DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning

Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus

(2018) Yan Zhang et al.   Nature Communications

Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction

(2018) Ziad Al Bkhetan et al.   Scientific Reports

Gene co-opening network deciphers gene functional relationships

(2017) Wenran Li et al.   Molecular BioSystems

Genome-wide characterization of mammalian promoters with distal enhancer functions

(2017) Lan T M Dao et al.   NATURE GENETICS

A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells

(2017) Yarui Diao et al.   NATURE METHODS

Modeling gene regulation from paired expression and chromatin accessibility data

(2017) Zhana Duren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) Biola M. Javierre et al.   CELL

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

(2016) David R. Kelley et al.   GENOME RESEARCH

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

(2016) Sean Whalen et al.   NATURE GENETICS

ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis

(2016) Guipeng Li et al.   NUCLEIC ACIDS RESEARCH

Constructing 3D interaction maps from 1D epigenomes

(2016) Yun Zhu et al.   Nature Communications

Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics

(2016) David Lamparter et al.   PLoS Computational Biology

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

(2015) Zhonghui Tang et al.   CELL

Genomic regulation of senescence and innate immunity signaling in the retinal pigment epithelium

(2015) Edward Chaum et al.   MAMMALIAN GENOME

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Deep learning for regulatory genomics

(2015) Yongjin Park et al.   NATURE BIOTECHNOLOGY

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

Walking on multiple disease-gene networks to prioritize candidate genes

(2015) Rui Jiang   Journal of Molecular Cell Biology

A Systematic Approach to Identify Candidate Transcription Factors that Control Cell Identity

(2015) Ana C. D’Alessio et al.   Stem Cell Reports

Metabolic Regulation of Immune Responses

(2014) Kirthana Ganeshan et al.   Annual Review of Immunology

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

(2014) Suhas S.P. Rao et al.   CELL

Genome-wide map of regulatory interactions in the human genome

(2014) Nastaran Heidari et al.   GENOME RESEARCH

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

The BioGRID interaction database: 2015 update

(2014) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Candidate genes and functional noncoding variants identified in a canine model of obsessive-compulsive disorder

(2014) Ruqi Tang et al.   GENOME BIOLOGY

Systematic identification of trans eQTLs as putative drivers of known disease associations

(2013) Harm-Jan Westra et al.   NATURE GENETICS

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The cellular and signaling networks linking the immune system and metabolism in disease

(2012) Olivia Osborn et al.   NATURE MEDICINE

Chlamydia pneumoniae heat shock protein 60 is associated with apoptotic signaling pathway in human atheromatous plaques of coronary artery disease patients

(2011) Hem Chandra Jha et al.   Journal of Cardiology

A common variant in the CDKN2B gene on chromosome 9p21 protects against coronary artery disease in Americans of African ancestry

(2011) Brian G Kral et al.   JOURNAL OF HUMAN GENETICS

9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response

(2011) Olivier Harismendy et al.   NATURE

Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease

(2011) Heribert Schunkert et al.   NATURE GENETICS

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

A multilocus genetic risk score for coronary heart disease: case-control and prospective cohort analyses

(2010) Samuli Ripatti et al.   LANCET

Reactome: a database of reactions, pathways and biological processes

(2010) D. Croft et al.   NUCLEIC ACIDS RESEARCH

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH