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  1. National Center for Toxicological Research

Stephen Harris

Computer Scientist — Division of Bioinformatics and Biostatistics

Stephen Harris, Computer Scientist NCTR

Stephen Harris
(870) 543-7391
NCTRResearch@fda.hhs.gov  

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About  |  Publications 


Background

Mr. Harris has been a software developer at NCTR for 19 years, as a contractor initially and as a government employee for the last 13 years. He holds a bachelor’s degree in mathematics from Cornell University, received in 1992. Mr. Harris has experience in a broad range of scientific computing areas, including development of chemical databases, quantitative structure-activity relationships (QSARs) and spectroscopic data activity relationship (SDAR) modeling, statistics, machine learning, full-stack web development, relational-database modeling and implementation, and No-SQL data-store development and management. He was a lead developer of the ArrayTrack application for microarray storage and analysis, did significant development for the MicroArray Quality Control (MAQC) project, and was the lead developer of the FDALabel web application and database system. Currently he is working on a high-profile laboratory-information management system for Office of Regulatory Affairs (ORA).

Research Interests

Mr. Harris’s primary interests are large-scale application architecture, system security, and knowledge representation in database systems. He also has interest in machine-learning algorithms, and feature selection in trained models resulting from machine-learning algorithms.

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Select Publications

FDA Drug Labeling: Rich Resources to Facilitate Precision Medicine, Drug Safety, and Regulatory Science.
Fang H., Harris S., Liu Z., Zhou G., Zhang G., Xu J., Howard P., and Tong W.
Drug Discovery Today. 2016, 21(10): 1566-1570.

Superconvergence of Weak Galerkin Finite Element Approximation for Second Order Elliptic Problems by L2-Projection Methods.disclaimer icon
Harris A. and Harris S.
Applied Mathematics and Computation. 2013.

The MAQC-II Project: A Comprehensive Study of Common Practices for the Development and Validation of Microarray-Based Predictive Models.
The MAQC Consortium.
Nature Biotechnology. 2010, 28:827–838.

EADB: An Estrogenic Activity Database for Assessing Potential Endocrine Activity.
Shen J., Xu L., Fang H., Richard A., Bray J., Judson R., Zhou G., Colatsky T., Aungst J., Teng C., Harris S., Ge W., Dai S., Su Z., Jacobs A., Harrouk W., Perkins R., Tong W., and Hong H.
Toxicological Science. 2013, 135(2), 277-291.

A Unifying Ontology to Integrate Histological and Clinical Observations for Drug-Induced Liver Injury.
Wang Y., Lin Z., Liu Z., Harris S., Kelly R., Zhang J., Ge W., Chen M., Borlak J., and Tong W.
American Journal of Pathology. 2013, 182(4):1180-1187.

SNPTrackTM – An Integrated Bioinformatics System for Genetic Association Studies.
Xu J., Kelly R., Zhou G., Turner S., Ding D., Harris S., Hong H., Fang H., and Tong W.
Human Genomics.  2012, 6(1), 5.

atBioNet – An Integrated Network Analysis Tool for Genomics and Biomarker Discovery.disclaimer icon
Ding Y., Chen M., Liu Z., Ding D., Ye Y., Zhang M., Kelly R., Guo L., Su Z., Harris S., Feng Q., Ge W., Fang H., Xu X., and Tong W.
BMC Genomics. 2012, 13(1), 325.

An FDA Bioinformatics Tool for Microbial Genomics Research on Molecular Characterization of Bacterial Foodborne Pathogens Using Microarrays.
Fang H., Xu J., Ding D., Jackson S., Patel I., Frye J., Nayak R., Foley S., Chen J., Su Z., Ye Y., Turner S., Harris S., Zhou G., Cerniglia C., and Tong W. 
BMC Bioinformatics. 2010, 11(Suppl 6): S4.

ISA Software Suite: Supporting Standards-Compliant Experimental Annotation and Enabling Curation at the Community Level.
Rocca-Serra P., Brandizi M., Maguire E., Sklyar N., Taylor C., Begley K., Field D., Harris S., Hide W., Hofmann O., Neumann S., Sterk P., Tong W., and Sansone S.
Bioinformatics. 2010, 26(18): 2354-2356.

