Stephen CJ Parker, PhD

Steven Parker
Professor of Computational Medicine and Bioinformatics
Professor of Human Genetics
Medical School and Professor of Biostatistics
School of Public Health
[email protected]
Available to mentor
Stephen CJ Parker, PhD
Steven Parker
Professor
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  • Center Memberships

    • Center Member
      Caswell Diabetes Institute
    • Center Member
      AI and Digital Health Innovation

    Research Overview

    We generate multiple high-throughput data sets on the genome, epigenome, and transcriptome across species and in disease-relevant tissues/cells at single-cell multi-omic resolution and use machine learning computational approaches to integrate and analyze this data. We aim to better understand the effects of genetic variation on chromatin architecture and transcriptional regulation at single-cell resolution. The major goal of the lab is to generate mechanistic knowledge about how disease susceptibility is encoded in the non-coding portion of the genome (from GWAS), with a focus on complex metabolic diseases including diabetes and related traits. We accomplish this through an interdisciplinary combination of molecular, cellular, and computational approaches.

    Links

    • Parker Lab

    Recent Publications

    See All Publications
    • Preprint
      Decoding the mystery of ultra-conservation in developmental enhancers: a role for nucleosome positioning, DNA structure and transcription factor binding.
      Woolfe A, Parker SC, Almouzni G. 2026 Jul 24; bioRxiv, DOI:10.64898/2026.07.16.739003
    • Journal Article
      Cross-cohort analysis of expression and splicing quantitative trait loci in TOPMed.
      Orchard P, Blackwell TW, Kachuri L, Castaldi PJ, Cho MH, Christenson SA, Durda P, Gabriel S, Hersh CP, Huntsman S, Hwang S, Joehanes R, Johnson M, Li X, Lin H, Liu C-T, Liu Y, Mak ACY, Manichaikul AW, Paik DT, Saferali A, Smith JD, Taylor KD, Tracy RP, Wang J, Wang M, Weinstock JS, Weiss J, Wheeler HE, Zhou Y, Zöllner S, Wu JC, Mestroni L, Graw S, Taylor MRG, Ortega VE, Johnson WC, Gan W, Abecasis G, Nickerson DA, Gupta N, Ardlie K, Woodruff PG, Bowler RP, Meyers DA, Reiner A, Kooperberg C, Ziv E, Vasan RS, Larson MG, Cupples LA, Silverman EK, Rich SS, Heard-Costa N, Tang H, Rotter JI, Smith AV, Levy D, NHLBI TOPMed Consortium Multi-Omics Working Group32 , NHLBI TOPMed Consortium32§ , Aguet F, Scott LJ, Raffield LM, Parker SCJ, Abe N, Almasy L, Ament S, Anugu P, Auer P, Avramopoulos D, Balasubramanian A, Barr RG, Barwick L, Beaty T, Becker D, Becker L, Beitelshees A, Benos T, Bezerra M, Bis J, Brody J, Broeckel U, Broome J, Bunting K, Buth E, Carey V, Carty C, Casaburi R, Chaffin M, Chang C, Chang Y-C, Chavan S, Chen B-J, Chen W-M, Choi SH, Chuang L-M, Chung R-H, Conomos M, Cornell E, Crandall C, Crapo J, Curtis J, Damcott C, David S, de Las Fuentes L, de Vries P, Deka R, DeMeo D, Devine S, Dinh H, Doddapaneni H, Duan Q, Duggirala R, Eaton C, Ekunwe L, El Boueiz A, Emery L, Farber C, Farek J, Franceschini N, Frazar C, Fu M, Fullerton SM, Fulton L, Gao S, Gao Y, Gass M, Geiger H, Ghosh A, Gignoux C, Glahn D, Gogarten S, Gong D-W, Goring H, Grine D, Gu CC, Guan Y, Hall M, Han Y, Harris D, Heavner B, Herrington D, Hobbs B, Hong E, Hoth K, Hsiung CA, Hu J, Hung Y-J, Huston H, Hwu CM, Jackson R, Jain D, Johnsen J, Johnston R, Jones K, Kessler M, Khan A, Khan Z, Kim W, Kimoff J, Kinney G, Kramer H, Lange C, Lange E, Laurie C, Laurie C, LeBoff M, Lee S, Lee W-J, Levine D, Lewis J, Li Y, Lin X, Liu S, Liu