STEPHEN L. MATHIAS
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.
PROFESSIONAL EXPERIENCE
Division of Biocomputing, University Of New Mexico School of Medicine
Albuquerque, New Mexico
A division of Biochemistry and Molecular Biology responsible for
informatics and computing support for genomics, proteomics,
bioinformatics and cheminformatics.
2002-present
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
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.
2003-2004
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
A startup company producing bioinformatics software tools for use in the pharmaceutical and biotechnology sectors.
1999-2002
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
A multi-national pharmaceutical company, and is now part of
GlaxoSmithKline.
1998-1999
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.
1996-1998
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, various methods of differential gene expression analysis, and
yeast two-hybrid system.
EDUCATION
Ph.D. - Human Genetics and Molecular Biology, 1992,
Johns Hopkins University
B.Sc. - Biochemistry, and Molecular and Cellular Biology (double major), 1987,
with honors,
University of Arizona