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  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Fontelo P, Faustorilla J, Gavino A, Marcelo A. Digital pathology - implementation challenges in low-resource countries. Anal Cell Pathol (Amst). 2012;35(1):31-6. doi: 10.3233/ACP-2011-0024.
  • Tran EE, Borgnia MJ, Kuybeda O, Schauder DM, Bartesaghi A, Frank GA, Sapiro G, Milne JL, Subramaniam S. Structural mechanism of trimeric HIV-1 envelope glycoprotein activation. PLoS Pathog. 2012;8(7):e1002797. doi: 10.1371/journal.ppat.1002797. Epub 2012 Jul 12.
  • Meyerson JR, White TA, Bliss D, Moran A, Bartesaghi A, Borgnia MJ, de la Cruz JV, Schauder D, Hartnell LM, Nandwani R, Dawood M, Kim B, Kim JH, Sununu J, Yang L, Bhatia S, Subramaniam C, Hurt DE, Gaudreault L, Subramaniam S. Determination of molecular structures of HIV envelope glycoproteins using cryo-electron tomography and automated sub-tomogram averaging. J Vis Exp. 2011 Dec 1;(58). pii: 2770. doi: 10.3791/2770.
  • Murphy GE, Narayan K, Lowekamp B, Hartnell LM, Heymann JA, Fu J, Subramaniam S. Correlative 3D imaging of whole mammalian cells with light and electron microscopy. J Struct Biol. 2011 Dec;176(3):268-78. doi: 10.1016/j.jsb.2011.08.013. Epub 2011 Sep 1.
  • Rahman MM, Antani SK, Thoma GR. A Query Expansion Framework in Image Retrieval Domain Based on Local and Global Analysis. Inf Process Manag. 2011 Sep 1;47(5):676-691.
  • Rahman MM, Antani SK, Thoma GR. A learning-based similarity fusion and filtering approach for biomedical image retrieval using SVM classification and relevance feedback. IEEE Trans Inf Technol Biomed. 2011 Jul;15(4):640-6. doi: 10.1109/TITB.2011.2151258. Epub 2011 Jun 16.
  • Caban JJ, Rheingans P, Yoo TS. An Evaluation of Visualization Techniques to Illustrate Statistical Deformation Models. Computer Graphics Forum. 2011 May-Jun;30(3):821-30. doi:10.1111/j.1467-8659.2011.01931.x.
  • Jaeger S, Antani S, Thoma GR. Tuberculosis Screening of Chest Radiographs. 2 June 2011, SPIE Newsroom. DOI: 10.1117/2.1201105.003732i.
  • Gururajan A, Kamalakannan S, Sari-Sharraf H, Shahriar M, Long LR, Antani SK. On the creation of a segmentation library for digitized cervical and lumbar spine radiographs. Comput Med Imaging Graph. 2011 Jun;35(4):251-65. doi: 10.1016/j.compmedimag.2010.11.006. Epub 2011 Mar 5.
  • Butan C, Hartnell LM, Fenton AK, Bliss D, Sockett RE, Subramaniam S, Milne JL. Spiral architecture of the nucleoid in Bdellovibrio bacteriovorus. J Bacteriol. 2011 Mar;193(6):1341-50. doi: 10.1128/JB.01061-10. Epub 2010 Dec 10.
  • Xue Z, Long LR, Antani SK, Neve L, Zhu Y, Thoma GR. A unified set of analysis tools for uterine cervix image segmentation. Comput Med Imaging Graph. 2010 Dec;34(8):593-604. doi: 10.1016/j.compmedimag.2010.04.002. Epub 2010 May 26.
  • 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.
  • 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.
  • 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.
  • 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.
  • Neve L, Long LR, Antani SK. Software: Boundary Marking Tool 2 (BMT2)
  • Lowekamp B, Chen D. A Framework for Improved Regression Testing Based Upon CTest and CDash. The Insight Journal. Web. 2009 Jul-Dec.
  • Lowekamp B, Chen D, Santoroski J, Yaniv Z, Yoo TS. Software: SimpleITK.
  • Bennett AE, Narayan K, Shi D, Hartnell LM, Gousset K, He H, Lowekamp BC, Yoo TS, Bliss D, Freed EO, Subramaniam S. Ion-abrasion scanning electron microscopy reveals surface-connected tubular conduits in HIV-infected macrophages. PLoS Pathog. 2009 Sep;5(9):e1000591. doi: 10.1371/journal.ppat.1000591. Epub 2009 Sep 25.
  • Xu X, Lee DJ, Antani SK, Long LR, Archiband JK. Using Relevance Feedback with Short-term Memory for Content-based Spine X-ray Image Retrieval. J Neurocomputing. June 2009;72(10-12):2259-69.
  • Lowekamp B. IO Streaming in ITK. Kitware Source. 2009 Apr;9:5-7.
  • Heymann JAW, Shi D, Kim S, Bliss D, Milne JLS, Subramaniam S. 3D imaging of mammalian cells with ion-abrasion scanning electron microscopy. J Struct Biol. 2009 Apr;166(1):1-7. doi: 10.1016/j.jsb.2008.11.005. Epub 2008 Dec 10.
