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 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
    • Journal Article
      Using a modular massively parallel reporter assay to discover context-dependent regulatory activity in type 2 diabetes-linked noncoding regions.
      Tovar A, Kyono Y, Nishino K, Bose M, Varshney A, Parker SCJ, Kitzman JO. HGG Adv, 2026 Apr 7; 100606 DOI:10.1016/j.xhgg.2026.100606
      PMID: 41952336
    • Preprint
      Genetic demultiplexing and transcript start site identification from nanopore sequencing of 10x Genomics multiome libraries
      Mears J, Orchard P, Varshney A, Bose M, Robertson CC, Piper M, Pashos E, Dolgachev V, Manickam N, Jean P, Kitzman DW, Fauman EB, Damilano F, Roth Flach RJ, Nicklas B, Parker SCJ. 2026 Apr 5; bioRxiv, DOI:10.64898/2026.03.31.715454
    • Journal Article
      RFX6 expression is central to the development and function of the neuroendocrine compartments of the pancreas and intestine and strongly affects diabetes risk
      Bate TSR, Huang Y, Luo X, Saunders DC, Walker JT, Rai V, Parker SCJ, Liu J, Brissova M. Diabetology International, 2026 Apr 1; 17 (2): DOI:10.1007/s13340-025-00867-1
    • Preprint
      Donor-matched iPSC model reveals context-dependent T2D genetic signals in fibro-adipogenic progenitors.
      Ventresca C, Varshney A, Orchard P, Vu HTH, Tsan Y-C, Monteiro da Rocha A, Erdos MR, Kinnunen L, Lakka TA, Saramies J, Laakso M, Tuomilehto J, Mohlke KL, Boehnke M, Scott LJ, Koistinen HA, Collins FS, Herron T, Bielas S, Parker SCJ. 2026 Feb 6; DOI:10.64898/2026.02.04.702388
      PMID: 41676558
    • Journal Article
      Genome writing and Targeted Delivery of the NKX6-3/ANK1 gene cluster and its Type 2 Diabetes GWAS Variants to Human iPSCs.
      Chalhoub N, Varshney A, Zhang W, Uhl S, Laurent JM, McLoughlin C, Ashe H, Mou X, Dale N, Ramnarine K, Paull D, Goldberg J, Maurano MT, Brosh R, Fenyö D, Cipriani F, Parker SCJ, Boeke JD. bioRxiv, 2026 Jan 4; DOI:10.64898/2026.01.04.697539
      PMID: PMC12776320
    • Journal Article
      Combining functional annotation and multi-trait fine-mapping methods improves fine-mapping resolution at glycaemic trait loci
      Soenksen J, Chen J, Varshney A, Martin S, Parker SCJ, Morris AP, Asimit JL, Barroso I. Human Molecular Genetics, 2026 Jan 1; 35 (2): DOI:10.1093/hmg/ddaf164
      PMID: 41251494
    • Journal Article
      CelLink: integrating single-cell multi-omics data with weak feature linkage and imbalanced cell populations
      Luo X, Huang Y, Zeng H, Tao Y, Bao X, Feng F, Hopkirk AL, Pham T, Bate TSR, Saunders DC, Orchard P, Robertson C, Shrestha S, Spraggins JM, Cartailler JP, Parker SCJ, Brissova M, Liu J. Nucleic Acids Research, 2025 Dec 11; 53 (22): DOI:10.1093/nar/gkaf1270
      PMID: 41335468
    • Preprint
      Inverse directions of association of higher physical activity and higher insulin resistance with human skeletal muscle cell type abundance and fiber-type-level 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. 2025 Nov 28; DOI:10.1101/2025.10.27.683567
      PMID: 41279274

    Featured News & Stories

         Diagram depicting the system's components in a circular format, showcasing their relationships and roles within the system.
    Department News

    A New Collaborative to Better Predict, Prevent, and Treat Type 1 Diabetes

    MAI-T1D is a major NIH-funded project using AI and multi-omics to map Type 1 Diabetes progression. The goal: better predict, prevent, and treat T1D.
         Steven C. J. Parker gives the C. Ronald Kahn Distinguished Lecture at Harvard University
    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.
         Photo portrait of Adelaide Tovar, PhD
    Department News

    Adelaide Tovar, Ph.D., received a MOSAIC K99/R00 Award from the NIH/NHGRI

    Adelaide Tovar, Ph.D., was awarded an NIH Maximizing Opportunities for Scientific and Academic Independent Careers (MOSAIC) K99/R00, a specialized career transition program intended for postdocs who are from underrepresented backgrounds and/or have demonstrated a commitment to increasing inclusivity and equity in the scientific workforce.
         Photos of DCMB promoted faculty: Yuanfang Guan, Ph.D., Jie Liu, Ph.D., Ryan Mills, Ph.D., Stephen C.J. Parker, Ph.D., and Arvind Rao, Ph.D.
    Department News

    Five DCMB faculty are promoted, congratulations!

    Five DCMB faculty were promoted. They are Yuanfang Guan, Ph.D., Jie Liu, Ph.D., Ryan Mills, Ph.D., Stephen C.J. Parker, Ph.D., and Arvind Rao, Ph.D. Congratulations!
         Professor Stephen Parker stands in his office
    Department News

    Stephen C.J. Parker, PhD, receives 2024 Outstanding Scientific Achievement Award from American Diabetes Association (ADA)

    Stephen C.J. Parker, Ph.D., is the recipient of the 2024 Outstanding Scientific Achievement Award from the American Diabetes Association (ADA).
         Aerial view of University of Michigan Health hospital located in Ann Arbor, Michigan.
    Department News

    A new Epigenomic Metabolic Medicine Center (EM2C) at the U-M Medical School

    Congratulations to Dr. Stephen Parker, Associate Professor of Computational Medicine and Bioinformatics, Human Genetics, and Biostatistics on the formation of the Epigenomic Metabolic Medicine Center (EM2C) at the U-M Medical School!