ArticleNAR genomics and bioinformatics2020
Phen2Gene: rapid phenotype-driven gene prioritization for rare diseases.
Article in NAR genomics and bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed, 84 citations in OpenAlex.
- Artificial Intelligence in Neuromuscular Diseases: Opportunities for a Data-Scarce Field.Neurology and therapy · 2026Review
- PhenoSS: phenotype semantic similarity-based approach for rare disease prediction and patient clustering.Journal of the American Medical Informatics Association : JAMIA · 2026Article
- RESCUE: An end-to-end multi-agent LLM system for proactive rare-disease patient screening in the EHR.medRxiv : the preprint server for health sciences · 2026Article
- Interpretable fine-tuned large language models facilitate making genetic test decisions for rare diseases.NPJ digital medicine · 2026Article
- PhenoSS: Phenotype semantic similarity-based approach for rare disease prediction and patient clustering.medRxiv : the preprint server for health sciences · 2026Article
- Reframing AI for Rare Disease Recognition.Research square · 2026Article
- Diagnostic Accuracy of Large Language Models for Rare Diseases: A Systematic Review and Meta-Analysis.medRxiv : the preprint server for health sciences · 2026Article
- GEN-KnowRD: Reframing AI for Rare Disease Recognition.medRxiv : the preprint server for health sciences · 2026Article
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- PERADIGM: Phenotype embedding similarity-based rare disease gene mapping.PLoS genetics · 2025Article
- Expanding the utility of variant effect predictions with phenotype-specific models.Nature communications · 2025Article
- geneEX: An Integrated Phenotype-Driven Algorithm for Rapid Identification of Causative Variants in Monogenic Disorders.Molecular genetics & genomic medicine · 2025Article
- A Hypergraph powered approach to Phenotype-driven Gene Prioritization and Rare Disease Prediction.Scientific reports · 2025Article
- PhenoDP: leveraging deep learning for phenotype-based case reporting, disease ranking, and symptom recommendation.Genome medicine · 2025Article
- AI-powered precision medicine: utilizing genetic risk factor optimization to revolutionize healthcare.NAR genomics and bioinformatics · 2025Review
- Single-cell data combined with phenotypes improves variant interpretation.BMC genomics · 2025Article
- Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease.Genome research · 2025Article
- Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework.BMC bioinformatics · 2025Article
- A clinical knowledge graph-based framework to prioritize candidate genes for facilitating diagnosis of Mendelian diseases and rare genetic conditions.BMC bioinformatics · 2025Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
13 authors at 3 institutions in 1 country.
Funding
Abstract
Human Phenotype Ontology (HPO) terms are increasingly used in diagnostic settings to aid in the characterization of patient phenotypes. The HPO annotation database is updated frequently and can provide detailed phenotype knowledge on various human diseases, and many HPO terms are now mapped to candidate causal genes with binary relationships. To further improve the genetic diagnosis of rare diseases, we incorporated these HPO annotations, gene-disease databases and gene-gene databases in a probabilistic model to build a novel HPO-driven gene prioritization tool, Phen2Gene. Phen2Gene accesses a database built upon this information called the HPO2Gene Knowledgebase (H2GKB), which provides weighted and ranked gene lists for every HPO term. Phen2Gene is then able to access the H2GKB for patient-specific lists of HPO terms or PhenoPacket descriptions supported by GA4GH (http://phenopackets.org/), calculate a prioritized gene list based on a probabilistic model and output gene-disease relationships with great accuracy. Phen2Gene outperforms existing gene prioritization tools in speed and acts as a real-time phenotype-driven gene prioritization tool to aid the clinical diagnosis of rare undiagnosed diseases. In addition to a command line tool released under the MIT license (https://github.com/WGLab/Phen2Gene), we also developed a web server and web service (https://phen2gene.wglab.org/) for running the tool via web interface or RESTful API queries. Finally, we have curated a large amount of benchmarking data for phenotype-to-gene tools involving 197 patients across 76 scientific articles and 85 patients' de-identified HPO term data from the Children's Hospital of Philadelphia.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.