epub 2015 May 28.
Dhombres F, Bodenreider O. Investigating
the lexico-syntactic properties of phenotype terms – Application to
interoperability between HPO and SNOMED CT. Proc Joint Bio-Ontologies and BioLINK ISMB'2015 SIG session "Phenotype Day" 2015:8-11.
Drawz PE, Archdeacon P, McDonald CJ, Powe NR, Smith KA, Norton J, Williams DE, Patel UD, Narva A. CKD as a Model for Improving Chronic Disease Care through Electronic Health Records. Clin J Am Soc Nephrol. 2015 Aug 7;10(8):1488-99. doi: 10.2215/CJN.00940115. Epub 2015 Jun 25.
Ruiz A, Allette K, Francis D, Lamping E, Jaeger S, Folio L, Apolo A. Patterns of soft tissue metastasis in patients with urothelial carcinoma using tumor volume heatmaps [Poster]. NIH Summer Research Program Poster Day, Aug 6, 2015.
Marceglia S, Fontelo P, Rossi E, Ackerman MJ. A Standards-Based Architecture Proposal for Integrating Patient mHealth Apps to Electronic Health Record Systems. Appl Clin Inform. 2015 Aug 5;6(3):488-505. doi: 10.4338/ACI-2014-12-RA-0115. eCollection 2015.
Yaniv Z, Linte CA. Applications of Augmented Reality in the Operating Room. Chapter 19 in Fundamentals of Wearable Computers and Augmented Reality, 2nd ed. CRC Press, 2015.
Read KB, Sheehan JR, Huerta MF, Knecht LS, Mork JG, Humphreys BL. Sizing the Problem of Improving Discovery and Access to NIH-Funded Data: A Preliminary Study. PLoS One. 2015 Jul 24;10(7):e0132735. doi: 10.1371/journal.pone.0132735. eCollection 2015.
Roberts K, Simpson M, Demner-Fushman D, Voorhees E, Hersh W. State-of-the-art
in biomedical literature retrieval for clinical cases: A survey of the
TREC 2014 CDS Track. . Inf Retrieval J. 2015.
Candemir S, Borovikov E, KC S, Antani SK, Thoma GR. RSILC: Rotation- and Scale-Invariant, Line-based Color-aware descriptor.
Image and Vision Computing, Volume 42, October 2015, Pages 1-12, ISSN
0262-8856. doi:10.1016/j.imavis.2015.06.010.
Gartrell K, Trinkoff AM, Storr CL, Wilson ML. Electronic Personal Health Record Use Among Nurses in the Nursing Informatics Community. Comput Inform Nurs. 2015 Jul;33(7):306-14. doi: 10.1097/CIN.0000000000000163.
Matheson NW, Ash JS
(Interviewer and Editor), Sittig DF (Interviewer and Editor), Goodwin RM
(Editor). The
Woman Behind the NLM’s Integrated Advanced Information Management
Systems (IAIMS) Initiative: 2005 Interview of Nina
Matheson. Conversations with Medical Informatics Pioneers: An oral history project.
Ackerman MJ. The Educational Value of Truly Interactive Science Publishing. J Electronic Pub. 2015 Spring:18(2). DOI: http://dx.doi.org/10.3998/3336451.0018.201.
Detmer
DE, Ash JS (Interviewer and Editor), Sittig DF (Interviewer and
Editor), Goodwin RM (Editor). Fostering Health Policy and the Biomedical Informatics Profession: 2006 Interview of Don Detmer. Conversations with Medical Informatics Pioneers: An oral history project.
Fontelo P, Liu F, Yagi Y. Evaluation of a smartphone for telepathology: Lessons learned. J Pathol Inform. 2015 Jun 23;6:35. doi: 10.4103/2153-3539.158912. eCollection 2015.
KC S, Vajda S, Antani SK, Thoma GR. Automatic Pulmonary Abnormality Screening using Thoracic Edge Map. IEEE, 28th International Symposium on Computer-Based Medical Systems (CBMS), pp. 360-361, 2015.
KC S, Antani SK, Thoma GR. Stitched Multipanel Biomedical Figure Separation. IEEE, 28th International Symposium on Computer-Based Medical Systems (CBMS), pp. 54-59, 2015.
Xue Z, You D, Candemir S, Jaeger S, Antani SK, Long LR, Thoma GR. Chest X-ray Image View Classification. The 28th IEEE International Symposium on Computer-Based Medical Systems
Kilicoglu H, Rosemblat G, Cairelli M, Rindflesch TC. A Compositional Interpretation of Biomedical Event Factuality.
Proc of the Second Workshop on Extra-Propositional Aspects of Meaning
in Computational Semantics (ExProM 2015).
Marchell R, Locatis CN, Ackerman MJ. High
definition live interactive and store and forward teledermatology:
initial qualitative observations. .
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Ayvas
S, Horn J, Hassanzadeh O, Zhu Q, Stan J, Tatonetti NP, Vilar S,
Brochhausen M8, Samwald M, Rastegar-Mojarad M, Dumontier M, Boyce
RD. Toward a complete dataset of drug-drug interaction information from publicly available sources. J Biomed Inform. 2015 Jun;55:206-17. doi: 10.1016/j.jbi.2015.04.006. Epub 2015 Apr 24.
Vajda S, Rangoni Y, Cecotti H. Semi-automatic
ground truth generation using unsupervised clustering and limited
manual labeling: Application to handwritten character
recognition. Pattern Recognit Lett. 2015 Jun 1;58:23-28.
Cairelli MJ, Fiszman M, Zhang H, Rindflesch TC. Networks of neuroinjury semantic predications to identify biomarkers for mild traumatic brain injury. J Biomed Semantics. 2015 May 18;6:25. doi: 10.1186/s13326-015-0022-4. eCollection 2015.
Peters LB, Bahr N, Bodenreider O. Evaluating drug-drug interaction information in NDF-RT and DrugBank. J Biomed Semantics. 2015 May 11;6:19. doi: 10.1186/s13326-015-0018-0. eCollection 2015.
Cho D, Mork JG, Aronson A, Demner-Fushman D, Schmidt S, Ozga D, Pash J, Kilbourne J. MeSH on demand: an easy way to identify relevant MeSH terms and related articles from text [Poster]. National Cancer Institute (NCI) Symposium "RNA Biology 2015".
Liu WL, Zhang K, Locatis C, Ackerman M. Cloud and traditional videoconferencing technology for telemedicine and distance learning. Telemed J E Health. 2015 May;21(5):422-6. doi: 10.1089/tmj.2014.0121. Epub 2015 Mar 18.
Deckard J, McDonald CJ, Vreeman DJ. Supporting interoperability of genetic data with LOINC. J Am Med Inform Assoc. 2015 May;22(3):621-7. doi: 10.1093/jamia/ocu012. Epub 2015 Feb 5.
Bunt CW, Burke HB, Towbin AJ, Hoang A, Stephens MB, Fontelo P, Liu F, Gimbel RW. Point-of-Care Estimated Radiation Exposure and Imaging Guidelines Can Reduce Pediatric Radiation Burden. J Am Board Fam Med. 2015 May-Jun;28(3):343-50. doi: 10.3122/jabfm.2015.03.140251.
Winnenburg R, Sorbello A, Bodenreider O. Exploring adverse drug events at the class level. J Biomed Semantics. 2015 May 1;6:18. doi: 10.1186/s13326-015-0017-1. eCollection 2015.
Gartrell K, Storr CL, Trinkoff AM, Wilson ML, Gurses AP. Electronic personal health record use among registerednurses. Nurs Outlook. 2015 May-Jun;63(3):278-87. doi: 10.1016/j.outlook.2014.11.013. Epub 2014 Nov 28.
Fung KW, Xu J. An
exploration of the properties of the CORE problem list subset and how
it facilitates the implementation of SNOMED CT. J Am Med Inform Assoc. 2015 May;22(3):649-58. doi: 10.1093/jamia/ocu022. Epub 2015 Feb 26.
Barnett
GO, Ash JS (Interviewer and Editor), Sittig DF (Interviewer and
Editor), Goodwin RM (Editor). From "Farm Boy" to Director of the Laboratory of Computer Science: 2004 Interview of G. Octo Barnett. Conversations with Medical Informatics Pioneers: An oral history project.
McDonald CJ, Kalisch ELM, Barratt JD, Caughey GE. An
international comparison of spontaneous adverse event reports and
potentially inappropriate medicine use associated with
dabigatran. Pharmacoepidemiol Drug Saf. 2015 Apr;24(4):399-405. doi: 10.1002/pds.3648. Epub 2014 May 20.
Warner HR, Sittig DF (Interviewer and Editor), Ash JS (Editor), Goodwin RM (Editor). Founder
of the HELP System and the Utah Medical Informatics Program: 2005
Interview of Homer R. Warner, Sr. Conversations with Medical Informatics Pioneers: An oral history project.
Ash JS (Interviewer and Editor), Sittig DF (Interviewer and Editor), Goodwin RM (Editor). Introduction. Conversations with Medical Informatics Pioneers: An oral history project.
Lindberg,
DAB, Ash JS (Interviewer and Editor), Sittig DF (Interviewer and
Editor), Goodwin RM (Editor). At the helm of the world's largest biomedical library: 2005 Interviews with Donald A.B. Lindberg, MD. Conversations with Medical Informatics Pioneers: An oral history project.
Antani SK. Automated Detection of Lung Diseases in Chest X-Rays . April 2015 Technical Report to the LHNCBC Board of Scientific Counselors.
Gartrell K, Trinkoff AM, Storr CL, Wilson ML, Gurses AP. Testing
the Electronic Personal Health Record Acceptance Model by Nurses for
Managing Their Own Health: A Cross-sectional Survey. Appl Clin Inform. 2015 Apr 8;6(2):224-47. doi: 10.4338/ACI-2014-11-RA-0107. eCollection 2015.
Jimeno Yepes AJ, Plaza L, Carrillo-de-Albornoz J, Mork JG, Aronson A. Feature engineering for MEDLINE citation categorization with MeSH. BMC Bioinformatics. 2015 Apr 8;16:113. doi: 10.1186/s12859-015-0539-7.
Marceglia S, Fontelo P, Ackerman MJ. Transforming consumer health informatics: connecting CHI applications to the health-IT ecosystem. J Am Med Inform Assoc. 2015 Apr;22(e1):e210-2. doi: 10.1093/jamia/ocu030. Epub 2015 Feb 8.
Abhyankar S, Goodwin RM, Sontag M, Yusuf C, Ojodu J, McDonald CJ. An update on the use of health information technology in newborn screening. Semin Perinatol. 2015 Apr;39(3):188-93. doi: 10.1053/j.semperi.2015.03.003. Epub 2015 Apr 29.
Zhu X, Cimino JJ. Clinicians' evaluation of computer-assisted medication summarization of electronic medical records. Comput Biol Med. 2015 Apr;59:221-31. doi: 10.1016/j.compbiomed.2013.12.006. Epub 2013 Dec 19.
Locatis CN, Gaines C, Liu WL, Gill MJ, Ackerman MJ. Lessons learned from ten years of distance learning outreach. J Med Libr Assoc. 2015 Apr;103(2):78-82. doi: 10.3163/1536-5050.103.2.004.
Cameron D, Kavuluru R, Rindflesch TC, Sheth AP, Thirunarayan K, Bodenreider O. Context-driven automatic subgraph creation for literature-based discovery. J Biomed Inform. 2015 Apr;54:141-57. doi: 10.1016/j.jbi.2015.01.014. Epub 2015 Feb 7.
Demner-Fushman D, Shooshan SE, Rodriguez L, Antani SK, Thoma GR. Annotation of Chest Radiology Reports for Indexing and Retrieval. Multimodal Retrieval in the Medical Domain 2015 (MRMD 2015), Vienna, Austria, March 29, 2015
Winnenburg R, Mortensen JM, Bodenreider O. Using description logics to evaluate the consistency of drug-class membership relations in NDF-RT. J Biomed Semantics. 2015 Mar 28;6:13. doi: 10.1186/s13326-015-0007-3. eCollection 2015.
Roberts K, Demner-Fushman D. Toward a Natural Language Interface for EHR Questions. AMIA Jt Summits Transl Sci Proc. 2015 Mar 25;2015:157-61. eCollection 2015.
Tao S, Cui L, Zhu W, Sun M, Bodenreider O, Zhang GQ. Mining Relation Reversals in the Evolution of SNOMED CT Using MapReduce. AMIA Jt Summits Transl Sci Proc. 2015 Mar 23;2015:46-50. eCollection 2015.
Zhang R, Adam TJ, Simon G, Cairelli MJ, Rindflesch T, Pakhomov S, Melton GB. Mining Biomedical Literature to Explore Interactions between Cancer Drugs and Dietary Supplements. AMIA Jt Summits Transl Sci Proc. 2015 Mar 23;2015:69-73. eCollection 2015.
Wei W, Demner-Fushman D, Wang S, Jiang X, Ohno-Machado L. Ranking Medical Subject Headings using a factor graph model. AMIA Jt Summits Transl Sci Proc. 2015 Mar 23;2015:56-63. eCollection 2015.
Xu T, Huang X, Kim E, Long LR, Antani SK. Multi-test cervical cancer diagnosis with missing data estimation.
Proc. SPIE. 9414, Medical Imaging 2015: Computer-Aided Diagnosis,
94140X. (March 20, 2015) doi: 10.1117/12.2080871.
Gopal AD, Desai NR, Tse T, Ross JS. Reporting of noninferiority trials in ClinicalTrials.gov and corresponding publications. JAMA. 2015 Mar 17;313(11):1163-5. doi: 10.1001/jama.2015.1697.
Xue Z, You D, Chachra S, Antani SK, Long LR, Demner-Fushman D, Thoma GR. Extraction of endoscopic images for biomedical figure classification.
Proc. SPIE. 9418, Medical Imaging 2015: PACS and Imaging Informatics:
Next Generation and Innovations, 94180P. (March 17, 2015) doi:
10.1117/12.2081033.
Candemir S, Antani SK, Jaeger SR, Thoma GR. Lung boundary detection in pediatric chest x-rays.
Proc. SPIE. 9418, Medical Imaging 2015: PACS and Imaging Informatics:
Next Generation and Innovations, 94180Q. (March 17, 2015) doi:
10.1117/12.2081060.
Rahman MM, Antani SK, Demner-Fushman D, Thoma GR. A visual concept-based interactive biomedical image retrieval using entropy and spatial information.
Proc. SPIE. 9418, Medical Imaging 2015: PACS and Imaging Informatics:
Next Generation and Innovations, 94180U. (March 17, 2015) doi:
10.1117/12.2081456.
Zhang Y, Baik SH, Newhouse JP. Use
of intelligent assignment to Medicare Part D plans for people with
schizophrenia could produce substantial savings. Health Aff (Millwood). 2015 Mar;34(3):455-60. doi: 10.1377/hlthaff.2014.1227.
Hristovski D, Dinevski D, Kastrin A, Rindflesch TC. Biomedical question answering using semantic relations. BMC Bioinformatics. 2015 Jan 16;16:6. doi: 10.1186/s12859-014-0365-3.
Zarin D, Tse T, Sheehan J. The proposed rule for U.S. clinical trial trials.gov: submission. N Engl J Med. 2015 Jan 8;372(2):174-80. doi: 10.1056/NEJMsr1414226. Epub 2014 Dec 24.
Amini S, Kilicoglu H, Hooft L, ter Riet G. Are
we expressing uncertainty of our claims enough? Towards automatic
detection of overstatement of claims [Poster]. 2015. World Conference on Research Integrity (WCRI).
Fu GE, Bolton NQ, Rosinach LI, Furlong V, Nguyen AP, Sheth O, Bodenreider O, Dumontier M. Exposing provenance metadata using different RDF models.
Proceedings of the International Conference on Semantic Web
Applications and Tools for Life Sciences (SWAT4LS 2015), 2015: p.
(electronic proceedings:
http://www.swat4ls.org/wp-content/uploads/2015/10/SWAT4LS_2015_paper_11.pdf).
KC S, Xue Z, Antani SK, Thoma GR. NLM at ImageCLEF 2015: Biomedical Multipanel Figure Separation.
Editors: Cappellato, L., Ferro, N., Jones, G., and San Juan, E., CLEF
2015 Labs and Workshops, Notebook Papers. CEUR WorkshopProceedings
(CEUR-WS.org), ISSN 1613-0073, http://ceur-ws.org/ Vol-1391/.
Simpson MS, You D, Rahman MM, Xue Z, Demner-Fushman D, Antani S, Thoma G. Literature-based biomedical image classification and retrieval. Comput Med Imaging Graph. 2015 Jan;39:3-13. doi: 10.1016/j.compmedimag.2014.06.006. Epub 2014 Jun 20.
Demner-Fushman D, Antani S, Kalpathy-Cramer J, Müller H. A decade of community-wide efforts in advancing medical image understanding and retrieval. Comput Med Imaging Graph. 2015 Jan;39:1-2. doi: 10.1016/j.compmedimag.2014.12.002.
Burke HB, Sessums LL, Hoang A, Becher DA, Fontelo P, Liu F, Stephens M, Pangaro LN, O'Malley PG, Baxi NS, Bunt CW, Capaldi VF 2nd, Chen JM, Cooper BA, Djuric DA, Hodge JA, Kane S, Magee C, Makary ZR, Mallory RM, Miller T, Saperstein A, Servey J, Gimbel RW. Electronic health records improve clinical note quality. J Am Med Inform Assoc. 2015 Jan;22(1):199-205. doi: 10.1136/amiajnl-2014-002726. Epub 2014 Oct 23.
Cohen KB, Demner-Fushman D. Biomedical Natural Language Processing. John Benjamins Publishing Company, 2014. DOI: 10.1075/nlp.11
Rance B, Le T, Bodenreider O. Fingerprinting Biomedical Terminologies--Automatic Classification and Visualization of Biomedical Vocabularies through UMLS Semantic Group Profiles. Stud Health Technol Inform. 2015;216:771-5.
Dhombres F, Winnenburg R, Case JT, Bodenreider O. Extending the coverage of phenotypes in SNOMED CT through post-coordination. Stud Health Technol Inform. 2015;216:795-9.
Hripcsak G,
Duke JD, Shah NH, Reich CG, Huser V, Schuemie MJ, Suchard MA, Park RW,
Wong IC, Rijnbeek PR, van der Lei J, Pratt N, Norén GN, Li YC, Stang PE,
Madigan D, Ryan PB. Observational
Health Data Sciences and Informatics (OHDSI): Opportunities for
Observational Researchers. Stud Health Technol Inform. 2015;216:574-8.
Hristovski D, Kastrin A, Dinevski D, Rindflesch TC. Constructing a Graph Database for Semantic Literature-Based Discovery. Stud Health Technol Inform. 2015;216:1094.
Kury F, Cimino JJ. Computationally
Comparing and Analyzing All Published Scoring Systems for Diagnosis of
Disseminated Intravascular Coagulation. Stud Health Technol Inform. 2015;216:956.
Song D, Kim E, Huang X, Patruno J, Munoz-Avila H, Heflin J, Long LR, Antani SK. Multimodal entity coreference for cervical dysplasia diagnosis. . IEEE Transactions on Medical Imaging, 34(1), January 2015, 229-245.
Kilicoglu H, Rogers W. A Hybrid System for Extracting Chemical-Disease Relationships from Scientific Literature. 2015. BioCreative 5 Proceedings.
KC S, Candemir S, Jaeger S, Folio L, Karargyris A, Antani SK, Thoma GR. Automatically detecting rotation in chest radiographs using principal rib-orientation measure for quality control. Int. J. Patt. Recogn. Artif. Intell, Vol 29 No. 2. DOI: 10.1142/S021800141.5570013.
Kalpathy-Cramer J, de Herrera AG, Demner-Fushman D, Antani S, Bedrick S, Müller H. Evaluating
performance of biomedical image retrieval systems--an overview of the
medical image retrieval task at ImageCLEF 2004-2013. Comput Med Imaging Graph. 2015 Jan;39:55-61. doi: 10.1016/j.compmedimag.2014.03.004. Epub 2014 Mar 27.
Kury F, Cimino JJ. Identifying
Repetitive Institutional Review Board Stipulations by Natural Language
Processing and Network Analysis. Stud Health Technol Inform. 2015;216:579-83.
Jaeger S. Detecting Disease in Radiographs with Intuitive Confidence. ScientificWorldJournal. 2015;2015:946793. doi: 10.1155/2015/946793. Epub 2015 Oct 1.
McDonald CJ. Lister Hill National Center for Biomedical Communications Annual Report FY2014. Lister Hill National Center for Biomedical Communications Annual Report FY2014.
Vajda S. Label
the many with a few: Semi-automatic medical image modality discovery in
a large image collection. IEEE Symposium Series on Computational Intelligence, Orlando, FL, Dec 9-12, 2014
Mishra R, Bian J, Fiszman M, Weir CR, Mostafa J, Fiol GD. Text summarization in the biomedical domain: a systematic review of recent research. J Biomed Inform. 2014 Dec;52:457-67. doi: 10.1016/j.jbi.2014.06.009. Epub 2014 Jul 10.
Shang N, Xu H, Rindflesch TC, Cohen T. Identifying plausible adverse drug reactions using knowledge extracted from the literature. J Biomed Inform. 2014 Dec;52:293-310. doi: 10.1016/j.jbi.2014.07.011. Epub 2014 Jul 19.
Cimino JJ, Ayres EJ, Remennik L, Rath S, Freedman R, Beri A, Chen Y, Huser V. The
National Institutes of Health's Biomedical Translational Research
Information System (BTRIS): design, contents, functionality and
experience to date. J Biomed Inform. 2014 Dec;52:11-27. doi: 10.1016/j.jbi.2013.11.004. Epub 2013 Nov 19.
Lau AF, Wang H, Weingarten RA, Drake SK, Suffredini AF, Chen Y, Gucek M, Youn JH, Stock F, Tso H, DeLeo J, Cimino JJ, Frank KM, Dekker JP. Reply
to "Tn4401 carrying blaKPC is inserted within another insertion in
pKpQIL and related plasmids". J Clin Microbiol. 2014 Dec;52(12):4450. doi: 10.1128/JCM.02614-14.
Jaeger S, Candemir S, Antani SK, Wang, Lu P, Thoma GR. Two public chest X-ray datasets for computer-aided screening of pulmonary diseases. Quant Imaging Med Surg. 2014 Dec;4(6):475-7. doi: 10.3978/j.issn.2223-4292.2014.11.20.
Xue Z, Bryant B, Long LR, Sari-Sarraf H, Thoma GR, Wachtel M. A
Client-Server Tool for Automatic Fast GPU-based Detection of Squamous
Epithelium Tissue Regions in Histology Images [Poster]. RSNA 2014. Chicago, USA, Nov 30-Dec 5, 2014
Roberts K, Cahan A, Demner-Fushman D. Error Propagation in EHRs via Copy/Paste: An Analysis of Relative Dates [Poster]. Proceedings of the American Medical Informatics Association Fall Symposium (AMIA), Washington, D.C., Nov 15-19, 2014.
Kayaalp M, Browne AC, Dodd Z, Sagan P, McDonald CJ. De-identification of Address, Date, and Alphanumeric Identifiers in Narrative Clinical Reports. AMIA Annu Symp Proc. 2014 Nov 14;2014:767-76. eCollection 2014.
Browne AC, Kayaalp M, Dodd Z, Sagan, P, McDonald CJ. The Challenges of Creating a Gold Standard for De-identification Research. AMIA Annu Symp Proc. 2014 Nov 14;2014:353-8. eCollection 2014.
Huser, V, Kayaalp M, Dodd Z, Cimino J. Piloting a deceased subject integrated data repository and protecting privacy of relatives. AMIA Annu Symp Proc. 2014 Nov 14;2014:719-28. eCollection 2014.
Lu C, Tormey D, McDreedy L, Browne AC. Using element words to generate (multi)words for the SPECIALIST Lexicon [Poster]. AMIA 2014 Annual Symposium, Washington, DC, November 15-19, 2014, p. 1499. Poster
Bodenreider O, Rodriguez L. Analyzing U.S. prescription lists with RxNorm and the ATC/DDD Index. AMIA Annu Symp Proc. 2014 Nov 14;2014:297-306. eCollection 2014.
Culbertson A, Fiszman M, Shin D, Rindflesch TC. Semantic processing to identify adverse drug event information from black box warnings. AMIA Annu Symp Proc. 2014 Nov 14;2014:442-8. eCollection 2014.
Ozturk S, Kayaalp M, McDonald CJ. Visualization of patient prescription history data in emergency care. AMIA Annu Symp Proc. 2014 Nov 14;2014:963-8. eCollection 2014.
Pan X, Cimino JJ. Locating
relevant patient information in electronic health record data using
representations of clinical concepts and database
structures. AMIA Annu Symp Proc. 2014 Nov 14;2014:969-75. eCollection 2014.
Cimino JJ, Remennick L. Adapting a Clinical Data Repository to ICD-10-CM through the use of a Terminology Repository. AMIA Annu Symp Proc. 2014 Nov 14;2014:405-13. eCollection 2014.
Fung KW, Richesson R, Bodenreider O. Coverage
of rare disease names in standard terminologies and implications for
patients, providers, and research. AMIA Annu Symp Proc. 2014 Nov 14;2014:564-72. eCollection 2014.
Roberts K, Kilicoglu H, Fiszman M, Demner-Fushman D. Automatically classifying question types for consumer health questions. AMIA Annu Symp Proc. 2014 Nov 14;2014:1018-27. eCollection 2014.
Uy RC, Sarmiento RF, Gavino A, Fontelo P. Confidence and Information Access in Clinical Decision-Making: An Examination of the Cognitive Processes that affect the Information-seeking Behavior of Physicians. AMIA Annu Symp Proc. 2014 Nov 14;2014:1134-40. eCollection 2014.
Winnenburg R, Bodenreider O. Desiderata for an authoritative Representation of MeSH in RDF. AMIA Annu Symp Proc. 2014 Nov 14;2014:1218-27. eCollection 2014.
Harpaz
R, Odgers D, Gaskin G, DuMouchel W, Winnenburg R, Bodenreider O, Ripple
AM, Szarfman A, Sorbello A, Horvitz E, White RW, Shah
NH. A time-indexed reference standard of adverse drug reactions. Sci Data. 2014 Nov 11;1:140043. doi: 10.1038/sdata.2014.43.
Rodriguez L, Huser V, Bodenreider O, Cimino J. Automatic coding of Free-Text Medication Data recorded by Research Coordinators [Poster]. AMIA Annu Symp Proc 2014:1565.
Gordon,
E, Ersoy, I, Jaeger S, Waisberg, M, Pena, M, Thoma GR, Antani SK,
Pierce, S, Palaniappan, K. Retinal Microcirculation Dynamics During an Active Malarial Infection [Poster]. Annual Meeting of the American Society of Tropical Medicine and Hygiene (ASTMH), 2014.
Winnenburg R, Bodenreider O. Desiderata for an authoritative representation of MeSH in RDF. AMIA Annu Symp Proc 2014:1218-1227.
McDonald CJ, Callaghan FM, Weissman A, Goodwin RM, Mundkur M, Kuhn T. Use of internist's free time by ambulatory care Electronic Medical Record systems. JAMA Intern Med. 2014 Nov;174(11):1860-3. doi: 10.1001/jamainternmed.2014.4506.
Wright A, Sittig DF, McGowan J, Ash JS, Weed LL. Bringing
science to medicine: an interview with Larry Weed, inventor of the
problem-oriented medical record.
J Am Med Inform Assoc. 2014 Nov-Dec;21(6):964-8. doi:
10.1136/amiajnl-2014-002776. Epub 2014 May 28.
Khatipov
E, Madden M, Chiang P, Chuang P, Nguyen D, D'Souza I, Winnenburg R,
Bodenreider O, Skapik J, McClure R, Emrick S. Creating, maintaining and publishing value sets in the VSAC [Poster]. AMIA Annu Symp Proc, 2014: p. 1459.
Ackerman MJ. Computer Briefs: But It's Only About Wellness. J Med Pract Manage. 2014 Sep-Oct;30(2):148-9.
Zhang R, Cairelli MJ, Fiszman M, Kilicoglu H, Rindflesch TC, Pakhomov SV, Melton GB. Exploiting Literature-derived Knowledge and Semantics to Identify Potential Prostate Cancer Drugs. Cancer Inform. 2014 Oct 14;13(Suppl 1):103-11. doi: 10.4137/CIN.S13889. eCollection 2014.
Richesson RL, Fung K, Bodenreider O. Coverage
of rare disease names in cinical coding systems and ontologies and
implications for electronic health records-based research
[Poster]. Proc 5th Int'l Conf Conference on Biomedical Ontology.
Bodenreider O, Peters L, Nguyen T. RxClass – Navigating between Drug Classes and RxNorm Drugs (Demo). Prc. ICBO 2014
Cohen T, Widdows D, Stephan C, Zinner R, Kim J, Rindflesch TC, Davies P. Predicting high-throughput screening results with scalable literature-based discovery methods. CPT Pharmacometrics Syst Pharmacol. 2014 Oct 8;3:e140. doi: 10.1038/psp.2014.37.
Kwon J, Burke DJ, Wang A, Boudreau HE, Lekstrom KJ, Korzeniowska A, Kim YS, Li L, Bunyak F, Jaeger S, Palaniappan K, Ambruso DR, Jackson SH, Leto TL. Peroxiredoxin
6 (Prdx6) supports NADPH oxidase1 (Nox1)-based reactive oxygen species
generation and cell migration: collaboration of oxidant generating and
scavenging systems [Poster]. NIH Research Festival 2014.
Rondonotti E, Koulaouzidis A,
Karargyris A, Giannakou A, Fini L, Soncini M, Pennazio M, Douglas S,
Shams A, Lachlan N, Zahid A, Mandelli G, Girelli C. Utility
of 3-dimensional image reconstruction in the diagnosis
ofsmall-bowel masses in capsule endoscopy (with
video). Gastrointest Endosc. 2014 Oct;80(4):642-51. doi: 10.1016/j.gie.2014.04.057. Epub 2014 Jul 3.
Kim I, Le DX, Thoma GR. Automated
method for extracting "citation sentences" from online biomedical
articles using SVM-based text summarization technique.
Proc. the 2014 IEEE Int'l Conf. on Systems, Man, and Cybernetics (SMC
2014), pp. 2006-2011, San Diego, October, 2014
Zhang GQ, Zhu W, Sun M, Tao S, Bodenreider O, Cui L. MaPLE: A MapReduce Pipeline for Lattice-based Evaluation and Its Application to SNOMED CT. Proc IEEE Int Conf Big Data. 2014 Oct;2014:754-759.
Collen MF, Sittig DF (Interviewer and Editor), Ash JS (Editor), Goodwin RM (Editor). Engineering Computerized Multiphasic Health Screening: 2005 Interview of Morris F. Collen, MD. Conversations with Medical Informatics Pioneers: An oral history project.
Bodenreider O, Winnenburg R. Drug Terminology and Ontology Integration -- Dissemination, Quality Assurance and Applications. September 2014 Technical Report to the LHNCBC Board of Scientific Counselors.
Huser V, Sincan M, Cimino JJ. Developing
genomic knowledge bases and databases to support clinical management:
current perspectives. Pharmgenomics Pers Med. 2014 Sep 9;7:275-83. doi: 10.2147/PGPM.S49904. eCollection 2014.
Burke HB, Hoang A, Becher D, Fontelo P, Liu F, Stephens M, Pangaro LN, Sessums LL, O'Malley P, Baxi NS, Bunt CW, Capaldi VF, Chen JM, Cooper BA, Djuric DA, Hodge JA, Kane S, Magee C, Makary ZR, Mallory RM, Miller T, Saperstein A, Servey J, Gimbel RW. QNOTE: an instrument for measuring the quality of EHR clinical notes. J Am Med Inform Assoc. 2014 Sep-Oct;21(5):910-6. doi: 10.1136/amiajnl-2013-002321. Epub 2014 Jan 2.
Rahman MM, You D, Simpson MS, Antani SK, Demner-Fushman D. Interactive
Cross and Multimodal Biomedical Image Retrieval Based on Automatic
Region-Of-Interest (ROI) Identification and
Classification. International Journal of Multimedia Information Retrieval (MMIR) 2014 Sep;3(3):131-146.
Abhyankar S, Demner-Fushman D, Callaghan FM, McDonald CJ. Combining
structured and unstructured data to identify a cohort of ICU patients
who received dialysis. J Am Med Inform Assoc. 2014 Sep-Oct;21(5):801-7. doi: 10.1136/amiajnl-2013-001915. Epub 2014 Jan 2.
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KC S, Wendling L, Antani SK, Thoma GR. Scalable arrow detection in biomedical images.
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CN, Roe MT, Gibson CM, Temple RJ, Pencina MJ, Zarin DA, Anstrom KJ,
Alexander JH, Sherman RE, Fiedorek FT, Mahaffey KW, Lee KL, Chow SC,
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Lau AF, Wang H, Weingarten RA, Drake SK, Suffredini AF, Garfield MK, Chen Y, Gucek M, Youn JH, Stock F, Tso H, DeLeo J, Cimino JJ, Frank KM, Dekker JP. A
rapid matrix-assisted laser desorption ionization-time of flight mass
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structure of a network of co-occurring MeSH terms: statistical analysis
of macroscopic properties. PLoS One. 2014 Jul 9;9(7):e102188. doi: 10.1371/journal.pone.0102188. eCollection 2014.
Kilicoglu H, Demner-Fushman D. Coreference Resolution for Structured Drug Product Labels. Proceedings of BioNLP 2014. pp. 44-53.
Chen G, Cairelli MJ, Kilicoglu H, Shin D, Rindflesch TC. Augmenting
microarray data with literature-based knowledge to enhance gene
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Zhang R, Cairelli MJ, Fiszman M, Rosemblat G, Kilicoglu H, Rindflesch TC, Pakhomov SV, Melton GB. Using semantic predications to uncover drug-drug interactions in clinical data. J Biomed Inform. 2014 Jun;49:134-47. doi: 10.1016/j.jbi.2014.01.004. Epub 2014 Jan 19.
KC S, Candemir S, Jaeger S, Folio L, Karargyris A, Antani SK, Thoma GR. Rotation detection in chest radiographs based on generalized line histogram of rib-orientations.
IEEE 27th International Symposium on Computer-Based Medical Systems,
New York, NY, USA, May 27-29, 2014: page 138-142.
Roberts K, Masterton K, Kilicoglu H, Fiszman M, Demner-Fushman D. Annotating Question Decomposition on Complex Medical Questions. LREC 2014.
Roberts K, Masterton K, Fiszman M, Kilicoglu H, Demner-Fushman D. Annotating Question Types for Consumer Health Questions. LREC 2014, BioTxtM workshop.
Roberts K, Kilicoglu H, Fiszman M, Demner-Fushman D. Decomposing consumer health questions. BioNLP 2014.
Del Fiol G, Workman TE, Gorman PN. Clinical questions raised by clinicians at the point of care: a systematic review. JAMA Intern Med. 2014 May;174(5):710-8. doi: 10.1001/jamainternmed.2014.368.
You D, Antani SK, Demner-Fushman D, Thoma GR. Does Figure-Text Improve Biomedical Article Retrieval? A Pilot Study. CBMS 2014. May 2014.
You D, Antani SK, Demner-Fushman D, Thoma GR. A MRF Model for Biomedical Image Segmentation. CBMS 2014. May 2014.
Ackerman MJ. The medical data tsunami. J Med Pract Manage. 2014 May-Jun;29(6):406-7.
Kayaalp M, Browne AC, Callaghan FM, Dodd Z, Divita G, Ozturk S, McDonald CJ. The
pattern of name tokens in narrative clinical text and a comparison of
five systems for redacting them. J Am Med Inform Assoc. 2014 May-Jun;21(3):423-31. doi: 10.1136/amiajnl-2013-001689. Epub 2013 Sep 11.
Xue Z, Antani SK, Long LR, Demner-Fushman D, Thoma GR. Body Segment Classification for Visible Human Cross Section Slices.
IEEE 27th International Symposium on Computer-Based Medical Systems
(CBMS), New York, NY, May 2014: pp. 199-204
Ren H, Campos-Nanez E, Yaniv Z, Banovac F, Abeledo H, Hata N, Cleary K. Treatment planning and image guidance for radiofrequency ablation of large tumors. IEEE J Biomed Health Inform. 2014 May;18(3):920-8. doi: 10.1109/JBHI.2013.2287202. Epub 2013 Oct 24.
