Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts

PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels

(2015) Yongwook Choi et al.   BIOINFORMATICS

Monoallelic and Biallelic Mutations in MAB21L2 Cause a Spectrum of Major Eye Malformations

(2014) Joe Rainger et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature

(2014) Reece K. Hart et al.   BIOINFORMATICS

Performance comparison of four exome capture systems for deep sequencing

(2014) Chandra Sekhar Chilamakuri et al.   BMC GENOMICS

Managing clinically significant findings in research: the UK10K example

(2014) Jane Kaye et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

SG-ADVISER CNV: copy-number variant annotation and interpretation

(2014) Galina A. Erikson et al.   GENETICS IN MEDICINE

Clinical Interpretation and Implications of Whole-Genome Sequencing

(2014) Frederick E. Dewey et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Guidelines for investigating causality of sequence variants in human disease

(2014) D. G. MacArthur et al.   NATURE

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

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

(2014) Joanna S. Amberger et al.   NUCLEIC ACIDS RESEARCH

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

Gene: a gene-centered information resource at NCBI

(2014) Garth R. Brown et al.   NUCLEIC ACIDS RESEARCH

CanvasDB: a local database infrastructure for analysis of targeted- and whole genome re-sequencing projects

(2014) A. Ameur et al.   Database-The Journal of Biological Databases and Curation

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

(2014) Davis J McCarthy et al.   Genome Medicine

Expansion of Ocular Phenotypic Features Associated With Mutations inADAMTS18

(2014) Aman Chandra et al.   JAMA Ophthalmology

dbNSFP v2.0: A Database of Human Non-synonymous SNVs and Their Functional Predictions and Annotations

(2013) Xiaoming Liu et al.   HUMAN MUTATION

RefSeq: an update on mammalian reference sequences

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

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

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

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations

(2013) Umadevi Paila et al.   PLoS Computational Biology

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

(2012) Pablo Cingolani et al.   FLY

A SNPshot of PubMed to associate genetic variants with drugs, diseases, and adverse reactions

(2012) Jörg Hakenberg et al.   JOURNAL OF BIOMEDICAL INFORMATICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

dbVar and DGVa: public archives for genomic structural variation

(2012) Ilkka Lappalainen et al.   NUCLEIC ACIDS RESEARCH

Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

(2012) J. A. Tennessen et al.   SCIENCE

The GNAT library for local and remote gene mention normalization

(2011) J. Hakenberg et al.   BIOINFORMATICS

Next generation genome-wide association tool: Design and coverage of a high-throughput European-optimized SNP array

(2011) Thomas J. Hoffmann et al.   GENOMICS

Translational bioinformatics: linking knowledge across biological and clinical realms: Figure 1

(2011) Indra Neil Sarkar et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

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

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

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

(2010) William McLaren et al.   BIOINFORMATICS

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

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

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

The Characterization of Twenty Sequenced Human Genomes

(2010) Kimberly Pelak et al.   PLoS Genetics

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

(2009) Prateek Kumar et al.   Nature Protocols