Qualifications
Twenty years professional experience as a manager/lead/team member of computational algorithm/software development and data analysis projects encompassing pattern recognition, optimization, statistical analysis and simulation techniques.
Experience
Exagen Diagnostics 2002-2012
Vice President, Discovery & Co-founder
➢ Developed and implemented (R/c++/MPI) Exagen's data mining platform for genomic data analysis on *nix-based clusters incorporating: modules for supervised classification and unsupervised clustering, genetic algorithm and exhaustive search for optimal feature subsets, outlier detection, and out-of-sample performance metrics
➢ Hired team incorporating computational and biological scientists to further develop and apply platform to identify prognostic and diagnostic biomarkers
➢ Used platform to discover biomarkers in autoimmune, cancer and other disease areas. Biomarkers validated in subsequent studies.
➢ 7 US patents awarded: 2 software algorithm & 5 biomarker
➢ 3 marketed diagnostic products based on discoveries
Quasar International 2000-2001
Senior Staff Scientist
➢ Evaluated pattern recognition techniques for the identification of defective forged and powdered metal parts utilizing ultrasound spectral data.
➢ Implemented (c++ & R) neural net, various discriminant analysis algorithms and genetic algorithm feature selector for use with ultrasound spectral data.
➢ Tested techniques on several synthetic and real part spectral datasets. Identified best solution and worked with GUI developer to implement windows software.
➢ Incorporated novel algorithm for robust evaluation of classifiers (US patent awarded)
➢ Trained internal and external clients on proper use of software
➢ Software installed in manufacturing plants worldwide
➢ Models developed with software currently evaluating ~150,000,000 parts/year (2007)
Veritas DGC 1990-1999
Senior Research Geophysicist
➢ Developed and implemented algorithms (c, fortran) suitable for large seismic data volume processing and imaging.
➢ Tested resulting programs on synthetic and real data.
➢ Presented results to both industry via technical conferences, and to individual oil company clients.
Algorithms developed include:
➢ Method for automated detection of seismic data events and subsequent imaging of detected events.
➢ Constrained nonlinear least-squares inversion technique for velocity model building from migration stacking velocities
➢ Kirchhoff and phase-shift imaging algorithms for heterogeneous subsurface velocities
Vice President, Discovery & Co-founder
➢ Developed and implemented (R/c++/MPI) Exagen's data mining platform for genomic data analysis on *nix-based clusters incorporating: modules for supervised classification and unsupervised clustering, genetic algorithm and exhaustive search for optimal feature subsets, outlier detection, and out-of-sample performance metrics
➢ Hired team incorporating computational and biological scientists to further develop and apply platform to identify prognostic and diagnostic biomarkers
➢ Used platform to discover biomarkers in autoimmune, cancer and other disease areas. Biomarkers validated in subsequent studies.
➢ 7 US patents awarded: 2 software algorithm & 5 biomarker
➢ 3 marketed diagnostic products based on discoveries
Quasar International 2000-2001
Senior Staff Scientist
➢ Evaluated pattern recognition techniques for the identification of defective forged and powdered metal parts utilizing ultrasound spectral data.
➢ Implemented (c++ & R) neural net, various discriminant analysis algorithms and genetic algorithm feature selector for use with ultrasound spectral data.
➢ Tested techniques on several synthetic and real part spectral datasets. Identified best solution and worked with GUI developer to implement windows software.
➢ Incorporated novel algorithm for robust evaluation of classifiers (US patent awarded)
➢ Trained internal and external clients on proper use of software
➢ Software installed in manufacturing plants worldwide
➢ Models developed with software currently evaluating ~150,000,000 parts/year (2007)
Veritas DGC 1990-1999
Senior Research Geophysicist
➢ Developed and implemented algorithms (c, fortran) suitable for large seismic data volume processing and imaging.
➢ Tested resulting programs on synthetic and real data.
➢ Presented results to both industry via technical conferences, and to individual oil company clients.
Algorithms developed include:
➢ Method for automated detection of seismic data events and subsequent imaging of detected events.
