The overall mission of the Biodata Mining and Discovery Section is to assist and to participate in biomedical research with Data Science and Bioinformatics approaches in support of the ultimate research goals of the NIAMS IRP.

We are currently integrating NGS data processing and data analysis related computational methods into a wide range of biological and biomedical studies, focusing on WES, ChIP-Seq, ATAC-Seq, RNA-Seq, and Single Cell RNA-Seq based research projects.

We also develop new data analysis strategies and customized computational solutions, and conduct research to evaluate emerging methods and techniques in the rapidly evolving field of applied bioinformatics and computational biology.


Since 2015, our team accomplished the following:

  • Provided bioinformatics support to over 160 researchers from 47 different labs
  • Processed and analyzed NGS data from more than 15,000 samples
  • Co-authored 58 research publications
  • Provided one-on-one data analysis training and mentoring to more than 70 researcher


The tools and utilities listed below have been developed by our team to support the ongoing research of the NIAMS.

PAPST (Peak Assignment and Profile Search Tool)
A Java desktop program for both gene centric and peak centric ChIP-Seq and ATAC-Seq data analysis. Learn more about the program.
DNA-Seq/Mutational data analysis pipeline.
A genetics data analysis pipeline, initially developed and used in a paper published in the New England Journal of Medicine.
ChIP-Seq data analysis pipeline
A Snakemake pipeline for fundamental ChIP-Seq data analysis including trimming, mapping, peak calling, and bigWig file generation for data visualization.
ATAC-Seq data analysis pipeline
A customized Snakemake pipeline for ATAC-Seq data analysis, initially developed and implemented for analyzing data in a paper published in Cell.
RNA-Seq data analysis pipeline
A Snakemake pipeline for fundamental RNA-Seq data analysis including trimming, mapping, PCR effect assessment, and gene expression value calculation.
scRNA-Seq data analysis pipeline
A Cell Ranger based pipeline for 10x genomics single cell data processing and analysis, initially implemented for analyzing data in a paper published in Nature Immunology.
CITE-Seq data analysis pipeline
A Cell Ranger based pipeline implemented for customized CITE-Seq data processing and analysis.
HiC data analysis pipeline
A JUICER based pipeline that performs PE read alignment, data filtering, data binning, and data normalization.
Bi-Seq data analysis pipeline
A Bismark package based pipeline for DNA methylation data analysis.
Enrichr based pathway analysis R code
An R code that facilitates Enrichr based pathway analysis and visualization.

In the Lab with NIAMS

This group facilitates biomedical research to support scientists and their discoveries. The facility uses computational and bioinformatics approaches to assist with data analysis.

Core Research Facilities

Labs at the NIAMS are supported by the following state-of-the-art facilities and services:

Image & Media Gallery

Scientific Publications

Selected Recent Publications

A central role for STAT5 in the transcriptional programing of T helper cell metabolism.

Villarino AV, Laurence AD, Davis FP, Nivelo L, Brooks SR, Sun HW, Jiang K, Afzali B, Frasca D, Hennighausen L, Kanno Y, O'Shea JJ
Sci Immunol.
2022 Nov 25;
doi: 10.1126/sciimmunol.abl9467
PMID: 36427325

MicroRNA-221 and -222 modulate intestinal inflammatory Th17 cell response as negative feedback regulators downstream of interleukin-23.

Mikami Y, Philips RL, Sciumè G, Petermann F, Meylan F, Nagashima H, Yao C, Davis FP, Brooks SR, Sun HW, Takahashi H, Poholek AC, Shih HY, Afzali B, Muljo SA, Hafner M, Kanno Y, O'Shea JJ
2021 Mar 9;
doi: 10.1016/j.immuni.2021.02.015
PMID: 33657395

BACH2 enforces the transcriptional and epigenetic programs of stem-like CD8(+) T cells.

Yao C, Lou G, Sun HW, Zhu Z, Sun Y, Chen Z, Chauss D, Moseman EA, Cheng J, D'Antonio MA, Shi W, Shi J, Kometani K, Kurosaki T, Wherry EJ, Afzali B, Gattinoni L, Zhu Y, McGavern DB, O'Shea JJ, Schwartzberg PL, Wu T
Nat Immunol.
2021 Mar;
doi: 10.1038/s41590-021-00868-7
PMID: 33574619

FoxO maintains a genuine muscle stem-cell quiescent state until geriatric age.

García-Prat L, Perdiguero E, Alonso-Martín S, Dell'Orso S, Ravichandran S, Brooks SR, Juan AH, Campanario S, Jiang K, Hong X, Ortet L, Ruiz-Bonilla V, Flández M, Moiseeva V, Rebollo E, Jardí M, Sun HW, Musarò A, Sandri M, Del Sol A, Sartorelli V, Muñoz-Cánoves P
Nat Cell Biol.
2020 Nov;
doi: 10.1038/s41556-020-00593-7
PMID: 33106654

Rapid Enhancer Remodeling and Transcription Factor Repurposing Enable High Magnitude Gene Induction upon Acute Activation of NK Cells.