Yaniv Z, Holmes DR III, editors. Medical Imaging 2014: Image-Guided Procedures, Robotic Interventions, and Modeling. Proceedings of conference held 2014 Feb 15-20; San Diego. Proc. SPIE 9036; 2014 Mar 12. 764 pages. ISBN: 9780819498298.
Nguyen V, Bodenreider O, Sheth AP. Don't Like RDF Reification? Making Statements about Statements Using Singleton Property. Proc Int World Wide Web Conf. 2014 Apr 11;2014:759-770.
Yoo TS, Ackerman MJ, Chen D, Lowekamp B, Kuybeda O, Santoroski J. 3D Informatics. April 2014 Technical Report to the LHNCBC Board of Scientific Counselors.
Callaghan FM, Leishear K, Abhyankar S, Demner-Fushman D, McDonald CJ. High
vitamin B12 levels are not associated with increased mortality risk for
ICU patients after adjusting for liver function: a cohort
study. ESPEN J. 2014 Apr 1;9(2):e76-e83.
Hartung DM, Zarin D, Guise JM, McDonagh M, Paynter R, Helfand M. Reporting
discrepancies between the ClinicalTrials.gov results database and
peer-reviewed publications. Ann Intern Med. 2014 Apr 1;160(7):477-83. doi: 10.7326/M13-0480.
Cimino JJ, Frisse ME, Halamka J, Sweeney L, Yasnoff W. Consumer-mediated health information exchanges: the 2012 ACMI debate. J Biomed Inform. 2014 Apr;48:5-15. doi: 10.1016/j.jbi.2014.02.009. Epub 2014 Feb 20.
Linte CA, Yaniv Z. When change happens: computer assistance and image guidance for minimally invasive therapy. Healthcare Technology Letters. 2014 Mar 25;1(1):2-5.
Pedrosa G, Rahman MM, Antani SK, Demner-Fushman D, Long LR, Traina A. Integrating visual words as bunch of n-grams for effective biomedical image classification. .
Proceedings of IEEE WACV 2014: IEEE Winter Conference on Applications
of Computer Vision. Steamboat Springs, CO. March 24-26, 2014.
Xue Z, You D, Antani SK, Long LR, Demner-Fushman D, Thoma GR. Classification of Visual Signs in Abdominal CT Image Figures in Biomedical Literature.
Proc. SPIE. 9039. Medical Imaging 2014: PACS and Imaging Informatics:
Next Generation and Innovations. 90390T.
Rahman MM, Antani SK, Demner-Fushman D, Thoma GR. Biomedical
image representation and classification using an entropy-weighted
probabilistic concept feature space.
Proc. SPIE. 9039. Medical Imaging 2014: PACS and Imaging Informatics:
Next Generation and Innovations. 90390G.
Gong RH, Jenkins B, Sze RW, Yaniv Z. A
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Guler, O, Yaniv Z. A tutorial on image guided therapy.
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Narayan K, Danielson
CM, Lagarec K, Lowekamp BC, Coffman P, Laquerre A, Phaneuf MW, Hope TJ,
Subramaniam S. Multi-resolution
correlative focused ion beam scanning electron microscopy: applications
to cell biology. J Struct Biol. 2014 Mar;185(3):278-84. doi: 10.1016/j.jsb.2013.11.008. Epub 2013 Dec 1.
Caudle KE, Klein TE, Hoffman
JM, Muller DJ, Whirl-Carrillo M, Gong L, McDonagh EM, Sangkuhl K, Thorn
CF, Schwab M, Agundez JA, Freimuth RR, Huser V, Lee MT, Iwuchukwu OF,
Crews KR, Scott SA, , Wadelius M, Swen JJ, Tyndale RF, Stein CM, Roden
D, Relling MV, Williams MS, Johnson SG. Incorporation
of pharmacogenomics into routine clinical practice: the Clinical
Pharmacogenetics Implementation Consortium (CPIC) guideline development
process. Curr Drug Metab. 2014 Feb;15(2):209-17.
Jaeger S, Karargyris A, Candemir S, Folio L, Siegelman J, Callaghan FM, Xue Z, Palaniappan K, Singh RK, Antani SK, Thoma GR, Wang, Lu P, McDonald CJ. Automatic tuberculosis screening using chest radiographs. IEEE Trans Med Imaging. 2014 Feb;33(2):233-45. doi: 10.1109/TMI.2013.2284099. Epub 2013 Oct 1.
Candemir
S, Jaeger S, Palaniappan K, Musco J, Singh RK, Xue Z, Karargyris A,
Antani SK, Thoma GR, McDonald CJ. Lung segmentation in chest radiographs using anatomical atlases with nonrigid registration. IEEE Trans Med Imaging. 2014 Feb;33(2):577-90. doi: 10.1109/TMI.2013.2290491. Epub 2013 Nov 13.
You D, Antani SK, Demner-Fushman D, Thoma GR. A Contour-based Shape Descriptor For Biomedical Image Classification and Retrieval. Proceedings of SPIE 2014, Vol. 9021, Document Recognition and Retrieval XXI. February 2014;9021.
Bekhuis T, Tseytlin E, Mitchell KJ, Demner-Fushman D. Feature
engineering and a proposed decision-support system for systematic
reviewers of medical evidence. PLoS One. 2014 Jan 27;9(1):e86277. doi: 10.1371/journal.pone.0086277. eCollection 2014.
Ripple AM, Mork JG, Schmidt SC, Thomson H, Knecht LS. Performance Comparison of MEDLINE Structured Abstract to Unstructured Abstracts [Poster]. 2014 NIH Research Festival.
Mork JG, Demner-Fushman D, Schmidt SC, Aronson A. Vocabulary Density Method for Personalized Indexing of MEDLINE Journals [Poster]. 2014 AMIA Symposium.
Mork JG, Demner-Fushman D, Schmidt SC, Aronson A. Recent Enhancements to the NLM Medical Text Indexer. . BioASQ 2014.
Jing X, Cimino JJ. A
complementary graphical method for reducing and analyzing large data
sets. Case studies demonstrating thresholds setting and
selection. Methods Inf Med. 2014;53(3):173-85. doi: 10.3414/ME13-01-0075. Epub 2014 Apr 14.
Winnenburg R, Bodenreider O. Coverage of human phenotypes in SNOMED CT [Poster]. SNOMED CT Implementation Showcase, 2014.
Osborne R, Aronson A, Cohen K. A repository of semantic types in the MIMIC II database clinical notes. . BioNLP 2014. pp. 93-97.
Kastrin A, Rindflesch TC, Hristovski D. Link prediction in a MeSH co-occurrence network: preliminary results. Stud Health Technol Inform. 2014;205:579-83.
Huser V, Cimino JJ. Don't take your EHR to heaven, donate it to science: legal and research policies for EHR post mortem. J Am Med Inform Assoc. 2014 Jan-Feb;21(1):8-12. doi: 10.1136/amiajnl-2013-002061. Epub 2013 Aug 21.
Ackerman MJ. Computer briefs: The EMR: more than just a record. J Med Pract Manage. 2014 Jan-Feb;29(4):266-7.
Bodenreider O. Multi-lingual features of the Unified Medical Language System. Proc. CLEF-ER 2013 workshop 2013.
Cohen T, Widdows D, Rindflesch TC. Expansion-by-analogy: A vector symbolic approach to semantic search. . AAAI-Fall 2014 Symposium on Quantum Informatics for Cognitive, Social, and Semantic Processes.
Roberts K, Shooshan SE, Rodriguez L, Abhyankar S, Kilicoglu H, Demner-Fushman D. Machine Learning Methods for Detecting Risk Factors for Heart Disease in EHRs. Proc i2b2 2014 Workshop
Winnenburg R, Bodenreider O. Evaluating the consistency of inferred drug-class membership relations in NDF-RT. Proc 17th ISMB'2014 SIG meeting "Bio-Ontologies"2014
Winnenburg R, Bodenreider O. Coverage of phenotypes in standard terminologies. Joint Bio-Ontologies and BioLINK ISMB'2014 SIG session "Phenotype Day"2014:41-44.
McDonald CJ, Tang PC, Hripcsak G. Electronic Health Record Systems. . In: Shortliffe EH, Cimino JJ, editors. Biomedical Informatics: Computer Applications in Healthcare and Biomedicine 4th ED [Internet]. London: Springer London; 2014. p. 391–421. Available from: http://link.springer.com/10.1007/978-1-4471-4474-8.
Goldbach
H, Chang AY, Kyer A, Ketshogileng D, Taylor L, Chandra A, Dacso M, Kung
SJ, Rijken T, Fontelo P, Littman-Quinn R, Seymour AK, Kovarik
CL. Evaluation of generic medical information accessed via mobile phones at the point of care in resource-limited settings. J Am Med Inform Assoc. 2014 Jan-Feb;21(1):37-42. doi: 10.1136/amiajnl-2012-001276. Epub 2013 Mar 27.
Kastrin A, Rindflesch TC, Hristovski D. Link prediction on the Semantic MEDLINE Network. . Proceedings of the 17th International conference on Discovery Science.
Lowekamp BC, Chen DT, Ibáñez L, Blezek D. The Design of SimpleITK. Front Neuroinform. 2013 Dec 30;7:45. doi: 10.3389/fninf.2013.00045. eCollection 2013.
Chachra S, Xue Z, Antani SK, Demner-Fushman D, Thoma GR. Extraction and Labeling High-resolution Images from PDF Documents.
Proc. SPIE 9021, Document Recognition and Retrieval XXI, 90210Q
(December 27, 2013). doi:10.1117/12.2042336.
Kilicoglu H, Fiszman M, Demner-Fushman D. Interpreting Consumer Health Questions: The Role of Anaphora and Ellipsis. Proceedings of BioNLP 2013. Pages 54-62.
Van Der Volgen J, Harris BR, Demner-Fushman D. Analysis of Consumer Health Questions for Development of Question-Answering Technology [Poster].
Proceedings of One HEALTH: Information in an Interdependent World, the
2013 Annual Meeting and Exhibition of the Medical Library Association
(MLA), 2013.
Schulz S, Balkanyi L, Cornet R, Bodenreider O. From concept representations to ontologies: a paradigm shift in health informatics?. Healthc Inform Res. 2013 Dec;19(4):235-42. doi: 10.4258/hir.2013.19.4.235. Epub 2013 Dec 31.
Bodenreider O. Disease Ontologies.
In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H, editors. Encyclopedia
of Systems Biology: Springer; 2013. p. 578-581.
Fontelo P, Gavino A, Sarmiento RF. Comparing data accuracy between structured abstracts and full-text journal articles: implications in their use for informing clinical decisions. Evid Based Med. 2013 Dec;18(6):207-11. doi: 10.1136/eb-2013-101272. Epub 2013 Jun 20.
Gavino AI, Ho BL, Wee PA, Marcelo AB, Fontelo P. Information-seeking trends of medical professionals and students from middle-income countries: a focus on the Philippines. Health Info Libr J. 2013 Dec;30(4):303-17. doi: 10.1111/hir.12032. Epub 2013 Jul 23.
Rosemblat G, Shin D, Kilicoglu H, Sneiderman C, Rindflesch TC. A methodology for extending domain coverage in SemRep. J Biomed Inform. 2013 Dec;46(6):1099-107. doi: 10.1016/j.jbi.2013.08.005. Epub 2013 Aug 21.
Karargyris A, Rondonotti E, Mandelli G, Koulaouzidis A. Evaluation of 4 three-dimensional representation algorithms in capsule endoscopy images. World J Gastroenterol. 2013 Nov 28;19(44):8028-33. doi: 10.3748/wjg.v19.i44.8028.
Lowekamp B, Chen D. BinShrink: A multi-resolution filter with cache efficient averaging. . Insight Journal. Web. 18 November 2013
Abhyankar S, Demner-Fushman D. A simple method to extract key maternal data from neonatal clinical notes. AMIA Annu Symp Proc. 2013 Nov 16;2013:2-9. eCollection 2013.
Cairelli MJ, Miller CM, Fiszman M, Workman TE, Rindflesch TC. Semantic
MEDLINE for discovery browsing: using semantic predications and the
literature-based discovery paradigm to elucidate a mechanism for the
obesity paradox. AMIA Annu Symp Proc. 2013 Nov 16;2013:164-73. eCollection 2013.
Cimino JJ, Overby CL, Devine EB, Hulse NC, Jing X, Maviglia SM, Del Fiol G. Practical choices for infobutton customization: experience from four sites. AMIA Annu Symp Proc. 2013 Nov 16;2013:236-45. eCollection 2013.
Demner-Fushman D, Mork JG, Aronson AR. Mining MEDLINE for problems associated with vitamin D. AMIA Annu Symp Proc. 2013 Nov 16;2013:300-8. eCollection 2013.
Fontelo P, Liu F. Mobile app versus Web app: a comparison using 2008-2012 "PubMed for Handhelds" server data. AMIA Annu Symp Proc. 2013 Nov 16;2013:445-50. eCollection 2013.
Huser V, Cimino JJ. Desiderata
for healthcare integrated data repositories based on architectural
comparison of three public repositories. AMIA Annu Symp Proc. 2013 Nov 16;2013:648-56. eCollection 2013.
Yepes AJ, Mork JG, Demner-Fushman D, Aronson AR. Comparison and combination of several MeSH indexing approaches. AMIA Annu Symp Proc. 2013 Nov 16;2013:709-18. eCollection 2013.
Lu C, Tormey D, McDreedy L, Browne AC. Implementing
comprehensive derivational features in Llexical tools using a
systematical approach [Poster]. AMIA 2013 Annual Symposium, Washington, DC, November 16-20, 2013, p. 904
Sheets L, Liu F, Sarmiento RF, Gavino A, Fontelo P. Optimizing the txt2MEDLINE search portal for low-resource clinical decision support. AMIA Annu Symp Proc. 2013 Nov 16;2013:1277-81. eCollection 2013.
Winnenburg R, Bodenreider O. Metrics for assessing the quality of value sets in clinical quality measures. AMIA Annu Symp Proc. 2013 Nov 16;2013:1497-505. eCollection 2013.
Workman TE, Rosemblat G, Fiszman M, Rindflesch TC. A literature-based assessment of concept pairs as a measure of semantic relatedness. AMIA Annu Symp Proc. 2013 Nov 16;2013:1512-21. eCollection 2013.
Mishra R, Del Fiol G, Kilicoglu H, Jonnalagadda S, Fiszman M. Automatically extracting clinically useful sentences from UpToDate to support clinicians' information needs. AMIA Annu Symp Proc. 2013 Nov 16;2013:987-92. eCollection 2013.
Borovikov E, Vajda S, Lingappa G, Candemir S, Antani SK, Gill MJ, Thoma GR. FaceMatch: visual search of missing persons during a disaster event [Poster]. NIH Intramural Research Festival, Bethesda MD, November 6-8, 2013.
Karargyris A, Candemir S, Jaeger S, Xue Z, Antani SK, Thoma GR. A Combined Approach for Lung Boundary Segmentation of Chest X-Ray Images [Poster]. NIH Intramural Research Festival, Bethesda MD, November 6-8, 2013.
Xue Z, Jaeger S, Karargyris A, Candemir S, Antani SK, Long LR, Thoma GR, McDonald CJ. A
System for Automated Screening for Tuberculosis using Digital Chest
X-rays for Resources-Constrained Regions [Poster]. NIH Intramural Research Festival, Bethesda MD, November 6-8, 2013.
Rahman MM, Antani SK, Demner-Fushman D, Thoma GR. An
Interactive Region-Of-interest (ROI)- Based Image Retrieval Approach of
Biomedical Articles in a Local Concept- Based Feature Space
[Poster]. NIH Intramural Research Festival, Bethesda MD, November 6-8, 2013.
You D, Antani SK, Demner-Fushman D, Thoma GR. Does figure-text improve biomedical image retrieval [Poster]. NIH Intramural Research Festival, Bethesda MD, November 6-8, 2013.
Karargyris A, Folio L, Siegelman J, Callaghan FM, Candemir S, Xue Z, Lu P-X, Wang, Antani SK, Thoma GR, Jaeger S. Comparing the Performance of Man and Machine for TB Screening in Chest Radiographs [Poster]. NIH Intramural Research Festival, Bethesda MD, November 6-8, 2013.
Le T, Rance B, Bodenreider O. Network visualization of UMLS source vocabularies using semantic groups. AMIA Annu Symp Proc, 2013: p. 90
Johnson HL, Fontelo P, Olsen CH, Jones KD, Gimbel RW. Family nurse practitioner student perception of journal abstract usefulness in clinical decision making: a randomized controlled trial. J Am Assoc Nurse Pract. 2013 Nov;25(11):597-603. doi: 10.1111/1745-7599.12013. Epub 2013 Mar 6.
Peters L, Nguyen T, Bodenreider O. Displaying drug classes in RxNav [Poster]. AMIA Annu Symp Proc, 2013: p. 1134.
McDonald CJ. Toward electronic medical record alerts that consume less physician time. JAMA Intern Med. 2013 Oct 14;173(18):1755-6. doi: 10.1001/jamainternmed.2013.9332.
Rosemblat G, Resnick MP, Auston I, Shin D, Sneiderman C, Fizsman M, Rindflesch TC. Extending SemRep to the Public Health Domain. J Am Soc Inf Sci Technol. 2013 Oct;64(10):1963-1974.
Friedman C, Rindflesch TC, Corn M. Natural
language processing: state of the art and prospects for significant
progress, a workshop sponsored by the National Library of
Medicine. J Biomed Inform. 2013 Oct;46(5):765-73. doi: 10.1016/j.jbi.2013.06.004. Epub 2013 Jun 25.
McDonald CJ. Lister Hill National Center for Biomedical Communications Annual Report FY2013. Lister Hill National Center for Biomedical Communications FY2013 Annual Report.
Gordon E, Waisberg M, Ersoy I, Pena M, Jaeger S, Pierce S. The eye as a window to investigate the CNS microvasculature during a dynamic malaria infection [Abstract]. Third Annual Seminar on Molecular Imaging of Infectious Diseases, September 23, 2013.
Karargyris A, Koulaouzidis A. Capsule-odometer: a concept to improve accurate lesion localisation. World J Gastroenterol. 2013 Sep 21;19(35):5943-6. doi: 10.3748/wjg.v19.i35.5943.
Kayaalp M, Browne AC, Dodd Z, Sagan P, McDonald CJ. Clinical Text De-Identification Research. September 2013 Technical Report to the LHNCBC Board of Scientific Counselors.
