C.A. Johnson, W.W. Lau, G. Wang, K. Collie, J.F. Jones, Jr., M. Vos, L. Krueger An Ensemble Classification System for Research Categorization and Decision Support in Portfolio Analysis
[Abstract] [Full Article] [Supplementary]

Yonqing Zhang, Supriyo De, John R. Garner, Kirstin Smith, S. Alex Wang, and Kevin G. Becker "Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information." BMC Medical Genomics, 2010 Jan 21;3:1. doi:10.1186/1755-8794-3-1
[Abstract] [Full Article]

Supriyo De, Yongqing Zhang, John R Garner, S. Alex Wang, and Kevin G. Becker Disease and phenotype gene set analysis of disease based gene expression in mouse and human. Physiol. Genomics (August 3, 2010). doi:10.1152/physiolgenomics.00008.2010
[Abstract] [Full Article]

C. Johnson, H. Cheung, R Martino, S. Bailey, D. Russ, A. Fletcher, B. Trus, "IRPgrid: A Feasibility Study of Grid Technologies for the NIH Intramural Research Program"
[Abstract] Presentation (2009)

Daniel E. Russ, Faye C. Austin, Carl A. Roth, Calvin A. Johnson, "Primary Assessment of High-Risk High-Reward Research at NIH Using Context-Sensitive Text Mining" NIH Research Festival 2009. Presentation (2009)

H. Cheung, T. Caruso, A. Frazin, A. Ravindran, T. Doan, A. Wang, C. Johnson," A Protocol Lifeycycle Tracking Tool for Clinical Research." NIH Research Festival 2009.
[Abstract] Presentation (2009) [Supplementary]

Lau W, Shum L, Johnson C "Salivary Proteome Wiki: A Collaborative Environment to Share and Annotate Proteomics Data." Clinical Proteomics (Proc. of 8th Human Proteome Organisation Congress). 5(Suppl. 1): 13, Sept, 2009 [Full Article] [Supplementary]

Nancy S. Longo, Patricia L. Lugar, Sule Yavuz, Wen Zhang, Peter H. L. Krijger, Daniel E. Russ, Dereje D. Jima, Sandeep S. Dave, Amrie C. Grammer and Peter E. Lipsky "Analysis of somatic hypermutation in X-HIgM syndrome reveals specific deficiencies in mutational targeting " Blood, preprint, doi:10.1182/blood-2008-10-183632
[Abstract] [Full Article]

Christopher D Dharmaraj, Anthony R Fletcher, Phuc N Doan, Nallathamby Devasahayam, Shingo Matsumato, Calvin Johnson, John A. Cook, James B. Mitchell, Sankaran Subramanian, Murali C Krishna "Reconstruction for Time-Domain In-Vivo EPR 3-D Multi-Gradient Oximetric Imaging - A Parallel Processing Perspective, " International Journal of Biomedical Imaging, vol. 2009, Article ID 528639, 2009. doi:10.1155/2009/528639
[Abstract] [Full Article]

Johnson C., Lau W., Bhandari A., and Hays T. , A Best-Fit Model for Concept Vectors in Biomedical Research Grants, Proc. AMIA Symp. 2008: 993.
[Abstract] [Full Article] [Supplementary]

D. E. Russ, F. C. Austin, G. Sun, W. Lau, C. A. Johnson "Context-Dependent Text Mining for the Retrospective Identification of High-Risk, High-Reward Research", Poster 2008 NIH Research Festival DCB Technical Report (2008) [Supplementary]

Ajay, Zavaleta A, Frazin A, Chintala S, and Cheung H. "Semantic Wiki for Collaborative Annotation of Chemical Biology Data."NIH Research Festival 2008. [Full Article]

Morgan AA, Lu Z, Wang X, Cohen AM, Fluck J, Ruch P, Divoli A, Fundel K, Leaman R, Hakenberg J, Sun C, Liu HH, Torres R, Krauthammer M, Lau WW, Liu H, Hsu CN, Schuemie M, Cohen KB, and Hirschman L. " Overview of BioCreative II Gene Normalization." Genome Biology. 9(S2):S3, 2008.
[Abstract] [Full Article]

Leitner F, Krallinger M, Rodriguez-Penagos C, Hakenberg J, Plake C, Kuo CJ, Hsu CN, Tasi RTH , Hung HC, Lau WW, Johnson CA, Stre R, Yoshida K, Kim S, Shin SY, Zhang BT, Baumgartner WA, Hunter L, Haddow B, Matthews M, Wang X, Ruch P, Ehrler F, Ozguro A, Erkan G, Radev DR, Krauthammer M, Luong TB, Hoffmann R, Sander C, and Valencia A "Introducing Meta-Services for Biomedical Information Extraction." Genome Biology. 9(S2):S6, 2008
[Abstract] [Full Article]

