Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome

Paternally inherited cis-regulatory structural variants are associated with autism

(2018) William M. Brandler et al.   SCIENCE

Computational Approaches to Prioritize Cancer Driver Missense Mutations

(2018) Feiyang Zhao et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies

(2017) Peter D. Stenson et al.   HUMAN GENETICS

Analysis of somatic microsatellite indels identifies driver events in human tumors

(2017) Yosef E Maruvka et al.   NATURE BIOTECHNOLOGY

Effects of short indels on protein structure and function in human genomes

(2017) Maoxuan Lin et al.   Scientific Reports

Frequency and Complexity of De Novo Structural Mutation in Autism

(2016) William M. Brandler et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Protein function in precision medicine: deep understanding with machine learning

(2016) Burkhard Rost et al.   FEBS LETTERS

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

(2016) Monkol Lek et al.   NATURE

Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability

(2016) Stefan H Lelieveld et al.   NATURE NEUROSCIENCE

MutaBind estimates and interprets the effects of sequence variants on protein–protein interactions

(2016) Minghui Li et al.   NUCLEIC ACIDS RESEARCH

The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes

(2016) Bernard Pereira et al.   Nature Communications

The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease

(2016) Jose Lugo-Martinez et al.   PLoS Computational Biology

Structure-Based Analysis Reveals Cancer Missense Mutations Target Protein Interaction Interfaces

(2016) H. Billur Engin et al.   PLoS One

Polymorphism Analysis Reveals Reduced Negative Selection and Elevated Rate of Insertions and Deletions in Intrinsically Disordered Protein Regions

(2015) Tahsin Khan et al.   Genome Biology and Evolution

Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel)

(2015) Christopher Douville et al.   HUMAN MUTATION

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Systematic discovery of complex insertions and deletions in human cancers

(2015) Kai Ye et al.   NATURE MEDICINE

ClinVar: public archive of interpretations of clinically relevant variants

(2015) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

A comprehensive study of small non-frameshift insertions/deletions in proteins and prediction of their phenotypic effects by a machine learning method (KD4i)

(2014) Carlos Bermejo-Das-Neves et al.   BMC BIOINFORMATICS

Clinical Interpretation and Implications of Whole-Genome Sequencing

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

Discriminating between deleterious and neutral non-frameshifting indels based on protein interaction networks and hybrid properties

(2014) Ning Zhang et al.   MOLECULAR GENETICS AND GENOMICS

Synaptic, transcriptional and chromatin genes disrupted in autism

(2014) Silvia De Rubeis et al.   NATURE

The contribution of de novo coding mutations to autism spectrum disorder

(2014) Ivan Iossifov et al.   NATURE

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

(2014) Martin Kircher et al.   NATURE GENETICS

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

The structural and functional signatures of proteins that undergo multiple events of post-translational modification

(2014) Vikas Pejaver et al.   PROTEIN SCIENCE

Determining Effects of Non-synonymous SNPs on Protein-Protein Interactions using Supervised and Semi-supervised Learning

(2014) Nan Zhao et al.   PLoS Computational Biology

MutPred Splice: machine learning-based prediction of exonic variants that disrupt splicing

(2014) Matthew Mort et al.   GENOME BIOLOGY

Predicting the functional consequences of cancer-associated amino acid substitutions

(2013) Hashem A. Shihab et al.   BIOINFORMATICS

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes

(2013) S. B. Montgomery et al.   GENOME RESEARCH

MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures

(2013) Noushin Niknafs et al.   HUMAN GENETICS

Towards Precision Medicine: Advances in Computational Approaches for the Analysis of Human Variants

(2013) Thomas A. Peterson et al.   JOURNAL OF MOLECULAR BIOLOGY

The eukaryotic linear motif resource ELM: 10 years and counting

(2013) Holger Dinkel et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2014 update

(2013) Donna Karolchik et al.   NUCLEIC ACIDS RESEARCH

Cancer Missense Mutations Alter Binding Properties of Proteins and Their Interaction Networks

(2013) Hafumi Nishi et al.   PLoS One

SIFT Indel: Predictions for the Functional Effects of Amino Acid Insertions/Deletions in Proteins

(2013) Jing Hu et al.   PLoS One

CanDrA: Cancer-Specific Driver Missense Mutation Annotation with Optimized Features

(2013) Yong Mao et al.   PLoS One

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

The mutational landscape of phosphorylation signaling in cancer

(2013) Jüri Reimand et al.   Scientific Reports

DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels

(2013) Huiying Zhao et al.   GENOME BIOLOGY

Whole-Genome Sequencing in Autism Identifies Hot Spots for De Novo Germline Mutation

(2012) Jacob J. Michaelson et al.   CELL

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

Bioinformatics challenges for personalized medicine

(2011) Guy Haskin Fernald et al.   BIOINFORMATICS

Disease mutations in disordered regions—exception to the rule?

(2011) Vladimir Vacic et al.   Molecular BioSystems

IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins

(2011) B. A. Shoemaker et al.   NUCLEIC ACIDS RESEARCH

The IntAct molecular interaction database in 2012

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

Analysis of protein function and its prediction from amino acid sequence

(2011) Wyatt T. Clark et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Using bioinformatics to predict the functional impact of SNVs

(2010) M. S. Cline et al.   BIOINFORMATICS

Sequence feature-based prediction of protein stability changes upon amino acid substitutions

(2010) Shaolei Teng et al.   BMC GENOMICS

In silico functional profiling of human disease-associated and polymorphic amino acid substitutions

(2010) Matthew Mort et al.   HUMAN MUTATION

The Simons Simplex Collection: A Resource for Identification of Autism Genetic Risk Factors

(2010) Gerald D. Fischbach et al.   NEURON

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

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

Automated inference of molecular mechanisms of disease from amino acid substitutions

(2009) B. Li et al.   BIOINFORMATICS

Cancer-Specific High-Throughput Annotation of Somatic Mutations: Computational Prediction of Driver Missense Mutations

(2009) H. Carter et al.   CANCER RESEARCH

COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer

(2009) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Influence of Sequence Changes and Environment on Intrinsically Disordered Proteins

(2009) Amrita Mohan et al.   PLoS Computational Biology

Gain and loss of phosphorylation sites in human cancer

(2008) P. Radivojac et al.   BIOINFORMATICS