Prioritizing non-coding regions based on human genomic constraint and sequence context with deep learning

Genome-wide rare variant analysis for thousands of phenotypes in over 70,000 exomes from two cohorts

(2020) Elizabeth T. Cirulli et al.   Nature Communications

A structural variation reference for medical and population genetics

(2020) Ryan L. Collins et al.   NATURE

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

Promoter CpG Density Predicts Downstream Gene Loss-of-Function Intolerance

(2020) Leandros Boukas et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Predicting Splicing from Primary Sequence with Deep Learning

(2019) Kishore Jaganathan et al.   CELL

Ranking of non-coding pathogenic variants and putative essential regions of the human genome

(2019) Alex Wells et al.   Nature Communications

The human noncoding genome defined by genetic diversity

(2018) Julia di Iulio et al.   NATURE GENETICS

Optimizing genomic medicine in epilepsy through a gene-customized approach to missense variant interpretation

(2017) Joshua Traynelis et al.   GENOME RESEARCH

A genomic perspective on HLA evolution

(2017) Diogo Meyer et al.   IMMUNOGENETICS

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

(2017) Yi-Fei Huang et al.   NATURE GENETICS

ClinVar: improving access to variant interpretations and supporting evidence

(2017) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

Orion: Detecting regions of the human non-coding genome that are intolerant to variation using population genetics

(2017) Ayal B. Gussow et al.   PLoS One

Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression

(2017) Camille Berthelot et al.   Nature Ecology & Evolution

Distinct patterns of simple sequence repeats and GC distribution in intragenic and intergenic regions of primate genomes

(2016) Wen-Hua Qi et al.   Aging-US

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

An expanded sequence context model broadly explains variability in polymorphism levels across the human genome

(2016) Varun Aggarwala et al.   NATURE GENETICS

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

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

denovo-db: a compendium of humande novovariants

(2016) Tychele N. Turner et al.   NUCLEIC ACIDS RESEARCH

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

SpeedSeq: ultra-fast personal genome analysis and interpretation

(2015) Colby Chiang et al.   NATURE METHODS

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

(2015) Jian Zhou et al.   NATURE METHODS

The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity

(2015) Slavé Petrovski et al.   PLoS Genetics

Gateways to the FANTOM5 promoter level mammalian expression atlas

(2015) Marina Lizio et al.   GENOME BIOLOGY

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

(2014) Daniel Quang et al.   BIOINFORMATICS

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

(2014) Martin Kircher et al.   NATURE GENETICS

Correction: Genic Intolerance to Functional Variation and the Interpretation of Personal Genomes

(2014) Slavé Petrovski et al.   PLoS Genetics

Phenotypic impact of genomic structural variation: insights from and for human disease

(2013) Joachim Weischenfeldt et al.   NATURE REVIEWS GENETICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

UCNEbase—a database of ultraconserved non-coding elements and genomic regulatory blocks

(2012) Slavica Dimitrieva et al.   NUCLEIC ACIDS RESEARCH

ENCODE Data in the UCSC Genome Browser: year 5 update

(2012) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Detection of nonneutral substitution rates on mammalian phylogenies

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

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS 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

Copy number variation and evolution in humans and chimpanzees

(2008) G. H. Perry et al.   GENOME RESEARCH