Genetic regulatory signatures underlying islet gene expression and type 2 diabetes

Genome Editing of Lineage Determinants in Human Pluripotent Stem Cells Reveals Mechanisms of Pancreatic Development and Diabetes

(2016) Zengrong Zhu et al.   Cell Stem Cell

Models of human core transcriptional regulatory circuitries

(2016) Violaine Saint-André et al.   GENOME RESEARCH

Clinical, Genetic, and Biochemical Characteristics of Early-Onset Diabetes in the Finnish Population

(2016) Hanna Huopio et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

The genetic regulatory signature of type 2 diabetes in human skeletal muscle

(2016) Laura J. Scott et al.   Nature Communications

Which Genetics Variants in DNase-Seq Footprints Are More Likely to Alter Binding?

(2016) Gregory A. Moyerbrailean et al.   PLoS Genetics

GREGOR: evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach

(2015) Ellen M. Schmidt et al.   BIOINFORMATICS

QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments

(2015) Stephen W. Hartley et al.   BMC BIOINFORMATICS

Type 2 Diabetes–Associated K+Channel TALK-1 Modulates β-Cell Electrical Excitability, Second-Phase Insulin Secretion, and Glucose Homeostasis

(2015) Nicholas C. Vierra et al.   DIABETES

Recent advances in understanding the genetic architecture of type 2 diabetes

(2015) Karen L. Mohlke et al.   HUMAN MOLECULAR GENETICS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo

(2015) Matthew T Maurano 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

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

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

Motif signatures in stretch enhancers are enriched for disease-associated genetic variants

(2015) Daniel X Quang et al.   Epigenetics & Chromatin

Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants

(2015) Fiona Allum et al.   Nature Communications

Coordinated regulatory variation associated with gestational hyperglycaemia regulates expression of the novel hexokinase HKDC1

(2015) Cong Guo et al.   Nature Communications

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

Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line

(2015) Marina Lizio et al.   Frontiers in Genetics

A Common Functional Regulatory Variant at a Type 2 Diabetes Locus Upregulates ARAP1 Expression in the Pancreatic Beta Cell

(2014) Jennifer R. Kulzer et al.   AMERICAN JOURNAL OF HUMAN GENETICS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

minimac2: faster genotype imputation

(2014) Christian Fuchsberger et al.   BIOINFORMATICS

Genetic and epigenetic fine mapping of causal autoimmune disease variants

(2014) Kyle Kai-How Farh et al.   NATURE

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

(2014) Lorenzo Pasquali et al.   NATURE GENETICS

Global genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism

(2014) J. Fadista et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RFX6 Regulates Insulin Secretion by Modulating Ca2+ Homeostasis in Human β Cells

(2014) Vikash Chandra et al.   Cell Reports

Rfx6 Maintains the Functional Identity of Adult Pancreatic β Cells

(2014) Julie Piccand et al.   Cell Reports

Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits

(2013) O. Corradin et al.   GENOME RESEARCH

Seeing is believing

(2013) Luc G Berthiaume   Nature Chemical Biology

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

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter 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

Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data

(2012) Goo Jun et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Chromatin marks identify critical cell types for fine mapping complex trait variants

(2012) Gosia Trynka et al.   NATURE GENETICS

Fast and accurate genotype imputation in genome-wide association studies through pre-phasing

(2012) Bryan Howie et al.   NATURE GENETICS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

AlleleSeq: analysis of allele-specific expression and binding in a network framework

(2011) J. Rozowsky et al.   Molecular Systems Biology

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

(2011) Jason Ernst et al.   NATURE

Robust relationship inference in genome-wide association studies

(2010) Ani Manichaikul et al.   BIOINFORMATICS

METAL: fast and efficient meta-analysis of genomewide association scans

(2010) C. J. Willer et al.   BIOINFORMATICS

Comparative Epigenomic Analysis of Murine and Human Adipogenesis

(2010) Tarjei S. Mikkelsen et al.   CELL

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

Rfx6 directs islet formation and insulin production in mice and humans

(2010) Stuart B. Smith et al.   NATURE

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

(2010) Oliver Stegle et al.   PLoS Computational Biology

Rfx6 is an Ngn3-dependent winged helix transcription factor required for pancreatic islet cell development

(2009) Josselin Soyer et al.   DEVELOPMENT

Identification and characterization of novel human tissue-specific RFX transcription factors

(2008) Syed Aftab et al.   BMC EVOLUTIONARY BIOLOGY