Single-cell chromatin accessibility identifies pancreatic islet cell type– and state-specific regulatory programs of diabetes risk

Patch-Seq Links Single-Cell Transcriptomes to Human Islet Dysfunction in Diabetes

(2020) Joan Camunas-Soler et al.   Cell Metabolism

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

(2019) Nathan Lawlor et al.   Cell Reports

Acquisition of Dynamic Function in Human Stem Cell-Derived β Cells

(2019) Leonardo Velazco-Cruz et al.   Stem Cell Reports

Interrogation of human hematopoiesis at single-cell and single-variant resolution

(2019) Jacob C. Ulirsch et al.   NATURE GENETICS

Navigating the Depths and Avoiding the Shallows of Pancreatic Islet Cell Transcriptomes

(2019) Alex M. Mawla et al.   DIABETES

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

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

(2019) Ilya Korsunsky et al.   NATURE METHODS

Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures

(2019) Vivek Rai et al.   Molecular Metabolism

A Common Type 2 Diabetes Risk Variant Potentiates Activity of an Evolutionarily Conserved Islet Stretch Enhancer and Increases C2CD4A and C2CD4B Expression

(2018) Ina Kycia et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

(2018) Jason D. Buenrostro et al.   CELL

Pseudotime Ordering of Single Human β-Cells Reveals States of Insulin Production and Unfolded Protein Response

(2018) Yurong Xin et al.   DIABETES

MafB Is Critical for Glucagon Production and Secretion in Mouse Pancreatic α Cells In Vivo

(2018) Megumi C. Katoh et al.   MOLECULAR AND CELLULAR BIOLOGY

Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression

(2018) Naomi R. Wray et al.   NATURE GENETICS

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation

(2018) Sebastian Preissl et al.   NATURE NEUROSCIENCE

Insulinpromoter in human pancreatic β cells contacts diabetes susceptibility loci and regulates genes affecting insulin metabolism

(2018) Xing Jian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci

(2018) Matthias Thurner et al.   eLife

Type 2 Diabetes Associated Genetic Variants Regulate Chromatin Accessibility in Human Islets

(2018) Shubham Khetan et al.   DIABETES

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

Biobank-driven genomic discovery yields new insight into atrial fibrillation biology

(2018) Jonas B. Nielsen et al.   NATURE GENETICS

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

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

Transcriptional Heterogeneity of Beta Cells in the Intact Pancreas

(2018) Lydia Farack et al.   DEVELOPMENTAL CELL

Shared genetic risk contributes to type 1 and type 2 diabetes etiology

(2018) Anthony Aylward et al.   HUMAN MOLECULAR GENETICS

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

All mixed up: defining roles for β-cell subtypes in mature islets

(2017) Jennifer S.E. Liu et al.   GENES & DEVELOPMENT

Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease

(2017) Katrina M de Lange et al.   NATURE GENETICS

Association analyses based on false discovery rate implicate new loci for coronary artery disease

(2017) Christopher P Nelson et al.   NATURE GENETICS

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

(2017) Alicia N Schep et al.   NATURE METHODS

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Genetic regulatory signatures underlying islet gene expression and type 2 diabetes

(2017) Arushi Varshney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations: A transethnic genome-wide meta-analysis

(2017) Eleanor Wheeler et al.   PLOS MEDICINE

The MAFB transcription factor impacts islet α-cell function in rodents and represents a unique signature of primate islet β-cells

(2016) Elizabeth Conrad et al.   AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM

Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes

(2016) Åsa Segerstolpe et al.   Cell Metabolism

Single-cell transcriptomes identify human islet cell signatures and reveal cell-type–specific expression changes in type 2 diabetes

