ArticleNucleic acids research2020
Novel phylogenetic methods are needed for understanding gene function in the era of mega-scale genome sequencing.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 48 citations in OpenAlex.
- Genome-Wide Dissection of the TCP Gene Family in Peach and Expression Analysis Under Drought Stress.International journal of molecular sciences · 2026Article
- Sequence dynamics and plastome evolution: decoding the complete chloroplast genome of Oenothera drummondii and comparative analysis within Oenothera (Onagraceae).Functional & integrative genomics · 2025Article
- From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions.Genome biology and evolution · 2025Review
- Genome-Wide Dissection of MATE Gene Family in Cultivated Peanuts and Unveiling Their Expression Profiles Under Aluminum Stress.International journal of molecular sciences · 2025Article
- Molecular and Functional Convergences Associated with Complex Multicellularity in Eukarya.Molecular biology and evolution · 2025Article
- Genome wide identification of MATE and ALMT gene family in lentil (Lens culinaris Medikus) and expression profiling under Al stress condition.BMC plant biology · 2025Article
- Hyperdimensional computing: A fast, robust, and interpretable paradigm for biological data.PLoS computational biology · 2024Review
- Inferences on the evolution of the ascorbic acid synthesis pathway in insects using Phylogenetic Tree Collapser (PTC), a tool for the automated collapsing of phylogenetic trees using taxonomic information.Journal of integrative bioinformatics · 2024Article
- Phylogenomics of the Ecdysteroid Kinase-like (EcKL) Gene Family in Insects Highlights Roles in Both Steroid Hormone Metabolism and Detoxification.Genome biology and evolution · 2024Article
- Culturomics- and metagenomics-based insights into the soil microbiome preservation and application for sustainable agriculture.Frontiers in microbiology · 2024Review
- Real-time expression and in silico characterization of pea genes involved in salt and water-deficit stress.Molecular biology reports · 2023Article
- CALANGO: A phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species.Patterns (New York, N.Y.) · 2023Article
- Defining hierarchical protein interaction networks from spectral analysis of bacterial proteomes.eLife · 2022Article
- Venom Gene Sequence Diversity and Expression Jointly Shape Diet Adaptation in Pitvipers.Molecular biology and evolution · 2022Article
- Genome-wide in silico identification of phospholipase D (PLD) gene family from Corchorus capsularis and Corchorus olitorius: reveals their responses to plant stress.Journal, genetic engineering & biotechnology · 2022Article
- ORTHOSCOPE*: A Phylogenetic Pipeline to Infer Gene Histories from Genome-Wide Data.Molecular biology and evolution · 2022Article
- Carotenoid modifying enzymes in metazoans.Methods in enzymology · 2022Article
- Article
- PlantTribes2: Tools for comparative gene family analysis in plant genomics.Frontiers in plant science · 2022Article
- Comparative Genomic Analysis of the DUF34 Protein Family Suggests Role as a Metal Ion Chaperone or Insertase.Biomolecules · 2021Article
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4 authors at 1 institution in 1 country.
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Abstract
Ongoing large-scale genome sequencing projects are forecasting a data deluge that will almost certainly overwhelm current analytical capabilities of evolutionary genomics. In contrast to population genomics, there are no standardized methods in evolutionary genomics for extracting evolutionary and functional (e.g. gene-trait association) signal from genomic data. Here, we examine how current practices of multi-species comparative genomics perform in this aspect and point out that many genomic datasets are under-utilized due to the lack of powerful methodologies. As a result, many current analyses emphasize gene families for which some functional data is already available, resulting in a growing gap between functionally well-characterized genes/organisms and the universe of unknowns. This leaves unknown genes on the 'dark side' of genomes, a problem that will not be mitigated by sequencing more and more genomes, unless we develop tools to infer functional hypotheses for unknown genes in a systematic manner. We provide an inventory of recently developed methods capable of predicting gene-gene and gene-trait associations based on comparative data, then argue that realizing the full potential of whole genome datasets requires the integration of phylogenetic comparative methods into genomics, a rich but underutilized toolbox for looking into the past.
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