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 at the University of Texas MD Anderson Cancer Center, where I work with Dr. Arjun Bhattacharya and Dr. Paul Scheet. A central challenge in human genetics is connecting genetic variation to molecular function and phenotype: most trait-associated loci remain mechanistically unresolved, in part because standard analyses aggregate expression across all transcripts of a gene, masking regulatory effects that act on individual isoforms. My research program closes this gap by building variant-to-function frameworks at isoform resolution, premised on the idea that regulatory variation acts at the level of individual transcripts, in specific cell types, developmental windows, and environmental contexts. I focus on human development, when gene regulation is most dynamic, most environmentally sensitive, and most consequential for lifelong health, and my primary system is the placenta, the interface of maternal-fetal communication and the conduit through which intrauterine exposures shape offspring phenotypes.

My program integrates three directions. First, I study how prenatal environmental exposures disrupt placental gene regulation to program development. I led the first placenta-specific long-read transcriptome reference, uncovering 14,985 novel isoforms absent from standard annotations, and I co-coordinate a multi-ancestry placental xQTL atlas harmonizing 2,222 placentas from nine international birth cohorts and four ancestry groups, mapping how gestational diabetes, maternal obesity, and PFAS exposure modify fetal genetic control of isoform expression and splicing, and testing whether disruption of parent-of-origin (imprinted) transcription links these exposures to offspring neurodevelopment. Second, I am developing family-based designs in large genotyped trio cohorts to decompose maternal indirect versus direct fetal genetic effects on childhood disease, including cancer. Third, I investigate the evolutionary origins and disease relevance of placental gene regulation, including the imprinting and transposable-element control shaped by intragenomic conflict, a throughline from my Ph.D. work on parent-of-origin effects in social insects.

My methods work gives these observational analyses a principled, testable basis for causal claims under unmeasured confounding. I developed ICONIC, an open-source R package that unifies genetic instrumental variables and negative-control calibration for causal mediation analysis of multi-omics data, stress-testing estimators across complementary confounding-control strategies with diagnostics calibrated to real omics covariance. 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
Overview of my research program: evolutionary-developmental origins of health and disease
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 )
ICONIC: An R Package for Integrating Instrumental Variable- and Negative-Control-Informed Causal Discovery and Diagnostics in Multiomic Studies
ICONIC: An R Package for Integrating Instrumental Variable- and Negative-Control-Informed Causal Discovery and Diagnostics in Multiomic Studies

Sean T. Bresnahan, Charis Xiong, Taylor Head, Yung-Han Chang, Arjun Bhattacharya, Jonathan Y Huang

medRxiv 2026 ; Preprint

ICONIC: An R Package for Integrating Instrumental Variable- and Negative-Control-Informed Causal Discovery and Diagnostics in Multiomic Studies

Sean T. Bresnahan, Charis Xiong, Taylor Head, Yung-Han Chang, Arjun Bhattacharya, Jonathan Y Huang

medRxiv 2026 ; Preprint

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