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.
Sean T. Bresnahan, Charis Xiong, Taylor Head, Yung-Han Chang, Arjun Bhattacharya, Jonathan Y Huang
medRxiv 2026 ; Preprint
Sean T. Bresnahan, Charis Xiong, Taylor Head, Yung-Han Chang, Arjun Bhattacharya, Jonathan Y Huang
medRxiv 2026 ; Preprint

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
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

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
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

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
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

S. Taylor Head, Sean T. Bresnahan, Nolan Cole, William Wu, Arjun Bhattacharya
bioRxiv 2025 ; in revision at Nature Genetics Preprint
S. Taylor Head, Sean T. Bresnahan, Nolan Cole, William Wu, Arjun Bhattacharya
bioRxiv 2025 ; in revision at Nature Genetics Preprint

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
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