ArticleNature communications2019
Improved measures for evolutionary conservation that exploit taxonomy distances.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Genomic Insights into Bacterioruberin and Halorhodopsin Biosynthetic Genes in 12 Halophilic Archaea Isolated from Korean Solar Salterns.Journal of microbiology and biotechnology · 2026Article
- Bioinformatics-driven identification of pathogenic missense nsSNPs in the human proto-oncogene SRC and cancer susceptibility.Journal, genetic engineering & biotechnology · 2025Article
- Assessing genetic conservation of human sociability-linked genes in C. elegans.Behavior genetics · 2025Article
- Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictors.Human genomics · 2024Article
- Variant Effect Prediction in the Age of Machine Learning.Cold Spring Harbor perspectives in biology · 2024Review
- Variant Impact Predictor database (VIPdb), version 2: Trends from 25 years of genetic variant impact predictors.bioRxiv : the preprint server for biology · 2024Article
- Purification, characterization and three-dimensional structure prediction of multicopper oxidase Laccases from Trichoderma lixii FLU1 and Talaromyces pinophilus FLU12.Scientific reports · 2024Article
- Disruption of metazoan gene regulatory networks in cancer alters the balance of co-expression between genes of unicellular and multicellular origins.Genome biology · 2024Article
- Dissecting genetic architecture of rare dystonia: genetic, molecular and clinical insights.Journal of medical genetics · 2024Article
- Tissue-specific atlas of trans-models for gene regulation elucidates complex regulation patterns.BMC genomics · 2024Article
- Structure-based pathogenicity relationship identifier for predicting effects of single missense variants and discovery of higher-order cancer susceptibility clusters of mutations.Briefings in bioinformatics · 2023Article
- Design of a Protein with Improved Thermal Stability by an Evolution-Based Generative Model.Angewandte Chemie (International ed. in English) · 2022Article
- Machine-learning of complex evolutionary signals improves classification of SNVs.NAR genomics and bioinformatics · 2022Article
- Novel variants in KAT6B spectrum of disorders expand our knowledge of clinical manifestations and molecular mechanisms.Molecular genetics & genomic medicine · 2021Article
- Low Diversity of Human Variation Despite Mostly Mild Functional Impact of De Novo Variants.Frontiers in molecular biosciences · 2021Article
- IDRMutPred: predicting disease-associated germline nonsynonymous single nucleotide variants (nsSNVs) in intrinsically disordered regions.Bioinformatics (Oxford, England) · 2020Article
- Analysis of APPL1 Gene Polymorphisms in Patients with a Phenotype of Maturity Onset Diabetes of the Young.Journal of personalized medicine · 2020Article
- Zebra2: advanced and easy-to-use web-server for bioinformatic analysis of subfamily-specific and conserved positions in diverse protein superfamilies.Nucleic acids research · 2020Article
- LIST-S2: taxonomy based sorting of deleterious missense mutations across species.Nucleic acids research · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Selective pressures on protein-coding regions that provide fitness advantages can lead to the regions' fixation and conservation in genome duplications and speciation events. Consequently, conservation analyses relying on sequence similarities are exploited by a myriad of applications across all biosciences to identify functionally important protein regions. While very potent, existing conservation measures based on multiple sequence alignments are so pervasive that improvements to solutions of many problems have become incremental. We introduce a new framework for evolutionary conservation with measures that exploit taxonomy distances across species. Results show that our taxonomy-based framework comfortably outperforms existing conservation measures in identifying deleterious variants observed in the human population, including variants located in non-abundant sequence domains such as intrinsically disordered regions. The predictive power of our approach emphasizes that the phenotypic effects of sequence variants can be taxonomy-level specific and thus, conservation needs to be interpreted accordingly.
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