Y, Make B, Manning A, Manson J, Martin L, Marton M, Mathai S, May S, McArdle P, McDonald M-L, McFarland S, McGoldrick D, McHugh C, Mei H, Meigs J, Menon V, Min N, Moll M, Momin Z, Montasser M, Mychaleckyj JC, Naik R, Naseri T, Natarajan P, Nelson SC, Neltner B, Nessner C, Nkechinyere O, O'Connell J, O'Connor T, Ochs-Balcom H, Okwuonu G, Pankow J, Parker C, Peloso G, Peralta JM, Perez M, Perry J, Peters U, Phillips LS, Pollin T, Becker JP, Boorgula MP, Psaty B, Qiao D, Rafaels N, Rajendran M, Rasmussen-Torvik L, Ratan A, Reed R, Regan E, Reupena MS, Robillard R, Roselli C, Ruczinski I, Runnels A, Russell P, Ryan K, Sabino EC, Salimi S, Salvi S, Salzberg S, Sandow K, Santibanez J, Schwander K, Sciurba F, Sériès F, Shetty A, Shetty A, Silver B, Skomro R, Smith T, Smoller S, Snively B, Stilp AM, Storm G, Streeten E, Su JL, Sung YJ, Sylvia J, Szpiro A, Taub M, Taylor S, Thornton TA, Threlkeld M, Tinker L, Tirschwell D, Tiwari H, Tong C, Tsai M, Vaidya D, Walker T, Wallace R, Walts A, Wang FF, Wang H, Watson K, Watt J, Weng L-C, Wessel J, Williams K, Wilson C, Wilson J, Winterkorn L, Wong Q, Wu B, Xu H, Yanek L, Yang I, Zekavat SM, Zhao SX, Zhao W, Zhu X. Science, 2026 Jul 16; 393 (6808): eadx2989 DOI:10.1126/science.adx2989
      PMID: 42462027
    • Preprint
      The Human Pancreas Cell Atlas defines a healthy reference framework for disease contextualization and translational benchmarking
      Parikh S, Strobl DC, Jiménez S, Beckmann JL, Arnoldt L, Roellin E, Vandenbempt V, Sterr M, Aije M, Vu HTH, Melton R, Liu J, Feng F, Cartailler J, Gaulton KJ, Parker SCJ, Ruland J, Conrad C, Brissova M, Carlotti F, Lickert H, Eils R, Balboa D, Luecken MD, Theis FJ. 2026 Jun 28; bioRxiv, DOI:10.64898/2026.06.22.733853
    • Preprint
      PanKbase Integrated Single-Cell Map: A Comprehensive Atlas of Human Pancreatic Islets.
      Vu HTH, Sun H, Kudtarkar P, Sharp SA, Brusman L, Wang Y, Huang Y, Mao R, Feng F, Corban S, Huber AK, Shilin A, Sun Y, Narayanaswamy S, Jang D, Jurgens JA, Robertson CC, Shrestha S, Bate T, Nguyen T, Smadbeck P, Zhang L, Brandes M, PanKbase Consortium , Flannick J, Burtt N, Chen S, Liu J, Cartailler J-P, Voight BF, Stitzel ML, Brissova M, Gloyn AL, Gaulton KJ, Parker SCJ. 2026 Jun 10; DOI:10.64898/2026.06.02.729719
      PMID: 42327171
    • Journal Article
      2395-P: PanKgraph: An Integrated Knowledge Graph for Type 1 Diabetes Research
      WANG Y, MAO R, FENG F, VU HT, HUANG Y, HAN Z, HUBER AK, CARTAILLER J-P, CHEN S, BRISSOVA M, PARKER S, LIU J. Diabetes, 2026 Jun 8; 75 (Supplement_1): DOI:10.2337/db26-2395-p
    • Journal Article
      3008-LB: Variant-to-Function analysis of the C2CD4A/B T2D GWAS Signal in Skeletal Muscle Fibers
      EPELLE L, TOVAR A, HUBER AK, VARSHNEY A, ORCHARD P, PARKER S. Diabetes, 2026 Jun 8; 75 (Supplement_1): DOI:10.2337/db26-3008-lb
    • Journal Article
      3109-LB: A Single-Cell Multiomic Atlas of the Developing Human Pancreas from the Neonatal Period through Childhood
      LIN S, HUBER AK, VU HT, ORCHARD P, JENKINS R, MEI S, COLDREN A, SAUNDERS DC, POWERS AC, BRISSOVA M, PARKER S, NONPANYA N, BERNAL-ASSIS OM, BOTTINO R. Diabetes, 2026 Jun 8; 75 (Supplement_1): DOI:10.2337/db26-3109-lb
    • Journal Article
      42-PUB: PanKgraph: An AI-Agent-Ready Knowledge Graph to Accelerate Type 1 Diabetes Research
      MAO R, WANG Y, VU HT, FENG F, HAN Z, HUANG Y, HUBER AK, CHEN S, BRISSOVA M, CARTAILLER J-P, LIU J, PARKER S. Diabetes, 2026 Jun 8; 75 (Supplement_1): DOI:10.2337/db26-42-pub

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