The paper uses a meta-analytic approach to identify sex-dependent splicing interactions in type 1 diabetes, finding higher prevalence in CD4 T cells than CD8 T cells.

bioRxiv · Jun 2, 2026 · PreprintGenomics

Manipulation of alternative splicing of IKZF1 elicits distinct gene regulatory responses in T cells

Lucía Pastor, Jeremy R. B. Newman, Colin M. Callahan, Rebecca Roche Pickin, Mark A. Atkinson, Suna Önengüt-Gümüşcü, PATRICK J. CONCANNON

The paper investigates how alternative splicing of IKZF1 affects gene regulation in T cells, finding significant changes in gene expression and chromatin accessibility.

Cells · Jan 24, 2026Peer-reviewedGenomics

Reduced function of the adaptor SH2B3 promotes T1D via altered γc cytokine-regulated, T cell intrinsic immune tolerance

Taylor K. Watson, Aaron B.I. Rosen, Travis Drow, Jacob A. Medjo, Matthew A. MacQuivey, Yan Ge, Denny Liggitt, Dane A. Grosvenor, Kimberly A. Dill‐McFarland, Matthew C. Altman, PATRICK J. CONCANNON, Jane Hoyt Buckner, David J. Rawlings, Eric J. Allenspach

This study identifies SH2B3 as a critical regulator of T cell tolerance in T1D, showing that its deficiency enhances cytokine signaling and promotes islet destruction.

Diabetes · Mar 6, 2025Peer-reviewedImmunology

Multi-omics profiling reveals ethylene signalling as a key pathway underlying both genetic and epigenetic responses to low-dose ionizing radiation in Arabidopsis

Jeremy R. B. Newman, Mingqi Zhou, J. Chris Pires, Rhonda L. Bacher, Michael P. Kladde, PATRICK J. CONCANNON

This study uses multi-omics profiling to show that low-dose ionizing radiation in Arabidopsis triggers genetic and epigenetic responses mediated by the ethylene signaling pathway.

bioRxiv · Oct 14, 2023 · PreprintGenomics

Shifts in isoform usage underlie transcriptional differences in regulatory T cells in type 1 diabetes

Jeremy R. B. Newman, Sarah Alice Long, Cate Speake, Carla J. Greenbaum, Karen M. Cerosaletti, Stephen S. Rich, Suna Önengüt-Gümüşcü, Lauren M. McIntyre, Jane Hoyt Buckner, PATRICK J. CONCANNON

The paper identifies shifts in isoform usage in Tregs associated with Type 1 Diabetes by comparing gene expression between cases and controls.

Communications Biology · Sep 27, 2023Peer-reviewedGenetics

Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes

Catherine C. Robertson, Jamie R. J. Inshaw, Suna Önengüt-Gümüşcü, Wei‐Min Chen, David Flores Santa Cruz, Hanzhi Yang, Antony J. Cutler, Daniel J. M. Crouch, Emily Farber, S. Louis Bridges, Jeffrey C. Edberg, Robert P. Kimberly, Jane Hoyt Buckner, Panos Deloukas, Jasmin Divers, , Stephen S. Rich

This study identifies causal variants, cells, genes, and drug targets for type 1 diabetes using large-scale genetic and functional genomic analyses.

Nature Genetics · Jun 14, 2021Peer-reviewedGenetics

Enhanced genetic analysis of type 1 diabetes by selecting variants on both effect size and significance, and by integration with autoimmune thyroid disease

Daniel J. M. Crouch, Jamie R. J. Inshaw, Catherine C. Robertson, Jiayuan Zhang, Wei‐Min Chen, Suna Önengüt-Gümüşcü, Antony J. Cutler, Carlo Sidore, Francesco Cucca, Flemming Pociot, PATRICK J. CONCANNON, Stephen S. Rich, John A. Todd

The paper identifies 302 new genetic signals for type 1 diabetes and autoimmune thyroid disease by combining effect size and significance, showing that only 28% of genome-wide significant signals have large effects.

bioRxiv · Feb 5, 2021 · PreprintGenetics

Genome-wide association study of cryptosporidiosis in infants implicates PRKCA

Genevieve L. Wojcik, Poonum S. Korpe, Chelsea S. Marie, Alexander J. Mentzer, Tommy Carstensen, Josyf C. Mychaleckyj, Beth D. Kirkpatrick, Stephen S. Rich, PATRICK J. CONCANNON, Abu Syed Golam Faruque, Rashidul Haque, William A. Petri, Priya Duggal

This paper conducts a GWAS to identify genetic variants associated with symptomatic cryptosporidiosis in infants, finding a strong association with an intronic SNP in PRKCA.

mBio · Feb 3, 2020Peer-reviewedGenetics

Machine Learning Methods to Identify Genetic Correlates of Radiation-Associated Contralateral Breast Cancer in the WECARE Study

Sangkyu Lee, Xiaolin Liang, Meghan Woods, Anne S. Reiner, Duncan C. Thomas, PATRICK J. CONCANNON, Leslie Bernstein, Charles F. Lynch, John D. Boice, Joseph O. Deasy, Jonine L. Bernstein, Jung Hun Oh

bioRxiv · Feb 12, 2019 · PreprintBioinformatics

Experimental design for large scale omic studies

Funda Ogut, Jeremy R. B. Newman, Rhonda L. Bacher, PATRICK J. CONCANNON, Koen J. F. Verhoeven, Lauren M. McIntyre

The paper discusses experimental design for large-scale omic studies, emphasizing the importance of balancing omics batches and accounting for experimental factors to improve statistical power.

bioRxiv · Jan 29, 2019 · PreprintGenetics

Genome-Wide Association Study Reveals Genetic Link Between Diarrhea-Associated Entamoeba histolytica Infection And Inflammatory Bowel Disease

Genevieve L. Wojcik, Chelsea S. Marie, Mayuresh M. Abhyankar, Nobuya Yoshida, Kôji Watanabe, Alexander J. Mentzer, Tommy Carstensen, Josyf C. Mychaleckyj, Beth D. Kirkpatrick, Stephen S. Rich, PATRICK J. CONCANNON, Rashidul Haque, George C. Tsokos, William A. Petri, Priya Duggal

This study identifies genetic variants associated with Entamoeba histolytica infection and links them to inflammatory bowel disease susceptibility.

mBio · Sep 18, 2018Peer-reviewedGenetics