Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data

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

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

A spectral approach integrating functional genomic annotations for coding and noncoding variants

(2016) Iuliana Ionita-Laza et al.   NATURE GENETICS

An integrative approach to predicting the functional effects of non-coding and coding sequence variation

(2015) Hashem A. Shihab et al.   BIOINFORMATICS

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

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

(2015) Zhonghui Tang et al.   CELL

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

(2015) Ya Guo et al.   CELL

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

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

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

A method for calculating probabilities of fitness consequences for point mutations across the human genome

(2015) Brad Gulko et al.   NATURE GENETICS

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

CEGA—a catalog of conserved elements from genomic alignments

(2015) Aline Dousse et al.   NUCLEIC ACIDS RESEARCH

ORegAnno 3.0: a community-driven resource for curated regulatory annotation

(2015) Robert Lesurf et al.   NUCLEIC ACIDS RESEARCH

A unified architecture of transcriptional regulatory elements

(2015) Robin Andersson et al.   TRENDS IN GENETICS

Krüppel Expression Levels Are Maintained through Compensatory Evolution of Shadow Enhancers

(2015) Zeba Wunderlich et al.   Cell Reports

The Ensembl Regulatory Build

(2015) Daniel R Zerbino et al.   GENOME BIOLOGY

DANN: a deep learning approach for annotating the pathogenicity of genetic variants

(2014) Daniel Quang et al.   BIOINFORMATICS

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

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

Functional annotation of noncoding sequence variants

(2014) Graham R S Ritchie et al.   NATURE METHODS

DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions

(2014) Ioannis S. Vlachos et al.   NUCLEIC ACIDS RESEARCH

The human splicing code reveals new insights into the genetic determinants of disease

(2014) H. Y. Xiong et al.   SCIENCE

8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage

(2014) Chris M. Rands et al.   PLoS Genetics

Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data

(2013) Inna Dubchak et al.   BIOINFORMATICS

The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine

(2013) Peter D. Stenson et al.   HUMAN GENETICS

Inference of Natural Selection from Interspersed Genomic Elements Based on Polymorphism and Divergence

(2013) Ilan Gronau et al.   MOLECULAR BIOLOGY AND EVOLUTION

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

(2013) Annabelle Haudry et al.   NATURE GENETICS

Genome-wide inference of natural selection on human transcription factor binding sites

(2013) Leonardo Arbiza et al.   NATURE GENETICS

ClinVar: public archive of relationships among sequence variation and human phenotype

(2013) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates

(2012) Mikhail Pachkov et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Kerstin Lindblad-Toh et al.   NATURE

Massive turnover of functional sequence in human and other mammalian genomes

(2010) S. Meader et al.   GENOME RESEARCH

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

Identifying novel constrained elements by exploiting biased substitution patterns

(2009) Manuel Garber et al.   BIOINFORMATICS

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequencing and Comparative Analysis of a Conserved Syntenic Segment in the Solanaceae

(2008) Y. Wang et al.   GENETICS

Selective Constraints in Experimentally Defined Primate Regulatory Regions

(2008) Daniel J. Gaffney et al.   PLoS Genetics

Patterns of Positive Selection in Six Mammalian Genomes

(2008) Carolin Kosiol et al.   PLoS Genetics