Portrait
Sean T. Bresnahan
Associate Data Scientist
Department of Epidemiology
MD Anderson Cancer Center
About Me

I am a computational and molecular geneticist and an Associate Data Scientist in the Department of Epidemiology and the Institute for Data Science in Oncology at the University of Texas MD Anderson Cancer Center, where I work with Dr. Arjun Bhattacharya and Dr. Paul Scheet. My research asks how early-life environmental exposures act through the genome, often through parent-of-origin and imprinting mechanisms, to shape lifelong disease risk. I first pursued this in evolutionary genomics, studying intragenomic conflict and gene-by-environment effects in social insects during my Ph.D., and I now study it in human placental biology, where the same conflict between parental genomes plays out in the tissue that governs fetal development.

My current program builds isoform-resolved maps of placental gene regulation and uses them to explain how genotype and prenatal exposure jointly program offspring health. Using long-read RNA sequencing, I assembled the largest placental transcriptome to date, uncovering 14,985 novel isoforms of known genes that are absent from standard adult-tissue annotations. On that foundation I am constructing the first multi-ancestry, isoform-resolved placental GxE-xQTL atlas across roughly 2,200 placentas from nine cohorts and five ancestry groups, mapping how gestational diabetes, pre-pregnancy obesity, and PFAS exposure modify fetal genetic control of isoform expression, splicing, and alternative transcript usage. This spans cis-xQTL mapping within and across ancestries, cross-ancestry fine-mapping and colocalization with childhood metabolic GWAS, locus-resolved heritability partitioning, and decomposition of genetic signals into direct fetal versus maternal indirect polygenic components. I also model parent-of-origin regulation and its disruption by exposure, accounting for somatic mosaicism in the placenta.

Much of my methods work makes these observational analyses causal. I develop mediation frameworks that combine genetically predicted expression as instruments with multi-omic negative controls, using generative adversarial networks to calibrate confounding bias, released in the open-source ICONIC R package. Alongside this, I run an independent bioinformatics consulting practice, evaluating therapeutic targets through pan-cancer TCGA and DepMap CRISPR analyses. I am currently seeking tenure-track Assistant Professor positions.

Curriculum Vitae
Education
  • The Pennsylvania State University
    Ph.D., Molecular, Cellular, and Integrative Biosciences
    2024
  • University of Nebraska at Omaha
    B.S., Neuroscience
    2019
Experience
  • MD Anderson Cancer Center
    Associate Data Scientist
    2024 - present
  • Vindhya Data Science
    Bioinformatics Data Science Contractor
    2026 - present
  • Merck & Co.
    Data & AI / Genome Sciences Intern
    2024
  • The Pennsylvania State University
    NSF Graduate Research Fellow
    2019 - 2024
Skills
  • Molecular & Laboratory: Nucleic-acid extraction & QC, PCR / qPCR, CRISPR/Cas9, RNAi, bacterial culture, ChIP, ATAC, sequencing library preparation, Illumina & Oxford Nanopore sequencing
  • Computational: Advanced: R (incl. package development), Bash, HPC, AWS. Intermediate: Python, MATLAB, C++
Selected Publications (view all )
Long-read transcriptome assembly reveals vast transcriptional complexity in the placenta associated with metabolic and endocrine function
Long-read transcriptome assembly reveals vast transcriptional complexity in the placenta associated with metabolic and endocrine function

Sean T. Bresnahan, Hannah Yong, William H. Wu, Sierra Lopez, Jerry K. Y. Chan, Fergus White, Pierre-Étienne Jacques, Marie-France Hivert, Shiao-Yng Chan, Michael I. Love, Jonathan Y. Huang, Arjun Bhattacharya

Nature Communications 2026

Long-read transcriptome assembly reveals vast transcriptional complexity in the placenta associated with metabolic and endocrine function

