ArticleGenome biology and evolution2018
Phylogenetic Clustering of Genes Reveals Shared Evolutionary Trajectories and Putative Gene Functions.
Article in Genome biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
20 citing papers in PubMed, 38 citations in OpenAlex.
- Sequence Conservation and Functional Significance of Charged Clusters in Mitochondria-Located Proteins of Green Plants.Journal of molecular evolution · 2026Article
- The Impact of Mitochondrial DNA Depletion on Mitochondrial Ultrastructure, Photosynthesis, and the mTERF Gene Family inInternational journal of molecular sciences · 2026Article
- CladeOScope-GSA: Revealing Evolutionary Associations Across Gene Sets.International journal of molecular sciences · 2026Article
- Unraveling Evolutionary Insights into AVT Peptide Conservation and Antimicrobial Motif Prediction Across Taxa.International journal of molecular sciences · 2025Article
- ParallelEvolCCM: Quantifying Coevolutionary Patterns Among Genomic Features.Genome biology and evolution · 2025Article
- Genome-wide analysis of the KCS gene family in Medicago truncatula and their expression profile under various abiotic stress.Scientific reports · 2025Article
- Genome-Wide Identification of β-Ketoacyl CoA Synthase Gene Family in Melon (Current issues in molecular biology · 2025Article
- The complete chloroplast genome ofMitochondrial DNA. Part B, Resources · 2025Article
- Using multi-scale genomics to associate poorly annotated genes with rare diseases.Genome medicine · 2024Article
- The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles.Systematic biology · 2023Article
- Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes.BMC bioinformatics · 2023Article
- Genome-wide identification and expression analysis of theFrontiers in plant science · 2023Article
- Article
- Exploring the mobilome and resistome ofMicrobial genomics · 2022Article
- A comparative whole-genome approach identifies bacterial traits for marine microbial interactions.Communications biology · 2022Article
- Genome-Wide Identification and Expression Profiling ofFrontiers in plant science · 2022Article
- Comprehensive Genome-Wide Identification and Expression Profiling ofFrontiers in plant science · 2022Article
- TAGOPSIN: collating taxa-specific gene and protein functional and structural information.BMC bioinformatics · 2021Article
- An Efficient, Nonphylogenetic Method for Detecting Genes Sharing Evolutionary Signals in Phylogenomic Data Sets.Genome biology and evolution · 2021Article
- CladeOScope: functional interactions through the prism of clade-wise co-evolution.NAR genomics and bioinformatics · 2021Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Homologous genes in prokaryotes can be described using phylogenetic profiles which summarize their patterns of presence or absence across a set of genomes. Phylogenetic profiles have been used for nearly twenty years to cluster genes based on measures such as the Euclidean distance between profile vectors. However, most approaches do not take into account the phylogenetic relationships amongst the profiled genomes, and overrepresentation of certain taxonomic groups (i.e., pathogenic species with many sequenced representatives) can skew the interpretation of profiles. We propose a new approach that uses a coevolutionary method defined by Pagel to account for the phylogenetic relationships amongst target organisms, and a hierarchical-clustering approach to define sets of genes with common distributions across the organisms. The clusters we obtain using our method show greater evidence of phylogenetic and functional clustering than a recently published approach based on hidden Markov models. Our clustering method identifies sets of amino-acid biosynthesis genes that constitute cohesive pathways, and motility/chemotaxis genes with common histories of descent and lateral gene transfer.
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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.