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

Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of-origin mapping from plasma DNA

(2017) Shicheng Guo et al.   NATURE GENETICS

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

Mechanisms and Disease Associations of Haplotype-Dependent Allele-Specific DNA Methylation

(2016) Catherine Do et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genetic dissection of the α-globin super-enhancer in vivo

(2016) Deborah Hay et al.   NATURE GENETICS

Genome-wide association study identifies multiple susceptibility loci for multiple myeloma

(2016) Jonathan S. Mitchell et al.   Nature Communications

Integrative epigenome-wide analysis demonstrates that DNA methylation may mediate genetic risk in inflammatory bowel disease

(2016) N. T. Ventham et al.   Nature Communications

Discovery and validation of sub-threshold genome-wide association study loci using epigenomic signatures

(2016) Xinchen Wang et al.   eLife

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation

(2015) Norihiro Kato 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

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

(2015) Hilary K Finucane et al.   NATURE GENETICS

Multiplexed analysis of chromosome conformation at vastly improved sensitivity

(2015) James O J Davies et al.   NATURE METHODS

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

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

Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci

(2015) Eilis Hannon et al.   NATURE NEUROSCIENCE

Discovery and Fine-Mapping of Glycaemic and Obesity-Related Trait Loci Using High-Density Imputation

(2015) Momoko Horikoshi et al.   PLoS Genetics

Transcript Expression Data from Human Islets Links Regulatory Signals from Genome-Wide Association Studies for Type 2 Diabetes and Glycemic Traits to Their Downstream Effectors

(2015) Martijn van de Bunt et al.   PLoS Genetics

Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements

(2015) Weiwei Zhang et al.   GENOME BIOLOGY

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

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

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

(2014) Martin J. Aryee et al.   BIOINFORMATICS

ADCY5 Couples Glucose to Insulin Secretion in Human Islets

(2014) D. J. Hodson et al.   DIABETES

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

(2014) Lorenzo Pasquali et al.   NATURE GENETICS

Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility

(2014) Anubha Mahajan et al.   NATURE GENETICS

DNA Sequence Explains Seemingly Disordered Methylation Levels in Partially Methylated Domains of Mammalian Genomes

(2014) Dimos Gaidatzis et al.   PLoS Genetics

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

Genome-Wide Associations between Genetic and Epigenetic Variation Influence mRNA Expression and Insulin Secretion in Human Pancreatic Islets

(2014) Anders H. Olsson et al.   PLoS Genetics

Genome-Wide DNA Methylation Analysis of Human Pancreatic Islets from Type 2 Diabetic and Non-Diabetic Donors Identifies Candidate Genes That Influence Insulin Secretion

(2014) Tasnim Dayeh et al.   PLoS Genetics

Impact of Type 2 Diabetes Susceptibility Variants on Quantitative Glycemic Traits Reveals Mechanistic Heterogeneity

(2013) Antigone S. Dimas et al.   DIABETES

Buccals are likely to be a more informative surrogate tissue than blood for epigenome-wide association studies

(2013) Robert Lowe et al.   Epigenetics

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Identification of active regulatory regions from DNA methylation data

(2013) Lukas Burger et al.   NUCLEIC ACIDS RESEARCH

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

Passive and active DNA methylation and the interplay with genetic variation in gene regulation

(2013) Maria Gutierrez-Arcelus et al.   eLife

Human β Cell Transcriptome Analysis Uncovers lncRNAs That Are Tissue-Specific, Dynamically Regulated, and Abnormally Expressed in Type 2 Diabetes

(2012) Ignasi Morán et al.   Cell Metabolism

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Bayesian refinement of association signals for 14 loci in 3 common diseases

(2012) Julian B Maller et al.   NATURE GENETICS

Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes

(2012)   NATURE GENETICS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

A genetically engineered human pancreatic β cell line exhibiting glucose-inducible insulin secretion

(2011) Philippe Ravassard et al.   JOURNAL OF CLINICAL INVESTIGATION

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

DNA-binding factors shape the mouse methylome at distal regulatory regions

(2011) Michael B. Stadler et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

(2011) Jordana T Bell et al.   GENOME BIOLOGY

LocusZoom: regional visualization of genome-wide association scan results

(2010) R. J. Pruim et al.   BIOINFORMATICS

A map of open chromatin in human pancreatic islets

(2010) Kyle J Gaulton et al.   NATURE GENETICS

Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis

(2010) Benjamin F Voight et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY