ReviewEXCLI journal2015
Data- and knowledge-based modeling of gene regulatory networks: an update.
Review in EXCLI journal, 2015. 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.
- Comprehensive map of the regulatory network triggered by MET exon 14 skipping reveals important involvement of the RAS-ERK signaling pathway.Cell death & disease · 2025Article
- Dietary Fermentation withInternational journal of molecular sciences · 2025Article
- Results and lessons learned from the sbv IMPROVER metagenomics diagnostics for inflammatory bowel disease challenge.Scientific reports · 2023Article
- DiffBrainNet: Differential analyses add new insights into the response to glucocorticoids at the level of genes, networks and brain regions.Neurobiology of stress · 2022Article
- A strategy to incorporate prior knowledge into correlation network cutoff selection.Nature communications · 2020Article
- Transcriptomic determinants of the response of ST-111 Pseudomonas aeruginosa AG1 to ciprofloxacin identified by a top-down systems biology approach.Scientific reports · 2020Article
- Integrated transcriptomics reveals master regulators of lung adenocarcinoma and novel repositioning of drug candidates.Cancer medicine · 2019Article
- Control of seminal fluid protein expression via regulatory hubs inProceedings. Biological sciences · 2018Article
- Expert curation for building network-based dynamical models: a case study on atherosclerotic plaque formation.Database : the journal of biological databases and curation · 2018Article
- Network Analyses in Plant Pathogens.Frontiers in microbiology · 2018Review
- Article
- Evaluation and improvement of the regulatory inference for large co-expression networks with limited sample size.BMC systems biology · 2017Article
- LASSIM-A network inference toolbox for genome-wide mechanistic modeling.PLoS computational biology · 2017Article
- Facing the challenges of multiscale modelling of bacterial and fungal pathogen-host interactions.Briefings in functional genomics · 2017Review
- How to Predict Molecular Interactions between Species?Frontiers in microbiology · 2016Review
- Cancer microarray data feature selection using multi-objective binary particle swarm optimization algorithm.EXCLI journal · 2016Article
- A comparative analytical assay of gene regulatory networks inferred using microarray and RNA-seq datasets.Bioinformation · 2016Article
- Data-based Reconstruction of Gene Regulatory Networks of Fungal Pathogens.Frontiers in microbiology · 2016Article
- Reconstruction of the temporal signaling network in Salmonella-infected human cells.Frontiers in microbiology · 2015Article
- A review on computational systems biology of pathogen-host interactions.Frontiers in microbiology · 2015Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene regulatory network inference is a systems biology approach which predicts interactions between genes with the help of high-throughput data. In this review, we present current and updated network inference methods focusing on novel techniques for data acquisition, network inference assessment, network inference for interacting species and the integration of prior knowledge. After the advance of Next-Generation-Sequencing of cDNAs derived from RNA samples (RNA-Seq) we discuss in detail its application to network inference. Furthermore, we present progress for large-scale or even full-genomic network inference as well as for small-scale condensed network inference and review advances in the evaluation of network inference methods by crowdsourcing. Finally, we reflect the current availability of data and prior knowledge sources and give an outlook for the inference of gene regulatory networks that reflect interacting species, in particular pathogen-host interactions.
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Registered trials
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