➢ Constrained nonlinear least-squares inversion technique for velocity model building from migration stacking velocities
➢ Kirchhoff and phase-shift imaging algorithms for heterogeneous subsurface velocities
Education
The Johns Hopkins University, Baltimore, MD
MA Physics, 1990
Continuing Education Courses
Statistical Modeling in S-PLUS, Insightful Corporation, 2007
Linux Cluster Institute Workshop, 2004
American Management Association:
Finance for Nonfinancial Managers, 1999
Project Management, 1997
Professional Affiliations
Institute of Electrical and Electronic Engineers CIS
Association for Computing Machinery SIGEVO
International Society for Computational Biology
Institute for Operations Research and the Management Sciences
Competitions
INFORMS 2010 Data Mining Competition, 1st place of 147
October 2010
http://viewer.zmags.com/publication/03b6e869#/03b6e869/42
Don't Overfit! Data Mining Competition, 4th place of 265
May 2011
http://www.kaggle.com/c/overfitting
The Johns Hopkins University, Baltimore, MD
MA Physics, 1990
Continuing Education Courses
Statistical Modeling in S-PLUS, Insightful Corporation, 2007
Linux Cluster Institute Workshop, 2004
American Management Association:
Finance for Nonfinancial Managers, 1999
Project Management, 1997
Professional Affiliations
Institute of Electrical and Electronic Engineers CIS
Association for Computing Machinery SIGEVO
International Society for Computational Biology
Institute for Operations Research and the Management Sciences
Competitions
INFORMS 2010 Data Mining Competition, 1st place of 147
October 2010
http://viewer.zmags.com/publication/03b6e869#/03b6e869/42
Don't Overfit! Data Mining Competition, 4th place of 265
May 2011
http://www.kaggle.com/c/overfitting
Selected Publications & Presentations
Generalizable Computational techniques
Cross-validation techniques pivotal in ranking stock price prediction models. C Harris, INFORMS 2010 Annual Meeting, Austin Texas, 2010
Biomarker Discovery Across Annotated and Unannotated Microarray Datasets Using Semi-Supervised Learning. Cole Harris and Noushin Ghaffari, BMC Genomics 2008, 9 (Supp 2);S7
Multi-objective optimization in the concurrent mining of disparate genomic datasets, C Harris and P Hraber, Genetic and Evolutionary Computation Conference, Washington DC, 2005
Discriminant analysis with unlabeled and mislabeled training data, C. Harris, Neural Information Systems Processing 2000 workshop: Using Unlabeled Data for Supervised Learning, Breckenridge 2000, invited talk
Biology/Medicine
Gene Expression Signatures Predictive of Infliximab Response in IBD. C. Harris, J. Alsobrook, L. Davis, American College of Gastroenterology Annual Meeting, Washington, DC, 2011, presentation P725
Transcriptional Patterns in Whole Blood Diagnostic of Systemic Lupus Erythematosus. T. Costello, C. Harris, American College of Rheumatology Annual Meeting, Chicago, 2011, presentation 2261
Combinations of Anti-Citrullinated Peptide Antibodies with Rheumatoid Factor Isotypes Reveal an Attribute Associated with Disease Activity in Rheumatoid Arthritis Patients Treated with Methtrexate. Thierry Dervieux, Cole Harris, Joel M. Kremer, American College of Rheumatology Annual Meeting, Chicago, 2011, presentation 329
The Contribution of Cell Bound Complement Activation Products to the Diagnosis of Systemic Lupus Erythematosus. K. C. Kalunian, W. Chatham, E. M. Massarotti, C. Harris, R. A. Furie, J. P. Buyon, E. F. Chakravarty, E. C. Somers, P. Chitkara, R. L. Gross, K. A. Kirou, J. Reyes-Thomas, R. Ramsey-Goldman, C. Hsieh, C. Putterman, T. Dervieux, A. Weinstein, American College of Rheumatology Annual Meeting, Chicago, 2011, presentation 597
Accurate differentiation between Crohn's Disease and Ulcerative Colitis using novel biomarkers from peripheral blood specimens. Cole Harris, Thomas Ma, Jonathan A. Leighton, Thomas Williams, Allison Treloar, Lisa Davis, John Alsobrook II, American College of Gastroenterology Annual Meeting, San Antonio, 2010, presentation P318
An integrated picture of IBD derived from mapping novel multi-genic disease markers onto regulatory pathways. Harris C, Alsobrook J, Davis, L, American College of Gastroenterology Annual Meeting, San Diego, 2009, poster presentation P314
Amplification patterns of three genomic regions predict distant recurrence in breast carcinoma. Davis LM, Harris C, Tang L, Doherty P, Hraber P, Sakai Y, Bocklage T, Doeden K, Hall B, Alsobrook J, Rabinowitz I, Williams TM, Hozier J. J Mol Diagn. 2007 Jul;9(3):327-36.
