Stephen CJ Parker, PhD
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Center Memberships
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Center MemberCaswell Diabetes Institute
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Center MemberAI 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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Woolfe A, Parker SC, Almouzni G. 2026 Jul 24; bioRxiv,PreprintDecoding the mystery of ultra-conservation in developmental enhancers: a role for nucleosome positioning, DNA structure and transcription factor binding.
DOI:10.64898/2026.07.16.739003 -
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 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, NHLBI TOPMed Consortium Multi-Omics Working Group32 , NHLBI TOPMed Consortium32§ , Aguet F, Scott LJ, Raffield LM, Parker SCJ, Abe N, Almasy L, Ament S, Anugu P, Auer P, Avramopoulos D, Balasubramanian A, Barr RG, Barwick L, Beaty T, Becker D, Becker L, Beitelshees A, Benos T, Bezerra M, Bis J, Brody J, Broeckel U, Broome J, Bunting K, Buth E, Carey V, Carty C, Casaburi R, Chaffin M, Chang C, Chang Y-C, Chavan S, Chen B-J, Chen W-M, Choi SH, Chuang L-M, Chung R-H, Conomos M, Cornell E, Crandall C, Crapo J, Curtis J, Damcott C, David S, de Las Fuentes L, de Vries P, Deka R, DeMeo D, Devine S, Dinh H, Doddapaneni H, Duan Q, Duggirala R, Eaton C, Ekunwe L, El Boueiz A, Emery L, Farber C, Farek J, Franceschini N, Frazar C, Fu M, Fullerton SM, Fulton L, Gao S, Gao Y, Gass M, Geiger H, Ghosh A, Gignoux C, Glahn D, Gogarten S, Gong D-W, Goring H, Grine D, Gu CC, Guan Y, Hall M, Han Y, Harris D, Heavner B, Herrington D, Hobbs B, Hong E, Hoth K, Hsiung CA, Hu J, Hung Y-J, Huston H, Hwu CM, Jackson R, Jain D, Johnsen J, Johnston R, Jones K, Kessler M, Khan A, Khan Z, Kim W, Kimoff J, Kinney G, Kramer H, Lange C, Lange E, Laurie C, Laurie C, LeBoff M, Lee S, Lee W-J, Levine D, Lewis J, Li Y, Lin X, Liu S, Liu Y, Make B, Manning A, Manson J, Martin L, Marton M, Mathai S, May S, McArdle P, McDonald M-L, McFarland S, McGoldrick D, McHugh C, Mei H, Meigs J, Menon V, Min N, Moll M, Momin Z, Montasser M, Mychaleckyj JC, Naik R, Naseri T, Natarajan P, Nelson SC, Neltner B, Nessner C, Nkechinyere O, O'Connell J, O'Connor T, Ochs-Balcom H, Okwuonu G, Pankow J, Parker C, Peloso G, Peralta JM, Perez M, Perry J, Peters U, Phillips LS, Pollin T, Becker JP, Boorgula MP, Psaty B, Qiao D, Rafaels N, Rajendran M, Rasmussen-Torvik L, Ratan A, Reed R, Regan E, Reupena MS, Robillard R, Roselli C, Ruczinski I, Runnels A, Russell P, Ryan K, Sabino EC, Salimi S, Salvi S, Salzberg S, Sandow K, Santibanez J, Schwander K, Sciurba F, Sériès F, Shetty A, Shetty A, Silver B, Skomro R, Smith T, Smoller S, Snively B, Stilp AM, Storm G, Streeten E, Su JL, Sung YJ, Sylvia J, Szpiro A, Taub M, Taylor S, Thornton TA, Threlkeld M, Tinker L, Tirschwell D, Tiwari H, Tong C, Tsai M, Vaidya D, Walker T, Wallace R, Walts A, Wang FF, Wang H, Watson K, Watt J, Weng L-C, Wessel J, Williams K, Wilson C, Wilson J, Winterkorn L, Wong Q, Wu B, Xu H, Yanek L, Yang I, Zekavat SM, Zhao SX, Zhao W, Zhu X. Science, 2026 Jul 16; 393 (6808): eadx2989Journal ArticleCross-cohort analysis of expression and splicing quantitative trait loci in TOPMed.
