Center for Spatial and Functional Genomics Publications

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Below is a list of selected publications from the Center for Spatial and Functional Genomics. View and download a full list of publications.

Palermo J, Chesi A, Zimmerman A, et al. Variant-to-gene mapping followed by cross-species genetic screening identifies GPI-anchor biosynthesis as a regulator of sleep. Sci Adv. 2023 Jan; 9(1):eabq0844. PMID: 36608130
Su C, Gao L, May CL, et al. 3D chromatin maps of the human pancreas reveal lineage-specific regulatory architecture of T2D risk. Cell Metab. 2022 Sep; 34(9):1394-1409.e4. PMID: 36070683
Lasconi C, Pahl MC, Pippin JA, et al. Variant-to-gene-mapping analyses reveal a role for pancreatic islet cells in conferring genetic susceptibility to sleep-related traits. Sleep. 2022 Aug; 45(8):zsac109. PMID: 35537191
Pahl MC, Le Coz C, Su C, et al. Implicating effector genes at COVID-19 GWAS loci using promoter-focused Capture-C in disease-relevant immune cell types. Genome Biol. 2022 Jun; 23(1):125. PMID: 35659055
Vujkovic M, Ramdas S, Lorenz KM, et al. A multiancestry genome-wide association study of unexplained chronic ALT elevation as a proxy for nonalcoholic fatty liver disease with histological and radiological validation. Nat Genet. 2022 Jun; 54(6):761-771. PMID: 35654975
Pahl MC, Doege CA, Hodge KM, et al.. Cis-regulatory architecture of human ESC-derived hypothalamic neuron differentiation aids in variant-to-gene mapping of relevant complex traits. Nat Commun. 2021 Nov; 12(1):6749. PMID: 34799566
Su C, Pahl MC, Grant SFA, Wells AD. Restriction enzyme selection dictates detection range sensitivity in chromatin conformation capture-based variant-to-gene mapping approaches. Hum Genet. 2021 Oct; 140(10):1441-1448. PMID: 34405268
Xu M, et al. UVB-responsive common variant at chromosome band 7p21.1 confers tanning response and melanoma risk via regulation of the aryl hydrocarbon receptor, AHR. Am J Hum Genet. 2021 Sep; 108(9):1611-1630. PMID: 34343493
Pippin JA, Chesi A, Wagley Y, Su C, Pahl MC, Hodge KM, Johnson ME, Wells AD, Hankenson KD, Grant SFA. CRISPR-Cas9-Mediated Genome Editing Confirms EPDR1 as an Effector Gene at the BMD GWAS-Implicated 'STARD3NL' Locus. JBMR Plus. 2021 Jul; 5(9):e10531. PMID: 34532616
Le Coz C, Nguyen DN, Su C, et al. Constrained chromatin accessibility in PU.1-mutated agammaglobulinemia patients. J Exp Med. 2021 Jul; 218(7):e20201750. PMID: 33951726
Pluta J, et al; Testicular Cancer Consortium. Identification of 22 susceptibility loci associated with testicular germ cell tumors. Nat Commun. 2021 Jul; 12(1):4487. PMID: 34301922
Su C, et al. 3D promoter architecture re-organization during iPSC-derived neuronal cell differentiation implicates target genes for neurodevelopmental disorders. Prog Neurobiol. 2021 Jun; 201:102000. PMID: 33545232
Lasconi C, et al. Variant-to-Gene-Mapping Analyses Reveal a Role for the Hypothalamus in Genetic Susceptibility to Inflammatory Bowel Disease. Cell Mol Gastroenterol Hepatol. 2021 Jan; 11(3):667-682. PMID: 33069917
Cousminer DL, et al. Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual. Genome Biol. 2021 Jan; 22(1):1. PMID: 33397451
Hammond RK, et al. Biological constraints on GWAS SNPs at suggestive significance thresholds reveal additional BMI loci. Elife. 2021 Jan; 10:e62206. PMID: 33459256
Su C, et al. Mapping effector genes at lupus GWAS loci using promoter Capture-C in follicular helper T cells. Nat Commun. 2020 Jul; 11(1):3294. PMID: 32620744
Çalışkan M, Manduchi E, Rao HS, et al. Genetic and Epigenetic Fine Mapping of Complex Trait Associated Loci in the Human Liver. Am J Hum Genet. 2019 Jul; 105(1):89-107. PMID: 31204013
Chesi A, Wagley Y, Johnson ME, et al. Genome-scale Capture C promoter interactions implicate effector genes at GWAS loci for bone mineral density. Nat Commun. 2019 Mar; 10(1):1260. PMID: 30890710
Gallagher MD, Posavi M, Huang P, et al. A Dementia-Associated Risk Variant near TMEM106B Alters Chromatin Architecture and Gene Expression. Am J Hum Genet. 2017 Nov; 101(5):643-663. PMID: 29056226
Xia Q, Chesi A, Manduchi E, et al. The type 2 diabetes presumed causal variant within TCF7L2 resides in an element that controls the expression of ACSL5. Diabetologia. 2016 Nov; 59(11):2360-2368. PMID: 27539148