Computational approaches to interpreting genomic sequence variation

Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits

(2014) Joseph K. Pickrell   AMERICAN JOURNAL OF HUMAN GENETICS

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

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

(2014) Martin Kircher et al.   NATURE GENETICS

Functional annotation of noncoding sequence variants

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

Choice of transcripts and software has a large effect on variant annotation

(2014) Davis J McCarthy et al.   Genome Medicine

A CpG Mutational Hotspot in a ONECUT Binding Site Accounts for the Prevalent Variant of Hemophilia B Leyden

(2013) Alister P.W. Funnell et al.   AMERICAN JOURNAL OF HUMAN GENETICS

VAAST 2.0: Improved Variant Classification and Disease-Gene Identification Using a Conservation-Controlled Amino Acid Substitution Matrix

(2013) Hao Hu et al.   GENETIC EPIDEMIOLOGY

Functional transcriptomics in the post-ENCODE era

(2013) J. M. Mudge et al.   GENOME RESEARCH

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

Activities at the Universal Protein Resource (UniProt)

(2013)   NUCLEIC ACIDS RESEARCH

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

The Next Generation of Transcription Factor Binding Site Prediction

(2013) Anthony Mathelier et al.   PLoS Computational Biology

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment

(2012) Lukas Habegger et al.   BIOINFORMATICS

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Annotation of functional variation in personal genomes using RegulomeDB

(2012) A. P. Boyle et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

A Combined Functional Annotation Score for Non-Synonymous Variants

(2012) Margarida C. Lopes et al.   HUMAN HEREDITY

Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models

(2012) Hashem A. Shihab et al.   HUMAN MUTATION

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions

(2012) L. D. Ward et al.   SCIENCE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

(2012) D. G. MacArthur et al.   SCIENCE

Improving the Assessment of the Outcome of Nonsynonymous SNVs with a Consensus Deleteriousness Score, Condel

(2011) Abel González-Pérez et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Using VAAST to Identify an X-Linked Disorder Resulting in Lethality in Male Infants Due to N-Terminal Acetyltransferase Deficiency

(2011) Alan F. Rope et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Rare-Variant Association Testing for Sequencing Data with the Sequence Kernel Association Test

(2011) Michael C. Wu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A probabilistic disease-gene finder for personal genomes

(2011) M. Yandell et al.   GENOME RESEARCH

Association of a functional variant downstream of TNFAIP3 with systemic lupus erythematosus

(2011) Indra Adrianto et al.   NATURE GENETICS

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

(2011) L. D. Ward et al.   NUCLEIC ACIDS RESEARCH

Pooled Association Tests for Rare Variants in Exon-Resequencing Studies

(2010) Alkes L. Price et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

A map of open chromatin in human pancreatic islets

(2010) Kyle J Gaulton et al.   NATURE GENETICS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

MutationTaster evaluates disease-causing potential of sequence alterations

(2010) Jana Marie Schwarz et al.   NATURE METHODS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

MOODS: fast search for position weight matrix matches in DNA sequences

(2009) J. Korhonen et al.   BIOINFORMATICS

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

Human Splicing Finder: an online bioinformatics tool to predict splicing signals

(2009) François-Olivier Desmet et al.   NUCLEIC ACIDS 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

SNAP predicts effect of mutations on protein function

(2008) Yana Bromberg et al.   BIOINFORMATICS