DOI:10.1126/science.adx2989 PMID: 42462027 -
Parikh S, Strobl DC, Jiménez S, Beckmann JL, Arnoldt L, Roellin E, Vandenbempt V, Sterr M, Aije M, Vu HTH, Melton R, Liu J, Feng F, Cartailler J, Gaulton KJ, Parker SCJ, Ruland J, Conrad C, Brissova M, Carlotti F, Lickert H, Eils R, Balboa D, Luecken MD, Theis FJ. 2026 Jun 28; bioRxiv,PreprintThe Human Pancreas Cell Atlas defines a healthy reference framework for disease contextualization and translational benchmarking
DOI:10.64898/2026.06.22.733853 -
Vu HTH, Sun H, Kudtarkar P, Sharp SA, Brusman L, Wang Y, Huang Y, Mao R, Feng F, Corban S, Huber AK, Shilin A, Sun Y, Narayanaswamy S, Jang D, Jurgens JA, Robertson CC, Shrestha S, Bate T, Nguyen T, Smadbeck P, Zhang L, Brandes M, PanKbase Consortium , Flannick J, Burtt N, Chen S, Liu J, Cartailler J-P, Voight BF, Stitzel ML, Brissova M, Gloyn AL, Gaulton KJ, Parker SCJ. 2026 Jun 10;PreprintPanKbase Integrated Single-Cell Map: A Comprehensive Atlas of Human Pancreatic Islets.
DOI:10.64898/2026.06.02.729719 PMID: 42327171 -
WANG Y, MAO R, FENG F, VU HT, HUANG Y, HAN Z, HUBER AK, CARTAILLER J-P, CHEN S, BRISSOVA M, PARKER S, LIU J. Diabetes, 2026 Jun 8; 75 (Supplement_1):Journal Article2395-P: PanKgraph: An Integrated Knowledge Graph for Type 1 Diabetes Research
DOI:10.2337/db26-2395-p -
EPELLE L, TOVAR A, HUBER AK, VARSHNEY A, ORCHARD P, PARKER S. Diabetes, 2026 Jun 8; 75 (Supplement_1):Journal Article3008-LB: Variant-to-Function analysis of the C2CD4A/B T2D GWAS Signal in Skeletal Muscle Fibers
DOI:10.2337/db26-3008-lb -
LIN S, HUBER AK, VU HT, ORCHARD P, JENKINS R, MEI S, COLDREN A, SAUNDERS DC, POWERS AC, BRISSOVA M, PARKER S, NONPANYA N, BERNAL-ASSIS OM, BOTTINO R. Diabetes, 2026 Jun 8; 75 (Supplement_1):Journal Article3109-LB: A Single-Cell Multiomic Atlas of the Developing Human Pancreas from the Neonatal Period through Childhood
DOI:10.2337/db26-3109-lb -
MAO R, WANG Y, VU HT, FENG F, HAN Z, HUANG Y, HUBER AK, CHEN S, BRISSOVA M, CARTAILLER J-P, LIU J, PARKER S. Diabetes, 2026 Jun 8; 75 (Supplement_1):Journal Article42-PUB: PanKgraph: An AI-Agent-Ready Knowledge Graph to Accelerate Type 1 Diabetes Research
DOI:10.2337/db26-42-pub
Featured News & Stories
Highlighted Publications: January - May 2026
A New Collaborative to Better Predict, Prevent, and Treat Type 1 Diabetes
Stephen Parker gave the C. Ronald Kahn Distinguished Lecture at Harvard University
Adelaide Tovar, Ph.D., received a MOSAIC K99/R00 Award from the NIH/NHGRI
Five DCMB faculty are promoted, congratulations!