Invasive ductal and invasive lobular carcinoma show a similar amplification profile of chromosomal markers prognostic for breast carcinoma recurrence. Carmichael B, Davis L, Harris C, Tang L, Doherty P, Alsobrook J, Williams TM, Doeden K, Hall B, Rabinowitz I, Hozier J, Bocklage T., San Antonio Breast Cancer Symposium, San Antonio, 2006, poster presentation
Prediction of Lymph Node Status Utilizing Selective Genomic Fluorescence In Situ Hybridization Markers in Invasive Breast Carcinoma, KS Doeden, T Bocklage, C Harris, L Davis, P Doherty, P Hraber, L Tang, B Hall, I Rabinowitz, T Williams, J Hozier, United States and Canadian College of Pathology Annual Meeting, San Antonio, 2005, poster presentation
Novel Tests Based on Genomic Markers, Assay Tutorial: Improving the Clinical Utility of Testing for Breast Cancer Recurrence, Suzanne Mattingly, Ph.D., Lisa Davis, Ph.D., and Cole Harris, Genetic Engineering News, Volume 25, Number 16, September 15, 2005
Discovery of multiplex genomic markers for predicting breast cancer recurrence, Harris C., San Antonio Breast Cancer Symposium, San Antonio, 2004, poster presentation
Validation of multiplex genomic markers for predicting breast cancer recurrence in a FISH assay format, Harris C., Doherty P., Hraber P., Tang L., Davis L., Bocklage T. Doeden K., Hall B., Rabinowitz I., Williams T., Hozier J., San Antonio Breast Cancer Symposium, San Antonio, 2004, poster presentation
Integration of CGH data and microarray gene expression data aids in the discovery of DNA-based diagnostic tumor markers, C. Harris, American Society of Human Genetics Annual Meeting, Los Angeles, 2003, poster presentation
Biomarker Discovery: Clinical and Research Applications, C. Harris, Annual Spring Bioinformatics Workshop 2002, National Center for Genome Resources, Santa Fe, invited talk
Magellan Biomarker Discovery in Microarray Data: Analysis of the MIT Leukemia and Rosetta Breast Cancer Datasets, C. Harris, Inaugural Genomics Symposium, University of New Mexico, Albuquerque 2002, poster presentation
Geophysics
MITAS, migration input trace aperture selection, C. Harris, M. Marcoux, and S. Bickel, SEG 68th Annual Meeting, New Orleans 1998, Expanded Abstracts p. 1373-1376
Aperture selection to improve Kirchhoff depth imaging using the maximum depth principle, C. Harris, M. Marcoux, and S. Bickel, 60th Conference and Technical Meeting, Leipzig 1998, Extended Abstracts vol 1, paper 1-56
Efficient depth migration for complex overburden by global inversion of RMO, C. Harris, EAGE 59th Conference and Technical Meeting, Geneva 1997, Extended Abstracts vol 1, paper A019
3-D prestack time migration and velocity - Depth modeling in GOM: E Cameron and Vermilion, Drummie, S., Gibson, R., Harris, C., Marcoux, M., O'Donnell, D., Schonbeck, S., Williams, R. G., Heron, S., Martin, J. and Putnam, M., 1996 66th Ann. Internat. Mtg: Soc. of Expl. Geophys., 551-554.
