Stephen L. Mathias Address: 1309 Arizona St NE Phone: (505) 385-1314 Albuquerque, NM 87110 E-mail: smathias@comcast.net ------------------------------------------------------------------------- BACKGROUND SUMMARY A geneticist and computational biologist with over 10 years of research experience in the fields of human genetics and molecullar biology, and 12 years experience developing and applying computational and database systems in the areas of genome biology, pharmacogenomics and genetic analysis in both industrial and academic settings. A self-motivated and creative worker with the ability to interface as a peer with both scientific domain experts and software engineers. Selected skills and areas of expertise include: - Broad range of experience in both the laboratory and computational aspects of molecular biology, genetics and drug discovery. - Demonstrated ability to design and develop software and database systems to help scientists manage data and accelerate research. - Extensive programming experience in Perl and PHP. Basic proficiency with the C/C++, Java, Python and Ruby programming languages. - Excellent skills in relational database design and management (Oracle, PostgreSQL and MySQL). - Demonstrated Linux/UNIX system administration skills. - Excellent web development skills, including extensive knowledge of HTML, CSS, CGI and Apache administration. Outstanding computer skills, including system administration, particularly in the UNIX environment. - Excellent skills in relational database design and management (Oracle, PostgreSQL and MySQL). - Extensive programming experience in Perl and PHP. Basic proficiency with the C/C++, Java, Python and Ruby programming languages. ------------------------------------------------------------------------- PROFESSIONAL EXPERIENCE Division of Biocomputing, University Of New Mexico School of Medicine, Albuquerque, New Mexico 2002-present A division of Biochemistry and Molecular Biology responsible for informatics and computing support for genomics, proteomics, bioinformatics and cheminformatics. Senior Research Scientist Principal staff scientist responsible for database application development and support of bioinformatics and genomics software. - Designed, developed and supported several scientific database applications, including: Roadrunner, a chemical database application supporting the New Mexico Molecular Libraries Screening Center; Genotation, a genomics workbench, the core of which is an extensive integrated database of gene annotation data; and UNMMD, database application for the storage, management and analysis of spotted microarray data. - Provided informatics support and services in numerous research collaborations. - Installed and maintained numerous bioinformatics databases and software packages to support genomics research within the Health Sciences Center. - Managed Linux servers on which the above services were made available. The Center for High Performance Computing Albuquerque, New Mexico 2003-2004 A strategic center of the University of New Mexico that a variety of high-performance computing platforms and supports both advanced systems and application research thrusts, including biocomputing. Senior Research Scientist Worked with the Database Group on developing data integration and warehousing strategies. - Developed object models, database schemas, web services, and the user interface for the GenomeDW project. Genomica Corporation, Boulder, Colorado 1999-2002 A startup company producing bioinformatics software tools for use in the pharmaceutical and biotechnology sectors. Senior Scientist, Research Principal staff scientist for product development in the areas of genetic analysis and pharmacogenomics. Reported to the President and Chief Scientist. - Defined the scientific content and served on the product steering teams for LinkMapper, dmCORE, and dmGENETICS. - Developed and maintained the domain object model supporting all products developed on the Java/Oracle platform. - Developed a Perl software development kit including an API to the Genomica domain object model, used this toolkit to build prototype applications, and applied it to research-oriented data management and analysis. SmithKline Beecham, London, England 1996-1999 A multi-national pharmaceutical company, and is now part of GlaxoSmithKline. Senior Investigator, Genome Bioinformatics Developed and supported specialist bioinformatics tools and resources to support genomics-based research in the Biopharmaceutical Department. - Built a web-client based database application used by lab-based scientists to manage in house SNP discovery data. - Developed a high-throughput system for the characterization of sequences for use in the production of DNA microarrays for gene expression analysis. Received an R&D Impact Award for this project. - Developed Perl libraries, used for the above projects and by others in the bioinformatics department, to automate database searching and sequence annotation. Investigator, Gene Informatics Applied of state of the art bioinformatics methods to data mining of proprietary and public EST and genomic sequence databases for novel drug targets. - Patented several novel gene sequences as drug targets in the therapeutic areas of diabetes and obesity. - Developed programs for the automation of database searching and sequence annotation activities. These programs were used on a daily basis by the investigators in the Gene Informatics group. - Worked closely with chemists and wet-bench biologists to effectively prioritize the discovery efforts of the Gene Informatics group to the needs of the therapeutic areas. University of Cambridge Department of Genetics, Cambridge, England 1992-1996 Post-doctoral Research Fellow in the laboratory of Peter N. Goodfellow. - Performed research aimed at identifying and characterizing genes involved in the mammalian testis-determining pathway. - Major techniques used included genetic linkage analysis, positional cloning, and various methods of differential gene and protein expression analysis. ------------------------------------------------------------------------- EDUCATION Ph.D. - Human Genetics and Molecular Biology, 1992. Johns Hopkins University B.Sc. - Biochemistry / Molecular and Cellular Biology (double major), 1987, with honors. University of Arizona