Xue Z, Antani SK, Long LR, Demner-Fushman D, Thoma GR. Classification of CT Figures in Biomedical Articles Based on Body Segments.
2013 IEEE International Conference on Healthcare Informatics (ICHI),
pp.264,268, 9-11 Sept. 2013. doi: 10.1109/ICHI.2013.17.
Jonnalagadda SR, Del Fiol G, Medlin R, Weir C, Fiszman M, Mostafa J, Liu H. Automatically extracting sentences from Medline citations to support clinicians' information needs. J Am Med Inform Assoc. 2013 Sep-Oct;20(5):995-1000. doi: 10.1136/amiajnl-2012-001347. Epub 2012 Oct 25.
Ackerman MJ. Computer briefs: the healthcare trifecta. J Med Pract Manage. 2013 Sep-Oct;29(2):140-1.
Borovikov E, Vajda S, Lingappa G, Antani SK, Thoma GR. Face matching for post-disaster family reunification. IEEE International Conference on Healthcare Informatics. Philadelphia, PA, USA. September 2013.
Fung K, Kayaalp M, Callaghan FM, McDonald CJ. Comparison
of electronic pharmacy prescription records with manually collected
medication histories in an emergency department. Ann Emerg Med. 2013 Sep;62(3):205-11. doi: 10.1016/j.annemergmed.2013.04.014. Epub 2013 May 18.
Kang YS, Kayaalp M. Extracting laboratory test information from biomedical text. J Pathol Inform. 2013 Aug 31;4:23. doi: 10.4103/2153-3539.117450. eCollection 2013.
Zarin D. Participant-level data and the new frontier in trial transparency [Letter]. N Engl J Med. 2013 Aug 1;369(5):468-9. doi: 10.1056/NEJMe1307268.
Kim J, Le DX, Thoma GR. Identification of Investigator Name Zones Using SVM Classifiers and Heuristic Rules.
12th international Conference on Document Analysis and Recognition
(ICDAR). Washington D.C., August 2013.
Zhang K, Liu WL, Locatis C, Ackerman M. Uncompressed high-definition videoconferencing tools for telemedicine and distance learning. Telemed J E Health. 2013 Aug;19(8):579-84. doi: 10.1089/tmj.2012.0219. Epub 2013 Jun 29.
Hersh WR,
Weiner MG, Embi PJ, Logan JR, Payne PR, Bernstam EV, Lehmann HP,
Hripcsak G, Hartzog TH, Cimino J, Saltz JH. Caveats
for the use of operational electronic health record data in comparative
effectiveness research. Med Care. 2013 Aug;51(8 Suppl 3):S30-7. doi: 10.1097/MLR.0b013e31829b1dbd.
Winnenburg R, Rodriguez L, Callaghan F, Sorbello A, Szarfman A, Bodenreider O. Aligning Pharmacologic Classes Between MeSH and ATC. 4th International Conference on Biomedical Ontology · ICBO 2013
Huser V, Cimino JJ. Linking ClinicalTrials.gov and PubMed to track results of interventional human clinical trials. PLoS One. 2013 Jul 9;8(7):e68409. doi: 10.1371/journal.pone.0068409. Print 2013.
Zarin D, Tse T. Trust but verify: trial registration and determining fidelity to the protocol [Letter]. Ann Intern Med. 2013 Jul 2;159(1):65-7. doi: 10.7326/0003-4819-159-1-201307020-00011.
Gimbel RW,
Fontelo P, Stephens MB, Olsen CH, Bunt C, Ledford CJ, Loveland Cook CA,
Liu F, Burke HB. Radiation
exposure and cost influence physician medical image decision making: a
randomized controlled trial. Med Care. 2013 Jul;51(7):628-32. doi: 10.1097/MLR.0b013e3182928fd5.
Jimeno-Yepes AJ, Plaza L, Mork JG, Aronson AR, Díaz A. MeSH indexing based on automatically generated summaries. BMC Bioinformatics. 2013 Jun 26;14:208. doi: 10.1186/1471-2105-14-208.
Huser V, Cimino JJ. Evaluating
adherence to the International Committee of Medical Journal Editors'
policy of mandatory, timely clinical trial registration. J Am Med Inform Assoc. 2013 Jun;20(e1):e169-74. doi: 10.1136/amiajnl-2012-001501. Epub 2013 Feb 9.
Jimeno-Yepes AJ, Sticco JC, Mork JG, Aronson AR. GeneRIF indexing: sentence selection based on machine learning. BMC Bioinformatics. 2013 May 31;14:171. doi: 10.1186/1471-2105-14-171.
Workman TE, Fiszman M, Rindflesch TC, Nahl D. Framing
Serendipitous Information Seeking Behavior for Facilitating
Literature-Based Discovery: A Proposed Model. . Journal of the American Society for Information Science and Technology 2013, in press.
Ross JS, Mocanu M, Lampropulos JF, Tse T, Krumholz HM. Time to publication among completed clinical trials. JAMA Intern Med. 2013 May 13;173(9):825-8. doi: 10.1001/jamainternmed.2013.136.
Ackerman MJ. Computer briefs: Blue Cross, Blue Shield, Blue Button. J Med Pract Manage. 2013 May-Jun;28(6):394-5.
Fung KW, Jao CS, Demner-Fushman D. Extracting
drug indication information from structured product labels using
natural language processing. J Am Med Inform Assoc. 2013 May 1;20(3):482-8. doi: 10.1136/amiajnl-2012-001291. Epub 2013 Mar 9.
Zarin D, Tse T. Clarification about ClinicalTrials.gov [Letter]. IRB. 2013 May-Jun;35(3):19.
Yepes AJ, Prieur-Gaston E, Névéol A. Combining
MEDLINE and publisher data to create parallel corpora for the automatic
translation of biomedical text. BMC Bioinformatics. 2013 Apr 30;14:146. doi: 10.1186/1471-2105-14-146.
Abhyankar S, McDonald CJ. Overweight, obesity, and all-cause mortality [Letter]. JAMA. 2013 Apr 24;309(16):1680-1. doi: 10.1001/jama.2013.3092.
Zarin DA, Williams RJ, Bergeris AM, Dobbins H, Ide NC, Loane RF, Robbins A, Tse T. ClinicalTrials.gov and Related Projects: Improving Access to Information about Clinical Trials. April 2013 Technical Report to the LHNCBC Board of Scientific Counselors.
Sheets L, Gavino A, Callaghan F, Fontelo P. Do language fluency and other socioeconomic factors influence the use of PubMed and MedlinePlus? Appl Clin Inform. 2013 Apr 10;4(2):170-84. doi: 10.4338/ACI-2013-01-RA-0006. Print 2013.
Schauder DM, Kuybeda O, Zhang J, Klymko K, Bartesaghi A, Borgnia MJ, Mayer ML, Subramaniam S. Glutamate
receptor desensitization is mediated by changes in quaternary structure
of the ligand binding domain. Proc Natl Acad Sci U S A. 2013 Apr 9;110(15):5921-6. doi: 10.1073/pnas.1217549110. Epub 2013 Mar 25.
McDonald CJ, Vreeman DJ, Abhyankar S. Comment on "time to integrate clinical and research informatics" [Letter]. Sci Transl Med. 2013 Apr 3;5(179):179le1. doi: 10.1126/scitranslmed.3005700.
Misra D, Thoma GR. Use
of descriptive metadata as a knowledgebase for analyzing data in large
textual collections. Proc. IS&T Archiving 2013. Washington
D.C. Proc. IS&T Archiving 2013. Washington D.C. pg 193-199.
Liu J, Subramanian KR, Yoo TS. An optical flow approach to tracking colonoscopy video. Comput Med Imaging Graph. 2013 Apr;37(3):207-23. doi: 10.1016/j.compmedimag.2013.01.010. Epub 2013 Mar 13.
Jaeger S, Karargyris A, Candemir S, Siegelman J, Folio L, Antani S, Thoma G. Automatic screening for tuberculosis in chest radiographs: a survey. Quant Imaging Med Surg. 2013 Apr;3(2):89-99. doi: 10.3978/j.issn.2223-4292.2013.04.03.
Marcelo A,
Gavino A, Isip-Tan IT, Apostol-Nicodemus L, Mesa-Gaerlan FJ, Firaza PN,
Faustorilla JF Jr., Callaghan FM, Fontelo P. A comparison of the accuracy of clinical decisions based on full-text articles and on journal abstracts alone: a study among residents in a tertiary care hospital. Evid Based Med. 2013 Apr;18(2):48-53. doi: 10.1136/eb-2012-100537. Epub 2012 Jul 10.
Jessup
CM, Balbus JM, Christian C, Haque E, Howe SE, Newton SA, Reid BC,
Roberts L, Wilhelm E, Rosenthal JP. Climate
change, human health, and biomedical research: analysis of the National
Institutes of Health research portfolio. Environ Health Perspect. 2013 Apr;121(4):399-404. doi: 10.1289/ehp.1104518. Epub 2013 Jan 18.
Cameron
D, Bodenreider O, Yalamanchili H, Danh T, Vallabhaneni S, Thirunarayan
K, Sheth AP, Rindflesch TC. A graph-based recovery and decomposition of Swanson's hypothesis using semantic predications. J Biomed Inform. 2013 Apr;46(2):238-51. doi: 10.1016/j.jbi.2012.09.004. Epub 2012 Sep 28.
Bryant B, Sari-Sarraf H, Wachtel M, Long LR, Antani SK. Fast
GPU-based segmentation of H&E stained squamous epithelium from
multi-gigapixel tiled virtual slides [Poster]. Proc. SPIE 8676, Medical Imaging 2013: Digital Pathology, 86760X (March 29, 2013); doi:10.1117/12.2007800
Harris
AK, Meyerson JR, Matsuoka Y, Kuybeda O, Moran A, Bliss D, Das SR,
Yewdell JW, Sapiro G, Subbarao K, Subramaniam S. Structure
and accessibility of HA trimers on intact 2009 H1N1 pandemic influenza
virus to stem region-specific neutralizing antibodies. Proc Natl Acad Sci U S A. 2013 Mar 19;110(12):4592-7. doi: 10.1073/pnas.1214913110. Epub 2013 Mar 4.
Huser V, Cimino J. Providing pharmacogenomics clinical decision support using whole genome sequencing data as input. AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:81. eCollection 2013.
Manning JD, Marciano BE, Cimino J. Visualizing
the data - using lifelines2 to gain insights from data drawn from a
clinical data repository. AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:168-72. eCollection 2013.
Hruby GW, Boland MR, Cimino J, Gao J, Wilcox AB, Hirschberg J, Weng C. Characterization of the biomedical query mediation process. AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:89-93. eCollection 2013.
Cimino JJ. Improving the electronic health record--are clinicians getting what they wished for?. JAMA. 2013 Mar 13;309(10):991-2. doi: 10.1001/jama.2013.890.
Apostolova E, You D, Xue Z, Antani SK, Demner-Fushman D, Thoma GR. Image
Retrieval From Scientific Publications: Text and Image Content
Processing To Separate Multipanel Figures.
JASIST (Journal of the American Society for Information Science and
Technology), 64(5):893–908, 2013.
Hristovski D, Rindflesch TC, Peterlin B. Using literature-based discovery to identify novel therapeutic approaches. Cardiovasc Hematol Agents Med Chem. 2013 Mar;11(1):14-24.
You D, Rahman MM, Antani SK, Demner-Fushman D, Thoma GR. Text- and content-based biomedical image modality classification. Proc. SPIE Medical Imaging. Orlando, FL. February 2013;8674-21.
Zhang X, Zou J, Le DX, Thoma GR. Combining
Discriminative SVM models for the Improved Recognition of Investigator
Names in Medical Articles. .
Proceedings of SPIE Volume 8658, Document Recognition and Retrieval XX,
IS&T/SPIE Electronic Imaging 2013.
Zarin DA, Tse T. Unambiguous identification of obesity trials [Letter]. N Engl J Med. 2013 Feb 7;368(6):580-1. doi: 10.1056/NEJMc1215018.
Tran EEH, Kuybeda O, Bartesaghi A, Milne JLS, Subramaniam S. Binding
of Neutralizing Antibodies Results in Distinct Quaternary Conformations
of Trimeric HIV-1 Envelope Glycoproteins. Biophysical Society 57th Annual Meeting; 2013 Feb 2-6; Philadelphia.
You D, Simpson M, Antani SK, Demner-Fushman D, Thoma GR. A
robust pointer segmentation in biomedical images toward building a
visual ontology for biomedical article retrieval.
Proc. SPIE 8658, Document Recognition and Retrieval XX, 86580Q
(February 4, 2013); doi:10.1117/12.2005934.
You D, Simpson M, Antani SK, Demner-Fushman D, Thoma GR. Annotating image ROIs with text descriptions for multimodal biomedical document retrieval.
Proc. SPIE 8658, Document Recognition and Retrieval XX, 86580Q
(February 4, 2013); doi:10.1117/12.2005934;
http://dx.doi.org/10.1117/12.2005934.
Kuybeda O, Frank GA, Bartesaghi A, Borgnia M, Subramaniam S, Sapiro G. A collaborative framework for 3D alignment and classification of heterogeneous subvolumes in cryo-electron tomography. J Struct Biol. 2013 Feb;181(2):116-27. doi: 10.1016/j.jsb.2012.10.010. Epub 2012 Oct 27.
Harris
AK, Meyerson JR, Matsuoka Y, Kuybeda O, Moran A, Bliss D, Das SR,
Yewdell J, Sapiro G, Subbarao K, Subramaniam S. Molecular
Structures of Native HA Trimers on 2009 H1N1 Pandemic Influenza Virus
Complexed with Neutralizing Antibodies. Biophysical Journal. 2013 Jan 29;104(2 Supp 1):414a. 57th Annual Meeting of the Biophysical Society; 2013 Feb 2-6; Philadelphia. DOI: http://dx.doi.org/10.1016/j.bpj.2012.11.2310.
Meyerson
JR, Tran EE, Kuybeda O, Chen W, Dimitrov DS, Gorlani A, Verrips T,
Lifson JD, Subramaniam S. Molecular structures of trimeric HIV-1 Env in complex with small antibody derivatives. Proc Natl Acad Sci U S A. 2013 Jan 8;110(2):513-8. doi: 10.1073/pnas.1214810110. Epub 2012 Dec 24.
Cimino JJ, Ayres EJ, Beri A, Freedman R, Oberholtzer E, Rath S. Developing a self-service query interface for re-using de-identified electronic health record data. Stud Health Technol Inform. 2013;192:632-6.
Zhang M, Del Fiol G, Grout RW,
Jonnalagadda S, Medlin R, Mishra R, Weir C, Liu H, Mostafa J, Fiszman
M. Automatic identification of comparative effectiveness research from medline citations to support clinicians' treatment information needs. Stud Health Technol Inform. 2013;192:846-50.
Locatis CN, Ackerman MJ. Three principles for determining the relevancy of store-and-forward and live interactive telemedicine: reinterpreting two telemedicine research reviews and other research. Telemed J E Health. 2013 Jan;19(1):19-23. doi: 10.1089/tmj.2012.0063. Epub 2012 Nov 27.
Jimeno Yepes A, Mork JG, Aronson A. Using the argumentative structure of scientific literature to improve information access [Poster]. BioNLP 2013.
Balkanyi L, Schulz S, Cornet R, Bodenreider O. Medical concept representation: the years beyond 2000 [Poster]. Stud Health Technol Inform. 2013;192:1011.
Mork JG, Jimeno Yepes A, Aronson A. The NLM Medical Text Indexer System for Indexing Biomedical Literature. . BioASQ 2013.
Jaeger S. The neurological principle: how traditional Chinese medicine unifies body and mind. Int. J. Functional Informatics and Personalised Medicine, Vol. 4, No. 2, 2013.
Maver A, Hristovski D, Rindflesch TC, Peterlin B. Integration
of data from omic studies with the literature-based discovery towards
identification of novel treatments for neovascularization in diabetic
retinopathy. Biomed Res Int. 2013;2013:848952. doi: 10.1155/2013/848952. Epub 2013 Nov 24.
Gallagher ME. Improving Software Sustainability: Lessons Learned from Profiles in Science. Archiving. 2013;2013:74-79.
Jimeno Yepes AJ, Mork JG, Aronson A. Identifying PublicationTypes Using Machine Learning. BioASQ Workshop 2013.
Demner-Fushman D, Seckman C, Fisher C, Thoma GR. Continual development of a personalized decision support system. Stud Health Technol Inform. 2013;192:175-9.
Montufar-Rueda C, Rodriguez L, Jarquin JD, Barboza A, Bustillo MC, Marin F, Ortiz G, Estrada F. Severe postpartum hemorrhage from uterine atony: a multicentric study. J Pregnancy. 2013;2013:525914. doi: 10.1155/2013/525914. Epub 2013 Dec 2.
Del Fiol G,
Curtis C, Cimino J, Iskander A, Kalluri AS, Jing X, Hulse NC, Long J,
Overby CL, Schardt C, Douglas DM. Disseminating
context-specific access to online knowledge resources within electronic
health record systems. Stud Health Technol Inform. 2013;192:672-6.
Zhang, H, Fiszman M, Shin D, Wilkowski B, Rindflesch TC. Clustering cliques for graph-based summarization of the biomedical research literature. . BMC Bioinformatics 14:182.
Rance B, Snyder M, Lewis J, Bodenreider O. Leveraging terminological resources for mapping between rare disease information sources. Stud Health Technol Inform. 2013;192:529-33.
Peters L, Mortensen J, Nguyen T, Bodenreider O. Enabling complex queries to drug information sources through functional composition. Stud Health Technol Inform. 2013;192:692-6.
Winnenburg R, Bodenreider O. Exploring pharmacoepidemiologic groupings of drugs from a clinical perspective. Stud Health Technol Inform. 2013;192:827-31.
Hunt S, Cimino J, Koziol DE. A comparison of clinicians' access to online knowledge resources using two types of information retrieval applications in an academic hospital setting. J Med Libr Assoc. 2013 Jan;101(1):26-31. doi: 10.3163/1536-5050.101.1.005.
Ackerman MJ. Computer briefs: privacy, M-health, and social media. J Med Pract Manage. 2013 Jan-Feb;28(4):264-5.