The EDKB: an Established Knowledge Base for Endocrine Disrupting Chemicals.
Ding D., Xu L., Fang H., Hong H., Perkins R., Harris S., Shi L., and Tong W. 
Bioinformatics. 2010, 11(Suppl 6): S5.

Investigation of Reproducibility of Differentially Expressed Genes in DNA Microarrays through Statistical Simulation.
Fan X., Shi L., Fang H., Harris S., Perkins P., and Tong W.
BMC Proceedings. 2009, 3(Suppl 2): S4.

FDA Bioinformatics Tool for Public Use – ArrayTrack.
Harris S., Fang H., Su Z., Chen M., Feng Q., Leming S., Arasappan D., Ge W., Fan X., Hong H., Xu J., Turner S., Bishop M., Jackson M., Perkins R., and Tong W.
Regulatory Research Perspectives. 2009, 8(1).

The Balance of Reproducibility, Sensitivity, and Specificity of Lists of Differentially Expressed Genes in Microarray Studies.
Shi L., Jones W., Jensen R., Harris S., Perkins R., Goodsaid F., Guo L., Croner L., Boysen C., Fang H., Qian F., Amur S., Bao W., Barbacioru C., Bertholet V., Cao X., Chu T., Collins P., Fan X., Frueh F., Fuscoe J., Guo X., Han J., Herman D., Hong H., Kawasaki E., Li Q., Luo Y., Ma Y., Mei N., Peterson R., Puri R., Shippy R., Su Z., Sun Y., Sun H., Thorn B., Turpaz Y., Wang C., Wang S., Warrington J., Willey J., Wu J., Xie Q., Zhang L., Zhang L., Zhong S., Wolfinger R., and Tong W.
BMC Bioinformatics. 2008, 9(Suppl 9): S10.

An Integrated Bioinformatics Infrastructure Essential for Advancing Pharmacogenomics and Personalized Medicine in the Context of the FDA's Critical Path Initiative.
Tong W., Harris S., Fang H., Shi L., Perkins R., Goodsaid F., and Frueh F.W.
Drug Discovery Today: Technologies. 2007, 4(1), 3-8.

The MicroArray Quality Control (MAQC) Project Shows Inter- and Intraplatform Reproducibility of Gene Expression Measurements.
The MAQC Consortium.
Nature Biotechnology. 2006, 24(9), 1151-1161.

Rat Toxicogenomic Study Reveals Analytical Consistency Across Microarray Platforms.
Guo L., Lobenhofer E., Wang C., Shippy R., Harris S., Zhang L., Mei N., Chen T., Herman D., Goodsaid F., Hurban P., Phillips K., Xu J., Deng X., Sun Y., Tong W., Dragan Y., and Shi L.
Nature Biotechnology, 2006, 24(9), 1162-1169.

Microarray Scanner Calibration Curves: Characteristics and Implications.
Shi L., Tong W., Su Z., Han T., Han J., Puri R., Fang H., Frueh F., Goodsaid F., Guo L., Branham W., Chen J., Xu Z., Harris S., Hong H., Xie Q., Perkins R., and Fuscoe J.
BMC Bioinformatics. 2005, 6 Suppl 2:S11.

Models of Steroid Binding Based on the Minimum Deviation of Structurally Assigned C-13 NMR Spectra Analysis (MiDSASA).
Beger R., Harris S., and Xie Q.
Journal of Chemical Information and Computer Sciences. 2004, 44(4):1489-1496.

Development of Public Toxicoinformatics Software for Microarray Data Management and Analysis.
Tong W., Cao X., Harris S., Sun H., Fang H., Fuscoe J., Harris A., Hong H., Xie Q., Perkins R., Shi L., and Casciano D.
Mutation Research. 2004, 549:241–253.

ArrayTrack--Supporting Toxicogenomic Research at the U.S. Food and Drug Administration National Center for Toxicological Research.
Tong W., Cao X., Harris S., Sun H., Fang H., Fuscoe J., Harris A., Hong H., Xie Q., Perkins R., Shi L., and Casciano D.
EHP Toxicogenomics. 2003, 111(15):1819–1826.

ArrayTrack – An FDA and Public Genomic Tool. disclaimer icon
Fang H., Harris C., Su Z., Chen M., Qian F., Shi L., Perkins R., and Tong W.
Protein Networks and Pathway Analysis. 2009, 379-398.

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Contact Information
Stephen Harris
(870) 543-7391
Expertise
Technology & Discipline