An Improved Phenotype-Driven Tool for Rare Mendelian Variant Prioritization: Benchmarking Exomiser on Real Patient Whole-Exome Data

Genetic Basis of Inherited Retinal Disease in a Molecularly Characterized Cohort of More Than 3000 Families from the United Kingdom

(2020) Nikolas Pontikos et al.   OPHTHALMOLOGY

Rapid and accurate interpretation of clinical exomes using Phenoxome: a computational phenotype-driven approach

(2019) Chao Wu et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

An ontological foundation for ocular phenotypes and rare eye diseases

(2019) Panagiotis I. Sergouniotis et al.   Orphanet Journal of Rare Diseases

Xrare: a machine learning method jointly modeling phenotypes and genetic evidence for rare disease diagnosis

(2019) Qigang Li et al.   GENETICS IN MEDICINE

DeepPVP: phenotype-based prioritization of causative variants using deep learning

(2019) Imane Boudellioua et al.   BMC BIOINFORMATICS

PhenoPro: a novel toolkit for assisting in the diagnosis of Mendelian disease

(2019) Zixiu Li et al.   BIOINFORMATICS

MutationDistiller: user-driven identification of pathogenic DNA variants

(2019) Daniela Hombach et al.   NUCLEIC ACIDS RESEARCH

Doc2Hpo: a web application for efficient and accurate HPO concept curation

(2019) Cong Liu et al.   NUCLEIC ACIDS RESEARCH

Variant filtering, digenic variants, and other challenges in clinical sequencing: a lesson from fibrillinopathies

(2019) Arash Najafi et al.   CLINICAL GENETICS

Deep Phenotyping on Electronic Health Records Facilitates Genetic Diagnosis by Clinical Exomes

(2018) Jung Hoon Son et al.   AMERICAN JOURNAL OF HUMAN GENETICS

GenIO: a phenotype-genotype analysis web server for clinical genomics of rare diseases

(2018) Daniel Koile et al.   BMC BIOINFORMATICS

Clinical sequencing: From raw data to diagnosis with lifetime value

(2018) S.M. Caspar et al.   CLINICAL GENETICS

Phrank measures phenotype sets similarity to greatly improve Mendelian diagnostic disease prioritization

(2018) Karthik A. Jagadeesh et al.   GENETICS IN MEDICINE

A recurrent de novo missense mutation in UBTF causes developmental neuroregression

(2018) Camilo Toro et al.   HUMAN MOLECULAR GENETICS

Predicting the clinical impact of human mutation with deep neural networks

(2018) Laksshman Sundaram et al.   NATURE GENETICS

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

The 100 000 Genomes Project: bringing whole genome sequencing to the NHS

(2018) Clare Turnbull et al.   BMJ-British Medical Journal

The 100 000 Genomes Project: bringing whole genome sequencing to the NHS

(2018) Clare Turnbull et al.   BMJ-British Medical Journal

ClinVar at five years: Delivering on the promise

(2018) Melissa J. Landrum et al.   HUMAN MUTATION

OMIM.org: leveraging knowledge across phenotype–gene relationships

(2018) Joanna S Amberger et al.   NUCLEIC ACIDS RESEARCH

CADD: predicting the deleteriousness of variants throughout the human genome

(2018) Philipp Rentzsch et al.   NUCLEIC ACIDS RESEARCH

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources

(2018) Sebastian Köhler et al.   NUCLEIC ACIDS RESEARCH

Using high-resolution variant frequencies to empower clinical genome interpretation

(2017) Nicola Whiffin et al.   GENETICS IN MEDICINE

Heterozygous Pathogenic Variant inDACT1Causes an Autosomal-Dominant Syndrome with Features Overlapping Townes-Brocks Syndrome

(2017) Bryn D. Webb et al.   HUMAN MUTATION

Settling the score: variant prioritization and Mendelian disease

(2017) Karen Eilbeck et al.   NATURE REVIEWS GENETICS

Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse

(2017) Cynthia L Smith et al.   NUCLEIC ACIDS RESEARCH

A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease

(2016) Damian Smedley et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

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

Phenotypic evolution of UNC80 loss of function

(2016) Elise Valkanas et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Variable expressivity and genetic heterogeneity involving DPT and SEMA3D genes in autosomal dominant familial Meniere’s disease

(2016) Carmen Martín-Sierra et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

A novel missense variant inPRKCBsegregates low-frequency hearing loss in an autosomal dominant family with Meniere’s disease

(2016) Carmen Martín-Sierra et al.   HUMAN MOLECULAR GENETICS

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

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

(2016) Karthik A Jagadeesh et al.   NATURE GENETICS

The Human Phenotype Ontology in 2017

(2016) Sebastian Köhler et al.   NUCLEIC ACIDS RESEARCH

A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics

(2016) Regis A. James et al.   Genome Medicine

An interactive genome browser of association results from the UK10K cohorts project

(2015) Matthias Geihs et al.   BIOINFORMATICS

OVA: Integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization

(2015) Agne Antanaviciute et al.   BIOINFORMATICS

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

(2015) Hashem A. Shihab et al.   BIOINFORMATICS

Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency

(2015) William P. Bone et al.   GENETICS IN MEDICINE

A method for calculating probabilities of fitness consequences for point mutations across the human genome

(2015) Brad Gulko et al.   NATURE GENETICS

Phenolyzer: phenotype-based prioritization of candidate genes for human diseases

(2015) Hui Yang et al.   NATURE METHODS

Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR

(2015) Hui Yang et al.   Nature Protocols

Next-generation diagnostics and disease-gene discovery with the Exomiser

(2015) Damian Smedley 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

Phevor Combines Multiple Biomedical Ontologies for Accurate Identification of Disease-Causing Alleles in Single Individuals and Small Nuclear Families

(2014) Marc V. Singleton et al.   AMERICAN JOURNAL OF HUMAN GENETICS

SAMBLASTER: fast duplicate marking and structural variant read extraction

(2014) G. G. Faust et al.   BIOINFORMATICS

DANN: a deep learning approach for annotating the pathogenicity of genetic variants

(2014) Daniel Quang et al.   BIOINFORMATICS

PhenoVar: a phenotype-driven approach in clinical genomics for the diagnosis of polymalformative syndromes

(2014) Yannis J Trakadis et al.   BMC Medical Genomics

Identification of two novel mutations in FAM136A and DTNA genes in autosomal-dominant familial Meniere's disease

(2014) T. Requena et al.   HUMAN MOLECULAR GENETICS

Jannovar: A Java Library for Exome Annotation

(2014) Marten Jäger et al.   HUMAN MUTATION

A missense mutation in the splicing factor geneDHX38is associated with early-onset retinitis pigmentosa with macular coloboma

(2014) Muhammad Ajmal et al.   JOURNAL OF MEDICAL GENETICS

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

(2014) Martin Kircher et al.   NATURE GENETICS

Phen-Gen: combining phenotype and genotype to analyze rare disorders

(2014) Asif Javed et al.   NATURE METHODS

A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies

(2014) Alejandro Alemán et al.   NUCLEIC ACIDS RESEARCH

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome

(2014) T. Zemojtel et al.   Science Translational Medicine

Identifying Mendelian disease genes with the Variant Effect Scoring Tool

(2013) Hannah Carter et al.   BMC GENOMICS

Improved exome prioritization of disease genes through cross-species phenotype comparison

(2013) P. N. Robinson et al.   GENOME RESEARCH

PhenoDB: A New Web-Based Tool for the Collection, Storage, and Analysis of Phenotypic Features

(2013) Ada Hamosh et al.   HUMAN MUTATION

PhenoTips: Patient Phenotyping Software for Clinical and Research Use

(2013) Marta Girdea et al.   HUMAN MUTATION

eXtasy: variant prioritization by genomic data fusion

(2013) Alejandro Sifrim et al.   NATURE METHODS

Rare-disease genetics in the era of next-generation sequencing: discovery to translation

(2013) Kym M. Boycott et al.   NATURE REVIEWS GENETICS

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

(2013) Sebastian Köhler et al.   NUCLEIC ACIDS RESEARCH

PhenoDigm: analyzing curated annotations to associate animal models with human diseases

(2013) D. Smedley et al.   Database-The Journal of Biological Databases and Curation

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

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

Representation of rare diseases in health information systems: The orphanet approach to serve a wide range of end users

(2012) Ana Rath et al.   HUMAN MUTATION

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

(2012)   NATURE

ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics

(2012) Douglas G. Howe et al.   NUCLEIC ACIDS RESEARCH

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

Exome sequencing as a tool for Mendelian disease gene discovery

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

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

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

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

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

Identifying novel constrained elements by exploiting biased substitution patterns

(2009) Manuel Garber et al.   BIOINFORMATICS

Gene copy number variation and common human disease

(2009) M Fanciulli et al.   CLINICAL GENETICS

Identification of deleterious mutations within three human genomes

(2009) S. Chun et al.   GENOME RESEARCH

The Human Phenotype Ontology: A Tool for Annotating and Analyzing Human Hereditary Disease

(2008) Peter N. Robinson et al.   AMERICAN JOURNAL OF HUMAN GENETICS