ArticlePLoS computational biology2009
Questioning the ubiquity of neofunctionalization.
Article in PLoS computational biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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
25 citing papers in PubMed.
- Protein Self-Interaction in Cellular Function and Network Evolution: Molecular Mechanisms, AI-Driven Insights, and Therapeutic Potentials.International journal of molecular sciences · 2026Review
- Evolutionary causes and consequences of gene duplication.Nature reviews. Genetics · 2026Review
- Mutational biases favor complexity increases in protein interaction networks after gene duplication.Molecular systems biology · 2024Article
- PICKLE RELATED 2 is a Neofunctionalized Gene Duplicate Under Positive Selection With Antagonistic Effects to the Ancestral PICKLE Gene on the Seed Transcriptome.Genome biology and evolution · 2023Article
- Genetic Channelization Mechanism of Four Chalcone Isomerase Homologous Genes for Synergistic Resistance to Fusarium wilt inInternational journal of molecular sciences · 2023Article
- Kinase regulators evolved into two families by gain and loss of ability to bind plant steroid receptors.Plant physiology · 2023Article
- The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction.Bioinformatics (Oxford, England) · 2020Article
- The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs.eLife · 2019Article
- The effect of Bu Zhong Yi Qi decoction on simulated weightlessness‑induced muscle atrophy and its mechanisms.Molecular medicine reports · 2017Article
- Evolution of the ability to modulate host chemokine networks via gene duplication in human cytomegalovirus (HCMV).Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2017Article
- Evolutionary and Comparative Genomics to Drive Rational Drug Design, with Particular Focus on Neuropeptide Seven-Transmembrane Receptors.Biomolecules & therapeutics · 2017Review
- A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human.Cell · 2016Article
- Proteome-wide prediction of self-interacting proteins based on multiple properties.Molecular & cellular proteomics : MCP · 2013Article
- The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks.PloS one · 2013Article
- Inferring evolution of gene duplicates using probabilistic models and nonparametric belief propagation.BMC genomics · 2013Article
- Functional divergence of gene duplicates - a domain-centric view.BMC evolutionary biology · 2012Article
- Gene duplications contribute to the overrepresentation of interactions between proteins of a similar age.BMC evolutionary biology · 2012Article
- Functional organization and its implication in evolution of the human protein-protein interaction network.BMC genomics · 2012Article
- Formins: emerging players in the dynamic plant cell cortex.Scientifica · 2012Review
- Drug target prediction based on the herbs components: the study on the multitargets pharmacological mechanism of qishenkeli acting on the coronary heart disease.Evidence-based complementary and alternative medicine : eCAM · 2012Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene duplication provides much of the raw material from which functional diversity evolves. Two evolutionary mechanisms have been proposed that generate functional diversity: neofunctionalization, the de novo acquisition of function by one duplicate, and subfunctionalization, the partitioning of ancestral functions between gene duplicates. With protein interactions as a surrogate for protein functions, evidence of prodigious neofunctionalization and subfunctionalization has been identified in analyses of empirical protein interactions and evolutionary models of protein interactions. However, we have identified three phenomena that have contributed to neofunctionalization being erroneously identified as a significant factor in protein interaction network evolution. First, self-interacting proteins are underreported in interaction data due to biological artifacts and design limitations in the two most common high-throughput protein interaction assays. Second, evolutionary inferences have been drawn from paralog analysis without consideration for concurrent and subsequent duplication events. Third, the theoretical model of prodigious neofunctionalization is unable to reproduce empirical network clustering and relies on untenable parameter requirements. In light of these findings, we believe that protein interaction evolution is more persuasively characterized by subfunctionalization and self-interactions.
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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.