ArticleBMC bioinformatics2015
Event inference in multidomain families with phylogenetic reconciliation.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 41 citations in OpenAlex.
- Identification and Classification of Fungal GPCR Gene Families.Journal of fungi (Basel, Switzerland) · 2025Article
- Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration.Journal of molecular evolution · 2025Review
- Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome.G3 (Bethesda, Md.) · 2025Article
- Proterozoic Acquisition of Archaeal Genes for Extracellular Electron Transfer: A Metabolic Adaptation of Aerobic Ammonia-Oxidizing Bacteria to Oxygen Limitation.Molecular biology and evolution · 2023Article
- Phylogenetic inference of the emergence of sequence modules and protein-protein interactions in the ADAMTS-TSL family.PLoS computational biology · 2023Article
- Human atlastin-3 is a constitutive ER membrane fusion catalyst.The Journal of cell biology · 2023Article
- Function and Constraint in Enhancer Sequences with Multiple Evolutionary Origins.Genome biology and evolution · 2022Article
- Phylogenetic reconciliation.PLoS computational biology · 2022Article
- Deciphering Microbial Gene Family Evolution Using Duplication-Transfer-Loss Reconciliation and RANGER-DTL.Methods in molecular biology (Clifton, N.J.) · 2022Article
- PANTHER: Making genome-scale phylogenetics accessible to all.Protein science : a publication of the Protein Society · 2022Review
- Ten Years of Collaborative Progress in the Quest for Orthologs.Molecular biology and evolution · 2021Article
- Improved inference of tandem domain duplications.Bioinformatics (Oxford, England) · 2021Article
- Achieving large and distant ancestral genome inference by using an improved discrete quantum-behaved particle swarm optimization algorithm.BMC bioinformatics · 2020Article
- Using Cellular Automata to Simulate Domain Evolution in Proteins.Frontiers in genetics · 2020Article
- Diversity and Evolutionary Dynamics of Antiphage Defense Systems inFrontiers in microbiology · 2020Article
- Phylogenetic reconciliation reveals the natural history of glycopeptide antibiotic biosynthesis and resistance.Nature microbiology · 2019Article
- Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies.BMC bioinformatics · 2019Article
- DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies.Genome biology and evolution · 2017Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundReconstructing evolution provides valuable insights into the processes of gene evolution and function. However, while there have been great advances in algorithms and software to reconstruct the history of gene families, these tools do not model the domain shuffling events (domain duplication, insertion, transfer, and deletion) that drive the evolution of multidomain protein families. Protein evolution through domain shuffling events allows for rapid exploration of functions by introducing new combinations of existing folds. This powerful mechanism was key to some significant evolutionary innovations, such as multicellularity and the vertebrate immune system. A method for reconstructing this important evolutionary process is urgently needed.
resultsHere, we introduce a novel, event-based framework for studying multidomain evolution by reconciling a domain tree with a gene tree, with additional information provided by the species tree. In the context of this framework, we present the first reconciliation algorithms to infer domain shuffling events, while addressing the challenges inherent in the inference of evolution across three levels of organization.
conclusionsWe apply these methods to the evolution of domains in the Membrane associated Guanylate Kinase family. These case studies reveal a more vivid and detailed evolutionary history than previously provided. Our algorithms have been implemented in software, freely available at http://www.cs.cmu.edu/˜durand/Notung.
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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.