ArticleBioinformatics (Oxford, England)2012
Genome-scale analysis of interaction dynamics reveals organization of biological networks.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- SAAMBE-MEM: a sequence-based method for predicting binding free energy change upon mutation in membrane protein-protein complexes.Bioinformatics (Oxford, England) · 2024Article
- Study on the detection method of biological characteristics of hepatoma cells based on terahertz time-domain spectroscopy.Biomedical optics express · 2023Article
- SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein-protein binding affinity.Bioinformatics (Oxford, England) · 2021Article
- Disease gene prediction for molecularly uncharacterized diseases.PLoS computational biology · 2019Article
- Latent Model-Based Clustering for Biological Discovery.iScience · 2019Article
- Integrated network analysis reveals distinct regulatory roles of transcription factors and microRNAs.RNA (New York, N.Y.) · 2016Article
- Protein complex detection based on partially shared multi-view clustering.BMC bioinformatics · 2016Article
- Spatial Colocalization of Human Ohnolog Pairs Acts to Maintain Dosage-Balance.Molecular biology and evolution · 2016Article
- BiCAMWI: A Genetic-Based Biclustering Algorithm for Detecting Dynamic Protein Complexes.PloS one · 2016Article
- A New Algorithm to Optimize Maximal Information Coefficient.PloS one · 2016Article
- DTW-MIC Coexpression Networks from Time-Course Data.PloS one · 2016Article
- Integrated web visualizations for protein-protein interaction databases.BMC bioinformatics · 2015Article
- Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks.PLoS computational biology · 2015Article
- ENCAPP: elastic-net-based prognosis prediction and biomarker discovery for human cancers.BMC genomics · 2015Article
- Detecting temporal protein complexes from dynamic protein-protein interaction networks.BMC bioinformatics · 2014Article
- RapidMic: Rapid Computation of the Maximal Information Coefficient.Evolutionary bioinformatics online · 2014Article
- Predicting cancer prognosis using functional genomics data sets.Cancer informatics · 2014Review
- Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways.Science signaling · 2013Article
- Schizophrenia at a genetics crossroads: where to now?Schizophrenia bulletin · 2013Article
- Simple topological features reflect dynamics and modularity in protein interaction networks.PLoS computational biology · 2013Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Analyzing large-scale interaction networks has generated numerous insights in systems biology. However, such studies have primarily been focused on highly co-expressed, stable interactions. Most transient interactions that carry out equally important functions, especially in signal transduction pathways, are yet to be elucidated and are often wrongly discarded as false positives. Here, we revisit a previously described Smith-Waterman-like dynamic programming algorithm and use it to distinguish stable and transient interactions on a genomic scale in human and yeast. We find that in biological networks, transient interactions are key links topologically connecting tightly regulated functional modules formed by stable interactions and are essential to maintaining the integrity of cellular networks. We also perform a systematic analysis of interaction dynamics across different technologies and find that high-throughput yeast two-hybrid is the only available technology for detecting transient interactions on a large scale.
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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.