Professor of Computational Medicine and Bioinformatics
Professor of Human Genetics
Professor of Biostatistics
[email protected]
Available to mentor
Stephen CJ Parker, PhD
Professor
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Center MemberCaswell Diabetes Institute
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Center MemberPrecision Health Initiative
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.
Parker Lab
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Walker EM, Pearson GL, Lawlor N, Stendahl AM, Lietzke A, Sidarala V, Zhu J, Stromer T, Reck EC, Li J, Levi-D'Ancona E, Pasmooij MB, Hubers DL, Renberg A, Mohamed K, Parekh VS, Zhang IX, Thompson B, Zhang D, Ware SA, Haataja L, Qi N, Parker SCJ, Arvan P, Yin L, Kaufman BA, Satin LS, Sussel L, Stitzel ML, Soleimanpour SA. Science, 2025 Feb 8; 388 (6743): eadf2034Journal ArticleRetrograde mitochondrial signaling governs the identity and maturity of metabolic tissues
DOI:10.1126/science.adf2034 PMID: 39913641 -
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 D, Saferali A, Smith JD, Taylor KD, Tracy RP, Wang J, Wang M, Weinstock JS, Weiss J, Wheeler HE, Zhou Y, Zoellner S, Wu JC, Mestroni L, Graw S, Taylor MRG, Ortega VE, Johnson CW, Gan W, Abecasis G, Nickerson DA, Gupta N, Ardlie K, Woodruff PG, Zheng Y, Bowler RP, Meyers DA, Reiner A, Kooperberg C, Ziv E, Ramachandran VS, Larson MG, Cupples LA, Burchard EG, Silverman EK, Rich SS, Heard-Costa N, Tang H, Rotter JI, Smith AV, Levy D, NHLBI TOPMed Consortium Multi-Omics Working Group , NHLBI TOPMed Consortium , Aguet F, Scott L, Raffield LM, Parker SCJ. 2025 Feb 21;PreprintCross-cohort analysis of expression and splicing quantitative trait loci in TOPMed.
DOI:10.1101/2025.02.19.25322561 PMID: 40034763 -
Jakubek YA, Ma X, Stilp AM, Yu F, Bacon J, Wong JW, Aguet F, Ardlie K, Arnett DK, Barnes K, Bis JC, Blackwell T, Becker LC, Boerwinkle E, Bowler RP, Budoff MJ, Carson AP, Chen J, Cho MH, Coresh J, Cox NJ, de Vries PS, DeMeo DL, Fardo DW, Fornage M, Guo X, Hall ME, Heard-Costa N, Hidalgo B, Irvin MR, Johnson AD, Jorgenson E, Kenny EE, Kessler MD, Levy D, Li Y, Lima JAC, Liu Y, Locke AE, Loos RJF, Machiela MJ, Mathias RA, Mitchell BD, Murabito JM, Mychaleckyj JC, North KE, Orchard P, Parker SCJ, Pershad Y, Peyser PA, Pratte KA, Psaty BM, Raffield LM, Redline S, Rich SS, Rotter JI, Shah SJ, Smith JA, Smith AP, Smith A, Taub MA, Tiwari HK, Tracy R, Tuftin B, Bick AG, Sankaran VG, Reiner AP, Scheet P, Auer PL. American Journal of Human Genetics, 2025 Feb 6; 112 (2): 276 - 290.Journal ArticleGenomic and phenotypic correlates of mosaic loss of chromosome Y in blood
DOI:10.1016/j.ajhg.2024.12.014 PMID: 39809269 -
Walker EM, Pearson GL, Lawlor N, Stendahl AM, Lietzke A, Sidarala V, Zhu J, Stromer T, Reck EC, Li J, Levi-D'Ancona E, Pasmooij MB, Hubers DL, Renberg A, Mohamed K, Parekh VS, Zhang IX, Thompson B, Zhang D, Ware SA, Haataja L, Qi N, Parker SCJ, Arvan P, Yin L, Kaufman BA, Satin LS, Sussel L, Stitzel ML, Soleimanpour SA. Science, 2025 Feb 6; eadf2034Journal ArticleRetrograde mitochondrial signaling governs the identity and maturity of metabolic tissues.
DOI:10.1126/science.adf2034 PMID: 39913641 -
Walker EM, Pearson GL, Lawlor N, Stendahl AM, Lietzke A, Sidarala V, Zhu J, Stromer T, Reck EC, Li J, Levi-D'Ancona E, Pasmooij MB, Hubers DL, Renberg A, Mohamed K, Parekh VS, Zhang IX, Thompson B, Zhang D, Ware SA, Haataja L, Qi N, Parker SCJ, Arvan P, Yin L, Kaufman BA, Satin LS, Sussel L, Stitzel ML, Soleimanpour SA. 2025 Feb 6;PresentationRetrograde mitochondrial signaling governs the identity and maturity of metabolic tissues.
DOI:10.1126/science.adf2034 PMID: 39913641 -
Nishino K, Kitzman JO, Parker SCJ, Tovar A. 2025 Jan 20;PreprintFunctional dissection of metabolic trait-associated gene regulation in steady state and stimulated human skeletal muscle cells.
DOI:10.1101/2024.11.28.625886 PMID: 39677760 -
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, Fernandes Silva L, 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. Nature Genetics, 2025 Jan 1; 57 (1): 180 - 192.Journal ArticleAdipose tissue eQTL meta-analysis highlights the contribution of allelic heterogeneity to gene expression regulation and cardiometabolic traits
DOI:10.1038/s41588-024-01982-6 PMID: 39747594 -
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. 2024 Dec 17;PreprintPopulation-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation.
DOI:10.1101/2023.12.15.571696 PMID: 38168419
Department News
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.
Department News
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.
Department News
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!
Department News
Stephen C.J. Parker, Ph.D., is the recipient of the 2024 Outstanding Scientific Achievement Award from the American Diabetes Association (ADA).
Department News
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
