ArticleCell2014
Expansion of biological pathways based on evolutionary inference.
Article in Cell, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed.
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- Profylo: A Python Package for Phylogenetic Profile Comparison and Analysis.Journal of molecular evolution · 2025Article
- CORGIAS: identifying correlated gene pairs by considering evolutionary history in a large-scale prokaryotic genome dataset.NAR genomics and bioinformatics · 2025Article
- Proximity-specific ribosome profiling reveals the logic of localized mitochondrial translation.Cell · 2025Article
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- Systematic mapping of mitochondrial calcium uniporter channel (MCUC)-mediated calcium signaling networks.The EMBO journal · 2024Article
- CilioGenics: an integrated method and database for predicting novel ciliary genes.Nucleic acids research · 2024Article
- Structure and interactions of the endogenous human Commander complex.Nature structural & molecular biology · 2024Article
- Mitochondrial proteome research: the road ahead.Nature reviews. Molecular cell biology · 2024Review
- Completion of mitochondrial division requires the intermembrane space protein Mdi1/Atg44.The Journal of cell biology · 2023Article
- A phylogenetic profiling approach identifies novel ciliogenesis genes in Drosophila and C. elegans.The EMBO journal · 2023Article
- The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles.Systematic biology · 2023Article
- Identification of hidden associations among eukaryotic genes through statistical analysis of coevolutionary transitions.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- An intermembrane space protein facilitates completion of mitochondrial division in yeast.bioRxiv : the preprint server for biology · 2023Article
- Composition, organization and mechanisms of the transition zone, a gate for the cilium.EMBO reports · 2022Review
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- ANGEL2 phosphatase activity is required for non-canonical mitochondrial RNA processing.Nature communications · 2022Article
- Exploring Newer Biosynthetic Gene Clusters in Marine Microbial Prospecting.Marine biotechnology (New York, N.Y.) · 2022Review
- Machine-learning of complex evolutionary signals improves classification of SNVs.NAR genomics and bioinformatics · 2022Article
11 more citing papers are in PubMed but not listed here.
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5 authors.
Funding
Abstract
The availability of diverse genomes makes it possible to predict gene function based on shared evolutionary history. This approach can be challenging, however, for pathways whose components do not exhibit a shared history but rather consist of distinct "evolutionary modules." We introduce a computational algorithm, clustering by inferred models of evolution (CLIME), which inputs a eukaryotic species tree, homology matrix, and pathway (gene set) of interest. CLIME partitions the gene set into disjoint evolutionary modules, simultaneously learning the number of modules and a tree-based evolutionary history that defines each module. CLIME then expands each module by scanning the genome for new components that likely arose under the inferred evolutionary model. Application of CLIME to ∼1,000 annotated human pathways and to the proteomes of yeast, red algae, and malaria reveals unanticipated evolutionary modularity and coevolving components. CLIME is freely available and should become increasingly powerful with the growing wealth of eukaryotic genomes.
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