An official website of the United States government
          Here’s how you know
        Here’s how you know**Official websites use .gov**A
              **.gov** website belongs to an official government
              organization in the United States.
        **Secure .gov websites use HTTPS**A
              **lock** (
              Locked padlock icon) or **https://** means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.
 Top Utility Nav
        
        
        Asian-Language Resources
        
        Portal en español


Site search Mega Menu
  

        

        Home
                  Health Topics
                                      
    
  Health Topics

    Arthritis and Rheumatic Diseases
          
    Muscle and Bone Diseases
          
    Skin Diseases
          
    All Diseases and Conditions
          
    Publication Catalog
                  Grants & Funding
                                      
    
  Grants & Funding

    Current Funding Opportunities
          
    Supported Scientific Programs
          
    NIAMS-Supported Programs
          
    Applying for a Grant
          
    NIH Policies and Guidance
          
    Peer Review and Grants Administration Resources
          
    Types of Funding Mechanisms (Activity Codes)
                  Labs @ NIAMS
                                      
    
  Labs @ NIAMS

    NIAMS Labs and Core Facilities
          
    Research Faculty
          
    Research Areas
          
    NIAMS Scientific Advances
          
    Training and Career Development
                  Clinical Trials
                                      
    
  Clinical Trials
      
            For Principal Investigators

    Clinical Trial Policies, Guidelines, and Templates
          
    Conducting Clinical Trials
          
    Register with ClinicalTrials.gov

For Patients

What is a Clinical Trial?
	Clinical Trials at NIAMS
	Clinical Trials in the Spotlight
                  News & Events
                                      
    
  Newsroom

    All NIAMS News
          
    NIAMS Newsletters
          
    Meetings & Events
                  About NIAMS
                                      
    
  About NIAMS

    Director's Page
          
    NIAMS Organization
          
    Strategic Plan Fiscal Years 2020-2024
          
    Staff Directory
          
    NIAMS Budget
          
    Partnerships
          
    Contact NIAMS
                  Community Outreach
                                      
    
  Community Outreach

    Bone Health
          
    Joint Health
          
    Muscle, Tendon, and Ligament Health
          
    Skin Health
          
    Health Information For Kids And Young Adults
          
    Health Information For Older Adults/Seniors
          
    Printable Materials for Community Events
          
    Resources in Other Languages
          
    Annual Health Observances
          
    Social Media Resources Breadcrumb
    Home
          Labs @ NIAMS
          Office of Science and Technology
          Biodata Mining and Discovery Section








Biodata Mining and Discovery Section


Hong-Wei Sun, Ph.D. FacebookEmailPrintFacebookEmail
        Title image showing data visualizations

      Overview

                                  Staff Scientist
      
  


Hong-Wei Sun, Ph.D.
      
  


            sunh1@mail.nih.gov
                                
            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.

Highlights

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 researcherTools

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:

Biodata Mining and Discovery
	Flow Cytometry
	Genomic Technology
	Laboratory Animal Care and Use
	Light Imaging
	Translational Immunology

                                    Staff
                            
            **Hong-Wei Sun, Ph.D.**Staff Scientistsunh1@mail.nih.gov
    **Stephen Brooks, Ph.D.**Staff Scientiststephen.brooks@nih.gov
    **Vijender Chaitankar, Ph.D.**Research Fellowvijender.chaitankar@nih.gov
    **Zuoming Deng, Ph.D.**Staff Scientistzuoming.deng@nih.gov
    **Kan Jiang, Ph.D.**Staff Scientistjiangk@mail.nih.gov
    **Seol Kyoung Jung, Ph.D.**Staff Scientistjungs3@mail.nih.gov
    **Binod Regmi, Ph.D.**Postdoctoral Fellowbinod.regmi@nih.gov
    **Andrew Uhlman, M.S.**Scientific Data Specialistandrew.uhlman@nih.gov
            
                                                Image & Media Gallery
              
            Integrated analysis of microbiome and transcriptome in Experimental Spondyloarthritis
Integrated analysis of microbiome and transcriptome in Experimental Spondyloarthritis
        ×
      Integrated analysis of microbiome and transcriptome in Experimental Spondyloarthritis
        Gill T et al, *Arthritis & Rheumatology*, 2019
    Transcriptomic, epigenetic, and functional analyses implicate neutrophil diversity in the pathogenesis of systemic lupus erythematosus. (1/3)
Transcriptomic, epigenetic, and functional analyses implicate neutrophil diversity in the pathogenesis of systemic lupus erythematosus. (1/3)
        ×
      PCA: discovery of SLE patient subgrouping
        Key discovery: SLE patients with LDGs can be sub-grouped based on the maturation stage of pathogenic neutrophils.

