Phen-Gen: combining phenotype and genotype to analyze rare disorders
Genomics
2015-03-02 v1
Abstract
We introduce Phen-Gen, a method which combines patient disease symptoms and sequencing data with prior domain knowledge to identify the causative gene(s) for rare disorders.
Keywords
Cite
@article{arxiv.1502.07829,
title = {Phen-Gen: combining phenotype and genotype to analyze rare disorders},
author = {Asif Javed and Saloni Agrawal and Pauline C. Ng},
journal= {arXiv preprint arXiv:1502.07829},
year = {2015}
}
Related papers
View all related →
Machine Learning · Computer Science
PhenoKG: Knowledge Graph-Driven Gene Discovery and Patient Insights from Phenotypes Alone
Kamilia Zaripova, Ege Özsoy, Nassir Navab, Azade Farshad
2025-06-17
Quantitative Methods · Quantitative Biology
Analysis of the human diseasome reveals phenotype modules across common, genetic, and infectious diseases
Robert Hoehndorf, Paul N Schofield, Georgios V Gkoutos
2015-05-26
Quantitative Methods · Quantitative Biology
Integrative analysis of gene expression and phenotype data
Min Xu
2015-06-30
Genomics · Quantitative Biology
From Genotype to Phenotype: polygenic prediction of complex human traits
Timothy G. Raben, Louis Lello, Erik Widen, Stephen D. H. Hsu
2021-01-18
Quantitative Methods · Quantitative Biology
Association in Facial Phenotype, Gene, Disease: A Dataset for Explainable Rare Genetic Diseases Diagnosis
Jie Song, Mengqiao He, Shumin Ren, Bairong Shen
2025-04-21
Applications · Statistics
Special section: Statistical methods for next-generation gene sequencing data
Karen Kafadar
2012-06-29
Machine Learning · Computer Science
GenePheno: Interpretable Gene Knockout-Induced Phenotype Abnormality Prediction from Gene Sequences
Jingquan Yan, Yuwei Miao, Lei Yu, Yuzhi Guo +3
2025-11-18
Machine Learning · Computer Science
Knowledge Graph Sparsification for GNN-based Rare Disease Diagnosis
Premt Cara, Kamilia Zaripova, David Bani-Harouni, Nassir Navab +1
2025-10-13
Quantitative Methods · Quantitative Biology
Gene-SGAN: a method for discovering disease subtypes with imaging and genetic signatures via multi-view weakly-supervised deep clustering
Zhijian Yang, Junhao Wen, Ahmed Abdulkadir, Yuhan Cui +24
2023-01-27
Genomics · Quantitative Biology
PhenoLinker: Phenotype-Gene Link Prediction and Explanation using Heterogeneous Graph Neural Networks
Jose L. Mellina Andreu, Luis Bernal, Antonio F. Skarmeta, Mina Ryten +3
2025-06-03
Quantitative Methods · Quantitative Biology
DNA Language Model and Interpretable Graph Neural Network Identify Genes and Pathways Involved in Rare Diseases
Ali Saadat, Jacques Fellay
2024-11-12
Applications · Statistics
Expectile Neural Networks for Genetic Data Analysis of Complex Diseases
Jinghang Lin, Xiaoran Tong, Chenxi Li, Qing Lu
2020-10-28
Biological Physics · Physics
A dynamic network approach for the study of human phenotypes
Cesar A. Hidalgo, Nicholas Blumm, Albert-Laszlo Barabasi, Nicholas Christakis
2015-05-14
Computer Vision and Pattern Recognition · Computer Science
Few-Shot Meta Learning for Recognizing Facial Phenotypes of Genetic Disorders
Ömer Sümer, Fabio Hellmann, Alexander Hustinx, Tzung-Chien Hsieh +2
2023-05-25
Quantitative Methods · Quantitative Biology
Comprehensive Detection of Genes Causing a Phenotype using Phenotype Sequencing and Pathway Analysis
Marc Harper, Luisa Gronenberg, James Liao, Christopher Lee
2014-03-18
Quantitative Methods · Quantitative Biology
From Cellular Characteristics to Disease Diagnosis: Uncovering Phenotypes with Supercells
Julián Candia, Ryan Maunu, Meghan Driscoll, Angélique Biancotto +9
2013-09-10
Genomics · Quantitative Biology
Compressed Genotyping
Yaniv Erlich, Assaf Gordon, Michael Brand, Gregory J. Hannon +1
2016-11-17
Machine Learning · Statistics
Explainable Genetic Inheritance Pattern Prediction
Edmond Cunningham, Dana Schlegel, Andrew DeOrio
2018-12-06
Genomics · Quantitative Biology
Combining exome and gene expression datasets in one graphical model of disease to empower the discovery of disease mechanisms
Aziz M. Mezlini, Fabio Fuligni, Adam Shlien, Anna Goldenberg
2015-09-01
Quantitative Methods · Quantitative Biology
Computational Approaches for Disease Gene Identification
Peng Yang
2017-05-23
Applications · Statistics
Improving sequence-based genotype calls with linkage disequilibrium and pedigree information
Baiyu Zhou, Alice S. Whittemore
2012-06-29
Artificial Intelligence · Computer Science
An artificial intelligence framework for end-to-end rare disease phenotyping from clinical notes using large language models
Cathy Shyr, Yan Hu, Rory J. Tinker, Thomas A. Cassini +7
2026-02-25
Physics and Society · Physics
Understanding diseases as increased heterogeneity: a complex network computational framework
Massimiliano Zanin, Juan Manuel Tuñas, Ernestina Menasalvas
2018-06-06
Quantitative Methods · Quantitative Biology
INDIGENA: inductive prediction of disease-gene associations using phenotype ontologies
Fernando Zhapa-Camacho, Robert Hoehndorf
2026-02-03
Genomics · Quantitative Biology
A guided network propagation approach to identify disease genes that combines prior and new information
Borislav H. Hristov, Bernard Chazelle, Mona Singh
2020-01-20