ArticlePeerJ2017
PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages.
Article in PeerJ, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed.
- Living on the Rocks: Genomic Analysis of Limestone Langurs Provides Novel Insights into the Adaptive Evolution in Extreme Karst Environments.Genomics, proteomics & bioinformatics · 2025Article
- Assembling bacterial puzzles: piecing together functions into microbial pathways.NAR genomics and bioinformatics · 2024Article
- Inverse Potts model improves accuracy of phylogenetic profiling.Bioinformatics (Oxford, England) · 2022Article
- Identifying protein function and functional links based on large-scale co-occurrence patterns.PloS one · 2022Article
- Co-evolution based machine-learning for predicting functional interactions between human genes.Nature communications · 2021Article
- GFICLEE: ultrafast tree-based phylogenetic profile method inferring gene function at the genomic-wide level.BMC genomics · 2021Article
- Ten Years of Collaborative Progress in the Quest for Orthologs.Molecular biology and evolution · 2021Article
- CladeOScope: functional interactions through the prism of clade-wise co-evolution.NAR genomics and bioinformatics · 2021Article
- Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes.PLoS computational biology · 2020Article
- Prediction of cancer driver genes through network-based moment propagation of mutation scores.Bioinformatics (Oxford, England) · 2020Article
- PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees.BMC evolutionary biology · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Direct and indirect functional links between proteins as well as their interactions as part of larger protein complexes or common signaling pathways may be predicted by analyzing the correlation of their evolutionary patterns. Based on phylogenetic profiling, here we present a highly scalable and time-efficient computational framework for predicting linkages within the whole human proteome. We have validated this method through analysis of 3,697 human pathways and molecular complexes and a comparison of our results with the prediction outcomes of previously published co-occurrency model-based and normalization methods. Here we also introduce PrePhyloPro, a web-based software that uses our method for accurately predicting proteome-wide linkages. We present data on interactions of human mitochondrial proteins, verifying the performance of this software. PrePhyloPro is freely available at http://prephylopro.org/phyloprofile/.
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What OpenQuestion holds
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.