(This group of three slides are all from this paper illustrating the discovery process)

**1) PCA: discovery of SLE patient subgrouping**

Mistry P et al., *PNAS*, 2019
    Transcriptomic, epigenetic, and functional analyses implicate neutrophil diversity in the pathogenesis of systemic lupus erythematosus. (2/3)
Transcriptomic, epigenetic, and functional analyses implicate neutrophil diversity in the pathogenesis of systemic lupus erythematosus. (2/3)
        ×
      Subgrouping supported by ATAC-Seq & scRNA-Seq
        **Key discovery**: SLE patients with LDGs can be sub-grouped based on the maturation stage of pathogenic neutrophils.

(This group of three slides are all from this paper illustrating the discovery process)

**2) Subgrouping supported by ATAC-Seq & scRNA-Seq**

Mistry P et al., *PNAS*, 2019
    Transcriptomic, epigenetic, and functional analyses implicate neutrophil diversity in the pathogenesis of systemic lupus erythematosus. (3/3)
Transcriptomic, epigenetic, and functional analyses implicate neutrophil diversity in the pathogenesis of systemic lupus erythematosus. (3/3)
        ×
      Novel motif enrichment analysis: each subgroup has uniquely enriched TF motifs.
        **Key discovery**: SLE patients with LDGs can be sub-grouped based on the maturation stage of pathogenic neutrophils.

(This group of three slides are all from this paper illustrating the discovery process)

**3) Novel motif enrichment analysis: each subgroup has uniquely enriched TF motifs.**

Mistry P et al., *PNAS*, 2019
    Discovery of disease-causing somatic mutations on MAP2K1 in Melorheostosis
Discovery of disease-causing somatic mutations on MAP2K1 in Melorheostosis
        ×
      Discovery of disease-causing somatic mutations on MAP2K1 in Melorheostosis
        Deng Z et al., *Nature Communications*, 2018
    Single-cell RNA-seq reveals TOX as a key regulator of CD8+ T cell persistence in chronic infection
Single-cell RNA-seq reveals TOX as a key regulator of CD8+ T cell persistence in chronic infection
        ×
      Single-cell RNA-seq reveals TOX as a key regulator of CD8+ T cell persistence in chronic infection
        Chen Y et al., *Nature Immunology*, 2019
    Developmental Acquisition of Regulomes Underlies Innate Lymphoid Cell Functionality
Developmental Acquisition of Regulomes Underlies Innate Lymphoid Cell Functionality
        ×
      Development of Regulomes
        Shih HY et al., *Cell*, 2016
            
                        
                        
                                    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;
        
                    7(77).
        
                    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
        

                    Immunity.
        
                    2021 Mar 9;
        
                    54(3).
        
                    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;
        
                    22(3).
        
                    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;
        
                    22(11).
        
                    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
        

                    Immunity.
        
                    2020 Oct 13;
        
                    53(4).
        
                    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;
        
                    117(28).
        
                    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;
        
                    130(4).
        
                    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;
        
                    20(7).
        
                    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;
        
                    71(11).
        
                    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;
        
                    75(6).
        
                    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;
        
                    116(50).
        
                    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;
        
                    139(8).
        
                    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;
        
                    34(6).
        
                    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
        

                    Immunity.
        
                    2019 Jan 15;
        
                    50(1).
        
                    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;
        
                    34(5).
        
                    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.
        
                    2019;
        
                    14(5).
        
                    doi: 10.1371/journal.pone.0216249
                            PMID: 31059533
            
                                    News & Highlights
              
            no-news-results



    FacebookEmailPrintFacebookEmail
        Last Updated: February 2024
 About NIAMS
                    Clinical Trials
                    Grants & Funding
                    Health Topics
                    Labs @ NIAMS
              News Room
                    NIAMS Multimedia Library
                    Disclaimer
                    FOIA
                    Contact us
              Privacy Statement
                    Accessibility
                    HHS Vulnerability Disclosure
                    Social Media Moderation Policy
                    NIAMS Archives
        Subscribe to Our E-Newsletters
            Click the button to see different options to sign up for newsletters.
            Click Here to Subscribe
          Follow us on
  
  About NIH
                  Accessibility Support
            FOIA requests
                  No FEAR Act data
            Office of the Inspector General
                  Performance reports
            Privacy Policy Back to Top