Accurate 3D time migration focusing in regions of lateral velocity gradients, C. Harris, EAGE 58th Conference and Technical Meeting, Amsterdam 1996, Extended Abstracts vol. 1, paper X019
Velocity modelling for depth migration using exact-time migration, Marcoux, M. O., Harris, C., Chernis, L. and Whiting, P., 1995, 11th Geophysical Conference, Austr. Soc. Expl. Geophys., 26, 461-467.
Depth migration and modeling from exact time migration, 64th Ann. Internat. Mtg: Marcoux, M. O., Harris, C. and Chernis, L., 1994 Soc. of Expl. Geophys., 1647-1650.
Smooth velocity-depth models from exact time migration, Marcoux, M. O., Chernis, L. and Harris, C., 1993, 63rd Ann. Internat. Mtg: Soc. of Expl. Geophys., 681-683.
Feasibility of exact time migration velocity inversion in 3D, C. Harris, SEG 65th Annual Meeting, Houston 1995, Expanded Abstracts p. 1018-1021
Cross-validation techniques pivotal in ranking stock price prediction models. C Harris, INFORMS 2010 Annual Meeting, Austin Texas, 2010
Biomarker Discovery Across Annotated and Unannotated Microarray Datasets Using Semi-Supervised Learning. Cole Harris and Noushin Ghaffari, BMC Genomics 2008, 9 (Supp 2);S7
Multi-objective optimization in the concurrent mining of disparate genomic datasets, C Harris and P Hraber, Genetic and Evolutionary Computation Conference, Washington DC, 2005
Discriminant analysis with unlabeled and mislabeled training data, C. Harris, Neural Information Systems Processing 2000 workshop: Using Unlabeled Data for Supervised Learning, Breckenridge 2000, invited talk
Biology/Medicine
Gene Expression Signatures Predictive of Infliximab Response in IBD. C. Harris, J. Alsobrook, L. Davis, American College of Gastroenterology Annual Meeting, Washington, DC, 2011, presentation P725
Transcriptional Patterns in Whole Blood Diagnostic of Systemic Lupus Erythematosus. T. Costello, C. Harris, American College of Rheumatology Annual Meeting, Chicago, 2011, presentation 2261
Combinations of Anti-Citrullinated Peptide Antibodies with Rheumatoid Factor Isotypes Reveal an Attribute Associated with Disease Activity in Rheumatoid Arthritis Patients Treated with Methtrexate. Thierry Dervieux, Cole Harris, Joel M. Kremer, American College of Rheumatology Annual Meeting, Chicago, 2011, presentation 329
The Contribution of Cell Bound Complement Activation Products to the Diagnosis of Systemic Lupus Erythematosus. K. C. Kalunian, W. Chatham, E. M. Massarotti, C. Harris, R. A. Furie, J. P. Buyon, E. F. Chakravarty, E. C. Somers, P. Chitkara, R. L. Gross, K. A. Kirou, J. Reyes-Thomas, R. Ramsey-Goldman, C. Hsieh, C. Putterman, T. Dervieux, A. Weinstein, American College of Rheumatology Annual Meeting, Chicago, 2011, presentation 597
Accurate differentiation between Crohn's Disease and Ulcerative Colitis using novel biomarkers from peripheral blood specimens. Cole Harris, Thomas Ma, Jonathan A. Leighton, Thomas Williams, Allison Treloar, Lisa Davis, John Alsobrook II, American College of Gastroenterology Annual Meeting, San Antonio, 2010, presentation P318
An integrated picture of IBD derived from mapping novel multi-genic disease markers onto regulatory pathways. Harris C, Alsobrook J, Davis, L, American College of Gastroenterology Annual Meeting, San Diego, 2009, poster presentation P314
Amplification patterns of three genomic regions predict distant recurrence in breast carcinoma. Davis LM, Harris C, Tang L, Doherty P, Hraber P, Sakai Y, Bocklage T, Doeden K, Hall B, Alsobrook J, Rabinowitz I, Williams TM, Hozier J. J Mol Diagn. 2007 Jul;9(3):327-36.
