Zachary Rodriguez, PhD — Genomics & Clinical Informatics

About Me

Hi, I'm Zach — a biologist, computing enthusiast, and geneticist.

I'm currently a Senior Bioinformatician at the Penn Medicine Biobank (PMBB), where I lead genomic pipeline development and data operations across the Setia-Verma, Verma, and Drivas labs at the Perelman School of Medicine, University of Pennsylvania. I completed my PhD at the Museum of Natural Science, Louisiana State University, investigating the genomic underpinnings of green-blooded lizards using phylogenomics and transcriptomics, followed by a postdoc in computational psychopathology analyzing digital phenotypes of serious mental illness.

I'm interested in integrating genomic, clinical EHR, and diverse demographic datasets to study the causes and treatments of human disease.

GitHub Google Scholar LinkedIn ORCID Resume

Projects

Clinical Informatics

PMBB Geno-Pheno Toolkit

Lead developer of a modular Nextflow suite for cross-biobank association analyses — GWAS, ExWAS, PheWAS, meta-analysis, and LD-based variant prioritization — benchmarked on PMBB (56K+ samples, 164M+ variants) and All of Us across local HPC, AWS, Azure, and GCP.

PMBB Geno Pheno Toolkit →

Rodriguez, Guare, Cardone, Carson, Caruth & Verma. PMBB Geno-Pheno Toolkit: A suite of scalable, reproducible pipelines for cross-biobank association analyses. Bioinformatics (under review). · Verma, Rodriguez, Guare, Cardone & Carson (2024). Command line to pipeLine: Cross-biobank analyses with Nextflow. PSB 2025 Proceedings, 696–701.

Nextflow GWAS ExWAS PheWAS AWS/GCP

PSB 2025 Workshop →

Clinical Informatics

Biobank Rare Variant (BRaVa) Consortium

Contributed PMBB data and analysis to a global, gene-based meta-analysis of rare coding variation across 10 biobanks (1.2M+ individuals, diverse ancestries), 33 clinical endpoints, and 11 quantitative traits — identifying 514 gene-trait associations, including 31 novel.

Palmer, Hill, Hodgson, et al., Rodriguez, et al., Verma, Zhou, Karczewski, Lindgren & Neale, for BRaVa (2026). medRxiv.

ExWAS Rare Variant Multi-ancestry Consortium

Preprint →

Clinical Informatics

Allostatic Load & Health Outcomes

Examining the impact of physiological burden on health outcomes using biobank-linked electronic health records, quantifying allostatic load as a composite marker of chronic stress exposure.

Rodriguez, Okeh, Drivas & Setia-Verma (2024). Bearing the Load. Department of Medicine Research Day, University of Pennsylvania.

EHR Biobank Clinical

Machine Learning & LLM

Undiagnosed Patient Project

Using agentic AI to identify undiagnosed patients within PMBB by scanning structured EHR data and unstructured clinician note summaries for diagnostic signal missed by conventional phenotyping.

LLM Agentic AI EHR NLP

Machine Learning & LLM

LLM-Based Psychometric Evaluation

Built NLP/ML pipelines to extract discussion topics and psychometric signal from ambulatory patient speech in schizophrenia and serious mental illness, informing frameworks for evaluating language-based clinical assessments and psychomotor slowing.

Cohen, Rodriguez, et al. (2022). Natural language processing and psychosis. Schizophrenia Bulletin. · Cowan, Rodriguez, et al. (2022). Talking about health. Behavioral Sciences. · Foltz, Chandler, Diaz-Asper, Cohen, Rodriguez, et al. (2022). Reflections on the nature of measurement. Schizophrenia Research. · Cohen, Rodriguez, et al. (2024). Evaluating speech latencies. Psychiatry Research.

NLP ML Clinical Schizophrenia

Machine Learning & LLM

Multimodal & Facial Affect Analysis

Developed computer-vision pipelines to objectively quantify blunted facial affect and paranoia-related digital phenotypes from video in serious mental illness research.

