ArticleBioinformatics (Oxford, England)2016
SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
73 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Brachypodium distachyon cold-acclimated plasma membrane proteome is primed for stress resistance.G3 (Bethesda, Md.) · 2021Pooled it
- Network based analysis identifies TP53m-BRCA1/2wt-homologous recombination proficient (HRP) population with enhanced susceptibility to Vigil immunotherapy.Cancer gene therapy · 2022Trial
- BOLL-Containing Aggregates Mediate the Translational Regulation During Human Oogenesis.Cell proliferation · 2026Article
- An Integrative Variant Scoring Function for Finding Novel Genes Associated with Ovarian and Thyroid Cancer.International journal of environmental research and public health · 2026Article
- Analysis of Roux-en-Y Gastric Bypass and High-Fat Feeding Reveals Hepatic Transcriptome Reprogramming: Ironing out the Details.Journal of clinical medicine · 2026Article
- Profylo: A Python Package for Phylogenetic Profile Comparison and Analysis.Journal of molecular evolution · 2025Article
- Multi-omics dissection of RAD21-PON1 axis reveals metabolic-immune crosstalk and prognostic significance in hepatocellular carcinoma.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Whole Transcriptome RNA-Seq Reveals Drivers of Pathological Dysfunction in a Transgenic Model of Alzheimer's Disease.Molecular neurobiology · 2025Article
- Dysregulation of Inositol Polyphosphate 5-Phosphatase OCRL in Alzheimer's Disease: Implications for Autophagy Dysfunction.International journal of molecular sciences · 2025Article
- Predicting Protein Function in the AI and Big Data Era.Biochemistry · 2025Review
- EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals.Nature communications · 2025Article
- A large-scale benchmark for network inference from single-cell perturbation data.Communications biology · 2025Article
- In Vitro Functional Validation of an Anti-FREM2 Nanobody for Glioblastoma Cell Targeting.Antibodies (Basel, Switzerland) · 2025Article
- Expression and immunological role of FUNDC2 in pan-cancer.PloS one · 2025Article
- Assembling bacterial puzzles: piecing together functions into microbial pathways.NAR genomics and bioinformatics · 2024Article
- PFAS and their association with the increased risk of cardiovascular disease in postmenopausal women.Toxicological sciences : an official journal of the Society of Toxicology · 2024Article
- Landscape of protein-protein interactions during hepatitis C virus assembly and release.Microbiology spectrum · 2024Article
- FAVA: high-quality functional association networks inferred from scRNA-seq and proteomics data.Bioinformatics (Oxford, England) · 2024Article
- An In Vitro Evaluation and Network Pharmacology Analysis of Prospective Anti-Prostate Cancer Activity fromPlants (Basel, Switzerland) · 2023Article
- Phylogenetic profiling in eukaryotes comes of age.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
13 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
unlabelledA successful approach for predicting functional associations between non-homologous genes is to compare their phylogenetic distributions. We have devised a phylogenetic profiling algorithm, SVD-Phy, which uses truncated singular value decomposition to address the problem of uninformative profiles giving rise to false positive predictions. Benchmarking the algorithm against the KEGG pathway database, we found that it has substantially improved performance over existing phylogenetic profiling methods. AVAILABILITY AND IMPLEMENTATION: The software is available under the open-source BSD license at https://bitbucket.org/andrea/svd-phy CONTACT: lars.juhl.jensen@cpr.ku.dk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Indexed as
Identifiers
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.