David W. Email & Phone Number

San Mateo, Ca, Us

Pioneered the integration of advanced deep learning methods, including Transformer and pretrained genome Large Language Model (LLM), to drive innovation in NGS product development and enhance CRISPR off-target prediction capabilities.Led the bioinformatics team in developing a comprehensive cancer panel for tumor molecular profiling, facilitating the detection of SNV/Indel, TMB, MSI, CNV, HRD, Fusion, RNA Splice, and more.Investigated machine learning for oligo synthesis error prediction in synthetic biology.

Redwood City

Led the bioinformatics team at the Redwood site, concentrating on NGS product development. Spearheaded the creation of groundbreaking initiatives, such as the development of the next-generation hybridization capture probe design engine, xGenV3, utilizing deep-learning neural networks. Additionally, pioneered the creation of a one-tube enrichment solution for targeted amplicon sequencing, as well as an all-in-one GUI-based serverless computing solution on the AWS cloud.

South San Francisco, Ca

Led the bioinformatics team in the development of multiple multiplex PCR-based NGS panels, such as the CFTR panel, solid tumor hotspot panel (52 genes), and pan-cancer panel (>400 genes). Focused efforts on content selection, assay design, and comprehensive data analysis.Developed innovative single-cell applications, including RNA/protein co-detection and immune cell profiling.

South San Francisco, Ca

Designed and implemented in-house DNA-Seq analysis pipelines to support the development of a range of DNA-Seq products, including targeted re-sequencing (Access Array) and single-cell DNA-Seq products (whole genome, whole exome, and targeted re-sequencing).Designed and implemented in-house RNA-Seq analysis pipelines to facilitate the development of various RNA-Seq products.Developed 1920 10-base barcodes for large-scale NGS screening, with 384 barcodes commercialized (PN 100-3770 I1) and the remaining 1500 barcodes validated by a third party at the University of London.Collaborated with R&D scientists and external partners to analyze mRNA-Seq data at single-cell resolution, resulting in publications in prestigious journals such as Nature Biotechnology and Nature.Developed an algorithm for error correction to accurately identify rare somatic mutations at the single-cell level, published in PLoS One.Designed functional assays for targeted re-sequencing and multiplex strategies for Genentech to enable high-throughput clinically relevant mutation detection, published in Clinical Cancer Research.Designed and implemented the Singular™ Analysis Toolset, an innovative, open-source R package for analyzing and visualizing gene expression data and mutation data at the single-cell level.Designed and implemented genomic assay design pipelines at Fluidigm for targeted re-sequencing (Access Array, PN 100-4189) and GTpipe for designing low-cost genotyping assays for genetic variant screening (SNPtype assay, PN 100-3464; US patent of 20150147755).Designed and developed a proprietary novel protein detection assay system using oligonucleotide extension reaction (OER) for multiplex protein detection by qPCR in single cells, published in Bioconjugate Chemistry.Contributed to a pioneer project using transposons to barcode single-cell genomes and conduct digital copy number variation (CNV) analysis, resulting in a US patent (2015032066).

Foster City, Ca

Developed and implemented a pipeline for designing SybrGreen and TaqMan real-time PCR assays to detect genome-wide DNA Methylation.Developed a Genplex pipeline for multiplexed SNP genotyping analysis.Played a pivotal role in providing bioinformatics support for all miRNA product lines at ABI, including individual miRNA TaqMan assays and TaqMan arrays. Responsibilities included assay design, database maintenance, updates, and troubleshooting.Designed, developed, and constructed infrastructure for the AB castPCR project aimed at detecting rare cancer mutations.Collaborated with R&D scientists to analyze NGS data, resulting in publications in prestigious journals such as Nature Methods (2009) and Cell Stem Cell (2010).

Austin, Tx

Developed the Ambion SilencerSelect siRNA product, pioneering the creation of a support vector machines (SVM) classifier for the selection of hyper-functional siRNAs (NAR 2009).Devised and executed a computational strategy to produce functional library panels for Ambion siRNAs.Conducted data analysis of non-coding small RNA from the ABI ultra-high-throughput sequencing platform SOLiD, as reported in Genome Biology (2011).Led the design and implementation of computational algorithms and pipelines for the generation of Ambion miRNA products, including mirVana miRNA AntimiR, PremiR, and Bioarrays.Developed a computational algorithm for systematically identifying microRNA functions by integrating target prediction and expression profiling (NAR 2006).Innovated a novel computational design strategy for RT primers aimed at amplifying the whole transcriptome while minimizing cDNA products derived from rRNA, leading to a US Patent (20110257039).

St. Louis, Mo

Explored the expression and regulation patterns of crystallins in mammalian lens epithelial cells.Conducted analysis of microarray data to discern the crucial factors contributing to lens cataract development.Integrated expression profiling with a computational algorithm to forecast and pinpoint co-motifs within genes.

Quebec, Canada

Investigated the penicillin resistance mechanism of Streptococcus pneumoniae.Analyzed DNA sequences and clinical data to identify biomarkers within drug-resistant genes and developed probes for use in microarrays to detect antibiotic resistance genes.

Beijing, China

Researched the adhesion gene and urease gene of Ureaplasma urealyticum.Pioneered a novel method to fabricate a genus-specific probe for Listeria species utilizing randomly amplified polymorphic DNA (RAPD).

Master Of Science (M.S.), Computer Science

Master Of Science (M.S.), Microbiology, & Molecular Biology