Mutation severity spectrum of rare alleles in the human genome is predictive of disease type

Modular epistasis and the compensatory evolution of gene deletion mutants

(2019) José I. Rojas Echenique et al.   PLoS Genetics

Heterozygous mutations cause genetic instability in a yeast model of cancer evolution

(2019) Miguel C. Coelho et al.   NATURE

The PSIPRED Protein Analysis Workbench: 20 years on

(2019) Daniel W A Buchan et al.   NUCLEIC ACIDS RESEARCH

OMA standalone: orthology inference among public and custom genomes and transcriptomes

(2019) Adrian M. Altenhoff et al.   GENOME RESEARCH

Assessing predictions on fitness effects of missense variants in calmodulin

(2019) Jing Zhang et al.   HUMAN MUTATION

The expanding phenotypes of cohesinopathies: one ring to rule them all!

(2019) Jessica Piché et al.   CELL CYCLE

Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations

(2019) Robert Fragoza et al.   Nature Communications

Compensatory mutations and epistasis for protein function

(2018) Jay F Storz   CURRENT OPINION IN STRUCTURAL BIOLOGY

Predicting the clinical impact of human mutation with deep neural networks

(2018) Laksshman Sundaram et al.   NATURE GENETICS

H3B-8800, an orally available small-molecule splicing modulator, induces lethality in spliceosome-mutant cancers

(2018) Michael Seiler et al.   NATURE MEDICINE

UniProt: the universal protein knowledgebase

(2018) The UniProt Consortium   NUCLEIC ACIDS RESEARCH

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding

(2018) Bálint Mészáros et al.   NUCLEIC ACIDS RESEARCH

Prediction and interpretation of deleterious coding variants in terms of protein structural stability

(2018) François Ancien et al.   Scientific Reports

The BioGRID interaction database: 2019 update

(2018) Rose Oughtred et al.   NUCLEIC ACIDS RESEARCH

Functional Analogy in Human Metabolism: Enzymes with Different Biological Roles or Functional Redundancy?

(2017) Rafael Mina Piergiorge et al.   Genome Biology and Evolution

Assessing predictions of fitness effects of missense mutations in SUMO-conjugating enzyme UBE2I

(2017) Jing Zhang et al.   HUMAN MUTATION

Mapping autosomal recessive intellectual disability: combined microarray and exome sequencing identifies 26 novel candidate genes in 192 consanguineous families

(2017) R Harripaul et al.   MOLECULAR PSYCHIATRY

Prevalence and architecture of de novo mutations in developmental disorders

(2017)   NATURE

Human gene essentiality

(2017) István Bartha et al.   NATURE REVIEWS GENETICS

Settling the score: variant prioritization and Mendelian disease

(2017) Karen Eilbeck et al.   NATURE REVIEWS GENETICS

Network propagation: a universal amplifier of genetic associations

(2017) Lenore Cowen et al.   NATURE REVIEWS GENETICS

DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins

(2017) Daniele Raimondi et al.   NUCLEIC ACIDS RESEARCH

ClinVar: improving access to variant interpretations and supporting evidence

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

The Reactome Pathway Knowledgebase

(2017) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Splicing Factor Mutations in Myelodysplasias: Insights from Spliceosome Structures

(2017) Jermaine L. Jenkins et al.   TRENDS IN GENETICS

High rate of adaptation of mammalian proteins that interact with Plasmodium and related parasites

(2017) Emily R. Ebel et al.   PLoS Genetics

PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology

(2017) Aris Gioutlakis et al.   PLoS One

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants

(2016) Nilah M. Ioannidis et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Multilevel biological characterization of exomic variants at the protein level significantly improves the identification of their deleterious effects

(2016) Daniele Raimondi et al.   BIOINFORMATICS

Explosive genetic evidence for explosive human population growth

(2016) Feng Gao et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Variation Interpretation Predictors: Principles, Types, Performance, and Choice

(2016) Abhishek Niroula et al.   HUMAN MUTATION

dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs

(2016) Xiaoming Liu et al.   HUMAN MUTATION

Integrative analyses reveal signaling pathways underlying familial breast cancer susceptibility

(2016) S. R. Piccolo et al.   Molecular Systems Biology

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

(2016) Monkol Lek et al.   NATURE

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

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

Analyzing and interpreting genome data at the network level with ConsensusPathDB

(2016) Ralf Herwig et al.   Nature Protocols

Robust classification of protein variation using structural modelling and large-scale data integration

(2016) Evan H. Baugh et al.   NUCLEIC ACIDS RESEARCH

DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants

(2016) Janet Piñero et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding

(2016) Yunhui Peng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Viruses are a dominant driver of protein adaptation in mammals

(2016) David Enard et al.   eLife

The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities

(2015) Jessica X. Chong et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2015) Yongwook Choi et al.   BIOINFORMATICS

Variegated RHOA mutations in adult T-cell leukemia/lymphoma

(2015) Y. Nagata et al.   BLOOD

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities

(2015) Traver Hart et al.   CELL

Yeast as a system for modeling mitochondrial disease mechanisms and discovering therapies

