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

Available to mentor
Stephen CJ Parker, PhD
Associate 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
    • Journal Article
      Cardiovascular risk reduction in older people with type 2 diabetes mellitus-a comprehensive narrative review
      Si PEH, Parker S, Abdelhafiz D, Summerbell A, Muzulu S, Abdelhafiz AH. Diabetes Research and Clinical Practice, 2024 May 1; 211: DOI:10.1016/j.diabres.2024.111662
    • Journal Article
      Genetic risk converges on regulatory networks mediating early type 2 diabetes.
      Walker JT, Saunders DC, Rai V, Chen H-H, Orchard P, Dai C, Pettway YD, Hopkirk AL, Reihsmann CV, Tao Y, Fan S, Shrestha S, Varshney A, Petty LE, Wright JJ, Ventresca C, Agarwala S, Aramandla R, Poffenberger G, Jenkins R, Mei S, Hart NJ, Phillips S, Kang H, Greiner DL, Shultz LD, Bottino R, Liu J, Below JE, HPAP Consortium , Parker SCJ, Powers AC, Brissova M. Nature, 2023 Dec; 624 (7992): 621 - 629. DOI:10.1038/s41586-023-06693-2
      PMID: 38049589
    • Preprint
      Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation.
      Varshney A, Manickam N, Orchard P, Tovar A, Zhang Z, Feng F, Erdos MR, Narisu N, Ventresca C, 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. 2023 Dec 15; DOI:10.1101/2023.12.15.571696
      PMID: 38168419
    • Journal Article
      FixItFelix: improving genomic analysis by fixing reference errors.
      Behera S, LeFaive J, Orchard P, Mahmoud M, Paulin LF, Farek J, Soto DC, Parker SCJ, Smith AV, Dennis MY, Zook JM, Sedlazeck FJ. Genome Biol, 2023 Feb 21; 24 (1): 31 DOI:10.1186/s13059-023-02863-7
      PMID: 36810122
    • Preprint
      Adipose tissue eQTL meta-analysis reveals the contribution of allelic heterogeneity to gene expression regulation and cardiometabolic traits.
      Brotman SM, El-Sayed Moustafa JS, Guan L, Broadaway KA, Wang D, Jackson AU, Welch R, Currin KW, Tomlinson M, Vadlamudi S, Stringham HM, Roberts AL, Lakka TA, Oravilahti A, Silva LF, Narisu N, Erdos MR, Yan T, Bonnycastle LL, Raulerson CK, Raza Y, Yan X, Parker SCJ, Kuusisto J, Pajukanta P, Tuomilehto J, Collins FS, Boehnke M, Love MI, Koistinen HA, Laakso M, Mohlke KL, Small KS, Scott LJ. 2023 Oct 27; DOI:10.1101/2023.10.26.563798
      PMID: 37961277
    • Preprint
      An integrative single-cell multi-omics profiling of human pancreatic islets identifies T1D associated genes and regulatory signals.
      Zhao Z, D'Oliveira Albanus R, Taylor H, Tang X, Han Y, Orchard P, Varshney A, Zhang T, Manickam N, Erdos M, Narisu N, Taylor L, Saavedra X, Zhong A, Li B, Zhou T, Naji A, Liu C, Collins F, Parker SC, Chen S. 2023 Oct 18; DOI:10.21203/rs.3.rs-3343318/v1
      PMID: 37886586
    • Preprint
      Using a modular massively parallel reporter assay to discover context-specific regulatory grammars in type 2 diabetes
      Tovar A, Kyono Y, Nishino K, Bose M, Varshney A, Parker SCJ, Kitzman J. 2023 bioRxiv, DOI:10.1101/2023.10.08.561391
    • Journal Article
      Noncoding variants alter GATA2 expression in rhombomere 4 motor neurons and cause dominant hereditary congenital facial paresis.
      Tenney AP, Di Gioia SA, Webb BD, Chan W-M, de Boer E, Garnai SJ, Barry BJ, Ray T, Kosicki M, Robson CD, Zhang Z, Collins TE, Gelber A, Pratt BM, Fujiwara Y, Varshney A, Lek M, Warburton PE, Van Ryzin C, Lehky TJ, Zalewski C, King KA, Brewer CC, Thurm A, Snow J, Facio FM, Narisu N, Bonnycastle LL, Swift A, Chines PS, Bell JL, Mohan S, Whitman MC, Staffieri SE, Elder JE, Demer JL, Torres A, Rachid E, Al-Haddad C, Boustany R-M, Mackey DA, Brady AF, Fenollar-Cortés M, Fradin M, Kleefstra T, Padberg GW, Raskin S, Sato MT, Orkin SH, Parker SCJ, Hadlock TA, Vissers LELM, van Bokhoven H, Jabs EW, Collins FS, Pennacchio LA, Manoli I, Engle EC. Nat Genet, 2023 Jul; 55 (7): 1149 - 1163. DOI:10.1038/s41588-023-01424-9
      PMID: 37386251
    Featured News & Stories
    Department News
    Stephen C.J. Parker, Ph.D., 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).
    Department News
    S. Parker's 'Nature' paper in NIH new Director’s Blog
    S. Parker's 'Nature' paper in NIH new Director’s Blog