Daryl Thomas
PhD in Bioinformatics (2006), MSc in Computer Science (2003) both from UC Santa Cruz, MS in Neuroscience from Stanford University (1994), BS in Chemistry from Carnegie Mellon University, Senior Bioinformatics Scientist at Navigenics, Inc since 2007
| Headline: | Scientist |
| Work status: | Living The Dream |
| Website: | http://www.soe.ucsc.edu/~daryl |
| Industries: | Biotech, Computing, Health, Nanotech |
| Skills: | C/C++, Databases, Design, Engineering, HTML / CSS, Java, Languages, Languages and Platforms, Perl, Product design, Software Engineering, SQL, System Administration, Unix, Web Development, Windows |
| Location: | San Francisco Bay Area |
| Interested in: | Brainstorming, Consulting opportunities, Helping friends, Learning about entrepreneurship, Meeting new people, Offering Expertise, Patenting my idea, Professional opportunities, Providing services to startups |
| Tags: | bioinformatics, genome browser |
| Schools: | Carnegie Mellon University, Stanford University, University of California System - Davis, University of California System - Santa Cruz |
WORK EXPERIENCE
| Employer: | Navigenics, Inc. |
| Position: | Senior Bioinformatics Scientist |
| Time period: | November 2007 - January 2010 |
| Description: | • Development of the Genetic Composite Index (GCI) to estimate the association
of a condition with the combined effect of a set of genetic variants. • Development of Affymetrix GW 6.0 and Applied Biosystems TaqMan Genotyping assays with validation against reference HapMap samples and customer saliva samples. • Analysis of complex genomic regions (e.g., HLA and APOE) using linkage disequilibrium to identify assayable variants across all populations. • Integration of disease-level data (heritability, prevalence, life time risk) with locus-specific details (risk/non-risk alleles, genotype frequencies, odds ratios) to support GCI calculations for all conditions in our products. • Creation and development of multiple reference databases and interfaces. |
| Employer: | Perlegen Sciences, Inc. |
| Position: | Bioinformatics Engineer |
| Time period: | March 2001 - September 2002 |
| Description: | • Development of client/server tools to manage query sequences, find their location
in the genome, store this information for subsequent retrieval, and display the results with related annotations in a database-driven GUI browser. • Creation, loading, and quality assurance of genomic annotations. • Development of a semi-automated pipeline for sequence processing, including acquisition, repeat masking, primer design, primer ordering, and primer tracking. |
| Employer: | Affymetrix, Inc. |
| Position: | Data Analyst |
| Time period: | February 1999 - March 2001 |
| Description: | • Tracking and analyzing data generated by the Polymorphisms group.
• Liaison to internal colleagues and to external clients and collaborators. • Used in-house applications to analyze chip image data for SNP identification. • Developed methods for improving data access, used these tools to track progress. • Coordinated ongoing and retrospective analyses of data quality and validation rates to identify inconsistencies in data quality and identify sources of variability. • Trained users on in-house software and worked with developers to make functional enhancements. |
| Employer: | Sentinel Biosciences, Inc |
| Position: | Senior Research Associate |
| Time period: | January 1997 - December 1998 |
| Description: | Purified and characterized antigens for immunization and antibody screening.
Developed IgG quantitation ELISA to increase sensitivity and decrease cost. Established tissue culture facility and selected optimum growth conditions for hybridoma cell lines by IgG quantitation ELISA and antigen binding ELISA. Screened polyclonal antisera from five rabbits for antibody titer and specificity. |
| Employer: | Howard Hughes Medical Institute, Stanford University |
| Position: | Research Technician II |
| Time period: | January 1992 - December 1995 |
| Description: | Biochemical purification and cloning of the transcription factor NF-ATc and paralogs.
Characterized NF-ATc clones by RNAse protection, Northern and Southern blot analysis, eukaryotic transienttransfection, reporter gene assays, cytosolic and nuclear protein extraction, and electrophoretic mobility shift assays. Curated and submitted nucleotide sequence data, searched databases for homologs and orthologs using BLAST, evaluated similarity using ALIGN. Created monoclonal antibodies using recombinant protein purification, mouse immunization, antiserum characterization, and Western blots. |
| Employer: | Protein and Nucleic Acid Facility, Stanford University |
| Position: | Research Associate |
| Time period: | January 1991 - December 1992 |
| Description: | Increased synthesis capacity three-fold to over 400 oligonucleotides per month.
Developed processes and protocols for new reagents and instrumentation. |
| Employer: | Clontech Laboratories, Inc. |
| Position: | Research Associate in Organic Chemistry |
| Time period: | January 1990 - December 1991 |
| Description: | Developed protocols for synthesis of Biotin-ON phosphoramidite and related reagents for incorporating chemical labels into synthetic oligonucleotides.
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EDUCATION
| University: | University of California System - Santa Cruz |
| Time period: | 2001 - 2006 |
| Degree: | Bioinformatics, PhD |
| University: | University of California System - Santa Cruz |
| Time period: | 2001 - 2003 |
| Degree: | Computer Science, MSc |
| University: | University of California System - Davis |
| Time period: | 1995 - 1997 |
| Degree: | Neuroscience, MSc |
| University: | Stanford University |
| Time period: | 1993 - 1994 |
| Degree: | Coursework in Biochemistry / Molecular Biology |
| University: | Carnegie Mellon University |
| Time period: | 1986 - 1990 |
| Degree: | Chemistry, BSc |
INFORMATION
| Memberships: | American Association for Cancer Research
International Genetic Epidemiology Society International Society for Computational Biology American Society for Human Genetics UCSC Extension Bioinformatics Certificate Steering Committee Bay Area Bioinformatics Discussion Group Society for Neuroscience American Association for the Advancement of Science American Chemical Society |