Sciumè G, Mikami Y, Jankovic D, Nagashima H, Villarino AV, Morrison T, Yao C, Signorella S, Sun HW, Brooks SR, Fang D, Sartorelli V, Nakayamada S, Hirahara K, Zitti B, Davis FP, Kanno Y, O'Shea JJ, Shih HY
2020 Oct 13;
doi: 10.1016/j.immuni.2020.09.008
PMID: 33010223

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
Proc Natl Acad Sci U S A.
2020 Jul 14;
doi: 10.1073/pnas.2003603117
PMID: 32601182

Distinct interferon signatures and cytokine patterns define additional systemic autoinflammatory diseases.

de Jesus AA, Hou Y, Brooks S, Malle L, Biancotto A, Huang Y, Calvo KR, Marrero B, Moir S, Oler AJ, Deng Z, Montealegre Sanchez GA, Ahmed A, Allenspach E, Arabshahi B, Behrens E, Benseler S, Bezrodnik L, Bout-Tabaku S, Brescia AC, Brown D, Burnham JM, Caldirola MS, Carrasco R, Chan AY, Cimaz R, Dancey P, Dare J, DeGuzman M, Dimitriades V, Ferguson I, Ferguson P, Finn L, Gattorno M, Grom AA, Hanson EP, Hashkes PJ, Hedrich CM, Herzog R, Horneff G, Jerath R, Kessler E, Kim H, Kingsbury DJ, Laxer RM, Lee PY, Lee-Kirsch MA, Lewandowski L, Li S, Lilleby V, Mammadova V, Moorthy LN, Nasrullayeva G, O'Neil KM, Onel K, Ozen S, Pan N, Pillet P, Piotto DG, Punaro MG, Reiff A, Reinhardt A, Rider LG, Rivas-Chacon R, Ronis T, Rösen-Wolff A, Roth J, Ruth NM, Rygg M, Schmeling H, Schulert G, Scott C, Seminario G, Shulman A, Sivaraman V, Son MB, Stepanovskiy Y, Stringer E, Taber S, Terreri MT, Tifft C, Torgerson T, Tosi L, Van Royen-Kerkhof A, Wampler Muskardin T, Canna SW, Goldbach-Mansky R
J Clin Invest.
2020 Apr 1;
doi: 10.1172/JCI129301
PMID: 31874111

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
Nat Immunol.
2019 Jul;
doi: 10.1038/s41590-019-0403-4
PMID: 31209400

Novel Inter-omic Analysis Reveals Relationships Between Diverse Gut Microbiota and Host Immune Dysregulation in HLA-B27-Induced Experimental Spondyloarthritis.

Gill T, Brooks SR, Rosenbaum JT, Asquith M, Colbert RA
Arthritis Rheumatol.
2019 Nov;
doi: 10.1002/art.41018
PMID: 31216122

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
Mol 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
Proc Natl Acad Sci U S A.
2019 Dec 10;
doi: 10.1073/pnas.1908576116
PMID: 31754025

SOX2 Epidermal Overexpression Promotes Cutaneous Wound Healing via Activation of EGFR/MEK/ERK Signaling Mediated by EGFR Ligands.

Uchiyama A, Nayak S, Graf R, Cross M, Hasneen K, Gutkind JS, Brooks SR, Morasso MI
J Invest Dermatol.
2019 Aug;
doi: 10.1016/j.jid.2019.02.004
PMID: 30772301

Inactivating Mutation in IRF8 Promotes Osteoclast Transcriptional Programs and Increases Susceptibility to Tooth Root Resorption.

Thumbigere-Math V, Foster BL, Bachu M, Yoshii H, Brooks SR, Coulter A, Chavez MB, Togi S, Neely AL, Deng Z, Mansky KC, Ozato K, Somerman MJ
J Bone Miner Res.
2019 Jun;
doi: 10.1002/jbmr.3690
PMID: 30840779

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

Melorheostotic Bone Lesions Caused by Somatic Mutations in MAP2K1 Have Deteriorated Microarchitecture and Periosteal Reaction.

Fratzl-Zelman N, Roschger P, Kang H, Jha S, Roschger A, Blouin S, Deng Z, Cabral WA, Ivovic A, Katz J, Siegel RM, Klaushofer K, Fratzl P, Bhattacharyya T, Marini JC
J Bone Miner Res.
2019 May;
doi: 10.1002/jbmr.3656
PMID: 30667555

The skin transcriptome in hidradenitis suppurativa uncovers an antimicrobial and sweat gland gene signature which has distinct overlap with wounded skin.

Coates M, Mariottoni P, Corcoran DL, Kirshner HF, Jaleel T, Brown DA, Brooks SR, Murray J, Morasso MI, MacLeod AS
PLoS One.
doi: 10.1371/journal.pone.0216249
PMID: 31059533

News & Highlights