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Sheng'en Shawn Hu, PhD

Sheng'en Shawn Hu, PhD

Assistant Professor, Public Health Sciences

Primary Phone Number
434.924.8430
Email
[email protected]

Bio & Overview

Sheng’en Shawn Hu, Ph.D., is an Assistant Professor of Genome Sciences since 2024. He has a training background in computational biology and expertise in modeling next-generation DNA sequencing data at bulk, single-cell, and spatial levels to understand how human cells are developed and regulated. He also investigates the machinery of gene regulation by analyzing super-resolution microscopy data. His work has contributed to understanding a wide range of subjects in molecular immunology, such as how the immune system responds to threats, how cancer develops and interacts with immunotherapy, and how immune cells function during lung COVID-19 infections. He continues to innovate new methods that use various high-throughput data to deepen our understanding of molecular biology and immunology. 

Google Scholar: https://scholar.google.com/citations?user=JwXm75kAAAAJ

 

Academic Information

Department
Public Health Sciences

Primary Education

  • Ph.D, undefinedTongji University, 2017

Other Affiliations

  • Genomic Sciences

Research Interests

Computational biology, Bioinformatics, Cancer immune therapy, Chimeric antigen receptor (CAR) T-cell therapy, Cancer epigenetics, Method development, Single-cell Genomics, Transcriptional regulation, Chromatin accessibility

Research Disciplines

  • Bioinformatics and Genomics
  • Biology
  • Cancer Biology
  • Computational Biology
  • Genetics
  • Immunology

Selected Publications

SELECTED PUBLICATIONS

  1. Zhao X*, Hu SS*, Zakrzewski JL, Mi Q, Rosenstein RK, Zang C, Ma X, Xue HH. Single-cell multiomics identifies Tcf1 and Lef1 as key initiators of early thymic progenitor fate. Science Immunology. 2025 Sep 12;10(111). PMID: 40938954.
  2. Hu SS, Xue HH, Zang C. IGN: Invariable gene set-based normalization for chromatin accessibility profile data analysis. Computational and Structural Biotechnology Journal. 2025. Volume 27, 501-507. PMID: 39931505.
  3. Narasimhan H*, Cheon IS*, Qian W*, Hu SS*, Parimon T, Li C, Goplen N, Wu Y, Wei X, Son YM, Fink E, de Almeida Santos G, Tang J, Yao C, Muehling L, Canderan G, Kadl A, Cannon A, Young S, Hannan R, Bingham G, Arish M, Sen Chaudhari A, Im JS, Mattingly CLR, Pramoonjago P, Marchesvsky A, Sturek J, Kohlmeier JE, Shim YM, Woodfolk J, Zang C, Chen P, Sun J. An aberrant immune-epithelial progenitor niche drives viral lung sequelae. Nature. 2024 Sep 4. PMID: 39232171.
  4. Zhao X, Hu W, Park SR, Zhu S, Hu SS, Zang C, Peng W, Shan Q, Xue HH. The transcriptional cofactor Tle3 reciprocally controls effector and central memory CD8+ T cell fates. Nat Immunol. 2024 Feb;25(2):294-306. PMID: 38238608.
  5. Baquero DP, Cvirkaite-Krupovic V, Hu SS, Fields JL, Liu X, Rensing C, Egelman EH, Krupovic M, Wang F. Extracellular cytochrome nanowires appear to be ubiquitous in prokaryotes. Cell. 2023 Jun 22;186(13):2853-2864.e8. PMID:37290436.
  6. Hu SS, Liu L, Li Q, Ma W, Guertin MJ, Meyer CA, Deng K, Zhang T, Zang C. Accurate estimation of intrinsic biases for improved analysis of chromatin accessibility sequencing data using SELMA. Nature Communications 13, 5533 (2022). PMID: 36130957.
  7. Turner AW*, Hu SS* (* co-first author), Mosquera JV, Ma W, Hodonsky CJ, Wong D, Auguste G, Sol-Church K, Farber E, Kundu Soumya, Kundaje A, Chang P, Lopez NG, Ma L, Ghosh S, Onengut-Gumuscu S, Ashley EA, Quertermous T, Finn AV, Leeper NJ, Kovacic JC, Björkgren JLM, Zang C, Miller CL. Single-cell chromatin landscape of human coronary artery resolves regulatory mechanisms of disease risk. Nature Genetics 54, 804–816 (2022) PMID: 35590109.
  8. Shan Q*, Hu SS* (*co-first author), Chen X, Badovinac VP, Zang C, Xue HH. Tcf1 preprograms glycolysis mobilization in central memory CD8+ T cells in recall response. Nature Immunology 23, 386–398 (2022). PMID: 35190717.
  9. Smith RJ*, Zhang H*, Hu SS* (*co-first author), Yung T, Francis R, Lee L, Onaitis MW, Dirks PB, Zang C, Kim T. Single-cell chromatin profiling of the primitive gut tube reveals regulatory dynamics underlying lineage fate decisions. Nature Communications 13, 2965 (2022). PMID: 35618699.
  10. Shan Q, Hu S*, Chen X, et al. Ectopic Tcf1 expression instills a stem-like program in exhausted CD8+ T cells to enhance viral and tumor immunity. Cell & Molecular Immunology. 2020
  11. Hu S*, Huo D*, Yu Z*, Chen Y*, Liu J, Liu L, Wu X$, Zhang Y$. ncHMR detector: a computational framework to systematically reveal non-classical functions of histone modification regulators. Genome Biology2020; 21: 48.
  12. Liu G*, Wang W*, Hu S*, Wang X, Zhang Y. Inherited DNA methylation primes the establishment of accessible chromatin during genome activation. Genome Research. 2018 May 29; 28: 998-1007.
  13. Huo X*, Hu S*, Zhao C, Zhang Y. Dr.seq: a quality control and analysis pipeline for droplet sequencing. Bioinformatics. 2016 Jul 15;32(14):2221-3.
  14. He HH*, Meyer CA*, Hu SS*, Chen MW, Zang C, Liu Y, Rao PK, Fei T, Xu H, Long H, Liu XS, Brown M. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification. Nature Methods. 2014 Jan;11(1):73-8.

* co-first authors