Cheung H., Wang A., Fann Y., Upender B., Chinatala S., Frazin A., Nie W., Martino R.L., and Johnson C. "A Web-Based, Meta-Data Driven, Clinical Research Platform for Managing Multiple Clinical Research Studies," Proceedings of the American Medical Informatics Association (AMIA) 2007 Annual Symposium, November, 2007, Chicago, IL, M-054
[Abstract] [Full Article] [Supplementary]

Becker KG, Zhang Y, Shenoy N, Smith KE, Karolchik D, Hsu F, Wang SA "GAD and GADview: a genomic view of common human disease" HUGOs 12th Human Genome Meeting, B.128 [Full Article]

M. Rodriguez, J.-S. Liow, S. Thada, M. Sibomana, S. Chelikani, T. Mulnix, C.A. Johnson, C. Michel, W.C. Barker, and R.E. Carson, "Count-Rate Dependent Component-Based Normalization for the HRRT", IEEE Transaction on Nuclear Science, vol. 54, no. 3, pp. 486-495 (2007).
[Abstract] [Full Article]

Lau, William W., Becker, Kevin G., and Johnson, Calvin A., "Rule-based Human Gene Normalization in Biomedical Text with Confidence Estimation", LSS Computational Systems Bioinformatics, San Diego, August, 2007, pp. 371-379.
[Abstract] [PubMed]

Lau WW, Johnson CA, "Rule-based Gene Normalization with Statistical and Heuristic Confidence Measure", Proceedings of the Second BioCreative Challenge Evaluation Workshop, Madrid, Spain, 2007, pp. 165 - 167.
[Abstract] [Full Article]

Sun G, Lau W, Wang A, Shenoy N, Becker K, Cheung H "Ranking and Presenting Gene-Disease Associations from Biomedical Literature." Poster. 2006 Summer Research Program Student Poster Day. [Full Article]

Lau WW "Survey of Clinical Knowledge Management and Analysis of Unstructured Text " Technical Report, 2006 Full Article

Sankaran Subramanian, Calvin A. Johnson, Nallathamby Devasahayam, Ken-ichiro Matsumoto1, Fuminori Hyodo, John Cook, and Murali C. Krishna.
"In Vivo Spectal-Spatial Imaging for Ocygen Mapping Using Single-Point, Time-Domain Electron Paramagnetic Resonance," Proceedings, the 2006 IEEE International Symposium on Biomedical Imaging, Crystal City, VA, 2006.

Martino, R.L., Russ, D.E., and Johnson, C.A., "Parallel Computing in the Analysis of Gene Expression Relationships." Chapter 11 in: A.Y. Zomaya, editor, Parallel Computing Bioinformatics, New York, N.Y.: Wiley, pp. 265-284.
[Abstract]

Dudko OK, Berezhkovskii AM, Weiss GH
"Time-dependent diffusion coefficients in periodic porous materials" J PHYS CHEM B 109 (45): 21296-21299

Shaohua A Wang, Yang Fann, Huey Cheung, Frank Pecjak, Barg Upender, Adam Frazin, Raj Lingam, Sarada Chintala, Gladys Wang, Marc Kellogg, Robert L. Martino, and Calvin A. Johnson"Performance of Using Oracle XMLDB in the Evaluation of CDISC ODM for a Clinical Study Informatics System." Proceedings 17th IEEE Symposium on Computer-Based Medical Systems 24-25 June 2004, Bethesda, MD; 594-599 Full Article

Huey Cheung, Yang Fann, Shaohua A. Wang, Barg Upender, Adam Frazin, Raj Lingam, Sarada Chintala, Frank Pecjak, Gladys Wang, Marc Kellogg, Robert L. Martino, and Calvin Johnson"A Web-Based Protocol Tracking Management System For Clinical Research. " 17th IEEE Symposium on Computer Based Medical Systems 24-25 June 2004, Bethesda, MD; 72-77 Full Article

Johnson CA, Shanthalaxmi Thada, Yongsheng Zhao, Anthony R. Iano-Fletcher, Jeih San Liow, W. Craig Barker, Robert L. Martino, and Richard E. Carson "Software achitecture of the MOLAR-HRRT reconstruction engine." IEEE Nuclear Science Symposium and Medical Imaging Conference Rome, Italy, 2004

Barker WC, Liow J-S, Zhao Y, Thada S, Iano-Fletcher A, Lenox M, Michel C, Johnson CA, Carson RE "Randoms estimation for list-mode reconstruction for the ECAT HRRT." IEEE Nuclear Science Symposium and Medical Imaging Conference Rome, Italy, 2004

Souto-Carneiro MM, Longo NS, Russ DE, Sun HW, Lipsky PE."Characterization of the human Ig heavy chain antigen binding complementarity determining region 3 using a newly developed software algorithm, JOINSOLVER" Journal of Immunology 2004 Jun 1;172(11):6790-6802.
[PubMed]