  • Greenspan H, Gordon S, Zimmerman G, Lotenberg S, Jeronimo J, Antani S, Long LR. Automatic Detection of Anatomical Landmarks In Uterine Cervix Images IEEE Trans Med Imaging. 2009 Mar;28(3):454-68
  • Deserno TM, Long LR, Greenspan H. Content-based Image Retrieval: Major Challenges for Biomedical Applications Intl Journal of Healthcare Information Systems and Informatics. January 2009;4(1):i-iii
  • Long LR, Antani SK, Deserno TM, Thoma GR. Content-based Image Retrieval in Medicine: Retrospective Assessment, State of the Art, and Future Directions Int J Healthc Inf Syst Inform. 2009 Jan 1;4(1):1-16
  • Du H, Yoo TS, Qin H. PDE-based medial axis extraction and shape manipulation of arbitrary meshes. Journal of Systems Science and Complexity. 2008 Dec;21(4):601-17.
  • Jeronimo J, Wentzensen N, Long R, Schiffman M, Dunst ST, Allen RA, Walker JL, Gold MA, Zuna RE, Sherman ME, Wacholder S, Wang SS. Evaluation of Linear Array Human Papillomavirus Genotyping Using Automatic Optical Imaging Software J Clin Microbiol. 2008 Aug;46(8):2759-65. Epub 2008 Jun 11
  • Zhu Y, Huang X, Wang W, Lopresti D, Long LR, Antani SA, Xue Z, Thoma GR. Balancing the Role of Priors in Multi-Observer Segmentation Evaluation J Signal Process Syst. 2008 May 28;55(1-3):185-207
  • Goedert JJ, Scoppio BM, Pfeiffer R, Neve L, Federici AB, Long LR, Dolan BM, Brambati M, Bellinvia M, Lauria C, Preiss L, Boneschi V, Whitby D, Brambilla L. Treatment of classic Kaposi sarcoma with a nicotine dermal patch: a phase II clinical trial. phase II clinical trial. J Eur Acad Dermatol Venereol. 2008 Sep;22(9):1101-9. doi: 10.1111/j.1468-3083.2008.02720.x. Epub 2008 Apr 1.r 1.
  • Stanley RJ, Antani S, Long LR, Thoma GR, Gupta K, Das M. Size-invariant Descriptors for Detecting Regions of Abnormal Growth in Cervical Vertebrae Comput Med Imaging Graph. 2008 Jan;32(1):44-52. Epub 2007 Oct 22
  • Xu X, Lee DJ, Antani S, Long LR. A Spine X-ray Image Retrieval System using Partial Shape Matching IEEE Trans Inf Technol Biomed. 2008 Jan;12(1):100-8.
  • Antani SK, Deserno TM, Long LR, Thoma GR. Geographically Distributed Complementary Content-Based Image Retrieval Systems for Biomedical Image Informatics Stud Health Technol Inform. 2007;129(Pt 1):493-7
  • Jeronimo J, Massad S, Castle PE, Schiffman M, NIH/ASCCP Research Group. Inter-observer Agreement in the Evaluation of Digitized Cervical Images Obstet Gynecol. Vol. 197, Issue 1, July 2007
  • Jeronimo J, Massad LS, Schiffman M for the NIH-ASCCP Research Group. Visual Appearance of the Uterine Cervix: Correlation with Human Papillomavirus Detection and Type Am J Obstet Gynecol. 2007 Jul;197(1):47.e1-8
  • Moorhead R, Johnson C, Munzner T, Pfister H, Rheingans P, Yoo TS. Visualization Corner: Visualization Research Challenges: A Report Summary. IEEE Computing in Science and Engineering. 2006 Jul-Aug;8(4):66-73. DOI: 10.1109/MCSE.2006.77.
  • Jeronimo J, Long R, Neve L, Ferris D, Noller K, Spitzer M, Mitra S, Guo J, Nutter B, Castle P, Herrero R, Rodriguez AC, Schiffman M. Preparing Digitized Cervigrams for Colposcopy Research and Education: Determination of Optimal Resolution and Compression Parameters J Low Genit Tract Dis. 2006 Jan;10(1):39-44
  • Munzner T, Johnson C, Moorhead R, Pfister H, Rheingans P, Yoo TS. Visualization Viewpoints: NIH-NSF Visualization Research Challenges Report Summary. IEEE Computer Graphics and Applications. 2006 Mar-Apr;26(2):20-24.
  • Jeronimo J, Long R, Neve L, Bopf M, Antani K, Schiffman M. Digital Tools for Collecting Data from Cervigrams for Research and Training in Colposcopy J Low Genit Tract Dis. 2006 Jan;10(1):16-25.
  • Castle PE, Jeronimo J, Schiffman M, Herroro R, Rodriguez AC, Bratti MC, Hildesheim A, Wacholder S, Long LR, Neve L, Pfeiffer R, Burk RD. Age-related changes of the cervix influence human papillomavirus type distribution Cancer Res. 2006 Jan 15;66(2):1218-24.
  • Yoo TS, Metaxas DN. Open science – combining open data and open source software: Medical image analysis with the Insight Toolkit. Med Image Anal. 2005 Dec;9(6):503-6. Epub 2005 Sep 19.
  • Long RL, Antani SK, Thoma GR. Image Informatics At a National Research Center Comput Med Imaging Graph. 2005 Mar-Apr;29(2-3):171-93. Epub 2004 Dec 21
  • Yoo TS, Ackerman MJ. Open Source Software for Medical Image Processing and Visualization. Communications of the ACM. 2005 Feb;48(2):55-9. DOI:10.1145/1042091.1042120.

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