Genome-wide enhancer maps link risk variants to disease genes

Enhancer Domains Predict Gene Pathogenicity and Inform Gene Discovery in Complex Disease

(2020) Xinchen Wang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A brief history of human disease genetics

(2020) Melina Claussnitzer et al.   NATURE

Pathway paradigms revealed from the genetics of inflammatory bowel disease

(2020) Daniel B. Graham et al.   NATURE

Towards a comprehensive catalogue of validated and target-linked human enhancers

(2020) Molly Gasperini et al.   NATURE REVIEWS GENETICS

Isolation and analysis of rereplicated DNA by Rerep-Seq

(2020) Johannes Menzel et al.   NUCLEIC ACIDS RESEARCH

A simple new approach to variable selection in regression, with application to genetic fine mapping

(2020) Gao Wang et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Global reference mapping of human transcription factor footprints

(2020) Jeff Vierstra et al.   NATURE

Inherited causes of clonal haematopoiesis in 97,691 whole genomes

(2020) Alexander G. Bick et al.   NATURE

Integrating predicted transcriptome from multiple tissues improves association detection

(2019) Alvaro N. Barbeira et al.   PLoS Genetics

Opportunities and challenges for transcriptome-wide association studies

(2019) Michael Wainberg et al.   NATURE GENETICS

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

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

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

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

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

(2019) Jeffrey M. Granja et al.   NATURE BIOTECHNOLOGY

Mixed-model association for biobank-scale datasets

(2018) Po-Ru Loh et al.   NATURE GENETICS

Comparative Analysis of Immune Cells Reveals a Conserved Regulatory Lexicon

(2018) Elisa Donnard et al.   Cell Systems

Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies

(2018) Wei Zhou et al.   NATURE GENETICS

ProGeM: a framework for the prioritization of candidate causal genes at molecular quantitative trait loci

(2018) David Stacey et al.   NUCLEIC ACIDS RESEARCH

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

Open Targets Platform: new developments and updates two years on

(2018) Denise Carvalho-Silva et al.   NUCLEIC ACIDS RESEARCH

Fine-mapping inflammatory bowel disease loci to single-variant resolution

(2017) Hailiang Huang et al.   NATURE

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Limited statistical evidence for shared genetic effects of eQTLs and autoimmune-disease-associated loci in three major immune-cell types

(2017) Sung Chun et al.   NATURE GENETICS

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

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

Reconstruction of enhancer–target networks in 935 samples of human primary cells, tissues and cell lines

(2017) Qin Cao et al.   NATURE GENETICS

Automatic identification of informative regions with epigenomic changes associated to hematopoiesis

(2017) Enrique Carrillo-de-Santa-Pau et al.   NUCLEIC ACIDS RESEARCH

Anti-inflammatory effect of IL-10 mediated by metabolic reprogramming of macrophages

(2017) W. K. Eddie Ip et al.   SCIENCE

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

(2016) Biola M. Javierre et al.   CELL

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

(2016) Lu Chen et al.   CELL

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

(2016) William J. Astle et al.   CELL

β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance

(2016) Boris Novakovic et al.   CELL

Local regulation of gene expression by lncRNA promoters, transcription and splicing

(2016) Jesse M. Engreitz et al.   NATURE

Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin

(2016) Sean Whalen et al.   NATURE GENETICS

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations

(2015) Jimmy Z Liu et al.   NATURE GENETICS

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

(2015) Hilary K Finucane et al.   NATURE GENETICS

MAGMA: Generalized Gene-Set Analysis of GWAS Data

(2015) Christiaan A. de Leeuw et al.   PLoS Computational Biology

From genome to function by studying eQTLs

(2014) Harm-Jan Westra et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Genetic and epigenetic fine mapping of causal autoimmune disease variants

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

In search of the determinants of enhancer–promoter interaction specificity

(2014) Joris van Arensbergen et al.   TRENDS IN CELL BIOLOGY

Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues

(2013) Jiang Zhu et al.   CELL

Physiologic Functions of Cyclophilin D and the Mitochondrial Permeability Transition Pore

(2013) John W. Elrod et al.   CIRCULATION JOURNAL

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

(2013) N. C. Sheffield et al.   GENOME RESEARCH

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

(2012) Luke Jostins et al.   NATURE

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

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

(2012) Julian B Maller 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

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Role of growth factors in the development of lymphangiogenesis driven by inflammatory bowel disease

(2010) Pablo M. Linares et al.   INFLAMMATORY BOWEL DISEASES

Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci

(2010) Andre Franke et al.   NATURE GENETICS

The UCSC Genome Browser database: update 2011

(2010) P. A. Fujita et al.   NUCLEIC ACIDS RESEARCH

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

Dendritic cells in intestinal homeostasis and disease

(2009) Maria Rescigno et al.   JOURNAL OF CLINICAL INVESTIGATION

Common variants at five new loci associated with early-onset inflammatory bowel disease

(2009) Marcin Imielinski et al.   NATURE GENETICS