Stephen CJ Parker, PhD
Professor of Computational Medicine and Bioinformatics
Professor of Human Genetics
Professor of Biostatistics
[email protected]

Available to mentor
Stephen CJ Parker, PhD
Professor
  • Center Memberships
  • Research Overview
  • Links
  • Recent Publications
    • Center Memberships
    • Center Member
      Caswell Diabetes Institute
    • Center Member
      Precision Health Initiative
    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
      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, MAGIC , Parker SCJ, Morris AP, Asimit JL, Barroso I. bioRxiv, DOI:10.1101/2024.11.13.623384
    • Preprint
      CelLink: Integrate single-cell multi-omics data with few linked features and imbalanced cell populations
      Luo X, Huang Y, Tao Y, Feng F, Hopkirk A, Bate TSR, Saunders DC, Orchard P, Robertson C, Shrestha S, Cartailler J-P, Parker SCJ, Brissova M, Liu J. bioRxiv, DOI:10.1101/2024.11.08.622745
    • Journal Article
      Human vascularized macrophage-islet organoids to model immune-mediated pancreatic β cell pyroptosis upon viral infection.
      Yang L, Han Y, Zhang T, Dong X, Ge J, Roy A, Zhu J, Lu T, Jeya Vandana J, de Silva N, Robertson CC, Xiang JZ, Pan C, Sun Y, Que J, Evans T, Liu C, Wang W, Naji A, Parker SCJ, Schwartz RE, Chen S. Cell Stem Cell, 2024 Nov 7; 31 (11): 1612 - 1629.e8. DOI:10.1016/j.stem.2024.08.007
      PMID: 39232561
    • Journal Article
      The methodological and ethical concerns of genetic studies of same-sex sexual behavior.
      Ventresca C, Martschenko DO, Wedow R, Civelek M, Tabery J, Carlson J, Parker SCJ, Ramos PS. Am J Hum Genet, 2024 Oct 3; 111 (10): 2107 - 2116. DOI:10.1016/j.ajhg.2024.08.007
      PMID: 39255798
    • Report
      CNTools: A computational toolbox for cellular neighborhood analysis from multiplexed images.
      Tao Y, Feng F, Luo X, Reihsmann CV, Hopkirk AL, Cartailler J-P, Brissova M, Parker SCJ, Saunders DC, Liu J. 2024 Aug; e1012344 DOI:10.1371/journal.pcbi.1012344
      PMID: 39196899
    • Journal Article
      Untangling the genetics of beta cell dysfunction and death in type 1 diabetes.
      Robertson CC, Elgamal RM, Henry-Kanarek BA, Arvan P, Chen S, Dhawan S, Eizirik DL, Kaddis JS, Vahedi G, Parker SCJ, Gaulton KJ, Soleimanpour SA. Mol Metab, 2024 Aug; 86: 101973 DOI:10.1016/j.molmet.2024.101973
      PMID: 38914291
    • Journal Article
      1468-P: Massively Parallel Reporter Assay Reveals Position-, Promoter-, and Strand-Dependent Effects in Islet TSSs Overlapping Type 2 Diabetes GWAS Loci
      BOSE ML, TOVAR A, VARSHNEY A, PARKER S, KITZMAN J, KYONO Y. Diabetes, 2024 Jun 14; 73 (Supplement_1): DOI:10.2337/db24-1468-p
    • Journal Article
      1731-P: Screening Human Islets to Identify Small Molecules Enhancing Glucagon Secretion under Hypoglycemia
      BATE TSR, REIHSMANN C, ARAMANDLA R, DAVIS C, MEI S, BRADLEY A, BAUER J, PARKER S, SAUNDERS DC, POWERS AC, BRISSOVA M. Diabetes, 2024 Jun 14; 73 (Supplement_1): DOI:10.2337/db24-1731-p
    Featured News & Stories 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!
    Department News
    S. Parker's 'Nature' paper in NIH new Director’s Blog
    S. Parker's 'Nature' paper in NIH new Director’s Blog