Bodenreider
O, Nguyen D, Chiang P, Chuang P, Madden M, Winnenburg R, McClure R,
Emrick S, D'Souza I. The NLM value set authority center (Poster). Stud Health Technol Inform. 2013;192:1224.
Antani SK, You D, Simpson M, Rahman M, Demner-Fushman D, Thoma GR. The role of image modality and visual characteristics in archiving biomedical images. Proc of IS&T Archiving Conference. Volume 2013, Number 1, 2013, pp. 31-35.
Sarmiento RF, Liu F, Fontelo P. A
Cross-Language Mobile Resource for Accessing MEDLINE/PubMed Based on an
Open-Source, Crowdsourced Controlled Medical Vocabulary for the
Philippines. Journal of Mobile Technology in Medicine. 2012 Dec;1:4S:28. DOI: 10.7309/jmtm.50.
Pearson G, Gill MJ. An Evaluation of Motion JPEG 2000 for Video Archiving. Proc. Archiving 2005. Washington, D.C. April 2005:237-43.
Abhyankar S, Leishear K, Callaghan FM, Demner-Fushman D, McDonald CJ. Lower
short- and long-term mortality associated with overweight and obesity
in a large cohort study of adult intensive care unit
patients. Crit Care. 2012 Dec 18;16(6):R235. doi: 10.1186/cc11903.
Locatis CN, Conde JG, Bhagwat MA. A Hands-on Distance Learning Strategy to Increase Access to Bioinformatics Training [Poster]. Research Centers in Minority Institutions (RCMI): 13th RCMI International Symposium on Health Disparities; 2012 Dec 9-13; San Juan, Puerto Rico.
Gallagher ME, Moffatt C. The Profiles in Science Digital Library: Behind the Scenes. Proc ACM/IEEE Joint Conf Digit Libr. 2012: 433–434. doi: 10.1145/2232817.2232928.
Kilicoglu H, Shin D, Fiszman M, Rosemblat G, Rindflesch TC. SemMedDB: a PubMed-scale repository of biomedical semantic predications. Bioinformatics. 2012 Dec 1;28(23):3158-60. doi: 10.1093/bioinformatics/bts591. Epub 2012 Oct 8.
Pearson G, Gill MJ, Antani SK, Neve L, Miernicki G, Phichaphop K, Kanduru A, Jaeger S, Thoma GR. The Role of Location For Family Reunification During Disasters. HealthGIS 2012. Redondo Beach, CA. November 2012.
Morrison SM, Cheh M, Calvo SC, Collins H, Fun J, Greenberg K, Forman-Neall L. Genetics Home Reference, Ten Years In: Where We Are Now [Poster]. American Society of Human Genetics, November 9, 2012, San Francisco, CA.
Fontelo P, Liu F. An Analysis of "PubMed for Handhelds" Server Utilization [Poster]. AMIA Annu Symp Proc [Proceedings of the American Medical Informatics Association Annual Symposium]; 2012 Nov 3-7; Chicago. p. 1736.
Liu F, Fontelo P, Gavino A. ClinicalTrials and DailyMed Links from Translational Science Search [Poster]. AMIA Annu Symp Proc [Proceedings of the American Medical Informatics Association Annual Symposium]; 2012 Nov 3-7; Chicago. p. 1841.
Gavino
A, Marcelo A, Isip-Tan IT, Apostol-Nicodemus L, Mesa-Gaerlan FJ, Firaza
PN, Faustorilla JF Jr., Fontelo P. Email2MEDLINE Use by Rural Health Physicians in Remote Areas of the Philippines [Poster]. AMIA Annu Symp Proc [Proceedings of the American Medical Informatics Association Annual Symposium]; 2012 Nov 3-7; Chicago. p. 1746.
Sheets L, Gavino A, Liu F, Fontelo P. Usability of Selected Databases for Low-Resource Clinical Decision Support [Poster]. AMIA Annu Symp Proc [Proceedings of the American Medical Informatics Association Annual Symposium]; 2012 Nov 3-7; Chicago. p. 1939.
Marcelo
A, Isip-Tan IT, Apostol-Nicodemus L, Mesa-Gaerlan FJ, Firaza PN,
Faustorilla JF Jr., Gavino A, Fontelo P. Use of Tablet Computers at the Point-of-Care: A Case Study from the Philippines [Poster]. AMIA Annu Symp Proc [Proceedings of the American Medical Informatics Association Annual Symposium]; 2012 Nov 3-7; Chicago. p. 1853.
Candemir S, Jaeger S, Palaniappan K, Antani SK, Thoma GR. Graph Cut Based Automatic Lung Boundary Detection in Chest Radiographs.
1st Annual IEEE Healthcare Innovation Conference of the IEEE EMBS
Houston, Texas USA, 7 - 9 November, 2012.
Lu C, Browne AC. Development of Sub-Term Mapping Tools (STMT) . AMIA 2012 Annual Symposium, Chicago, IL, November 3-7, 2012
Kawamoto K, Jacobs J, Welch BM,
Huser V, Paterno MD, Del Fiol G, Shields D, Strasberg HR, Huag PJ, Liu
Z, Jenders RA, Rowed DW, Chertcoff D, Fehre K, Adlassnig KP, Curtis
C. Clinical information system services and capabilities desired for scalable, standards-based, service-oriented decision support: consensus assessment of the Health Level 7 clinical decision support Work Group. AMIA Annu Symp Proc. 2012;2012:446-55. Epub 2012 Nov 3.
Huser V, Cimino JJ. Precision and negative predictive value of links between ClinicalTrials.gov and PubMed. AMIA Annu Symp Proc. 2012;2012:400-8. Epub 2012 Nov 3.
Lu C, Browne AC. Development of sub-term mapping tools (STMT) [Poster].
AMIA 2012 Annual Symposium, Chicago, IL, November 3-7, 2012, p. 1845
(AMIA, 2012 Distinguished Poster Award) Poster.
Fung KW, Bodenreider O. Knowledge representation and ontologies.
Richesson RL, Andrews JE (Eds.). Clinical Research Informatics, Health
Informatics, DOI 10.1007/978-1-84882-448-5_14, Springer-Verlag London
Limited Publishing 2012.
Peters L, Nguyen T, Bodenreider O. RxBatch – Batch operations for RxNorm and NDF-RT APIs (Poster). AMIA Annu Symp Proc, 2012: p. 1897.
Yoo TS, Bliss D, Lowekamp B, Chen D, Murphy GE, Narayan K, Hartnell LM, Do T, Subramaniam S. Visualizing cells and humans in 3D: Biomedical image analysis at nanometer and meter scales. IEEE Computer Graphics and Applications. 2012 Sep-Oct;32(5):39-49. DOI: 10.1109/MCG.2012.68.
Abhyankar S, Demner-Fushman D, Callaghan F, Leishear K, McDonald CJ. MIMIC-II: a database of 30,000+ patients for ICU research. NIH Intramural Research Festival, Bethesda MD, October 9-12, 2012.
Jaeger S, Karargyris A, Antani SK, Thoma GR. Automatic Screening For Lung Diseases In Chest Radiographs: a Global Health Initiative [Poster]. NIH Research Festival. October 2012.
Callaghan F, Jackson MT, Demner-Fushman D, Abhyankar S, McDonald C. Analysis
of data that has been extracted from free-text using natural language
processing: a likelihood model for misclassification with an application
to medical informatics. .
International Conference on Advances in Interdisciplinary Statistics
and Combinatorics (AISC2012), Greensboro, NC, October
2012
Caban JJ, Rosebrock A, Yoo TS. Automatic identification of prescription drugs using shape distribution models. In: 19th IEEE International Conference on Image Processing (ICIP); 2012 Sep 30-Oct 3; Lake Buena Vista, Florida. p. 1005-8. DOI: 10.1109/ICIP.2012.6467032
Rance B, Doughty E, Demner-Fushman D, Kann MG, Bodenreider O. A mutation-centric approach to identifying pharmacogenomic relations in text. J Biomed Inform. 2012 Oct;45(5):835-41. doi: 10.1016/j.jbi.2012.05.003. Epub 2012 Jun 7.
Jaeger S. An information-theoretic neural model based on concepts in Chinese medicine. 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW).
Borovikov E. FaceMatch: visual search for pictures of missing persons during a disaster event. NIH Research Festival. October 2012.
McDonald CJ. Lister Hill National Center for Biomedical Communications FY2012 Annual Report . September 2012
Rahman MM, You D, Simpson M. An
interactive image retrieval framework for biomedical articles based on
visual region-of-interest (ROI) identification and classification
[Abstract].
The 2nd IEEE Conference on Healthcare Informatics, Imaging, and Systems
Biology Analyzing Big Data for Healthcare and Biomedical Sciences (HISB
2012). La Jolla, CA. September 2012.
Simpson M, You D, Rahman MM, Demner-Fushman D, Antani SK, Thoma GR. ITI's participation in the ImageCLEF 2012 medical retrieval and classification tasks. CLEF 2012 Working Notes. Rome, Italy. September 2012.
Sheets L, Callaghan F, Gavino A, Liu F, Fontelo P. Usability of selected databases for low-resource clinical decision support. Applied Clinical Informatics. 2012;3(3):326-33. DOI: http://dx.doi.org/10.4338/ACI-2012-06-RA-0024.
Rindflesch
TC, Fiszman M, Kilicoglu H, Rosemblat G, Shin D, Cairelli M, Chen G,
Miller CM, Workman E. Semantic Knowledge Representation Project: Advanced Information Management for Biomedical Research. September 2012 Technical Report to the LHNCBC Board of Scientific Counselors.
Callaghan F, Jackson MT, Demner-Fushman D, Abhyankar S, McDonald CJ. NLP-derived
information improves the estimates of risk of disease compared to
estimates based on manually extracted data alone.
5th International Symposium on Semantic Mining in Biomedicine (SMBM
2012), 2012 Sept 3-4, Zurich, Switzerland.
Ackerman MJ. Computer briefs: big data. J Med Pract Manage. 2012 Sep-Oct;28(2):153-4.
He L, Long LR, Antani SK, Thoma GR. Histology image analysis for carcinoma detection and grading. Comput Methods Programs Biomed. 2012 Sep;107(3):538-56. doi: 10.1016/j.cmpb.2011.12.007. Epub 2012 Mar 20.
Jaeger S, Karargyris A, Antani SK, Thoma GR. Detecting tuberculosis in radiographs using combined lung masks. 34th Int. Conf. of the IEEE Engineering in Medicine & Biology Society (EMBC). San Diego, CA. August 2012:4978-4981. doi: 10.1109/EMBC.2012.6347110.
Huston M, Williams RJ, Bergeris A, Fun J, Tse T. New style and new content for ClinicalTrials.gov. NLM Tech Bull. 2012 Jul-Aug;(387):e5.
Huser V, Taft L, Cimino J. Suitability
of LOINC document ontology as a reference terminology for clinical
document types: a case report of a research-oriented EHR. NIH Poster Day 2012.
Abhyankar S, Demner-Fushman D, McDonald CJ. Standardizing clinical laboratory data for secondary use. J Biomed Inform. 2012 Aug;45(4):642-50. doi: 10.1016/j.jbi.2012.04.012. Epub 2012 May 3.
Vreeman D, Chiaravalloti MT, Hook J, McDonald CJ. Enabling international adoption of LOINC through translation. J Biomed Inform. 2012 Aug;45(4):667-73. doi: 10.1016/j.jbi.2012.01.005. Epub 2012 Jan 21.
Lin MC, Vreeman DJ, McDonald CJ, Huff SM. Auditing
consistency and usefulness of LOINC use among three large institutions -
using version spaces for grouping LOINC codes. J Biomed Inform. 2012 Aug;45(4):658-66. doi: 10.1016/j.jbi.2012.01.008. Epub 2012 Jan 28.
Kim I, Le DX, Thoma GR. Identifying
“comment-on” citation data in online biomedical articles using
SVM-based text summarization technique. Proc. Int’l Conf. Artificial Intelligence (ICAI’12), vol. 1, pp. 431-437, Las Vegas, July 2012.
Tse T, Zarin D, Williams R, Ide N. The role and importance of clinical trial registries and results databases.
In: Gallin JI, Ognibene FP, eds, Principles and Practice of Clinical
Research. 3rd ed. Amsterdam: Academic Press; 2012: 171-81.
Ackerman MJ. Computer briefs: M-health revisited. J Med Pract Manage. 2012 Jul-Aug;28(1):72-3.
Bekhuis T, Demner-Fushman D. Screening nonrandomized studies for medical systematic reviews: a comparative study of classifiers. Artif Intell Med. 2012 Jul;55(3):197-207. doi: 10.1016/j.artmed.2012.05.002. Epub 2012 Jun 5.
Lu C, McCreedy L, Tormey D, Browne AC. A Systematic Approach for Automatically Generating Derivational Variants in Lexical Tools Based on theSPECIALIST Lexicon . IEEE IT Professional Magazine, May/June, 2012;36-42.
Jimeno-Yepes A, Mork J, Demner-Fushman D, Aronson AR. A one-size-fits-all indexing method does not exist: automatic selection based on meta-learning. JCSE, vol. 6, no. 2, pp.151-160, 2012.
Demner-Fushman D, Abhyankar S. Syntactic-semantic frames for clinical cohort identification queries. .
Data Integration in the Life Sciences (DILS) June 2012, LNBI 7348
proceedings. Lecture Notes in Computer Science.
2012;7348:100-112
Demner-Fushman D, Antani SK, Simpson M, Thoma GR. Design and Development of a Multimodal Biomedical Information Retrieval System. JCSE. June 2012;6(2):168-177.
Misra D, Hall RH, Payne SM, Thoma GR. Digital
preservation and knowledge discovery based on documents from an
international health science program. Proc. 12th ACM/IEEE-CS JCDL, pg 23-26 (2012). doi: 10.1145/2232817.2232823.
McDonald CJ, Tierney WM. The effect of electronic health records on test ordering [Letter}. Health Aff (Millwood). 2012 Jun;31(6):1365; author reply 1366. doi: 10.1377/hlthaff.2012.0471.
Workman TE, Fiszman M, Hurdle JF. Text summarization as a decision support aid. BMC Med Inform Decis Mak. 2012 May 23;12:41. doi: 10.1186/1472-6947-12-41.
Califf RM, Zarin DA, Kramer JM, Sherman RE, Aberle LH, Tasneem A. Characteristics of clinical trials registered in ClinicalTrials.gov, 2007-2010. JAMA. 2012 May 2;307(17):1838-47. doi: 10.1001/jama.2012.3424.
Pan
H, Tryka KA, Vreeman DJ, Huggins W, Phillips MJ, Mehta JP, Phillips JH,
McDonald C, Junkins HA, Ramos EM, Hamilton CM. Using PhenX measures to identify opportunities for cross-study analysis. Hum Mutat. 2012 May;33(5):849-57. doi: 10.1002/humu.22074. Epub 2012 Apr 3.
Thoma G, Antani SK, Gill MJ, Pearson G, Neve L. People Locator: A System for Family Reunification. IT Professional Volume 14 Issue 3, May 2012 Pages 13-21 DOI: 10.1109/MITP.2012.25
Lu C, Tormey D, McCreedy L, Browne AC. A Systematic Approach for Automatically Generating Derivational Variants in Lexical Tools Based on the SPECIALIST Lexicon. IEEE IT Professional Magazine, May/June, 2012, p. 36-42.
Aronson AR, Mork J, Lang FM, Rogers W, Jimeno-Yepes A, Sticco JC. The NLM Indexing Initiative: Current Status and Role in Improving Access to Biomedical Information. April 2012 Technical Report to the LHNCBC Board of Scientific Counselors.
Workman TE, Stoddart JM. Rethinking information delivery: using a natural language processing application for point-of-care data discovery. J Med Libr Assoc. 2012 Apr;100(2):113-20. doi: 10.3163/1536-5050.100.2.009.
Zarin D. Factual
Errors about ClinicalTrials.gov and other federal mandates in special
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Jimeno-Yepes A, Aronson AR. Knowledge-based biomedical word sense disambiguation: comparison of approaches. BMC Bioinformatics. 2010 Nov 22;11:569. doi: 10.1186/1471-2105-11-569.
Cardenas I, Marcelo AB, Fontelo P. Development of a health informatics community-generated, open-source controlled medical vocabulary. AMIA Annu Symp Proc [Proceedings of the American Medical Informatics Association Annual Symposium]; 2010 Nov 13-17; Washington DC. p. 998.
Olson R, James E, Fontelo P. Information access trends among clinicians at a community hospital in northeast Georgia. AMIA Annu Symp Proc [Proceedings of the American Medical Informatics Association Annual Symposium]; 2010 Nov 13-17; Washington DC. p. 975.
Fontelo P, Liu F, Banez RJ. Mobile Devices, Smartphones and ‘PubMed for Handhelds’. AMIA Annu Symp Proc [Proceedings of the American Medical Informatics Association Annual Symposium]; 2010 Nov 13-17; Washington DC. p. 1044.
Banez RJ, Fontelo P, Marcelo AB, Liu F. QRefer: Using 2D-Barcode Technology for Patient Referral Systems. AMIA Annu Symp Proc [Proceedings of the American Medical Informatics Association Annual Symposium]; 2010 Nov 13-17; Washington DC. p. 975.
Kovarik C, Fontelo P, Liu F, Armstrong K, Littman-Quinn R, Banez R, Seymour A, Shih T, Mazhani L. txt2MEDLINE and SMS Practice Guidelines for Clinicians in Botswana. AMIA Annu Symp Proc [Proceedings of the American Medical Informatics Association Annual Symposium]; 2010 Nov 13-17; Washington DC. p. 1043.
Liu F, Fontelo P. Automatic translations of MEDLINE abstracts using Google Translate. AMIA Annu Symp Proc [Proceedings of the American Medical Informatics Association Annual Symposium]; 2010 Nov 13-17; Washington DC. p. 1148.
Abhyankar
S, Lloyd-Puryear MA, Goodwin R, Copeland S, Eichwald J, Therrell BL,
Zuckerman A, Downing G, McDonald CJ. Standardizing newborn screening results for health information exchange. AMIA Annu Symp Proc. 2010 Nov 13;2010:1-5.
Bodenreider O, Demner-Fushman D. Investigating
drug classes in biomedical terminologies from the perspective of
clinical decision support. AMIA Annu Symp Proc. 2010 Nov 13;2010:56-60.
Vreeman DJ, McDonald CJ, Huff SM. Representing Patient Assessments in LOINC®. AMIA Annu Symp Proc. 2010 Nov 13;2010:832-6.
