3D chromatin maps of the human pancreas reveal lineage-specific regulatory architecture of T2D risk

Variant-to-gene-mapping analyses reveal a role for pancreatic islet cells in conferring genetic susceptibility to sleep-related traits

(2022) Chiara Lasconi et al.   SLEEP

FoxA-dependent demethylation of DNA initiates epigenetic memory of cellular identity

(2021) Yitzhak Reizel et al.   DEVELOPMENTAL CELL

3D promoter architecture re-organization during iPSC-derived neuronal cell differentiation implicates target genes for neurodevelopmental disorders

(2021) Chun Su et al.   PROGRESS IN NEUROBIOLOGY

Comprehensive analysis of single cell ATAC-seq data with SnapATAC

(2021) Rongxin Fang et al.   Nature Communications

A fast and efficient colocalization algorithm for identifying shared genetic risk factors across multiple traits

(2021) Christopher N. Foley et al.   Nature Communications

Interpreting type 1 diabetes risk with genetics and single-cell epigenomics

(2021) Joshua Chiou et al.   NATURE

Genome-wide enhancer maps link risk variants to disease genes

(2021) Joseph Nasser et al.   NATURE

The trans-ancestral genomic architecture of glycemic traits

(2021) Ji Chen et al.   NATURE GENETICS

Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2

(2020) Arya Kaul et al.   Nature Protocols

Discovery of 318 new risk loci for type 2 diabetes and related vascular outcomes among 1.4 million participants in a multi-ancestry meta-analysis

(2020) Marijana Vujkovic et al.   NATURE GENETICS

High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells

(2020) Joep Beumer et al.   CELL

Pan-cancer study detects genetic risk variants and shared genetic basis in two large cohorts

(2020) Sara R. Rashkin et al.   Nature Communications

Genetic mapping of etiologic brain cell types for obesity

(2020) Pascal N Timshel et al.   eLife

A Multi-omic Integrative Scheme Characterizes Tissues of Action at Loci Associated with Type 2 Diabetes

(2020) Jason M. Torres et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Bulk tissue cell type deconvolution with multi-subject single-cell expression reference

(2019) Xuran Wang et al.   Nature Communications

Multiomic Profiling Identifies cis-Regulatory Networks Underlying Human Pancreatic β Cell Identity and Function

(2019) Nathan Lawlor et al.   Cell Reports

Genome-wide association study identifies genetic loci for self-reported habitual sleep duration supported by accelerometer-derived estimates

(2019) Hassan S. Dashti et al.   Nature Communications

Genome-wide association analyses of chronotype in 697,828 individuals provides insights into circadian rhythms

(2019) Samuel E. Jones et al.   Nature Communications

The Integrated Islet Distribution Program Answers the Call for Improved Human Islet Phenotyping and Reporting of Human Islet Characteristics in Research Articles

(2019) Marcela Brissova et al.   DIABETES

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes

(2019) Irene Miguel-Escalada et al.   NATURE GENETICS

Pancreatic islet chromatin accessibility and conformation reveals distal enhancer networks of type 2 diabetes risk

(2019) William W. Greenwald et al.   Nature Communications

WITHDRAWN: Global and regional diabetes prevalence estimates for 2019 and projections for 2030 and 2045: results from the International Diabetes Federation Diabetes Atlas, 9th edition

(2019) Pouya Saeedi et al.   DIABETES RESEARCH AND CLINICAL PRACTICE

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Circadian Entrainment Triggers Maturation of Human In Vitro Islets

(2019) Juan R. Alvarez-Dominguez et al.   Cell Stem Cell

Multi-ethnic genome-wide association study for atrial fibrillation

(2018) Carolina Roselli et al.   NATURE GENETICS

The role of the carboxyl ester lipase ( CEL ) gene in pancreatic disease

(2018) Bente B. Johansson et al.   PANCREATOLOGY

HiCcompare: an R-package for joint normalization and comparison of HI-C datasets

(2018) John C. Stansfield et al.   BMC BIOINFORMATICS

A Chromatin Basis for Cell Lineage and Disease Risk in the Human Pancreas

(2018) H. Efsun Arda et al.   Cell Systems

Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps

(2018) Anubha Mahajan et al.   NATURE GENETICS

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

(2017) Tao Yang et al.   GENOME RESEARCH

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

HiTAD: detecting the structural and functional hierarchies of topologically associating domains from chromatin interactions

(2017) Xiao-Tao Wang et al.   NUCLEIC ACIDS RESEARCH

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

(2016) Biola M. Javierre et al.   CELL

Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets

(2016) Zhihong Zhu et al.   NATURE GENETICS

Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes

(2016) Amanda M. Ackermann et al.   Molecular Metabolism

LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants: Fig. 1.

(2015) Mitchell J. Machiela et al.   BIOINFORMATICS

Role of transcription factors in the transdifferentiation of pancreatic islet cells

(2015) T. van der Meulen et al.   JOURNAL OF MOLECULAR ENDOCRINOLOGY

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

The diabetes gene Hhex maintains  -cell differentiation and islet function

(2014) J. Zhang et al.   GENES & DEVELOPMENT

Depression of Type I Diacylglycerol Kinases in Pancreatic β-Cells From Male Mice Results in Impaired Insulin Secretion

(2013) Yukiko Kurohane Kaneko et al.   ENDOCRINOLOGY

Dynamic regulation of transcriptional states by chromatin and transcription factors

(2013) Ty C. Voss et al.   NATURE REVIEWS GENETICS

Network for Pancreatic Organ Donors with Diabetes (nPOD): developing a tissue biobank for type 1 diabetes

(2012) Martha Campbell-Thompson et al.   DIABETES-METABOLISM RESEARCH AND REVIEWS

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

Transcriptional regulation of α-cell differentiation

(2011) N. C. Bramswig et al.   DIABETES OBESITY & METABOLISM

Isolation of mouse pancreatic alpha, beta, duct and acinar populations with cell surface markers

(2011) Craig Dorrell et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Foxa1 and Foxa2 Maintain the Metabolic and Secretory Features of the Mature β-Cell

(2010) Nan Gao et al.   MOLECULAR ENDOCRINOLOGY

Prediction and Interaction in Complex Disease Genetics: Experience in Type 1 Diabetes

(2009) David G. Clayton   PLoS Genetics

Is Pancreatic Diabetes (Type 3c Diabetes) Underdiagnosed and Misdiagnosed?

(2008) P. D. Hardt et al.   DIABETES CARE

Dynamic regulation of Pdx1 enhancers by Foxa1 and Foxa2 is essential for pancreas development

(2008) N. Gao et al.   GENES & DEVELOPMENT

A HapMap harvest of insights into the genetics of common disease

(2008) Teri A. Manolio et al.   JOURNAL OF CLINICAL INVESTIGATION

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS

Genetic Mapping in Human Disease

(2008) D. Altshuler et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY