CV
You can download a PDF version of my resume here.
Education
- B.Sc. in Biotechnology, California State Polytechnic University, Pomona (2008)
- Ph.D. in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine (2016)
Skills
- Programming
- R & Shiny; Python; Bash
- SQL; Git & Github
- CWL; Snakemake
- Platforms
- Sun Grid Engine; Slurm; Docker
- Amazon Web Services; Seven Bridges Genomics
- Data analysis
- Biostatistics; microarray & NGS;
- Genomics, epigenomics, transcriptomics
- Machine learning
Professional experience
- Bioinformatics Scientist (Jun 2020 - Current)
- Arcus Biosciences Inc
- Bioinformatics Department
- Broad bioinformatics functionalities to support data-driven drug discovery.
- Lead bioinformatics functions of early stage, preclinical immuno-oncology projects in multi-functional teams.
- Analyze Phase 1/2 clinical trial NGS data for biomarker discovery.
- Create data harmonization framework and internal database of over 8TB of -omics data to support drug discovery and translational decisions, such as hypothesis testing, model selection, and indication assessment.
- Develop analysis frameworks, computational methods, and software for -omics data analysis.
- Spearhead efforts for data-driven discovery of new drug targets using bioinformatics approaches.
- Design and implement infrastructure, NGS pipelines, and Shiny applications.
- Manage and mentor direct reports and interns to successful completion of several projects.
- Establish relationships with vendors for bioinformatics needs and NGS applications.
- Post-doctoral Fellow (Dec 2016 - May 2019)
- Kennedy Krieger Institute & Johns Hopkins University
- PI: Dr. Jonathan Pevsner
- Characterization of somatic mosaicism in neurobehavioral disorders
- Analyzed NGS (genomic, transcriptomic, 10X Genomics) datasets to identify somatic variants associated with disease
- Designed phase-aware computational methods for somatic variant discovery and prioritization that led to increased specificity in variant calling.
- Developed and maintained Dockerfiles and bioinformatics pipelines for high performance cluster or cloud computing to enable efficient genomic analysis and promote reproducibility.
- Generated a 14TB public resource of genomic variant call format (GVCF) files from 1000 Genomes to increase variant calling sensitivity using the Seven Bridges Genomics cloud computing platform.
- PhD Candidate (Sep 2010 - Nov 2016)
- Johns Hopkins University School of Medicine
- PIs: Drs. Saraswati Sukumar, Christopher Umbricht, Leslie Cope
- Multi-omics analysis of archival tissue for biomarker discovery in breast and thyroid cancer
- Designed statistical framework & computational tools for integrative genomic & epigenomic analysis.
- Developed the Epicopy program for estimating copy number variation from methylation microarrays, effectively increasing the amount of data obtained from methylation microarray experiments.
- Optimized protocols for DNA/RNA extraction from archival tissue and microarray analysis leading to greater yield and microarray quality.
- Actively collaborated on interdisciplinary teams to make decisions and discoveries for grants and research projects, resulting in thirteen publications.
- Led the development of bioinformatics research strategy, generated pilot data, and successfully co-wrote two competitively funded grants totaling $300,000.
- Graduate Intern, Computational Biology (Aug 2015 - Oct 2015)
- Pfizer
- Multi-omics analysis of breast cancer
- Led the analysis of genomic and transcriptomic data of a unique breast cancer cohort, resulting in a peer-reviewed publication in Nature Communications.
- Research Associate (June 2008 - May 2010)
- City of Hope National Cancer Center
- PI: Dr. Michael Jensen
- Immuno-oncology research in chimeric antigen receptor (CAR) T-cells
- Designed and constructed lentiviral vectors of CARs for T-cell therapy research as an active member of a translational research team.
- Undergraduate Researcher (Oct 2007 - June 2008)
- California State Polytechnic University, Pomona
- PI: Dr. Weijen Lin
- Development of a transposon system for gene delivery in Gram-positive bacteria
- Modified and optimized the use of transposon Tn5 for large gene delivery through electroporation.
Publications
Invited Talks
- Epicopy: Measuring DNA copy number using Illumina 450K methylation microarrays (2014)
- Computational Genomics Symposium, Johns Hopkins Hospital
Posters
- Characterization of metastatic follicular thyroid cancer by RNA-seq. (2016)
- American Thyroid Association Annual Meeting, Denver CO
- Epicopy: Measuring DNA copy number variation using Illumina high density methylation microarrays. (2015)
- American Cancer Association Annual Meeting, Philadelphia PA
Teaching
Service and leadership
- Journal reviewer:
- Cancer Epidemiology, Biomarkers and Prevention
- Cancer Research
- Clinical Cancer Research
- Frontiers in Oncology
- Molecular Cancer Research
- Molecular Carcinogenesis
- Oncogene