Resume

Zhenguo Zhang

Passionate Bioinformatics Scientist and Mentor · zhangz.sci@gmail.com · GitHub · LinkedIn

Executive Summary

Bioinformatics Scientist with 20+ years of R&D expertise in multi-omic data analysis, biomarker discovery, and translational research, backed by 20+ peer-reviewed publications across gene regulation, genome evolution, and cancer genomics. Experienced across the full R&D lifecycle—from idea initiation and experimental design to computational execution and commercial product delivery. Over the past decade, engineered dozens of Nextflow pipelines, automated reporting via RMarkdown, and identified dozens of DNA methylation and RNA cancer markers for novel diagnostic products. Recipient of a 2024 Annual Employee Award for cross-functional scientific leadership and dedicated mentorship of junior scientists.

Technical Skills

• Cloud & Pipeline Infrastructure: Nextflow, AWS (Batch, EC2, S3, SageMaker, Athena), Docker, GitHub Actions (CI/CD), Slurm, Databricks, DNAnexus, Git.
• Programming & Data Engineering: R, Python, SQL, Linux, C, Perl, Groovy, Pandas, NumPy, Apache Arrow, DuckDB, Sparklyr, Parquet.
• Biostatistics & Machine Learning: Classical statistical testing, ElasticNet regression, random forests, SVM, neural networks, Scikit-learn, TensorFlow.
• Bioinformatics: DESeq2, edgeR, Seurat, Cell Ranger, GATK, SnpEff, bismark, bcftools, STAR, Bedtools, Leafcutter, DEXSeq, PAML, MEGA.
• Genomic Databases: TCGA, GTEx, DepMap, CCLE, GEO, COSMIC, ClinVar, MSigDB, gnomAD, ENSEMBL, UCSC, dbSNP.
• Data Visualization: RMarkdown, ggplot2, Shiny, Streamlit, Jupyter, Plotly, Pkgdown, Confluence.
• Generative & Agentic AI: Agentic AI frameworks, Model Context Protocol (MCP), RAG, Claude Code, GitHub Copilot, AWS Bedrock, ChatGPT, Gemini, Perplexity.
• Domain Expertise & Assays: Epigenomics, cancer diagnostics, liquid biopsy, RNA regulation, WGS, WGBS, RNA-seq, ChIP-seq, hybrid capture, CLIA/CAP/IVD.

Professional Experience

Exact Sciences (now Abbott)

San Diego, CA

Staff Bioinformatics Scientist · March 2026–September 2026

• Drove departmental research forward through strategic planning, pipeline architecture, technical analysis oversight, and AI adoption.
• Spearheaded cancer biomarker discovery across FFPE, liquid biopsy, and stool samples using DNA fragmentomics and RNA expression/splicing profiles.
• Applied AI workflows to shorten programming cycles by 50%, drive ideation, and enhance predictive modeling.

Senior Bioinformatics Scientist · April 2023–February 2026

• Discovered dozens of DNA methylation cancer biomarkers via integrative analysis of blood and tissue data from hundreds of samples, enabling commercial product development.
• Advanced departmental goals by building dozens of pipelines and RMarkdown reporting templates, reducing analysis time by 70%.
• Built a machine learning model utilizing blood-derived RNA biomarkers, achieving an AUC of 0.7.
• Built custom R Shiny and Streamlit apps, enabling 15 lab scientists to self-serve pipeline execution and result visualization.
• Drove seamless collaboration across DevOps, wet-lab scientists, and bioinformaticians through goal alignment, reproducible analyses, and effective communication.

Zymo Research Corp.

Bioinformatics Scientist · March 2017–February 2023 · Irvine, CA

• Co-developed commercial NGS assays (PicoMethyl, ATAC-seq, cfDNA) by leading tailored bioinformatics analyses, earning a Team Excellence Award.
• Boosted liquid biopsy diagnostic performance by estimating cell-type compositions via DNA-methylation-based deconvolution.
• Engineered scalable Nextflow pipelines on AWS for omics data, shortening turnaround times and ensuring reproducibility.
• Upskilled junior team members through technical training, scientific guidance, and hands-on practice.

University of Rochester

Postdoctoral Research Associate · May 2014–March 2017 · Rochester, NY

• Advanced X-linked gene translation understanding by discovering slower translation despite more use of optimal codons (MBE).
• Advanced aneuploidy understanding by discovering novel translational compensation using multi-omic analysis (NAR).
• Expedited gene expression analysis by developing an RNAseq pipeline and deploying to a Slurm HPC cluster.

Pennsylvania State University

Postdoctoral Scholar · November 2009–April 2014 · State College, PA

• Informed virus outbreak prevention by retracing H7N9/H6N1 origin using phylogenetic analysis of genomic sequences.
• Published three peer-reviewed papers on the distinct impacts of nonsense-mediated mRNA decay, alternative splicing, and microRNAs on gene regulation and evolution.
• Quantified the impact of fluctuating natural selection on human genetic variations using population genomics models.

Education

• Ph.D. in Genetics (Bioinformatics) — Shanghai Institutes for Biological Sciences, Chinese Academy of Science · Shanghai, China · 2004–2009.
• B.S. in Biotechnology — Nanjing University · Nanjing, China · 2000–2004.

Awards and Scholarships

Technical Projects

• Technical knowledge base — Technical knowledge recorded in my blog.
• Nextflow dashboard — Shiny app tracking Nextflow pipeline execution.
• PDF database builder — Automated parsing of PDF papers into searchable databases.
• Programming learning notes — Curated code references, snippets, and tips.
• Agent skills — Verified AI workflows to accelerate daily work.
• MCP servers — Model Context Protocol servers for DevOps.

Certificates and Trainings

Talks and Posters