Cowan, Rodriguez, Strauss, Raugh & Cohen (2024). Computerized analysis of facial expression. Eur Arch Psychiatry Clin Neurosci. · Cohen, Rodriguez & Warren (2022). Developing a Multimodal Digital Phenotyping Paranoia Measure. ISCTM.

Computer Vision Multimodal Digital Phenotyping

Evolution & Comparative Genomics

Evolution of Green Blood in Lizards

PhD dissertation research uncovering multiple independent origins of green (biliverdin-based) blood in New Guinea lizards through phylogenomics and comparative genomics. Coverage by NPR, The Atlantic, AP, and Science News.

Rodriguez, Perkins & Austin (2018). Multiple origins of green blood in New Guinea lizards. Science Advances, 4(5), eaao5017. · Rodriguez (2020). Evolution of Green Blood in New Guinea Lizards [Doctoral Dissertation], LSU.

Phylogenomics Comparative Genomics NGS

Science Advances →

Evolution & Comparative Genomics

Evolution of the Albumin Protein Family in Reptiles

Co-authored analysis of albumin gene family evolution across reptiles, tracing duplication and diversification patterns tied to physiological adaptation.

Broussard, Rodriguez & Austin (2022). Evolution of the albumin protein family in reptiles. Molecular Phylogenetics and Evolution, 169, 107435.

Comparative Genomics Evolutionary Biology

Skills

Programming & Infrastructure

Python R Bash/Shell SQL Nextflow Snakemake Docker Singularity Git SLURM/PBS

Cloud & DevOps

AWS Azure Google Cloud Databricks CI/CD HPC

Clinical Informatics & Genomics

GWAS ExWAS PheWAS GSEA TWAS PLINK SAIGE VEP EHR / HIPAA IRB Compliance

Statistics & Machine Learning

Predictive Modeling Bayesian Methods PCA / Clustering NLP LLMs Network Analysis

Soft Skills

Mentorship Scientific Writing Science Communication DEI Advocacy Project Management

Experience

Senior Bioinformatician

2023 – present

Penn Medicine Biobank (PMBB) · Philadelphia, PA

Curate, process, and analyze the annual PMBB release (300K+ participants), integrating phenotype, exome, genotype, imputed, and clinical EHR data across release cycles
Project manager for 5+ genomic research teams; oversee bioinformatics workflows and statistical rigor across the Setia-Verma, Verma, and Drivas labs
Directed development of scalable Nextflow pipelines (GWAS, ExWAS, PheWAS) for 500K+ sample datasets across local HPC and cloud platforms
Manages genomic data requests, cohort queries, and variant-level extractions for researchers without direct database access

Nextflow GWAS Biobank HPC/Cloud Leadership

Postdoctoral Researcher, Computational Mental Health

2020 – 2023

Center for Computation & Technology, Louisiana State University · Baton Rouge, LA

Developed ML and NLP analytical pipelines to predict mental health symptoms from archival clinical data
Supervised the technical side of 5 research projects (statistical frameworks, NLP, ML models), resulting in peer-reviewed publications
Ensured HIPAA- and IRB-compliant data integration across diverse sources; developed EHR data management plans
Collaborated internationally with academic and industry researchers

NLP ML Mental Health HIPAA

NSF Graduate Research Fellow

2014 – 2020

Museum of Natural Science, Louisiana State University · Baton Rouge, LA

Led 3 independent research projects on reptile genomics (green blood, adhesive toe pads, live birth), from study design to publication
Secured $180,000+ in external funding (NSF GRFP, LA-BRIDGE, institutional grants)
Ran HPC jobs (280,000 CPU-hours) analyzing next-generation sequencing data for phylogenomic and comparative-genomic analyses
Disseminated results via Science Advances, NPR, The Atlantic, AP, and more

Phylogenomics NGS HPC Fieldwork

Education

PhD, Ecology, Evolution, & Genetics

2020

Museum of Natural Science, Louisiana State University · Baton Rouge, LA

Dissertation: Evolution of Green Blood in New Guinea Lizards: Phylogenomics, Biogeography, and Comparative Genomics. Advisor: Dr. Christopher Austin.