ArticleJournal of computational biology : a journal of computational molecular cell biology2013
Simultaneous reconstruction of multiple signaling pathways via the prize-collecting steiner forest problem.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed.
- PCIPG: A comprehensive framework for protein complex identification based on a probabilistic graphical model.PLoS computational biology · 2026Article
- A Framework for Benchmarking Pathway Reconstruction Algorithms.bioRxiv : the preprint server for biology · 2026Article
- A module-based approach for post-omics, post-GWAS network-based gene classification.Bioinformatics (Oxford, England) · 2026Article
- Extracellular matrix-driven patient stratification and network modeling reveal distinct molecular grades with potential clinical implications.NPJ systems biology and applications · 2026Article
- Computational Approaches for Pathway-Centric Analysis of Protein Post-Translational Modifications.Proteomics · 2025Review
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- Image2Reg: Linking chromatin images to gene regulation using genetic and chemical perturbation screens.Cell systems · 2025Article
- An integrative systems-biology approach defines mechanisms of Alzheimer's disease neurodegeneration.Nature communications · 2025Article
- CellPHIE: Integrating Pathway Discovery With Pooled Profiling of Perturbations Uncovers Pathways of Huntington's Disease, Including Genetic Modifiers of Neuronal Development and Morphology.bioRxiv : the preprint server for biology · 2025Article
- Lipidomics of Huntington's Disease: A Comprehensive Review of Current Status and Future Directions.Metabolites · 2025Review
- Mutant huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure.Nature communications · 2024Article
- Prioritizing drug targets by perturbing biological network response functions.PLoS computational biology · 2024Article
- Transcriptional programs mediating neuronal toxicity and altered glial-neuronal signaling in aGenome research · 2024Article
- Transcriptional programs mediating neuronal toxicity and altered glial-neuronal signaling in abioRxiv : the preprint server for biology · 2024Article
- Current and future directions in network biology.Bioinformatics advances · 2024Article
- Integrative analysis reveals a conserved role for the amyloid precursor protein in proteostasis during aging.Nature communications · 2023Article
- De novo identification of maximally deregulated subnetworks based on multi-omics data with DeRegNet.BMC bioinformatics · 2022Article
- Context dependent isoform specific PI3K inhibition confers drug resistance in hepatocellular carcinoma cells.BMC cancer · 2022Article
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- Risk-aware temporal cascade reconstruction to detect asymptomatic cases.Knowledge and information systems · 2022Article
8 more citing papers are in PubMed but not listed here.
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8 authors.
Funding
Abstract
Signaling and regulatory networks are essential for cells to control processes such as growth, differentiation, and response to stimuli. Although many "omic" data sources are available to probe signaling pathways, these data are typically sparse and noisy. Thus, it has been difficult to use these data to discover the cause of the diseases and to propose new therapeutic strategies. We overcome these problems and use "omic" data to reconstruct simultaneously multiple pathways that are altered in a particular condition by solving the prize-collecting Steiner forest problem. To evaluate this approach, we use the well-characterized yeast pheromone response. We then apply the method to human glioblastoma data, searching for a forest of trees, each of which is rooted in a different cell-surface receptor. This approach discovers both overlapping and independent signaling pathways that are enriched in functionally and clinically relevant proteins, which could provide the basis for new therapeutic strategies. Although the algorithm was not provided with any information about the phosphorylation status of receptors, it identifies a small set of clinically relevant receptors among hundreds present in the interactome.
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