dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs

dbMTS: A comprehensive database of putative human microRNA target site SNVs and their functional predictions

(2020) Chang Li et al.   HUMAN MUTATION

Predicting Splicing from Primary Sequence with Deep Learning

(2019) Kishore Jaganathan et al.   CELL

Predicting the clinical impact of human mutation with deep neural networks

(2018) Laksshman Sundaram et al.   NATURE GENETICS

ClinPred: Prediction Tool to Identify Disease-Relevant Nonsynonymous Single-Nucleotide Variants

(2018) Najmeh Alirezaie et al.   AMERICAN JOURNAL OF HUMAN GENETICS

CADD: predicting the deleteriousness of variants throughout the human genome

(2018) Philipp Rentzsch et al.   NUCLEIC ACIDS RESEARCH

PERCH: A Unified Framework for Disease Gene Prioritization

(2017) Bing-Jian Feng   HUMAN MUTATION

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

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

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

(2017) Daniele Raimondi et al.   NUCLEIC ACIDS RESEARCH

Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes

(2017) Suganthi Balasubramanian et al.   Nature Communications

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

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

UCSC Data Integrator and Variant Annotation Integrator

(2016) Angie S. Hinrichs et al.   BIOINFORMATICS

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

The performance of deleteriousness prediction scores for rare non-protein-changing single nucleotide variants in human genes

(2016) Xiaoming Liu et al.   JOURNAL OF MEDICAL GENETICS

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

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

M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity

(2016) Karthik A Jagadeesh et al.   NATURE GENETICS

An integrative approach to predicting the functional effects of non-coding and coding sequence variation

(2015) Hashem A. Shihab et al.   BIOINFORMATICS

Big Data: the challenge for small research groups in the era of cancer genomics

(2015) Aisyah Mohd Noor et al.   BRITISH JOURNAL OF CANCER

WGSA: an annotation pipeline for human genome sequencing studies

(2015) Xiaoming Liu et al.   JOURNAL OF MEDICAL GENETICS

SIFT missense predictions for genomes

(2015) Robert Vaser et al.   Nature Protocols

A Statistical Framework to Predict Functional Non-Coding Regions in the Human Genome Through Integrated Analysis of Annotation Data

(2015) Qiongshi Lu et al.   Scientific Reports

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

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

MutationTaster2: mutation prediction for the deep-sequencing age

(2014) Jana Marie Schwarz et al.   NATURE METHODS

In silico prediction of splice-altering single nucleotide variants in the human genome

(2014) Xueqiu Jian et al.   NUCLEIC ACIDS RESEARCH

The human splicing code reveals new insights into the genetic determinants of disease

(2014) H. Y. Xiong et al.   SCIENCE

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

(2014) Davis J McCarthy et al.   Genome Medicine

Identifying Mendelian disease genes with the Variant Effect Scoring Tool

(2013) Hannah Carter et al.   BMC GENOMICS

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

(2013) Xiaoming Liu et al.   HUMAN MUTATION

Sequencing studies in human genetics: design and interpretation

(2013) David B. Goldstein et al.   NATURE REVIEWS GENETICS

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

(2012) Pablo Cingolani et al.   FLY

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

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

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

APPRIS: annotation of principal and alternative splice isoforms

(2012) Jose Manuel Rodriguez et al.   NUCLEIC ACIDS RESEARCH

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

Clan Genomics and the Complex Architecture of Human Disease

(2011) James R. Lupski et al.   CELL

dbNSFP: A lightweight database of human nonsynonymous SNPs and their functional predictions

(2011) Xiaoming Liu et al.   HUMAN MUTATION

Exome sequencing as a tool for Mendelian disease gene discovery

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

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

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

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

BioMart Central Portal: an open database network for the biological community

(2011) J. M. Guberman et al.   Database-The Journal of Biological Databases and Curation

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

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

Identification of deleterious mutations within three human genomes

(2009) S. Chun et al.   GENOME RESEARCH

Widespread Genomic Signatures of Natural Selection in Hominid Evolution

(2009) Graham McVicker et al.   PLoS Genetics