AIMC Topic: Genes
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A compendium of human gene functions derived from evolutionary modelling.
Nature
Feb 26, 2025
A comprehensive, computable representation of the functional repertoire of all macromolecules encoded within the human genome is a foundational resource for biology and biomedical research. The Gene Ontology Consortium has been working towards this g...
On knowing a gene: A distributional hypothesis of gene function.
Cell systems
May 28, 2024
As words can have multiple meanings that depend on sentence context, genes can have various functions that depend on the surrounding biological system. This pleiotropic nature of gene function is limited by ontologies, which annotate gene functions w...
Pathway information extracted from 25 years of pathway figures.
Genome biology
Nov 9, 2020
Thousands of pathway diagrams are published each year as static figures inaccessible to computational queries and analyses. Using a combination of machine learning, optical character recognition, and manual curation, we identified 64,643 pathway figu...
Genes, the brain, and artificial intelligence in evolution.
Journal of human genetics
Jul 27, 2020
Three important systems, genes, the brain, and artificial intelligence (especially deep learning) have similar goals, namely, the maximization of likelihood or minimization of cross-entropy. Animal brains have evolved through predator-prey interactio...
Deep Collaborative Filtering for Prediction of Disease Genes.
IEEE/ACM transactions on computational biology and bioinformatics
Mar 26, 2019
Accurate prioritization of potential disease genes is a fundamental challenge in biomedical research. Various algorithms have been developed to solve such problems. Inductive Matrix Completion (IMC) is one of the most reliable models for its well-est...
MaGIC: a machine learning tool set and web application for monoallelic gene inference from chromatin.
BMC bioinformatics
Feb 28, 2019
BACKGROUND: A large fraction of human and mouse autosomal genes are subject to random monoallelic expression (MAE), an epigenetic mechanism characterized by allele-specific gene expression that varies between clonal cell lineages. MAE is highly cell-...
FunMappOne: a tool to hierarchically organize and visually navigate functional gene annotations in multiple experiments.
BMC bioinformatics
Feb 15, 2019
BACKGROUND: Functional annotation of genes is an essential step in omics data analysis. Multiple databases and methods are currently available to summarize the functions of sets of genes into higher level representations, such as ontologies and molec...
Universal method for robust detection of circadian state from gene expression.
Proceedings of the National Academy of Sciences of the United States of America
Sep 10, 2018
Circadian clocks play a key role in regulating a vast array of biological processes, with significant implications for human health. Accurate assessment of physiological time using transcriptional biomarkers found in human blood can significantly imp...
NMFGO: Gene Function Prediction via Nonnegative Matrix Factorization with Gene Ontology.
IEEE/ACM transactions on computational biology and bioinformatics
Jul 30, 2018
Gene Ontology (GO) is a controlled vocabulary of terms that describe molecule function, biological roles, and cellular locations of gene products (i.e., proteins and RNAs), it hierarchically organizes more than 43,000 GO terms via the direct acyclic ...
Multi-Factored Gene-Gene Proximity Measures Exploiting Biological Knowledge Extracted from Gene Ontology: Application in Gene Clustering.
IEEE/ACM transactions on computational biology and bioinformatics
Jun 21, 2018
To describe the cellular functions of proteins and genes, a potential dynamic vocabulary is Gene Ontology (GO), which comprises of three sub-ontologies namely, Biological-process, Cellular-component, and Molecular-function. It has several application...
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