(2016) Nathan Lawlor et al.   GENOME RESEARCH

Identification of proliferative and mature β-cells in the islets of Langerhans

(2016) Erik Bader et al.   NATURE

The genetic architecture of type 2 diabetes

(2016) Christian Fuchsberger et al.   NATURE

A reference panel of 64,976 haplotypes for genotype imputation

(2016)   NATURE GENETICS

Genome-wide mapping and analysis of chromosome architecture

(2016) Anthony D. Schmitt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

RNA splicing is a primary link between genetic variation and disease

(2016) Yang I. Li et al.   SCIENCE

Human islets contain four distinct subtypes of β cells

(2016) Craig Dorrell et al.   Nature Communications

CD93 and dystroglycan cooperation in human endothelial cell adhesion and migration

(2016) Federico Galvagni et al.   Oncotarget

4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments

(2016) Ramya Raviram et al.   PLoS Computational Biology

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

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

Comprehensive alpha, beta and delta cell transcriptomes reveal that ghrelin selectively activates delta cells and promotes somatostatin release from pancreatic islets

(2016) Michael R. DiGruccio et al.   Molecular Metabolism

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure

(2016) Maayan Baron et al.   Cell Systems

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Genetic studies of body mass index yield new insights for obesity biology

(2015) Adam E. Locke et al.   NATURE

Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus

(2015) James Bentham et al.   NATURE GENETICS

Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci

(2015) Kyle J Gaulton et al.   NATURE GENETICS

A method to predict the impact of regulatory variants from DNA sequence

(2015) Dongwon Lee et al.   NATURE GENETICS

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

(2015) Hilary K Finucane et al.   NATURE GENETICS

An atlas of genetic correlations across human diseases and traits

(2015) Brendan Bulik-Sullivan et al.   NATURE GENETICS

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

(2015) Brendan K Bulik-Sullivan et al.   NATURE GENETICS

Urocortin3 mediates somatostatin-dependent negative feedback control of insulin secretion

(2015) Talitha van der Meulen et al.   NATURE MEDICINE

WASP: allele-specific software for robust molecular quantitative trait locus discovery

(2015) Bryce van de Geijn et al.   NATURE METHODS

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans

(2015) Melina Claussnitzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways

(2015) Heather J. Cordell et al.   Nature Communications

Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits

(2014) Joseph K. Pickrell   AMERICAN JOURNAL OF HUMAN GENETICS

Leveraging Cross-Species Transcription Factor Binding Site Patterns: From Diabetes Risk Loci to Disease Mechanisms

(2014) Melina Claussnitzer et al.   CELL

MafA is critical for maintenance of the mature beta cell phenotype in mice

(2014) Wataru Nishimura et al.   DIABETOLOGIA

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Reversal of diabetes with insulin-producing cells derived in vitro from human pluripotent stem cells

(2014) Alireza Rezania et al.   NATURE BIOTECHNOLOGY

Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants

(2014) Lorenzo Pasquali et al.   NATURE GENETICS

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

TFClass: a classification of human transcription factors and their rodent orthologs

(2014) Edgar Wingender et al.   NUCLEIC ACIDS RESEARCH

Identification of a Regulatory Variant That Binds FOXA1 and FOXA2 at the CDC123/CAMK1D Type 2 Diabetes GWAS Locus

(2014) Marie P. Fogarty et al.   PLoS Genetics

Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease

(2013) Jean-Charles Lambert et al.   NATURE GENETICS

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

(2013) S. C. J. Parker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways

(2012) Robert A Scott et al.   NATURE GENETICS

A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance

(2012) Alisa K Manning et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Paracrine and autocrine interactions in the human islet: More than meets the eye

(2012) Alejandro Caicedo   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Genome-Wide Association Identifies Nine Common Variants Associated With Fasting Proinsulin Levels and Provides New Insights Into the Pathophysiology of Type 2 Diabetes

(2011) R. J. Strawbridge et al.   DIABETES

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A map of open chromatin in human pancreatic islets

(2010) Kyle J Gaulton et al.   NATURE GENETICS

Genetic variation in GIPR influences the glucose and insulin responses to an oral glucose challenge

(2010) Richa Saxena et al.   NATURE GENETICS

New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk

(2010) Josée Dupuis et al.   NATURE GENETICS

Transcriptional Control of Endothelial Cell Development

(2009) Sarah De Val et al.   DEVELOPMENTAL CELL

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH