Phen2Disease: a phenotype-driven model for disease and gene prioritization by bidirectional maximum matching semantic similarities

PhenoApt leverages clinical expertise to prioritize candidate genes via machine learning

(2022) Zefu Chen et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases

(2022) Xiao Yuan et al.   BRIEFINGS IN BIOINFORMATICS

PhenoTagger: A Hybrid Method for Phenotype Concept Recognition using Human Phenotype Ontology

(2021) Ling Luo et al.   BIOINFORMATICS

Exome sequencing reveals genetic architecture in patients with isolated or syndromic short stature

(2021) Xin Fan et al.   Journal of Genetics and Genomics

Deciphering the mutational signature of congenital limb malformations

(2021) Liying Sun et al.   Molecular Therapy-Nucleic Acids

Diagnostic yield and clinical impact of exome sequencing in early-onset scoliosis (EOS)

(2020) Sen Zhao et al.   JOURNAL OF MEDICAL GENETICS

AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature

(2020) Johannes Birgmeier et al.   Science Translational Medicine

Interpretable Clinical Genomics with a Likelihood Ratio Paradigm

(2020) Peter N. Robinson et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Human Phenotype Ontology in 2021

(2020) Sebastian Köhler et al.   NUCLEIC ACIDS RESEARCH

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

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

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

(2019) Qigang Li et al.   GENETICS IN MEDICINE

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

(2019) Cong Liu et al.   NUCLEIC ACIDS RESEARCH

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

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

A new method to measure the semantic similarity from query phenotypic abnormalities to diseases based on the human phenotype ontology

(2018) Xiaofeng Gong et al.   BMC BIOINFORMATICS

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

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

TAF1 Variants Are Associated with Dysmorphic Features, Intellectual Disability, and Neurological Manifestations

(2015) Jason A. O’Rawe et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Clinical application of whole-exome sequencing across clinical indications

(2015) Kyle Retterer et al.   GENETICS IN MEDICINE

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

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders

(2015) Jenny C Taylor et al.   NATURE GENETICS

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

(2015) Hui Yang et al.   NATURE METHODS

Phenotype-driven strategies for exome prioritization of human Mendelian disease genes

(2015) Damian Smedley et al.   Genome Medicine

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

Molecular Findings Among Patients Referred for Clinical Whole-Exome Sequencing

(2014) Yaping Yang et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Clinical Exome Sequencing for Genetic Identification of Rare Mendelian Disorders

(2014) Hane Lee et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

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

(2014) Asif Javed et al.   NATURE METHODS

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

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

eXtasy: variant prioritization by genomic data fusion

(2013) Alejandro Sifrim et al.   NATURE METHODS

Clinical Whole-Exome Sequencing for the Diagnosis of Mendelian Disorders

(2013) Yaping Yang et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genetic Considerations in Hypertrophic Cardiomyopathy

(2012) Carolyn Y. Ho   PROGRESS IN CARDIOVASCULAR DISEASES

Rapid Whole-Genome Sequencing for Genetic Disease Diagnosis in Neonatal Intensive Care Units

(2012) C. J. Saunders et al.   Science Translational Medicine

Enhancing MEDLINE document clustering by incorporating MeSH semantic similarity

(2009) Shanfeng Zhu et al.   BIOINFORMATICS

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

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