Becker, K.G., Barnes, K.C., Bright, T.J. & Wang, S.A.
"The Genetic Association Database" Nature Genetics 36: 431-432 [PubMed]

Xiaobo Zhou, Xiaodong Wang, Edward R. Dougherty, Daniel Russ, Edward Suh
"Gene Clustering Based on Clusterwide Mutual Information." Journal of Computational Biology 11:147-161
[PubMed]

T. Brody, et al., "A search for targets of the drosophila neuroblast temporal network," Developmental Biology, vol. 259, p. 93, 2003. [Full Article]

Carson RE, Barker WC, Liow J-S, Adler S, Johnson CA
"Design of a motion-compensation OSEM List-mode Algorithm for Resolution-Recovery Reconstruction of the HRRT." Conf. Record of the IEEE Nuclear Science Symposium and Medical Imaging Conference Portland, OR, 2003, M16-6.

Deirdre A. Joy, Xiaorong Feng, Jianbing Mu, Tetsuya Furuya, Kesinee Chotivanich, Antoniana U. Krettli, May Ho, Alex Wang, Nicholas J. White, Edward Suh, Peter Beerli, Xin-zhuan Su
"Early Origin and Recent Expansion of Plasmodium falciparum." Science 300: 318-321
[PubMed]

Tohru Kobayashi, Motoko Yamaguchi, Seungchan Kim, Jun Morikawa, Satoshi Ueno, Edward Suh, Edward Dougherty, Ilya Shmulevich, Hiroshi Shiku, and Wei Zhang
"Gene Expression Profiling Identifies Strong Feature Genes that Classify de novo CD5+ and CD5- Diffuse Large B-Cell Lymphoma and Mantle Cell Lymphoma." Cancer Research 63:60-66

Johnson CA, Cook JA, McGarry DP, Devasahayam N, Mitchell JB, Subramanian S, Krishna M
"Maximim Entropy Reconstruction Methods in Electron Paramagnetic Resonance Imaging." Annals of Operations Research 119 (1-4): 101-118

Suh EB, Wang A, Cheung H, Martino RL
"A Web-based Medical Image Archive System." Proceedings of the Medical Imaging 2002 San Diego, California, International Society for Optical Engineering, February 23-28 Full Article

Suh EB, Russ DE, Dougherty ER, Kim S, Chen Y, Bittner M, Martino RL
"Parallel Computation and Visualization Tools for Codetermination Analysis of Multivariate Gene-Expression." Computational and Statistical Approaches to Genomics Wei Zhang and Ilya Shmulevich (Editors), Kluwer Academic Publishers, Boston

Hunsberger S, Albert PS, Follmann DA, Suh EB"Parametric and Semiparametric Approaches to Testing for Seasonal Trend in Serial Count Data." Biostatistics Oxford University Press, June 2002, vol. 3, no. 2.
[PubMed]

Albert PS, Follmann DA, Wang A, Suh EB
"A Latent Autoregressive Model for Longitudinal Binary Data Subject to Informative Missingness." Biometrics 58: 631-642
[PubMed]

Kim S, Li H, Dougherty ER, Cao N, Chen Y, Bittner M, Suh EB
"Can Markov Chain Mimic Biological Regulation." Journal of Biological Systems 10 (4): 431-445

Suh, E.B., D.E. Russ, E.R. Dougherty, S. Kim, M.L. Bittner, Y. Chen, and R.L. Martino
"Parallel Computation for Coefficients of Determination in the Context of Multivariate Gene-Expression Analysis." International Journal of Computer Research 11(4):419-429

Suh EB, Diougherty ER, Kim S, Russ DE, Martino RL
"Parallel Computing Methods for Microarray Data Analysis." Proceedings of the Biomedical Optics (BiOS) 2001 San Jose, California, International Society for Optical Engineering, January 20-26

Johnson CA, Sofer A. "A primal-dual method for large-scale image reconstruction in emission tomography." SIAM Journal on Optimization 11: 691-715

Suh EB, Narahari B, Simha R
"Dynamic Load Balancing Schemes for Computing Accessible Surface Areas of Protein Molecules." Proceedings, International Conference on High Performance Computing (HiPC98) December 17-20, 1998, Chennai (Madras), India.

Suh EB, Lee BK, Narahari B, Choudhary A, Martino RL"Parallel computation of solvent accessible surface area of protein molecules." Proceedings of the Seventh International Parallel Processing Symposium IEEE Computer Society, Washington, DC; 1993; 685-689

Martino RL, Johnson CA, Trus BL, Yap TK, Suh EB, Pfeifer JC, Brooks RB
"Highly Parallel Computing at the National Institutes of Health." Proceedings of Supercomputing USA/Pacific 91