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

Insights into genetics, human biology and disease gleaned from family based genomic studies

(2019) Jennifer E. Posey et al.   GENETICS IN MEDICINE

AVADA: toward automated pathogenic variant evidence retrieval directly from the full-text literature

(2019) Johannes Birgmeier et al.   GENETICS IN MEDICINE

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

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

A gene–phenotype relationship extraction pipeline from the biomedical literature using a representation learning approach

(2018) Wenhui Xing et al.   BIOINFORMATICS

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

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

PubCaseFinder: A Case-Report-Based, Phenotype-Driven Differential-Diagnosis System for Rare Diseases

(2018) Toyofumi Fujiwara et al.   AMERICAN JOURNAL OF HUMAN GENETICS

ClinPhen extracts and prioritizes patient phenotypes directly from medical records to expedite genetic disease diagnosis

(2018) Cole A. Deisseroth et al.   GENETICS IN MEDICINE

OMIM.org: leveraging knowledge across phenotype–gene relationships

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

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

(2018) Sebastian Köhler et al.   NUCLEIC ACIDS RESEARCH

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

ClinVar: improving access to variant interpretations and supporting evidence

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

Deriving genomic diagnoses without revealing patient genomes

(2017) Karthik A. Jagadeesh et al.   SCIENCE

An analysis of disease-gene relationship from Medline abstracts by DigSee

(2017) Jeongkyun Kim et al.   Scientific Reports

Clinical Practice Guidelines for Rare Diseases: The Orphanet Database

(2017) Sonia Pavan et al.   PLoS One

Systematic reanalysis of clinical exome data yields additional diagnoses: implications for providers

(2016) Aaron M. Wenger et al.   GENETICS IN MEDICINE

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

(2016) Monkol Lek et al.   NATURE

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

(2016) Karthik A Jagadeesh et al.   NATURE GENETICS

Genenames.org: the HGNC and VGNC resources in 2017

(2016) Bethan Yates et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Text Mining Genotype-Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine

(2016) Ayush Singhal et al.   PLoS Computational Biology

Phenotypic Variability of Childhood Charcot-Marie-Tooth Disease

(2016) Kayla M.D. Cornett et al.   JAMA Neurology

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

The European Genome-phenome Archive of human data consented for biomedical research

(2015) Ilkka Lappalainen et al.   NATURE GENETICS

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

(2015) Hui Yang et al.   NATURE METHODS

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

(2015) Damian Smedley et al.   Nature Protocols

PhenoMiner: from text to a database of phenotypes associated with OMIM diseases

(2015) Nigel Collier et al.   Database-The Journal of Biological Databases and Curation

DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes

(2015) J. Pinero et al.   Database-The Journal of Biological Databases and Curation

GNormPlus: An Integrative Approach for Tagging Genes, Gene Families, and Protein Domains

(2015) Chih-Hsuan Wei et al.   Biomed Research International

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

The usefulness of whole-exome sequencing in routine clinical practice

(2014) Alejandro Iglesias et al.   GENETICS IN MEDICINE

Clinical Interpretation and Implications of Whole-Genome Sequencing

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

“Is it Going to Hurt?”: The Impact of the Diagnostic Odyssey on Children and Their Families

(2014) Nikkola Carmichael et al.   Journal of Genetic Counseling

Large-scale discovery of novel genetic causes of developmental disorders

(2014) T. W. Fitzgerald et al.   NATURE

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

(2014) Asif Javed et al.   NATURE METHODS

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

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

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

PubTator: a web-based text mining tool for assisting biocuration

(2013) Chih-Hsuan Wei et al.   NUCLEIC ACIDS RESEARCH

Genic Intolerance to Functional Variation and the Interpretation of Personal Genomes

(2013) Slavé Petrovski et al.   PLoS Genetics

Harmonization of gene/protein annotations: towards a gold standard MEDLINE

(2012) David Campos et al.   BIOINFORMATICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature

(2010) Emily Doughty et al.   BIOINFORMATICS

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

(2010) M. Valiev et al.   COMPUTER PHYSICS COMMUNICATIONS

Using text to build semantic networks for pharmacogenomics

(2010) Adrien Coulet et al.   JOURNAL OF BIOMEDICAL INFORMATICS

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

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

Clinical Diagnostics in Human Genetics with Semantic Similarity Searches in Ontologies

(2009) Sebastian Köhler et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Exome sequencing identifies the cause of a mendelian disorder

(2009) Sarah B Ng et al.   NATURE GENETICS

Identifying gene-disease associations using centrality on a literature mined gene-interaction network

(2008) A. Ozgur et al.   BIOINFORMATICS

PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites

(2008) D. Cheng et al.   NUCLEIC ACIDS RESEARCH