ArticleJournal of computational biology : a journal of computational molecular cell biology2011
Inferring mechanisms of compensation from E-MAP and SGA data using local search algorithms for max cut.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 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.
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Who cites it
7 citing papers in PubMed.
- A novel ILP framework to identify compensatory pathways in genetic interaction networks with GIDEON.Bioinformatics (Oxford, England) · 2026Article
- A Novel ILP Framework to Identify Compensatory Pathways in Genetic Interaction Networks with GIDEON.bioRxiv : the preprint server for biology · 2026Article
- Exploring weighting schemes for the discovery of informative generalized between pathway models to uncover pathways in genetic interaction networks.Scientific reports · 2025Article
- Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems.Cell systems · 2016Article
- Constructing module maps for integrated analysis of heterogeneous biological networks.Nucleic acids research · 2014Article
- Genecentric: a package to uncover graph-theoretic structure in high-throughput epistasis data.BMC bioinformatics · 2013Article
- Article
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Authors and funding
4 authors.
Funding
Abstract
A new method based on a mathematically natural local search framework for max cut is developed to uncover functionally coherent module and BPM motifs in high-throughput genetic interaction data. Unlike previous methods, which also consider physical protein-protein interaction data, our method utilizes genetic interaction data only; this becomes increasingly important as high-throughput genetic interaction data is becoming available in settings where less is known about physical interaction data. We compare modules and BPMs obtained to previous methods and across different datasets. Despite needing no physical interaction information, the BPMs produced by our method are competitive with previous methods. Biological findings include a suggested global role for the prefoldin complex and a SWR subcomplex in pathway buffering in the budding yeast interactome.
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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.