ArticleComputational and structural biotechnology journal2021
Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data.
Article in Computational and structural biotechnology journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 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
8 citing papers in PubMed, 13 citations in OpenAlex.
- RSEA: A Web Server for Pathway Enrichment Analysis of Metabolic Reaction Sets.Biotechnology and bioengineering · 2025Article
- drexml: A command line tool and Python package for drug repurposing.Computational and structural biotechnology journal · 2024Article
- Single cell RNA sequencing of human FAPs reveals different functional stages in Duchenne muscular dystrophy.Frontiers in cell and developmental biology · 2024Article
- In Silico Clinical Trials: Is It Possible?Methods in molecular biology (Clifton, N.J.) · 2024Article
- Functional Profiling of Soft Tissue Sarcoma Using Mechanistic Models.International journal of molecular sciences · 2023Article
- Crosstalk between Metabolite Production and Signaling Activity in Breast Cancer.International journal of molecular sciences · 2023Article
- Integrating knowledge and omics to decipher mechanisms via large-scale models of signaling networks.Molecular systems biology · 2022Review
- Discovering potential interactions between rare diseases and COVID-19 by combining mechanistic models of viral infection with statistical modeling.Human molecular genetics · 2022Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome-scale mechanistic models of pathways are gaining importance for genomic data interpretation because they provide a natural link between genotype measurements (transcriptomics or genomics data) and the phenotype of the cell (its functional behavior). Moreover, mechanistic models can be used to predict the potential effect of interventions, including drug inhibitions. Here, we present the implementation of a mechanistic model of cell signaling for the interpretation of transcriptomic data as an R/Bioconductor package, a Cytoscape plugin and a web tool with enhanced functionality which includes building interpretable predictors, estimation of the effect of perturbations and assessment of the effect of mutations in complex scenarios.
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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 Socratic graph.