Stephen CJ Parker, PhD

 Steven Parker
Professor of Computational Medicine and Bioinformatics
Professor of Human Genetics, Medical School
Professor of Biostatistics, School of Public Health
Email:
[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

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    • Journal Article
      Genetic integration reveals causal effects of chromatin accessibility on nucleosome positioning across diverse muscle cells
      Wang X, Robertson CC, Varshney A, Manickam N, Orchard P, Laakso M, Tuomilehto J, Lakka TA, Mohlke KL, Boehnke M, Scott LJ, Koistinen HA, Collins FS, Parker SCJ. Nature Communications, 2026 Oct 29; DOI:10.1038/s41467-026-78760-x
    • Journal Article
      Population-scale single-nucleus multi-omic profiling of skeletal muscle reveals extensive context-specific genetic regulation.
      Varshney A, Manickam N, Orchard P, Tovar A, Ventresca C, Zhang Z, Feng F, Mears J, Erdos MR, Narisu N, Nishino K, Rai V, Stringham HM, Jackson AU, Tamsen T, Gao C, Yang M, Koues OI, Welch JD, Burant CF, Williams LK, Jenkinson C, DeFronzo RA, Norton L, Saramies J, Lakka TA, Laakso M, Tuomilehto J, Mohlke KL, Kitzman JO, Koistinen HA, Liu J, Boehnke M, Collins FS, Scott LJ, Parker SCJ. Nat Genet, 2026 Oct 28; DOI:10.1038/s41588-026-02786-6
      PMID: 42951906
    • Journal Article
      Inverse directions of association of higher physical activity and higher insulin resistance with human skeletal muscle fiber-type gene expression
      Ciotlos DL, Hanks SC, Varshney A, Erdos MR, Manickam N, Stringham HM, Orchard P, Hill-Burns EM, Narisu N, Bonnycastle LL, Sweeney MD, Saramies J, Laakso M, Tuomilehto J, Lakka TA, Mohlke KL, Boehnke M, Collins FS, Koistinen HA, Parker SCJ, Scott LJ. Iscience, 2026 Oct 16; 29 (10): DOI:10.1016/j.isci.2026.117293
    • Preprint
      Single-nucleus multi-omics reveals reversible molecular signatures in skeletal muscle of patients with heart failure with preserved ejection fraction
      Bose M, Varshney A, Carruthers NJ, Orchard P, Piper M, Pashos E, Dolgachev V, Manickam N, Curka E, Jean-Beltran PM, Kitzman DW, Fauman EB, Damilano F, Roth Flach RJ, Nicklas B, Brubaker P, Parker SC. 2026 Oct 11; bioRxiv, DOI:10.64898/2026.10.07.756854
    • Journal Article
      Letter to the American Diabetes Association Board of Directors From Members of the Mentor Advisory Committee, ADA Pathway to Stop Diabetes Program.
      Anderson B, Anderson M, D'Alessio D, de Groot M, Eckel R, Harlan D, Herold K, Huang E, Kulkarni R, Laffel L, Newgard C, Page K, Parker S, Pennathur S, Phillipson L, Quinn L, Saltiel A, Schaffer J, Shah V, Stewart A, Talmadge K, Weissberg-Benchell J, White P. Diabetes, 2026 Oct 6; DOI:10.2337/dbi26-0053
      PMID: 42853875
    • Preprint
      Erosion of regenerative regulation: age-associated shifts in the skeletal muscle fiber epigenome and transcriptome
      Moo KG, Orchard P, Varshney A, Albanus RD, Manickam N, Kinnunen L, Lakka TA, Saramies J, Laakso M, Tuomilehto J, Mohlke KL, Boehnke M, Scott L, Koistinen HA, Collins FS, Parker SCJ. 2026 Aug 27; bioRxiv, DOI:10.64898/2026.08.19.744884
    • Preprint
      Integrated Analysis of Skeletal Muscle Transcriptional Networks Characterizes Dysregulation in Pathways and Trait-Associated Regulatory Regions in Type 2 Diabetes
      Maddox A, Manickam N, Orchard P, Erdos MR, Narisu N, Stringham HM, Lakka TA, Saramies J, Laakso M, Tuomilehto J, Mohlke KL, Boehnke M, Scott LJ, Koistinen HA, Collins FS, Varshney A, Rao A, Parker SC. 2026 Aug 23; bioRxiv, DOI:10.64898/2026.08.17.745340
    • 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 CT, 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, Aguet F, Scott LJ, Raffield LM, Parker SCJ. Science, 2026 Jul 16; 393 (6808): DOI:10.1126/science.adx2989
      PMID: 42462027

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    Department News

    Stephen Parker gave the C. Ronald Kahn Distinguished Lecture at Harvard University

    Thursday, November 21, 2024, Steven Parker, Ph.D., gave the C. Ronald Kahn Distinguished Lecture at the Joslin Diabetes Center at Harvard University. Parker's lecture, titled "Beyond Genes: How Epigenomic Contexts Shape Diabetes Predisposition," presented the Parker Lab's research on how epigenomic contexts shape diabetes predisposition. This recognition highlights the growing impact of his research and the reputation of his group as leaders in the field.