Lin M-C, Vreeman DJ, McDonald CJ, Huff SM. Correctness of Voluntary LOINC Mapping for Laboratory Tests in Three Large Institutions. AMIA Annu Symp Proc. 2010 Nov 13;2010:447-51.
Mougin F, Bodenreider O, Burgun A. Looking
for Anemia (and Other Disorders) in SNOMED CT: Comparison of Three
Approaches and Practical Implications. AMIA Annu Symp Proc. 2010 Nov 13;2010:527-31.
Peters L, Kapusnik-Uner JE, Bodenreider O. Methods for managing variation in clinical drug names. AMIA Annu Symp Proc. 2010 Nov 13;2010:637-41.
Simpson M, Demner-Fushman D, Thoma GR. Evaluating
the Importance of Image-related Text for Ad-hoc and Case-based
Biomedical Article Retrieval. AMIA Annu Symp Proc. 2010 Nov 13;2010:752-6.
Fiszman M, Shin D, Sneiderman CA, Jin H, Rindflesch TC. A Knowledge Intensive Approach to Mapping Clinical Narrative to LOINC. AMIA Annu Symp Proc. 2010 Nov 13;2010:227-31.
Zhang GQ, Bodenreider O. Large-scale, Exhaustive Lattice-based Structural Auditing of SNOMED CT. AMIA Annu Symp Proc. 2010 Nov 13;2010:922-6.
Xue Z, Antani SK, Long LR, Thoma GR. An online segmentation tool for cervicographic image analysis.
ACM International Health Informatics Symposium, IHI 2010, Arlington,
VA, USA, November 11 - 12, 2010, Proceedings; 01/2010.
Zhang G-Q, Bodenreider O. Using SPARQL to Test for Lattices: Application to Quality Assurance in Biomedical Ontologies.
In: Patel-Schneider PF, Pan Y, Hitzler P, Mika P, Zhang L, Pan JZ, et
al., editors. Proceedings of the 9th International Semantic Web
Conference (ISWC 2010), Shanghai, China, November 7-11, 2010. Berlin,
Heidelberg: Springer; 2010. p. 273-288.
Fontelo P, Liu F. Are Consensus MEDLINE Abstracts Useful For Guiding Clinical Decisions? Evidence 2010 -- Transforming Healthcare; 2010 Nov 1-2; BMA House, London.
Fung K, Scichilone R, Giannangelo K. Benefits and Use Cases of a SNOMED CT to ICD-10 Map. . AMIA Annu Symp Proc 2010: 1049.
Mork JG, Aronson AR. The Medical Text Indexer (MTI) system for indexing biomedical literature.
book chapter submitted to monograph Indexing Specialities: Medicine.
Edited by L. Pilar Wyman. Medford, NJ: Information Today, Inc., in
association with the American Society of Indexers, Phoenix, AZ.
2010.
Zhu VJ, Fung K. Extraction and Comparison of Drug Class Information From Standard Terminologies. AMIA Annu Symp Proc. November 2010:1327.
Fung KW, McDonald C, Srinivasan S. The
UMLS-CORE project: a study of the problem list terminologies used in
large healthcare institutions. J Am Med Inform Assoc. 2010 Nov-Dec;17(6):675-80. doi: 10.1136/jamia.2010.007047.
Pathak J, Peters L, Chute CG, Bodenreider O. Comparing and evaluating terminology services application programming interfaces: RxNav, UMLSKS and LexBIG. J Am Med Inform Assoc. 2010 Nov-Dec;17(6):714-9. doi: 10.1136/jamia.2009.001149.
Ackerman MJ. Computer briefs: M-health: modern and mobile. J Med Pract Manage. 2010 Nov-Dec;26(3):191-2.
Xue Z, Long LR, Antani SK, Thoma GR. Automatic Extraction of Mosaic Patterns In Uterine Cervix Images.
23rd IEEE International Symposium on Computer-Based Medical Systems
(CBMS) 2010. Perth, Australia. October 2010:273-8.
Willams RJ, Tse T, Harlan WR, Zarin DA. Registration of observational studies: is it time?. CMAJ. 2010 Oct 19;182(15):1638-42. doi: 10.1503/cmaj.092252. Epub 2010 Jul 19.
Workman TE, Fiszman M, Hurdle JF, Rindflesch TC. Biomedical
text summarization to support genetic database curation: using Semantic
MEDLINE to create a secondary database of genetic
information. J Med Libr Assoc. 2010 Oct;98(4):273-81. doi: 10.3163/1536-5050.98.4.003.
Ducut E, Liu F, Avila JM, Encinas MA, Diwa M, Fontelo P. Virtual Microscopy in a Developing Country: A Collaborative Approach to Building an Image Library. Journal of eHealth Technology and Application. 2010 Sep;8(2):112-5.
Jimeno-Yepes A, Aronson AR. Improving an automatically extracted corpus for UMLS Metathesaurus word sense disambiguation. BioSEPLN 2010, Sept. 2010.
McDonald CJ. Lister Hill National Center for Biomedical Communications Annual Report FY2010. September 2010.
Ceccarelli MA, Curioso WH, Liu F, Fontelo P. Do
machine translations increase the usefulness of summaries of MEDLINE
abstracts? A preliminary study with medical students and physicians in
Peru. In: Stud Health Technol Inform [Studies in Health Technology and Informatics] -- MEDINFO 2010: Proceedings of the 13th World Congress on Medical and Health Informatics; 2010 Sep 12-15; Cape Town, South Africa;160:1414.
Demner-Fushman D, Antani SA, Simpson M, Rahman MM. Combining Text and Visual Features for Biomedical Information Retrieval and Ontologies. September 2010 Technical Report to the LHNCBC Board of Scientific Counselors.
Mork
JG, Bodenreider O, Demner-Fushman D, Dogan RI, Lang FM, Lu Z, Névéol A,
Peters L, Shooshan SE, Aronson AR. Extracting Rx information from clinical narrative. J Am Med Inform Assoc. 2010 Sep-Oct;17(5):536-9. doi: 10.1136/jamia.2010.003970.
Rahman MM, Antani SK, Thoma GR. Biomedical
Image Retrieval In a Fuzzy Feature Space With Affine Region Detection
and Vector Quantization of a Scale-Invariant Descriptor. 6th International Symposium on Visual Computing (ISVC) 2010. Las Vegas, NV. November 2010.
Rahman MM, Antani SK, Thoma GR. Bag
of Keypoints-Based Biomedical Image Search With Affine Covariant Region
Detection and Correlation-Enhanced Similarity Matching.
23rd IEEE International Symposium on Computer-Based Medical Systems
(CBMS ) 2010. Perth, Australia. October 2010:261-6.
He L, Long LR, Antani SK, Thoma GR. Local
and Global Gaussian Mixture Models For Hematoxylin and Eosin Stained
Histology Image Segmentation. 20th International Conference on Hybrid Intelligence Systems. Atlanta, GA. August 2010:223-8
Kilicoglu H, Fiszman M, Rosemblat G, Marimpietri S, Rindflesch TC. Arguments of Nominals in Semantic Interpretation of Biomedical Text. BioNLM Workshop Proc, Assoc. for Computational Linguistics 2010
Resnick MP, Ripple AM, Auston I, Rindflesch TC. An Ontology for Public Health to Support Enhanced Information Retrieval. AMIA Annu Symp Proc. 2010
Demner-Fushman D, Mork JG, Shooshan SE, Aronson AR. UMLS content views appropriate for NLP processing of the biomedical literature vs. clinical text. J Biomed Inform. 2010 Aug;43(4):587-94. doi: 10.1016/j.jbi.2010.02.005. Epub 2010 Feb 10.
Murphy GE, Lowekamp B, Zerfas PM, Chandler RJ, Narasimha R, Venditti CP, Subramaniam S. Ion-abrasion
scanning electron microscopy reveals distorted liver mitochondrial
morphology in murine methylmalonic acidemia. J Struct Biol. 2010 Aug;171(2):125-32. doi: 10.1016/j.jsb.2010.04.005. Epub 2010 Apr 23.
Cheng B, Stanley RJ, Antani SK, Thoma GR. A Novel Computational Intelligence-based Approach For Medical Image Artifacts Detection.
Proceedings of the 2010 International Conference on Artificial
Intelligence and Pattern Recognition. Orlando, FL. July
2010:113-20
Felts
RL, Narayan K, Estes JD, Shi D, Trubey CM, Fu J, Hartnell LM, Ruthel
GT, Schneider DK, Nagashima K, Bess JW Jr, Bavari S, Lowekamp B, Bliss
D, Lifson JD, Subramaniam S. 3D visualization of HIV transfer at the virological synapse between dendritic cells and T cells. Proc Natl Acad Sci U S A. 2010 Jul 27;107(30):13336-41. doi: 10.1073/pnas.1003040107. Epub 2010 Jul 12.
Thoma GR, Ford G, Antani SK, Demner-Fushman D, Chung M, Simpson M. Interactive Publication: The document as a research tool. Web Semant. 2010 Jul 1;8(2-3):145-150.
Ackerman MJ. Computer briefs: Med, Fed, and IT. J Med Pract Manage. 2010 Jul-Aug;26(1):61-2.
Rahman MM, Antani SK, Thoma GR. Local
Concept-Based Medical Image Retrieval With Correlation-Enhanced
Similarity Matching Based On Global Analysis.
IEEE Computer Society Workshop on Mathematical Methods in Biomedical
Image Analysis (MMBIA10) in conjunction with IEEE International
Conference on Computer Vision and Pattern Recognition (CVPR) 2010. June
2010:87-94
Zhang X, Zou J, Le DX, Thoma GR. Investigator
Name Recognition From Medical Journal Articles: A Comparative Study of
SVM and Structural SVM. International Workshop on Document Analysis Systems. June 2010:121-8
Caban JJ, Rheingans P, Yoo TS. An MRF-based Statistical Deformation Model for Morphological Image Analysis. IEEE Computer Society Workshop on Mathematical Models in Biomedical Image Analysis (MMBIA); 2010 Jun 14; San Francisco:31-8.
Lowekamp B, Chen D. A Streaming IO Base Class and Support for Streaming the MRC and VTK File Format. Insight Journal. Web. 2010 Jun 9.
Zou J, Le DX, Thoma GR. Locating and parsing bibliographic references in HTML medical articles. Int J Doc Anal Recognit. 2010 Jun 1;13(2):107-119.
Kamalakannan S, Gururajan A, Sari-Sarraf H, Long LR, Antani SK. Double-edge detection of radiographic lumbar vertebrae images using pressurized open DGVF snakes. IEEE Trans Biomed Eng. 2010 Jun;57(6):1325-34. doi: 10.1109/TBME.2010.2040082. Epub 2010 Feb 17.
Qian X, Tagare HD, Fulbright RK, Long LR, Antani SK. Optimal embedding for shape indexing in medical image databases. Med Image Anal. 2010 Jun;14(3):243-54. doi: 10.1016/j.media.2010.01.001. Epub 2010 Jan 20.
Demner-Fushman D, Karpinski J, Thoma GR. Automatically building a repository to support evidence-based practice. .
Proceedings of the 2nd Workshop on Building and evaluating resources
for biomedical text mining (BioTxtM 2010), 7th Language Resources and
Evaluation Conference (LREC 2010). Valetta, Malta. May
2010.
Armstrong K, Liu F, Seymour A, Rahman M, Fontelo P, Kovarik C. Design and Evaluation of txt2MEDLINE and SMS Optimized, Searchable Clinical Guidelines for Clinicians in Botswana.
Telemedicine J E Health;16(S1):S-93. American Telemedicine Association
15th Annual International Meeting and Exposition; 2010 May 16-18; San
Antonio, Texas.
Banez RJ, Sarmiento R, Marcelo A, Fontelo P, Du B. An SMS Appointment Reminder System for Prenatal Care in Urban Health Care Centers in the Philippines.
Telemed J E Health;16(S1):S-38. American Telemedicine Association 15th
Annual International Meeting and Exposition; 2010 May 16-18; San
Antonio, Texas.
Friedlin J, McDonald CJ. An evaluation of medical knowledge contained in Wikipedia and its use in the LOINC database. J Am Med Inform Assoc. 2010 May-Jun;17(3):283-7. doi: 10.1136/jamia.2009.001180.
Chen D, Chittajallu DR, Passalis G, Kakadiaris IA. Computational tools for quantitative breast morphometry based on 3D scans. Ann Biomed Eng. 2010 May;38(5):1703-18. doi: 10.1007/s10439-010-9971-z. Epub 2010 Mar 19.
Aronson AR, Lang FM. An overview of MetaMap: historical perspective and recent advances. J Am Med Inform Assoc. 2010 May-Jun;17(3):229-36. doi: 10.1136/jamia.2009.002733.
Bodenreider O. Quality Assurance in Biomedical Terminologies and Ontologies. April 2010 Technical Report to the LHNCBC Board of Scientific Counselors.
Locatis C, Williamson D, Gould-Kabler C, Zone-Smith L, Detzler I, Roberson J, Maisiak R, Ackerman MJ. Comparing in-person, video, and telephonic medical interpretation. J Gen Intern Med. 2010 Apr;25(4):345-50. doi: 10.1007/s11606-009-1236-x. Epub 2010 Jan 27.
Guan H, Antani S, Long LR, Thoma GR. Minimizing the Semantic Gap In Biomedical Content-based Image Retrieval.
Proc SPIE, Medical Imaging: Advanced PACS-based Imaging Informatics,
and Therapeutic Applications. March 2010;7628:762807-1
Kim E, Huang X, Tan G, Long LR, Antani S. A Hierarchical SVG Image Abstraction Layer for Medical Imaging.
Medical Imaging 2010: Advanced PACS-based Imaging Informatics and
Therapeutic Applications. San Diego, California. March
2010;7628
Xue Z, Antani S, Long LR, Thoma GR. Web-accessible Cervigram Automatic Segmentation Tool. SPIE Medical Imaging Conference. March 2010;7628
Ackerman MJ. Computer briefs: meaningful use?. J Med Pract Manage. 2010 Mar-Apr;25(5):320-1.
Ackerman MJ, Siegel, E, Wood, F. Interactive Science Publishing: A joint OSA-NLM project. Information Services & Use. 2010 Jan-Feb;30:39-50. DOI: 10.3233/ISU-2010-0612.
Liu J, Subramanian K, Yoo TS. Accurate motion parameter estimation for colonoscopy tracking using a regression method. In: Karssemeijer N, Summer RM, editors. Proceedings of SPIE Medical Imaging 2010: Computer-Aided Diagnosis; 2010 Feb 13-18; San Diego;7624:11 pages. DOI: 10.1117/12.844433.
Rahman MM, Antani S, Long LR, Demner-Fushman D, Thoma GR. Multi-Modal Query Expansion Based on Local Analysis for Medical Image Retrieval.
Lecture Notes in Computer Science. First MICCAI International Workshop
on Medical Content-Based Retrieval for Clinical Decision Support
(MCBR-CDS 2009); part of the 12th International Conference on Medical
Image Computing and Computer Assisted Interventio February
2010;5853/2010(doi: 10.1007/978-3-642-11769-5):110-9..
Locatis C, Berner ES, Hammack G, Smith S, Maisiak R, Ackerman MJ. An
exploratory study of co-location as a factor in synchronous,
collaborative medical informatics distance education. BMC Res Notes. 2010 Feb 2;3:30. doi: 10.1186/1756-0500-3-30.
Bodenreider O, Mougin F, Burgun A. Automatic Determination of Anti-coagulation Status with NDF-RT. Proceedings of the 13th ISMB'2010 SIG meeting Bio-ontologies 2010:140-143
Chen S, Misra D, Thoma GR. Efficient Automatic OCR Word Validation Using Word Partial Format Derivation and Language Model.
Document Recognition and Retrieval XVII. Proceedings of the SPIE. San
Jose, CA. January 2010;7534:75340O-75340O-8
Dumontier
M, Andersson B, Batchelor C, Domarew C, Jentzsch A, Luciano J, Pichler
E, Prud'hommeaux E, Whetzel PL, Bodenreider O, Clark T, Harland L,
Kashyap V, Kos P, Kozlovsky J, McGurk J, Ogbuji C, Samwald M, Schriml L,
Tonellato PJ, Zhao J, Stephens S. The
Translational Medicine Ontology: Driving Personalized Medicine by
Bridging the Gap from Bedside to Bench. Proceedings of the 13th ISMB'2010 SIG meeting Bio-ontologies 2010:120-123
Kim J, Le DX, Thoma GR. Naive
Bayes and SVM Classifiers For Classifying Databank Accession Number
Sentences From Online Biomedical Articles.
IS&T/SPIE's 22nd Annual Symposium on Electronic Imaging. San Jose,
CA. January 2010;7534:75340U-1 - 8
You D, Antani S, Demner-Fushman D, Rahman MM, Govindarju V, Thoma GR. Biomedical Article Retrieval Using Multimodal Features and Image Annotations In Region-based CBIR.
Document Recognition and Retrieval XVII. Edited by Likforman-Sulem,
Laurence; Agam, Gady. Proceedings of the SPIE. San Jose, CA. January
2010;7534:75340V-75340V-12.
Zhang X, Zou J, Le DX, Thoma GR. A
Stacked Sequential Learning Method For Investigator Name Recognition
From Web-based Medical Articles.
17th Document Recognition and Retrieval Conference (SPIE-DR&R). San
Jose, CA. January 2010;7534:753404-7
Rahman MM, Antani SK, Thoma GR. A Classification-Driven Similarity Matching Framework For Retrieval of Biomedical Images. 11th ACM International Conference on Multimedia Information Retrieval (MIR 2010). 2010:147-154.
Sahoo SS, Bodenreider O, Hitzler P, Sheth A, Thirunarayan K. Provenance Context Entity (PaCE): Scalable Provenance Tracking for Scientific RDF Data. SSDBM: Springer, 2010. p. 461-470
Cohen T, Widdows D, Schvaneveldt RW, Rindflesch TC. Logical Leaps and Quantum Connectives: Forging Paths through Predication Space. AAAI-Fall 2010 Symposium on Quantum Informatics for Cognitive, Social, and Semantic Processes
Keselman A, Rosemblat G, Kilicoglu H, Fiszman M, Jin H, Shin D, Rindflesch TC. Adapting
Semantic Natural Language Processing Technology to Address Information
Overload in Influenza Epidemic Management.
