ArticleBioinformatics (Oxford, England)2017
CausalR: extracting mechanistic sense from genome scale data.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- MultiOmicsXplorer, a tool to browse, access and analyse multi-omics data.BMC bioinformatics · 2026Article
- Analysis of Genomic and Transcriptomic Data Revealed Key Genes and Processes in the Development of Major Depressive Disorder.International journal of molecular sciences · 2025Article
- Towards an interpretable deep learning model of cancer.NPJ precision oncology · 2025Review
- Analysis of transcription profiles for the identification of master regulators as the key players in glioblastoma.Computational and structural biotechnology journal · 2024Article
- Drug Repurposing Using Molecular Network Analysis Identifies Jak as Targetable Driver in Necrobiosis Lipoidica.JID innovations : skin science from molecules to population health · 2024Article
- SignalingProfiler 2.0 a network-based approach to bridge multi-omics data to phenotypic hallmarks.NPJ systems biology and applications · 2024Article
- Prioritizing drug targets by perturbing biological network response functions.PLoS computational biology · 2024Article
- A Causal Regulation Modeling Algorithm for Temporal Events with Application toInternational journal of molecular sciences · 2024Article
- Characterizing alternative splicing effects on protein interaction networks with LINDA.Bioinformatics (Oxford, England) · 2023Article
- Benchmarking causal reasoning algorithms for gene expression-based compound mechanism of action analysis.BMC bioinformatics · 2023Article
- Mechanism of action deconvolution of the small-molecule pathological tau aggregation inhibitor Anle138b.Alzheimer's research & therapy · 2023Article
- Integrating knowledge and omics to decipher mechanisms via large-scale models of signaling networks.Molecular systems biology · 2022Review
- Computational analyses of mechanism of action (MoA): data, methods and integration.RSC chemical biology · 2022Review
- The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling.Briefings in bioinformatics · 2021Article
- Modeling in systems biology: Causal understanding before prediction?Patterns (New York, N.Y.) · 2021Article
- The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST).Bioinformatics (Oxford, England) · 2021Article
- CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination.Bioinformatics (Oxford, England) · 2019Article
- Footprint-based functional analysis of multiomic data.Current opinion in systems biology · 2019Review
- From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL.NPJ systems biology and applications · 2019Article
- Computational systems biology approaches for Parkinson's disease.Cell and tissue research · 2018Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryUtilization of causal interaction data enables mechanistic rather than descriptive interpretation of genome-scale data. Here we present CausalR, the first open source causal network analysis platform. Implemented functions enable regulator prediction and network reconstruction, with network and annotation files created for visualization in Cytoscape. False positives are limited using the introduced Sequential Causal Analysis of Networks approach. AVAILABILITY AND IMPLEMENTATION: CausalR is implemented in R, parallelized, and is available from Bioconductor. CONTACT: glyn.x.bradley@gsk.com. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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