ArticleJournal of computational biology : a journal of computational molecular cell biology2023
Stochastic Modeling of Gene Expression Evolution Uncovers Tissue- and Sex-Specific Properties of Expression Evolution in the
Article in Journal of computational biology : a journal of computational molecular cell biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 13 citations in OpenAlex.
- Lineage-aware stochastic modeling reveals gene-expression dynamics in development and disease.bioRxiv : the preprint server for biology · 2026Article
- Article
- A framework for identifying transcript orthologs: the evolution of sex bias in alternative transcript structure in Drosophila.bioRxiv : the preprint server for biology · 2026Article
- Conservation and divergence of sex-biased gene expression across 50 million years of Drosophila evolution.Molecular biology and evolution · 2026Article
- Article
- Paralog-Dependent Specialization of Paf1C Subunit, Ctr9, for Sex Chromosome Gene Regulation and Male Germline Differentiation in Drosophila.Genes to cells : devoted to molecular & cellular mechanisms · 2025Article
- GeneAgent: self-verification language agent for gene-set analysis using domain databases.Nature methods · 2025Article
- Quantifying Transcriptome Turnover on Phylogenies by Modeling Gene Expression as a Binary Trait.Molecular biology and evolution · 2025Article
- Stochastic modeling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones.Cell systems · 2025Article
- cis- and trans-regulatory contributions to a hierarchy of factors influencing gene expression variation.Communications biology · 2024Article
- Stochastic modelling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones.bioRxiv : the preprint server for biology · 2024Article
- Evolution of chemosensory tissues and cells across ecologically diverse Drosophilids.Nature communications · 2024Article
- The seminal odorant binding protein Obp56g is required for mating plug formation and male fertility ineLife · 2023Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Gene expression evolution is typically modeled with the stochastic Ornstein-Uhlenbeck (OU) process. It has been suggested that the estimation of within-species variations using replicated data can increase the predictive power of such models, but this hypothesis has not been fully tested. We developed EvoGeneX, a computationally efficient implementation of the OU-based method that models within-species variation. Using extensive simulations, we show that modeling within-species variations and appropriate selection of species improve the performance of the model. Further, to facilitate a comparative analysis of expression evolution, we introduce a formal measure of evolutionary expression divergence for a group of genes using the rate and the asymptotic level of divergence. With these tools in hand, we performed the first-ever analysis of the evolution of gene expression across different body-parts, species, and sexes of the
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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.