Journal of the American Society for Information Science and Technology
(JASIST), 61(12):2531-2543, 2010
Zuckerman AE, Downs SM, McDonald CJ, Weisman JL, Ross DA. Newborn Screening as the Model for Interoperable Genetic Data. AMIA Annu Symp Proc. 2010
Cardillo E, Hernandez, Jr G, Bodenreider O. Integrating
consumer-oriented vocabularies with selected professional ones from the
UMLS using Semantic Web Technologies. Proceedings of the eHealth 2010 conference, 2010: p. (paper 10579 - electronic proceedings).
Ackerman MJ, Filart R, Burgess LP, Lee I, Poropatich RK. Developing
next-generation telehealth tools and technologies: patients, systems,
and data perspectives. Telemed J E Health. 2010 Jan-Feb;16(1):93-5. doi: 10.1089/tmj.2009.0153.
Downs SM, van Dyck PC, Rinaldo P, McDonald CJ, Howell RR, Zuckerman A, Downing G. Improving
newborn screening laboratory test ordering and result reporting using
health information exchange. J Am Med Inform Assoc. 2010 Jan-Feb;17(1):13-8. doi: 10.1197/jamia.M3295.
Bodenreider O, Burgun A. A framework for comparing phenotype annotations of orthologous genes. Stud Health Technol Inform. 2010;160(Pt 2):1309-13.
Vreeman DJ, McDonald C, Huff SM. LOINC®
- A Universal Catalog of Individual Clinical Observations and Uniform
Representation of Enumerated Collections. Int J Funct Inform Personal Med. 2010;3(4):273-291. Epub 2011 May 23.
Erdogan H, Erdem E, Bodenreider O. Exploiting UMLS semantics for checking semantic consistency among UMLS concepts. Stud Health Technol Inform. 2010;160(Pt 1):749-53.
Fiszman M, Bray B, Shin D, Kilicoglu H, Bennett GC, Bodenreider O, Rindflesch TC. Combining relevance assignment with quality of the evidence to support guideline development. Stud Health Technol Inform. 2010;160(Pt 1):709-13.
Wei D, Bodenreider O. Using
the abstraction network in complement to description logics for quality
assurance in biomedical terminologies - a case study in SNOMED
CT. Stud Health Technol Inform. 2010;160(Pt 2):1070-4.
Bekhuis T, Demner-Fushman D. Towards automating the initial screening phase of a systematic review. Stud Health Technol Inform. 2010;160(Pt 1):146-50.
Mortensen J, Bodenreider O. Comparing Pharmacologic Classes in NDF-RT and SNOMED CT. Proc SMBM 2010:119-124.
Zeng-Treitler Q, Kim H, Rosemblat G, Kesselman A. Can
multilingual machine translation help make medical record content more
comprehensible to patients?. Stud Health Technol Inform. 2010;160(Pt 1):73-7.
Liu J, Subramanian K, Yoo TS. Region flow: a multi-stage method for colonoscopy tracking. Med Image Comput Comput Assist Interv. 2010;13(Pt 2):505-13.
Baorto D, Li L, Cimino JJ. Practical Experience with the Maintenance of a Large Ontology for an Academic Medical Center. Journal of Biomedical Informatics; 2009 Jun;42(3):494-503)
Lowekamp B, Chen D. A Framework for Improved Regression Testing Based Upon CTest and CDash. The Insight Journal. Web. 2009 Jul-Dec.
Humphrey SM, Névéol A, Gobeil J, Ruch P, Darmoni SJ, Browne AC. Comparing a Rule Based vs. Statistical System for Automatic Categorization of MEDLINE Documents According to Biomedical Specialty. J Am Soc Inf Sci Technol. 2009 Dec 1;60(12):2530-2539.
Fontelo P, Liu F. A novel tool for translational research discovery. Clin Transl Sci. 2009 Dec;2(6):391. doi: 10.1111/j.1752-8062.2009.00139.x.
Demner-Fushman D, Simpson M, Antani S, Thoma GR. Annotation and retrieval of clinically relevant images. Int J Med Inform. 2009 Dec;78(12):e59-67. doi: 10.1016/j.ijmedinf.2009.05.003. Epub 2009 Jul 9.
Williams R, Tse T. ClinicalTrials.gov: A public database of clinical research. .
Presented at: American Public Health Association 137th Annual Meeting
and Expo; November 2009; Philadelphia, PA.
Mork
JG, Bodenreider O, Demner-Fushman D, Doagan RI, Lang F-M, Lu Z, Névéol
A, Peters L, Shooshan SE, Aronson AR. NLM's I2B2 tool system description.
Third i2b2 Workshop on Natural Language Processing Challenges for
Clinical Records, November, San Francisco, 2009
Sneiderman C, Rosemblat G, Bray B, Fiszman M, Rindflesch TC. Matching Clinical Observations in Published Cardiology Case Reports to LOINC [Abstract]. AMIA Annu Symp Proc; 2009 Nov 14-18; San Francisco. p. 1036.
Mougin F, Bodenreider O, Burgun A. Identifying anatomical concepts associated with ICD10 diseases.
Proceedings of the 8th Conference on Terminology and Artificial
Intelligence (TIA 2009), 2009: p. (electronic proceedings:
http://www.irit.fr/TIA09/start_here.htm).
Lu C, Humphrey SM, Rogers W, Browne AC. Development of a semantic type based WSD tool [Abstract]. AMIA Annu Symp Proc 2009:943.
Kasiviswanathan K, Fontelo P. Connecting the OLPC: a Model for Developing Countries. AMIA Annu Symp Proc; 2009 Nov 14-18; San Francisco. p. 904.
Liu F, Fontelo P. Infobuttons Linked to Indivo, a Patient Controlled Health Record. AMIA Annu Symp Proc; 2009 Nov 14-18; San Francisco. p. 940.
Ducut E, Liu F, Quion N, Fontelo P. TB-SMS: A Short Messaging Service (SMS) Medication Reminder Application for DOTS. AMIA Annu Symp Proc; 2009 Nov 14-18; San Francisco. p. 827.
Encinas MA, Ducut E, Liu F, Avila JM, Diwa M, Fontelo P. Development of a Virtual Slide Library in a Developing Country. AMIA Annu Symp Proc; 2009 Nov 14-18; San Francisco. p. 836.
Fontelo P, Liu F. Consensus TBL Summaries for Clinical Decision-making. AMIA Annu Symp Proc; 2009 Nov 14-18; San Francisco. p. 846.
Fontelo P, Liu F, Cravedi K. Found in Translation: Tracking and Tagging Translational Research. AMIA Annu Symp Proc. 2009 Nov 14-18; San Francisco. p. 823.
Aronson AR, Lang FM. The Evolution of MetaMap, a Concept Search Program for Biomedical Text. AMIA Annu Symp Proc. 2009 Nov:22
Cohen T, Schvaneveldt R, Rindflesch TC. Predication-based
semantic indexing: permutations as a means to encode predications in
semantic space. AMIA Annu Symp Proc. 2009 Nov 14;2009:114-8.
Geller J, Morrey CP, Xu J, Halper M, Elhanan G, Perl Y, Hripcsak G. Comparing inconsistent relationship configurations indicating UMLS errors. AMIA Annu Symp Proc. 2009 Nov 14;2009:193-7.
Hristovski D, Kastrin A, Peterlin P, Rindflesch TC. Semantic relations for interpreting DNA microarray data. AMIA Annu Symp Proc. 2009 Nov 14;2009:255-9.
Cimino JJ. The
contribution of observational studies and clinical context information
for guiding the integration of infobuttons into clinical information
systems. AMIA Annu Symp Proc. 2009 Nov 14;2009:109-13.
Haerian K, McKeeby J, DiPatrizio G, Cimino JJ. Use of clinical alerting to improve the collection of clinical research data. AMIA Annu Symp Proc. 2009 Nov 14;2009:218-22.
Bodenreider O. Using SNOMED CT in combination with MedDRA for reporting signal detection and adverse drug reactions reporting. AMIA Annu Symp Proc. 2009 Nov 14;2009:45-9.
Burgun A, Mougin F, Bodenreider O. Two approaches to integrating phenotype and clinical information. AMIA Annu Symp Proc. 2009 Nov 14;2009:75-9.
An L, Obradovic Z, Smith D, Bodenreider O, Megalooikonomou V. Mining Association Rules among Gene Functions in Clusters of Similar Gene Expression Maps.
Workshop proceedings of the IEEE International Conference on
Bioinformatics and Biomedicine (BIBM09) -- Workshop on Data Mining in
Functional Genomics 2009: p. 254-259
Ackerman MJ. Computer briefs: personalized medicine. J Med Pract Manage. 2009 Nov-Dec;25(3):194-5.
Bodenreider O. Provenance information in biomedical knowledge repositories – A use case.
Proceedings of the First International Workshop on the role of Semantic
Web in Provenance Management (SWPM 2009), 2009: p. (electronic
proceedings: http://ceur-ws.org/Vol-526/).
Fung K, Berglund D, Scichilone R, Brear H, Giannangelo K. SNOMED CT to ICD-10 map development process diagram.
Meeting of the WHO Collaborating Centers for the Family of
International Classifications. October 2009.
Fung K, Berglund D, Scichilone R, Brear H, Giannangelo K. SNOMED CT to ICD-10 mapping project update - a joint task for IHTSDO and WHO-FIC.
Meeting of the WHO Collaborating Centers for the Family of
International Classifications. October 2009.
Yoo TS, Silver D, Correa C, Chen D, Moran A. Volumetric Bodies - the Exhibition. IEEE VisWeek 2009 Interactive Demo & Art Exhibit; 2009 Oct 12-16; Atlantic City, New Jersey.
Névéol A, Mork JG, Aronson AR. Comment on 'MeSH-up: effective MeSH text classification for improved document retrieval'[Letter]. Bioinformatics. 2009 Oct 15;25(20):2770-1; author reply 2772. doi: 10.1093/bioinformatics/btp483. Epub 2009 Aug 11.
Névéol A, Shooshan SE, Humphrey SM, Mork JG, Aronson AR. A recent advance in the automatic indexing of the biomedical literature. J Biomed Inform. 2009 Oct;42(5):814-23. doi: 10.1016/j.jbi.2008.12.007. Epub 2008 Dec 30.
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Simonaitis L, McDonald CJ. Using
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Kim I, Chien SI. Speed-up of error backpropagation algorithm with class-selective relevance. Neurocomputing. 2002 Oct 1;48(1):1009-14. doi: http://dx.doi.org/10.1016/S0925-2312(02)00594-5
Ackerman MJ. Computer Briefs: Last Mile Broadband: The Experiment. J Med Pract Manage. 2002 Jul-Aug;18(1):52-3.
Tse T, Johnson SO, Ripple AM. Update: Expanded ClinicalTrials.gov search capabilities. NLM Tech Bull. 2002 Jul-Aug;(327):e5.
Ackerman MJ. Computer Briefs: Going the Last Mile. J Med Pract Manage. 2002 May-Jun;17(6):295-6.
Ackerman MJ, Craft R, Ferrante F, Kratz M, Mandil S, Sapci H. Telemedicine/telehealth: an international perspective. Telemedicine technology. Telemed J E-Health. 2002 Spring;8(1):71-8.
Burgun A, Bodenreider O. Mapping the UMLS Semantic Network into General Ontologies. Proc AMIA Symp. 2001:81-5.
Aronson AR. Effective Mapping of Biomedical Text to the UMLS Metathesaurus: The MetaMap Program. Proc AMIA Symp. 2001:17-21.
McCray AT, Bodenreider O, Malley JD, Browne AC. Evaluating UMLS Strings for Natural Language Processing. AMIA Annu Symp Proc. 2001;():448-52.
Kim W, Aronson AR, Wilbur WJ. Automatic MeSH Term Assignment and Quality Assessment. Proc AMIA Symp. 2001:319-23.
Nishinaga N, Tatsumi H, Gill M, Akashib A, Nogawa H, Reategui I. Trans-Pacific Demonstration of Visible Human. Space Communications. 2002 March; 17(4):303-311.
Ackerman MJ. Computer Briefs: DSL and Other Last Mile Solutions. J Med Pract Manage. 2002 Jan-Feb;17(4):200-201.
Yoo T, Ackerman MJ, Lorensen W, Schroeder W, Chalana V, Aylward S, Metaxas D, Whitaker R. Engineering and Algorithm Design for an Image Processing API: A Technical Report on ITK - The Insight Toolkit. In: Westwood JD, Hoffman HM, Robb RA, Stredney D, editors. Stud Health Technol Inform [Studies in Health Technology and Informatics] - Proceedings of the 10th annual Medicine Meets Virtual Reality conference – Digital Upgrades: Applying Moore’s Law to Health; 2002 Jan 23-26; Newport Beach, California;85:586-92. Amsterdam: IOS Press.
Burgun A, Bodenreider O. Methods for Exploring the Semantics of the Relationships Between Co-Occurring UMLS Concepts. Medinfo. 2001 ;10(Pt 1):171-5.
McCray AT, Burgun A, Bodenreider O. Aggregating UMLS Semantic Types for Reducing Conceptual Complexity. Medinfo. 2001 ;10(Pt 1):216-20.
Bodenreider O. An Object-Oriented Model for Representing Semantic Locality in the UMLS. Medinfo. 2001 ;10(Pt 1):161-5.
Schadow G, Grannis S, McDonald CJ. Privacy-Preserving Distributed Queries for a Clinical Case Research Network.
IEEE International Conference on Data Mining Workshop on Privacy,
Security, and Data Mining City: Maebashi City, Japan 2002 vol: 14 pp:
55-65.
Overhage JM, Dexter PR, Perkins SM, Cordell WH, McGoff J, McGrath R, McDonald CJ. A randomized, controlled trial of clinical information shared from another institution. Ann Emerg Med. 2002 Jan;39(1):14-23.
Locatis CN. Instructional design and technology in healthcare. Chapter 17 in: Reiser RA, Dempsey JV, editors. Trends and Issues in Instructional Design and Technology. Upper Saddle River, New Jersey: Merrill Prentice Hall; 2002 Jan 1.
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Locatis C. Design Considerations for Multimedia Programs.
Chapter 18 in: Medsker K, Holdsworth KM, editors. Models and Strategies
for Training Design. Silver Spring, Maryland: International Society for
Performance Improvement; 2001. p. 355-73.
Morris J, Yoo TS, Chen D, Burgess J, Richardson AC. Computer Assisted Pedicle Screw Trajectory Guidance Using Fused Deposition Modeling. Abstract in Computer Assisted Surgery. 2001.
Fraser L, Locatis C. Effects
of Link Annotations on Search Performance in Layered and Unlayered
Hierarchically Organized Information Spaces. Journal of the American Society for Information Science and Technology. 2001;52(14):1255-61.
Rodgers RPC, Sherwin Z. A Management System for Network Sharable Locally Installed Software: Merging RPM and the Depot Scheme under Solaris. LISA XV: Proceedings of the Fifteenth Systems Administration Conference. 2001 Dec;: 267-272.
Schadow G, Russler DC, McDonald CJ. Conceptual alignment of electronic health record data with guideline and workflow knowledge. Int J Med Inform. 2001 Dec;64(2-3):259-74.
McDonald CJ. Hickam 2000: the maturation of, and linkages between, medical informatics and bioinformatics. J Lab Clin Med. 2001 Dec;138(6):359-66.
Bodenreider O. Circular
hierarchical relationships in the UMLS: etiology, diagnosis, treatment,
complications and prevention. Proc AMIA Symp. 2001:57-61.
Bodenreider O, Zweigenbaum P. Identifying Proper Names in Parallel Medical Terminologies. Stud Health Technol Inform. 2000;77:443-7
Schadow G, Barnes MR, McDonald CJ. Representing and querying conceptual graphs with relational database management systems is possible. Proc AMIA Symp. 2001:598-602.
Overhage JM, Aisen A, Barnes M, Tucker M, McDonald CJ. Integration of radiographic images with an electronic medical record. Proc AMIA Symp. 2001:513-7.
Kroth PJ, Belsito A, Overhage JM, McDonald CJ. Bedside vital signs capture for the non-ICU setting-an open source, PC-based solution. Proc AMIA Symp. 2001:344-8.
Thomas SM, Overhage JM, Warvel J, McDonald CJ. A comparison of a printed patient summary document with its electronic equivalent: early results. Proc AMIA Symp. 2001:701-5.
Weiner M, Schadow G, Lindbergh D, Warvel J, Abernathy G, Dexter P, McDonald CJ. Secure Internet video conferencing for assessing acute medical problems in a nursing facility. Proc AMIA Symp. 2001:751-5.
Overhage JM, Suico J, McDonald CJ. Electronic laboratory reporting: barriers, solutions and findings. J Public Health Manag Pract. 2001 Nov;7(6):60-6.
Cooper GF, Buchanan BG, Chapman W, Hanbury P, Kayaalp M, Saul M. IPS: A System That Uses Machine Learning to Help Locate Patient Records for Clinical Research. Proc AMIA Symp. 2001: : 813.
Humphrey SM, Rindflesch TC, Aronson AR. Automatic Indexing by Discipline and High-Level Categories: Methodology and Potential Applications. Advances in classification research. Proc. of the 11th ASIST SIG/CR Classification Research Workshop. 2001.
Ackerman MJ. Computer Briefs: POTS and Other Channels. J Med Pract Manage. 2001 Sep-Oct;17(2):112-3.
Yoo TS, Machiraju R, editors. From Transfer Functions to Level Sets: Advanced Topics in Volume Image Processing. Tutorial Notes for IEEE Visualization 2001; 2001 Oct 21-26; San Diego. 100 pages.
Yoo TS, Morris J, Chen DT, Burgess J, Richardson AC. Template
Guided Intervention: Interactive Visualization and Design for Medical
Fused Deposition Models. In: Niessen WJ, Viergever MA, editors. Proceedings of the Fourth International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI); 2001 Oct 14-17; Utrecht, The Netherlands. Lecture Notes in Computer Science 2208. Springer; 2001. p. 45-8.
Yoo TS, Subramanian KR. Implicit Snakes: Active Constrained Implicit Models. In: Niessen WJ, Viergever MA, editors. Proceedings of the Fourth International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI); 2001 Oct 14-17; Utrecht, The Netherlands. Lecture Notes in Computer Science 2208. Springer; 2001. p. 1379-81.