(2015) J.-P. Lasserre et al.   Disease Models & Mechanisms

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology

(2015) Sue Richards et al.   GENETICS IN MEDICINE

On Human Disease-Causing Amino Acid Variants: Statistical Study of Sequence and Structural Patterns

(2015) Marharyta Petukh et al.   HUMAN MUTATION

Genetic studies in intellectual disability and related disorders

(2015) Lisenka E. L. M. Vissers et al.   NATURE REVIEWS GENETICS

Haploinsufficiency predictions without study bias

(2015) Julia Steinberg et al.   NUCLEIC ACIDS RESEARCH

MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins

(2015) Sarah E. Calvo et al.   NUCLEIC ACIDS RESEARCH

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

(2015) Tauno Metsalu et al.   NUCLEIC ACIDS RESEARCH

Inactivating mutations in GNA13 and RHOA in Burkitt’s lymphoma and diffuse large B-cell lymphoma: a tumor suppressor function for the Gα13/RhoA axis in B cells

(2015) M O'Hayre et al.   ONCOGENE

The human gene damage index as a gene-level approach to prioritizing exome variants

(2015) Yuval Itan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene essentiality and synthetic lethality in haploid human cells

(2015) V. A. Blomen et al.   SCIENCE

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome

(2015) István Bartha et al.   PLoS Computational Biology

Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies

(2015) C. Dong et al.   HUMAN MOLECULAR GENETICS

DISOPRED3: precise disordered region predictions with annotated protein-binding activity

(2014) David T. Jones et al.   BIOINFORMATICS

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

(2014) Martin Kircher et al.   NATURE GENETICS

A framework for the interpretation of de novo mutation in human disease

(2014) Kaitlin E Samocha et al.   NATURE GENETICS

Essential Plasticity and Redundancy of Metabolism Unveiled by Synthetic Lethality Analysis

(2014) Oriol Güell et al.   PLoS Computational Biology

Identifying Mendelian disease genes with the Variant Effect Scoring Tool

(2013) Hannah Carter et al.   BMC GENOMICS

Contribution of rare and common variants determine complex diseases—Hirschsprung disease as a model

(2013) Maria M. Alves et al.   DEVELOPMENTAL BIOLOGY

Molecular Mechanisms of Disease-Causing Missense Mutations

(2013) Shannon Stefl et al.   JOURNAL OF MOLECULAR BIOLOGY

Large-scale gene function analysis with the PANTHER classification system

(2013) Huaiyu Mi et al.   Nature Protocols

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

(2013) S. C. J. Parker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Clinical Genomic Database

(2013) B. D. Solomon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction

(2013) Renxiang Yan et al.   Scientific Reports

Interpretation of Genomic Variants Using a Unified Biological Network Approach

(2013) Ekta Khurana et al.   PLoS Computational Biology

From Mouse to Human: Evolutionary Genomics Analysis of Human Orthologs of Essential Genes

(2013) Benjamin Georgi et al.   PLoS Genetics

DAVID-WS: a stateful web service to facilitate gene/protein list analysis

(2012) X. Jiao et al.   BIOINFORMATICS

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

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

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

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

Correlating disease-related mutations to their effect on protein stability: A large-scale analysis of the human proteome

(2011) Rita Casadio et al.   HUMAN MUTATION

Exome sequencing as a tool for Mendelian disease gene discovery

(2011) Michael J. Bamshad et al.   NATURE REVIEWS GENETICS

The IntAct molecular interaction database in 2012

(2011) S. Kerrien et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

Defining the Role of Essential Genes in Human Disease

(2011) Jonathan E. Dickerson et al.   PLoS One

Structural Variation in the Human Genome and its Role in Disease

(2010) Paweł Stankiewicz et al.   Annual Review of Medicine

Easy retrieval of single amino-acid polymorphisms and phenotype information using SwissVar

(2010) Anaïs Mottaz et al.   BIOINFORMATICS

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Characterising and Predicting Haploinsufficiency in the Human Genome

(2010) Ni Huang et al.   PLoS Genetics

Genetic Redundancy: New Tricks for Old Genes

(2009) Ran Kafri et al.   CELL

Identification of deleterious mutations within three human genomes

(2009) S. Chun et al.   GENOME RESEARCH

A genome-wide linkage and association scan reveals novel loci for autism

(2009) Lauren A. Weiss et al.   NATURE

Genetics of human gene expression: mapping DNA variants that influence gene expression

(2009) Vivian G. Cheung et al.   NATURE REVIEWS GENETICS

Human genetic variation and its contribution to complex traits

(2009) Kelly A. Frazer et al.   NATURE REVIEWS GENETICS

Dosage Effects of Cohesin Regulatory Factor PDS5 on Mammalian Development: Implications for Cohesinopathies

(2009) Bin Zhang et al.   PLoS One

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Human Protein Reference Database--2009 update

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