Sean T. Bresnahan, Hannah Yong, William H. Wu, Sierra Lopez, Jerry K. Y. Chan, Fergus White, Pierre-Étienne Jacques, Marie-France Hivert, Shiao-Yng Chan, Michael I. Love, Jonathan Y. Huang, Arjun Bhattacharya

Nature Communications 2026

Natural variation in transplacental transfer efficiency exposes distinct transcriptional network architectures of PFAS effects on birth weight and gestational age
Natural variation in transplacental transfer efficiency exposes distinct transcriptional network architectures of PFAS effects on birth weight and gestational age

Sean T. Bresnahan, Hannah E. J. Yong, Martin G. Drelichman, Sarah N. Campbell, Anna E. Trapse, Gabriela R. Romo, Christina M. Cellini, Sierra Lopez, Jerry K. Yen Chan, Shiao-Yng Chan, Elana R. Elkin, Arjun Bhattacharya, Jonathan Y. Huang

bioRxiv 2026 ; in revision at Environmental Health Perspectives Preprint

Natural variation in transplacental transfer efficiency exposes distinct transcriptional network architectures of PFAS effects on birth weight and gestational age

Sean T. Bresnahan, Hannah E. J. Yong, Martin G. Drelichman, Sarah N. Campbell, Anna E. Trapse, Gabriela R. Romo, Christina M. Cellini, Sierra Lopez, Jerry K. Yen Chan, Shiao-Yng Chan, Elana R. Elkin, Arjun Bhattacharya, Jonathan Y. Huang

bioRxiv 2026 ; in revision at Environmental Health Perspectives Preprint

Improving isoform-level eQTL and integrative genetic analyses of breast cancer risk with long-read RNA transcript assemblies
Improving isoform-level eQTL and integrative genetic analyses of breast cancer risk with long-read RNA transcript assemblies

S. Taylor Head, Aryun Nemani, Yung-Han Chang, Tabitha A. Harrison, Sean T. Bresnahan, Joseph H. Rothstein, Weiva Sieh, Sara Lindström, Arjun Bhattacharya

bioRxiv 2026 ; in revision at Nature Genetics Preprint

Improving isoform-level eQTL and integrative genetic analyses of breast cancer risk with long-read RNA transcript assemblies

S. Taylor Head, Aryun Nemani, Yung-Han Chang, Tabitha A. Harrison, Sean T. Bresnahan, Joseph H. Rothstein, Weiva Sieh, Sara Lindström, Arjun Bhattacharya

bioRxiv 2026 ; in revision at Nature Genetics Preprint

Quantification method affects replicability of eQTL analysis, colocalization, and TWAS
Quantification method affects replicability of eQTL analysis, colocalization, and TWAS

S. Taylor Head, Sean T. Bresnahan, Nolan Cole, William Wu, Arjun Bhattacharya

bioRxiv 2025 ; in revision at Nature Genetics Preprint

Quantification method affects replicability of eQTL analysis, colocalization, and TWAS

S. Taylor Head, Sean T. Bresnahan, Nolan Cole, William Wu, Arjun Bhattacharya

bioRxiv 2025 ; in revision at Nature Genetics Preprint

Isoform-level analyses of 6 cancers uncover extensive genetic risk mechanisms undetected at the gene level
Isoform-level analyses of 6 cancers uncover extensive genetic risk mechanisms undetected at the gene level

Yung-Han Chang, Sean T. Bresnahan, S. Taylor Head, Tabitha Harrison, Yao Yu, Chad D. Huff, Bogdan Pasaniuc, Sara Lindström, Arjun Bhattacharya

British Journal of Cancer, 133, 874-885. 2025

Isoform-level analyses of 6 cancers uncover extensive genetic risk mechanisms undetected at the gene level

Yung-Han Chang, Sean T. Bresnahan, S. Taylor Head, Tabitha Harrison, Yao Yu, Chad D. Huff, Bogdan Pasaniuc, Sara Lindström, Arjun Bhattacharya

British Journal of Cancer, 133, 874-885. 2025

All publications