McDonald CJ. Is the placebo powerless? [Letter]. N Engl J Med. 2001 Oct 25;345(17):1276-7; author reply 1278-9.
Kratz M, Ackerman MJ, Hanss T, Corbato S. NGI and Internet2: Accelerating the Creation of Tomorrow's Internet. In: Patel VL, Rogers R, Haux R, editors. Stud Health Technol Inform [Studies in Health Technology and Informatics] – MEDINFO 2001: Proceedings of the 10th World Congress on Medical Informatics (2001 Sep 2-5; London);84(Part I):28-32. Amsterdam: IOS Press.
Ackerman MJ, Yoo T, Jenkins D. From Data to Knowledge - The Visible Human Project Continues. In: Patel VL, Rogers R, Haux R, editors. Stud Health Technol Inform [Studies in Health Technology and Informatics] – MEDINFO 2001: Proceedings of the 10th World Congress on Medical Informatics (2001 Sep 2-5; London);84(Part II):887-90. Amsterdam: IOS Press.
Kim I, Chien SI. Analysis of 3D hand trajectory gestures using stroke-based composite hidden Markov models. Applied Intelligence. 2001 Sept/Oct;15(2):131-43.
McDonald CJ, Schadow G, Suico J, Overhage JM. Data standards in health care. Ann Emerg Med. 2001 Sep;38(3):303-11.
Dexter PR, Perkins S, Overhage JM, Maharry K, Kohler RB, McDonald CJ. A computerized reminder system to increase the use of preventive care for hospitalized patients. N Engl J Med. 2001 Sep 27;345(13):965-70.
Marcelo AB, Fontelo P. Web-based Health Applications on Handheld Devices. Arch Pathol Lab Med. 2001 Aug;125(8):1015.
Marcelo AB, Fontelo P. A
Pathology Report Metadata Registry: Framework for Semantic
Interoperability Across Disparate Systems. Arch Pathol Lab Med. 2001 Aug;125(8):1014-1015.
Weeber M, Mork JG, Aronson AR. Developing a Test Collection for Biomedical Word Sense Disambiguation. Proc AMIA Symp. 2001:746-50.
Yoo TS, Machiraju R, editors. Image Processing for Volume Graphics. Tutorial Notes for ACM SIGGRAPH 2001; 2001 Aug 12-17; Los Angeles. 333 pages.
Kim I, Kim DS, Chien SI. Selective
attention based speed-up of error backpropagation algorithm:
Application to speaker adaptation. Proc. IASTED Int'l Conf. Signal and Image Processing, pp. 231-235, Hawaii, Aug. 2001.
Cheung NT, Fung K, Wong KC, Cheung A, Cheung J, Ho W, Cheung C, Shung E, Fung V, Fung H. Medical Informatics-the State of the Art In the Hospital Authority. Int J Med Inform. July 2001;62(2-3):113-9.
Overhage JM, Perkins S, Tierney WM, McDonald CJ. Controlled
trial of direct physician order entry: effects on physicians' time
utilization in ambulatory primary care internal medicine
practices. J Am Med Inform Assoc. 2001 Jul-Aug;8(4):361-71.
Morse B, Yoo TS, Rheingans P, Chen DT, Subramanian KR. Interpolating
Implicit Surfaces From Scattered Surface Data Using Compactly Supported
Radial Basis Functions.
In: Werner R, editor. Proceedings of the SMI 2001 International
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Fung K, Lau Y, Fielding R, Or A, Yip AW. The
impact of mastectomy, breast-conserving treatment and immediate breast
reconstruction on the quality of life of Chinese women. ANZ J Surg. April 2001;71(4):202-6.
Yoo TS, Morse B, Subramanian KR, Rheingans P, Ackerman MJ. Anatomical Modeling from Unstructured Samples Using Variational Implicit Surfaces.
In: Westwood JD, Hoffman HM, Mogel GT, Stredney D, Robb RA, editors.
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2001;81:594-600. Amsterdam: IOS Press.
Bodenreider O, Bean CA. Relationships Among Knowledge Structures: Vocabulary Integration Within a Subject Domain.
In: Bean A, Green R, editors. Relationships in the organization of
knowledge. Springer; 2001. pp. 81-98.
McCray AT, Dorfman E, Ripple A, Ide NC, Jha M, Katz DG, Loane RF, Tse T. Usability Issues in Developing a Web-Based Consumer Health Site. Proc AMIA Symp. 2000:556-60.
Bodenreider O. Using UMLS semantics for classification purposes. Proc AMIA Symp. 2000:86-90.
Weeber M, Klein H, Aronson AR, Mork JG, de Jong-van den Berg LT, Vos R. Text-Based Discovery in Biomedicine: The Architecture of the DAD-System. AMIA Annu Symp Proc. 2000 ;():903-7.
Rindflesch TC, Bean CA, Sneiderman CA. Argument
Identification for Arterial Branching Predications Asserted in Cardiac
Catheterization Reports. Proc AMIA Symp. 2000:704-8.
Hole WT, Srinivasan S. Discovering Missed Synonymy in a Large Concept-Orientated Methathesaurus. AMIA Annu Symp Proc. 2000;():354-8.
Oh HH, Kim IC, Chien SI. Experiments on various visual speech features for Korean vowel lipreading. Proc. IASTED Int'l Conf. Signal and Image Processing, pp. 225-230, Hawaii, Aug. 2001.
Ackerman MJ, Banvard RA, guest editors. Computerized Medical Imaging and Graphics;24(3). Elsevier; 2000.
Rindflesch TC, Tanabe L, Weinstein JN, Hunter L. EDGAR: extraction of drugs, genes and relations from the biomedical literature. Pac Symp Biocomput. 2000:517-28.
Kakadiaris IA, Chen D, Miller MJ, Loftin RB, Patrick C. Simulation-based determination of breast tissue engineering design patterns. Third Biennial Tissue Engineering Society International Meeting; 2000 Nov 30-Dec 3; Orlando, Florida.
Marcelo A, Fontelo P, Parolan M, Cualing H. Effect of Image Compression on Telepathology; A Randomized Clinical Trial. AMIA Annu Symp Proc; 2000 Nov 4-8; Los Angeles. p. 354-8.
Schadow G, Russler DC, Mead CN, McDonald CJ. Integrating medical information and knowledge in the HL7 RIM. Proc AMIA Symp. 2000:764-8.
Kayaalp M, Cooper GF, Clemont G. Predicting ICU mortality: a comparison of stationary and nonstationary temporal models. Proc AMIA Symp. 2000:418-22.
McDonald CJ, Weiner M, Hui SL. How many deaths are due to medical errors? [Letter]. JAMA. 2000;284(17):2187. doi:10.1001/jama.284.17.2184
Aronson AR, Bodenreider O, Chang HF, Humphrey SM, Mork JG, Nelson SJ, Rindflesch TC, Wilbur WJ. The NLM Indexing Initiative. Proc AMIA Symp. 2000:17-21.
Ackerman MJ. Computer Briefs: Is 21st Century E-Health Care Really Self Care?. J Med Pract Manage. 2000 Sep-Oct;16(2):108-9.
Lin C, Loftin RB, Kakadiaris IA, Chen D, Su S. Interaction with Medical Volume Data on a Projection Workbench. 10th International Conference on Artificial Reality and Telexistence (ICAT 2000); 2000 Oct 25-27; National Taiwan University, Taipei, Taiwan.
McCray AT. Better access to information about clinical trials. Ann Intern Med. 2000 Oct 17;133(8):609-14.
Yoo TS, Ackerman MJ, Vannier M. Toward a Common Validation Methodology for Segmentation and Registration Algorithms. In: Delp SL, DiGioia AM, Jaramaz B, editors. Proceedings of the Third International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI); 2000 Oct 11-14; Pittsburgh. Lecture Notes in Computer Science 1935. Berlin: Springer-Verlag; 2000. p. 422-31.
Chen D, Kakadiaris IA, Miller MJ, Loftin RB, Patrick C. Modeling for Plastic and Reconstructive Breast Surgery. In: Delp SL, DiGioia AM, Jaramaz B, editors. Proceedings of the Third International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI); 2000 Oct 11-14; Pittsburgh. Lecture Notes in Computer Science 1935. Springer; 2000. p. 1040-50. DOI: 10.1007/978-3-540-40899-4_108.
Yoo TS, Machiraju R, editors. Image Processing for Volume Graphics and Analysis. Tutorial Notes for IEEE Visualization 2000; 2000 Oct 8-13; Salt Lake City. 125 pages.
Lu CJ, Bangalore A, Tse T. Developing Web Browser Recording Tools Using Server-Side Programming Technology.
Proc. of WebNet 2000, World conference on WWW and Internet: Association
for the Advancement of Computing in Education.
2000;:372-7.
Weeber M, Vos R. Extracting the Lowest-Frequency Words: Pitfalls and Possibilities. Computational Linguistics. 2000;26(3):301-17.
Tse T. Searching ClinicalTrials.gov. NLM Tech Bull. 2000 Sep-Oct;(316):e1.
Fung V, Cheung NT, Chu YC, Chow YY, Tung Y, Wong KC, Fung KW, et al.. Statistical data collection as a by-product of clinical documentation. APAMI – MIC 2000 Conference. September 2000.
Kwok CK, Cheung NT, Fung KW, et al.. The electronic patient record in the hospital authority. APAMI – MIC 2000 Conference. September 2000.
Fan Y, Hwang K, Gill M, Huang HK. Some Connectivity and Security Issues of NGI in Medical Imaging Applications. Journal of High Speed Networks. 2000;9: 3-13.
McDonald CJ, Schadow G, Suico J, Heilmann K. Sprechen Sie LOINC. HL7 Mitteilugen, Germany. 2000. P 6-11.
Xiaocheng L, Prettyman M, Antonucci R. Agent-based system expansion and integration in HSTAT.
Proceedings of the Fourth World Multiconference on Systemics,
Cybernetics, and Informatics (SCI2000). July 2000.
McDonald CJ, Weiner M, Hui SL. Deaths due to medical errors are exaggerated in Institute of Medicine report. JAMA. 2000 Jul 5;284(1):93-5.
Ackerman MJ, Banvard RA. Imaging Outcomes from the National Library of Medicine's Visible Human Project. Comput Med Imaging Graph. 2000 May-Jun;24(3):125-6.
Ackerman MJ. Computer Briefs: Virtual Reality. J Med Pract Manage. 2000 May-Jun;15(6):304-5.
Ackerman MJ, Yoo T, Jenkins D. The Visible Human Project: From Data to Knowledge. In: Lemke HU, Vannier MW, Inamura K, Farman AG, Doi K, editors. Proceedings of the 14th International Congress and Exhibition of Computer Assisted Radiology and Surgery (CARS2000); 2000 Jun 28-Jul 1; San Francisco. Amsterdam: Elsevier; 2000 Jun 1. p. 11-6.
Kim I, Chien SI. Selectively attentive learning of multilayer perceptron for fast speaker adaptation.
Proc. Int’l. Conf. Artificial Intelligence (ICAI'2000), vol.3, pp.
1259-1264, Las Vegas, June 2000.
Rodgers RP. Searching for biomedical information on the World Wide Web. J Med Pract Manage. 2000 May-Jun;15(6):306-13.
Ackerman MJ. Electronics and Health Care Revisited: Thirty-Eight Years Later. Proc IEEE. 2000;88(5):706-7. DOI: 10.1109/5.849172.
Ebert D, McClanahan T, Rheingans P, Yoo TS. Direct Volume Rendering from Photographic Data.
In: deLeeuw W, van Liere R, editors. DataVisualization 2000:
Proceedings of the Joint EUROGRAPHICS and IEEE TCVG [Technical Committee
on Visualization and Graphics] Symposium on Visualization; 2000 May
29-30; Amsterdam, The Netherlands. Berlin: Springer-Verlag; 2000 May 19.
p. 137-46.
McCray AT, Ide NC. Design and implementation of a national clinical trials registry. J Am Med Inform Assoc. 2000 May-Jun;7(3):313-23.
Ackerman MJ. Computer Briefs: Welcome to the New Millennium. J Med Pract Manage. 2000 Jan-Feb;15(4):211-2.
Yoo TS. Advances Toward Understanding of Multimodal Volume Data. Proceedings of High Care 2000: Innovations in Medicine; 2000 Feb 25-27; Ruhr University, Bochum, Germany.
Murray MD, Aguirre B, McDonald CJ. Inhaled Corticosteroids and adverse Gastrointestinal Effects. Pharmacoepidemiology and Drug Safety, 9: S1-S70 (2000).
Olesen
H, Ibsen I, Bruunshuus I, Kenny D, Dybkaer R, Fuentes-Arderiu X, Hill
G, Soares de Araujo P, McDonald CJ. Properties and Units in the Clinical Laboratory Sciences. Part X. Pure Appl Chem 2000 vol: 72 (5) pp: 889-962.
Schadow G, Russler DC, McDonald CJ. Conceptual integration of guidelines and workflow into the electronic health record. Stud Health Technol Inform. 2000;77:807-11.
Yoo TS, Ackerman MJ. A New Research Program in Medical Image Processing.
In: Westwood JD, Hoffman HM, Mogel GT, Robb RA, Stredney D, editors.
Stud Health Technol Inform [Studies in Health Technology and
Informatics] - Proceedings of Medicine Meets Virtual Reality
2000;70:385-91. Amsterdam: IOS Press.
Aronis JM, Cooper GF, Kayaalp M, Buchanan BG. Identifying patient subgroups with simple Bayes'. Proc AMIA Symp. 1999:658-62.
Kroenke K, Stump T, Clark DO, Callahan CM, McDonald CJ. Symptoms in hospitalized patients: outcome and satisfaction with care. Am J Med. 1999 Nov;107(5):425-31.
West RT. IAIMS:
an interview with Dick West. Integrated Advanced Information Management
Systems. Interview by Joan S Ash and Frances E Johnson. J Am Med Inform Assoc. 1999 Nov-Dec;6(6):447-56.
Prettyman, M, Antonucci, R, Lynch P, Mericle L. Electronic Publication of Health Information in an Objected-Oriented Environment.
Proceedings of the 62nd Annual Meeting of the American Society for
Information Science. Washington, DC, October 1999.
McDonald CJ. Quality measures and electronic medical systems. JAMA. 1999 Sep 22-29;282(12):1181-2.
McDonald
CJ, Overhage JM, Tierney WM, Dexter PR, Martin DK, Suico JG, Zafar A,
Schadow G, Blevins L, Glazener T, Meeks-Johnson J, Lemmon L, Warvel J,
Porterfield B, Cassidy P, Lindbergh D, Belsito A, Tucker M, Williams B,
Wodniak C. The Regenstrief Medical Record System: a quarter century experience. Int J Med Inform. 1999 Jun;54(3):225-53.
Overhage J, Tierney W, McDonald CJ. Clinical Decision Support in Ambulatory Care Tools, Trials, and Tribulations. J Health Manag 1999 vol: 13 (2) pp: 67-79.
McCray AT, Gallagher ME, Flannick MA. Extending the role of metadata in a digital library system.
In: Proceedings of the IEEE Forum on Research and Technology Advances
in Digital Libraries, pp. 190-9, 1999.
Zafar A, Overhage JM, McDonald CJ. Continuous speech recognition for clinicians. J Am Med Inform Assoc. 1999 May-Jun;6(3):195-204.
Schadow G, McDonald CJ, Suico JG, Fohring U, Tolxdorff T. Units of measure in clinical information systems. J Am Med Inform Assoc. 1999 Mar-Apr;6(2):151-62.
Russler DC, Schadow G, Mead C, Snyder T, Quade LM, McDonald CJ. Influences of the Unified Service Action Model on the HL7 Reference Information Model. Proc AMIA Symp. 1999:930-4.
Clark DO, Kroenke K, Callahan CM, McDonald CJ. Validity and utility of patient-reported health measures on hospital admission. J Clin Epidemiol. 1999 Jan;52(1):65-71.
Davis D, Sager T, Senn S, Altman D, McDonald CJ. Claims for Glandular Supplements Still Unsubstantiated [LetterToEd]. J of Applied Nutrition 1999 vol: 51 pp: 3-4.
Cooper GF, Buchanan BG, Kayaalp M, Saul M, Vries JK. Using computer modeling to help identify patient subgroups in clinical data repositories. Proc AMIA Symp. 1998:180-4.
McDonald CJ, Overhage JM, Dexter PR, Blevins L, Meeks-Johnson J, Suico JG, Tucker MC, Schadow G. Canopy computing: using the Web in clinical practice. JAMA. 1998 Oct 21;280(15):1325-9.
Howe SE, executive editor. Networked Computing for the 21st Century: Supplement to the President's FY 1999 Budget.
Subcommittee on Computing, Information, and Communications R&D;
Committee on Technology; National Science and Technology
Council.
Huff
SM, Rocha RA, McDonald CJ, De Moor GJ, Fiers T, Bidgood WD Jr, Forrey
AW, Francis WG, Tracy WR, Leavelle D, Stalling f, Griffin B, Maloney P,
Leland D, Charles L, Hutchins K, Baenziger J. Development of the Logical Observation Identifier Names and Codes (LOINC) vocabulary. J Am Med Inform Assoc. 1998 May-Jun;5(3):276-92.
McDonald CJ, Overhage JM, Dexter P, Takesue B, Suico JG. What is done, what is needed and what is realistic to expect from medical informatics standards. Int J Med Inform. 1998 Feb;48(1-3):5-12.
McDonald CJ. Perspective: Need for Standards In Health Information[Letter]. Health Aff (Millwood). 1998 Nov-Dec;17(6):44-6.
Howe SE, editor. High
Performance Computing and Communications: Foundation for America's
Information Future - Supplement to the President's FY 1996
Budget. Committee on Information and Communication, National Science and Technology Council.
Howe SE, editor. High Performance Computing & Communications: Technology for a National Information Infrastructure - Supplement to the President's Fiscal Year 1995 Budget. Committee on Information and Communication, National Science and Technology Council.
Howe SE, editor. High Performance Computing & Communications: Toward a National Information Infrastructure - The FY 1994 U.S. Research and Development Program.
Committee on Physical, Mathematical, and Engineering Sciences; Federal
Coordinating Council on Science, Engineering, and Technology; Office of
Science and Technology Policy; Executive Office of the
President.
McDonald CJ, Park BH, Blevins L. Grocers, Physicians, and Electronic Data Processing. . AMA Cont Med Ed Newsl. 1983;12:5-8.