Dr. Sun received his Ph.D. from The University of Iowa and conducted his post-doc research at Yale University where he solved the X-ray crystal structure of a cytokine (MIF). He is a founding member of four Bioinformatics groups, a co-author of a Medical Bioinformatics textbook, a co-inventor of nine issued patents, and a co-author of two published Java programs for biomedical research (JOINSOLVER & PAPST).

Research Statement

As the institute’s bioinformatics core facility, Biodata Mining and Discovery Section focuses on applying computational approaches of Data Sciences to biomedical research. We also develop and implement computational algorithms and methods mostly used in analyzing NGS data such as those from RNA-Seq, ChIP-Seq, ATAC-Seq, and single cell RNA-Seq.

Scientific Publications

Sex differences in neutrophil biology modulate response to type I interferons and immunometabolism.

Gupta S, Nakabo S, Blanco LP, O'Neil LJ, Wigerblad G, Goel RR, Mistry P, Jiang K, Carmona-Rivera C, Chan DW, Wang X, Pedersen HL, Gadkari M, Howe KN, Naz F, Dell'Orso S, Hasni SA, Dempsey C, Buscetta A, Frischmeyer-Guerrerio PA, Kruszka P, Muenke M, Franco LM, Sun HW, Kaplan MJ
Proceedings of the National Academy of Sciences of the United States of America.
2020 Jul 14;
doi: 10.1073/pnas.2003603117
PMID: 32601182

Single-cell RNA-seq reveals TOX as a key regulator of CD8+ T cell persistence in chronic infection.

Yao C, Sun HW, Lacey NE, Ji Y, Moseman EA, Shih HY, Heuston EF, Kirby M, Anderson S, Cheng J, Khan O, Handon R, Reilley J, Fioravanti J, Hu J, Gossa S, Wherry EJ, Gattinoni L, McGavern DB, O'Shea JJ, Schwartzberg PL, Wu T
Nature immunology.
2019 Jul;
doi: 10.1038/s41590-019-0403-4
PMID: 31209400

The Magnitude of IFN-γ Responses Is Fine-Tuned by DNA Architecture and the Non-coding Transcript of Ifng-as1.

Petermann F, Pękowska A, Johnson CA, Jankovic D, Shih HY, Jiang K, Hudson WH, Brooks SR, Sun HW, Villarino AV, Yao C, Singleton K, Akondy RS, Kanno Y, Sher A, Casellas R, Ahmed R, O'Shea JJ
Molecular cell.
2019 Sep 19;
doi: 10.1016/j.molcel.2019.06.025
PMID: 31377117

Transcriptomic, epigenetic, and functional analyses implicate neutrophil diversity in the pathogenesis of systemic lupus erythematosus.

Mistry P, Nakabo S, O'Neil L, Goel RR, Jiang K, Carmona-Rivera C, Gupta S, Chan DW, Carlucci PM, Wang X, Naz F, Manna Z, Dey A, Mehta NN, Hasni S, Dell'Orso S, Gutierrez-Cruz G, Sun HW, Kaplan MJ
Proceedings of the National Academy of Sciences of the United States of America.
2019 Dec 10;
doi: 10.1073/pnas.1908576116
PMID: 31754025

Retinoic Acid Receptor Alpha Represses a Th9 Transcriptional and Epigenomic Program to Reduce Allergic Pathology.

Schwartz DM, Farley TK, Richoz N, Yao C, Shih HY, Petermann F, Zhang Y, Sun HW, Hayes E, Mikami Y, Jiang K, Davis FP, Kanno Y, Milner JD, Siegel R, Laurence A, Meylan F, O'Shea JJ
2019 Jan 15;
doi: 10.1016/j.immuni.2018.12.014
PMID: 30650370

Argonaute-miRNA Complexes Silence Target mRNAs in the Nucleus of Mammalian Stem Cells.

Sarshad AA, Juan AH, Muler AIC, Anastasakis DG, Wang X, Genzor P, Feng X, Tsai PF, Sun HW, Haase AD, Sartorelli V, Hafner M
Molecular cell.
2018 Sep 20;
doi: 10.1016/j.molcel.2018.07.020
PMID: 30146314

A Muscle-Specific Enhancer RNA Mediates Cohesin Recruitment and Regulates Transcription In trans.

Tsai PF, Dell'Orso S, Rodriguez J, Vivanco KO, Ko KD, Jiang K, Juan AH, Sarshad AA, Vian L, Tran M, Wangsa D, Wang AH, Perovanovic J, Anastasakis D, Ralston E, Ried T, Sun HW, Hafner M, Larson DR, Sartorelli V
Molecular cell.
2018 Jul 5;
doi: 10.1016/j.molcel.2018.06.008
PMID: 29979962

The effects of shared information on semantic calculations in the gene ontology.

Bible PW, Sun HW, Morasso MI, Loganantharaj R, Wei L
Computational and structural biotechnology journal.
doi: 10.1016/j.csbj.2017.01.009
PMID: 28217262

Developmental Acquisition of Regulomes Underlies Innate Lymphoid Cell Functionality.

Shih HY, Sciumè G, Mikami Y, Guo L, Sun HW, Brooks SR, Urban JF Jr, Davis FP, Kanno Y, O'Shea JJ
2016 May 19;
doi: 10.1016/j.cell.2016.04.029
PMID: 27156451

PAPST, a User Friendly and Powerful Java Platform for ChIP-Seq Peak Co-Localization Analysis and Beyond.

Bible PW, Kanno Y, Wei L, Brooks SR, O'Shea JJ, Morasso MI, Loganantharaj R, Sun HW
PloS one.
doi: 10.1371/journal.pone.0127285
PMID: 25970601


University of Iowa, Iowa City, Iowa

University of Toronto, Toronto, Canada


Biodata Mining and Discovery Section, OST, NIAMS, NIH

Senior Staff Scientist, Bioinformatics
Gene Logic Inc.

Staff Scientist, Bioinformatics
Bayer Corporation

Post-doc, Structural Biology
Yale University

Last Updated: July 2020