David Williamson Email & Phone Number

Seattle, Wa, Us

Bangalore, Karnataka, In

Designed and developed NGS bioinformatics workflows and reporting systems to detect and monitor AML blood cancer using DuplexSeq, and Nextflow on AWS. Developed clinical laboratory systems in preparation for regulatory compliance.Lead team of production bioinformatics software engineers.

Studied piano and guitar.Parenting.

Seattle, Wa, Us

Designed primary bioinformatics workflow algorithm.Engineered CLIA approved bioinformatics pipeline to process clinical NGS diagnostic immunoassays (TCRA, TCRB, TCRG, IgH, IGK/L), ImmunoSeq.Established CLIA approved reporting system for identifying and tracking clones of interest in TCell and BCell cancers (MRD - monitoring minimum residual disease), ClonoSEQ.Established quality control systems for monitoring and improving the productivity of NGS workflows.Developed normalization methods to control for artifacts of multiplex PCR amplification.Verification and Validation, developed and supported customer facing analytical platform, ImmunoSeq.Managed tier 3 support for customer services.Managed all production and RandD data sets.Managed small bioinformatics team.

San Diego, Ca, Us

Lead the bioinformatics development for the TruSeq whole exome and custom targeted enrichment capture technologies.Conducted a 9 month pilot study as the primary analyst for Pfizer, identifying and annotating somatic mutations from the exomes of 23 pairs of tumor/normal samples using Agilent SureSelect enrichment technologies, materializing a multimillion dollar WGS services contract with Pfizer for Illumina.Worked with marketing to define custom enrichment and custom amplicon product specifications.Developed and validated the TruSeq custom enrichment and MiSeq custom amplicon oligo probe multiplex assays.Developed and validated targeted sequencing coverage analysis workflow.Produced a comparative analysis of custom enrichment technologies (Raindance, Roche, NimbleGen, Agilent SureSelect, Illumina TruSeq).Supported the sales and marketing teams as a customer facing bioinformatics expert.Developed technical competitive marketing materials.Trained sales and marketing teams on technical aspects pertaining custom enrichment assay design and analysis.Developed DNA/RNA NGS workflow and QC validation.Automated the detection and annotation of SNPs, Indels, somatic mutations, and structural variation detection in tumor/normal pairs (cancer).Automated the detection of differentially expressed genes using RNASeq.Presented seminars at webinars, and both national and international conferences.

San Diego, Ca, Us

San Diego, Ca, Us

Developed DNASeq/RNASeq/ChIPSeq and exome capture workflows including sequence alignment, polymorphism detection, genome visualization, RNA fusion transcript discovery, and small bacterial genome de novo assembly.Improved the robustness and biological relevance of early access software by critically evaluating beta versions, identifying and documenting bugs, and suggesting fixes and feature requests.Managed the transfer and archiving of large volume data sets over a multisite network.Presented analytical methods, and finalized resultant data to service customers to promote sales.Planned CLIA lab development.

San Francisco, California, Us

Ph.D. DissertationGenetic and Bioinformatic Approaches to Identify Polymorphic Modulators of Transcription Factor Binding and Disease Phenotypes Including HIV1 Viremia.Genetic Survey - To conduct a genetic survey of four genes (CCR5, TLR9, IRF5, APOE) in order to identify associations between genotype/haplotype frequencies and viremia levels, in a population of HIV positive Americans primarily derived from the San Francisco SCOPE cohort.Computational Survey - To computationally survey the database of human single nucleotide polymorphisms (SNPs) in order to identify and rank prioritize which polymorphisms are likely to have allele-specific transcription factor recruitment. Transcription factor binding site matrices provided by the BIOBASE TRANSFAC database are pattern matched against human genome sequence to derive quantitative scores reflecting allele-specific transcription factor binding affinity.Software Development (Delta-MATCH) - To produce a user friendly, web-based tool (Delta-MATCH). Predictions made by the computational survey also integrate data from a broad number of external bioinformatics resources (UCSC human genome, dbSNP, HAPMAP, Gene Ontology, Affymetrix, Illumina, Perlegen, PReMod), and are used to identify important candidate SNPs that may be genotyped and further investigated for association with inheritable disease.Polymorphism Selection - To produce discrete lists of high-value candidate single nucleotide polymorphisms (SNPs) to investigate the following disease phenotypes: cardiovascular disease, obesity, dyslipidemia, diabetes mellitus, multiple sclerosis, autoimmunity, prostate cancer, glioma, and Alzheimer’s disease. These candidate SNPs are being genotyped in the appropriate genetic cohorts through collaborations at UCSF.

Conducted genotype/haplotype association studies.Investigated more than 130 polymorphisms in candidate genes (ApoE, LIPC, CETP, MTP, APM1, FABP2, AKAP10, TLR9, CCR5, IRF5) for association with disease phenotypes: dyslipidemia, cardiovascular disease, insulin resistance, obesity, the metabolic syndrome, Tcell activation, and HIV-1 viremia/progression.Designed polymorphism detection assays and genotyped more than 80,000 single nucleotide polymorphisms (SNPs) using Restriction Fragment Length Polymorphism (RFLP), Allele Specific Oligo (ASO) hybridization, High-Performance Liquid Chromatography (HPLC), and Taqman assays.Conducted genetic analyses (case/control, pedigree, TDT inheritance, linkage).Primer design, PCR, sequencing, array analysis (Illumina and Affymetrix arrays).Database curator for the Turkish Heart Study (THS) (> 12,000 biological samples).Validated predicted gene associations using advanced techniques in molecular biology.Engineered a transgenic mouse strain overexpressing human protein disulfide isomerase.Developed a Dual-LuciferaseTM Reporter (DLR) promoter expression assay.Evaluated the affect of polymorphisms on protein function using 3-D modeling.

San Francisco, California, Us

Administrated and graded exams for 80+ PharmD students.Digitally recorded, distributed and archived digitizer lecture materials.

Seattle, Wa, Us

Curated colonies of eight lines of knockout mice.Investigated tumorigenesis in tumor suppressor knockout mouse models.PCR genotyping.

Washington, District Of Columbia, Us

Constructed sustainable fresh water fisheries and integrated agricultural farming systems.Combatted the spread of HIV/AIDS by hosting educational seminars.Ambassador to the Peace Corps mission.Generated positive change.

Ph.D., Biological And Medical Informatics

Ecology And Systematic Biology

Bs, Cellular & Molecular Biology