ArticleBioinformatics (Oxford, England)2016
Reconstructing the temporal progression of HIV-1 immune response pathways.
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 5 papers.
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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
5 citing papers in PubMed.
- Genetic Signatures of Positive Selection in Human Populations Adapted to High Altitude in Papua New Guinea.Genome biology and evolution · 2024Article
- Transcriptome Analysis Identifies Altered Biological Processes and Novel Markers in Human Immunodeficiency Virus-1 Long-Term Non-Progressors.Infection & chemotherapy · 2021Article
- A dual controllability analysis of influenza virus-host protein-protein interaction networks for antiviral drug target discovery.BMC bioinformatics · 2019Article
- Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data.Cell reports · 2018Article
- Transcriptome analyses identify key cellular factors associated with HIV-1-associated neuropathogenesis in infected men.AIDS (London, England) · 2017Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
motivationMost methods for reconstructing response networks from high throughput data generate static models which cannot distinguish between early and late response stages.
resultsWe present TimePath, a new method that integrates time series and static datasets to reconstruct dynamic models of host response to stimulus. TimePath uses an Integer Programming formulation to select a subset of pathways that, together, explain the observed dynamic responses. Applying TimePath to study human response to HIV-1 led to accurate reconstruction of several known regulatory and signaling pathways and to novel mechanistic insights. We experimentally validated several of TimePaths' predictions highlighting the usefulness of temporal models. AVAILABILITY AND IMPLEMENTATION: Data, Supplementary text and the TimePath software are available from http://sb.cs.cmu.edu/timepath CONTACT: zivbj@cs.cmu.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.