Invasive ductal and invasive lobular carcinoma show a similar amplification profile of chromosomal markers prognostic for breast carcinoma recurrence. Carmichael B, Davis L, Harris C, Tang L, Doherty P, Alsobrook J, Williams TM, Doeden K, Hall B, Rabinowitz I, Hozier J, Bocklage T., San Antonio Breast Cancer Symposium, San Antonio, 2006, poster presentation
Prediction of Lymph Node Status Utilizing Selective Genomic Fluorescence In Situ Hybridization Markers in Invasive Breast Carcinoma, KS Doeden, T Bocklage, C Harris, L Davis, P Doherty, P Hraber, L Tang, B Hall, I Rabinowitz, T Williams, J Hozier, United States and Canadian College of Pathology Annual Meeting, San Antonio, 2005, poster presentation
Novel Tests Based on Genomic Markers, Assay Tutorial: Improving the Clinical Utility of Testing for Breast Cancer Recurrence, Suzanne Mattingly, Ph.D., Lisa Davis, Ph.D., and Cole Harris, Genetic Engineering News, Volume 25, Number 16, September 15, 2005
Discovery of multiplex genomic markers for predicting breast cancer recurrence, Harris C., San Antonio Breast Cancer Symposium, San Antonio, 2004, poster presentation
Validation of multiplex genomic markers for predicting breast cancer recurrence in a FISH assay format, Harris C., Doherty P., Hraber P., Tang L., Davis L., Bocklage T. Doeden K., Hall B., Rabinowitz I., Williams T., Hozier J., San Antonio Breast Cancer Symposium, San Antonio, 2004, poster presentation
Integration of CGH data and microarray gene expression data aids in the discovery of DNA-based diagnostic tumor markers, C. Harris, American Society of Human Genetics Annual Meeting, Los Angeles, 2003, poster presentation
Biomarker Discovery: Clinical and Research Applications, C. Harris, Annual Spring Bioinformatics Workshop 2002, National Center for Genome Resources, Santa Fe, invited talk
Magellan Biomarker Discovery in Microarray Data: Analysis of the MIT Leukemia and Rosetta Breast Cancer Datasets, C. Harris, Inaugural Genomics Symposium, University of New Mexico, Albuquerque 2002, poster presentation
Geophysics
MITAS, migration input trace aperture selection, C. Harris, M. Marcoux, and S. Bickel, SEG 68th Annual Meeting, New Orleans 1998, Expanded Abstracts p. 1373-1376
Aperture selection to improve Kirchhoff depth imaging using the maximum depth principle, C. Harris, M. Marcoux, and S. Bickel, 60th Conference and Technical Meeting, Leipzig 1998, Extended Abstracts vol 1, paper 1-56
Efficient depth migration for complex overburden by global inversion of RMO, C. Harris, EAGE 59th Conference and Technical Meeting, Geneva 1997, Extended Abstracts vol 1, paper A019
3-D prestack time migration and velocity - Depth modeling in GOM: E Cameron and Vermilion, Drummie, S., Gibson, R., Harris, C., Marcoux, M., O'Donnell, D., Schonbeck, S., Williams, R. G., Heron, S., Martin, J. and Putnam, M., 1996 66th Ann. Internat. Mtg: Soc. of Expl. Geophys., 551-554.
Accurate 3D time migration focusing in regions of lateral velocity gradients, C. Harris, EAGE 58th Conference and Technical Meeting, Amsterdam 1996, Extended Abstracts vol. 1, paper X019
Velocity modelling for depth migration using exact-time migration, Marcoux, M. O., Harris, C., Chernis, L. and Whiting, P., 1995, 11th Geophysical Conference, Austr. Soc. Expl. Geophys., 26, 461-467.
Depth migration and modeling from exact time migration, 64th Ann. Internat. Mtg: Marcoux, M. O., Harris, C. and Chernis, L., 1994 Soc. of Expl. Geophys., 1647-1650.
Smooth velocity-depth models from exact time migration, Marcoux, M. O., Chernis, L. and Harris, C., 1993, 63rd Ann. Internat. Mtg: Soc. of Expl. Geophys., 681-683.
Feasibility of exact time migration velocity inversion in 3D, C. Harris, SEG 65th Annual Meeting, Houston 1995, Expanded Abstracts p. 1018-1021