ArticleNucleic acids research2015
PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 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
26 citing papers in PubMed, 47 citations in OpenAlex.
- CladeOScope-GSA: Revealing Evolutionary Associations Across Gene Sets.International journal of molecular sciences · 2026Article
- SLC25A48 controls mitochondrial choline import and metabolism.Cell metabolism · 2024Article
- Matreex: Compact and Interactive Visualization for Scalable Studies of Large Gene Families.Genome biology and evolution · 2024Article
- Mitochondrial choline import regulates purine nucleotide pools via SLC25A48.bioRxiv : the preprint server for biology · 2024Article
- The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles.Systematic biology · 2023Article
- Phylogenetic profiling in eukaryotes comes of age.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Machine-learning of complex evolutionary signals improves classification of SNVs.NAR genomics and bioinformatics · 2022Article
- Multi-omics data integration analysis identifies the spliceosome as a key regulator of DNA double-strand break repair.NAR cancer · 2022Article
- Computational methods, databases and tools for synthetic lethality prediction.Briefings in bioinformatics · 2022Review
- Florigen and its homologs of FT/CETS/PEBP/RKIP/YbhB family may be the enzymes of small molecule metabolism: review of the evidence.BMC plant biology · 2022Review
- Co-evolution based machine-learning for predicting functional interactions between human genes.Nature communications · 2021Article
- Article
- GFICLEE: ultrafast tree-based phylogenetic profile method inferring gene function at the genomic-wide level.BMC genomics · 2021Article
- CladeOScope: functional interactions through the prism of clade-wise co-evolution.NAR genomics and bioinformatics · 2021Article
- Reversal of diet-induced hepatic steatosis by peripheral CB1 receptor blockade in mice is p53/miRNA-22/SIRT1/PPARα dependent.Molecular metabolism · 2020Article
- ACE2 Co-evolutionary Pattern Suggests Targets for Pharmaceutical Intervention in the COVID-19 Pandemic.iScience · 2020Article
- A network of RNA-binding proteins controls translation efficiency to activate anaerobic metabolism.Nature communications · 2020Article
- MYORG Mutations: a Major Cause of Recessive Primary Familial Brain Calcification.Current neurology and neuroscience reports · 2019Review
- Loss of Wood Formation Genes in Monocot Genomes.Genome biology and evolution · 2019Article
- Mapping global and local coevolution across 600 species to identify novel homologous recombination repair genes.Genome research · 2019Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Proteins that function in the same pathways, protein complexes or the same environmental conditions can show similar patterns of sequence conservation across phylogenetic clades. In species that no longer require a specific protein complex or pathway, these proteins, as a group, tend to be lost or diverge. Analysis of the similarity in patterns of sequence conservation across a large set of eukaryotes can predict functional associations between different proteins, identify new pathway members and reveal the function of previously uncharacterized proteins. We used normalized phylogenetic profiling to predict protein function and identify new pathway members and disease genes. The phylogenetic profiles of tens of thousands conserved proteins in the human, mouse, Caenorhabditis elegans and Drosophila genomes can be queried on our new web server, PhyloGene. PhyloGene provides intuitive and user-friendly platform to query the patterns of conservation across 86 animal, fungal, plant and protist genomes. A protein query can be submitted either by selecting the name from whole-genome protein sets of the intensively studied species or by entering a protein sequence. The graphic output shows the profile of sequence conservation for the query and the most similar phylogenetic profiles for the proteins in the genome of choice. The user can also download this output in numerical form.
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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.