ArticleCells2013
Reverse engineering cellular networks with information theoretic methods.
Article in Cells, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- A comparative analysis of mutual information methods for pairwise relationship detection in metagenomic data.BMC bioinformatics · 2024Article
- An order independent algorithm for inferring gene regulatory network using quantile value for conditional independence tests.Scientific reports · 2021Article
- Article
- Review of Causal Discovery Methods Based on Graphical Models.Frontiers in genetics · 2019Review
- Neurotransmitter identity and electrophysiological phenotype are genetically coupled in midbrain dopaminergic neurons.Scientific reports · 2018Article
- Next-generation, personalised, model-based critical care medicine: a state-of-the art review of in silico virtual patient models, methods, and cohorts, and how to validation them.Biomedical engineering online · 2018Review
- The best models of metabolism.Wiley interdisciplinary reviews. Systems biology and medicine · 2017Review
- Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures.Cell systems · 2017Article
- Reconstruction of Complex Directional Networks with Group Lasso Nonlinear Conditional Granger Causality.Scientific reports · 2017Article
- Data-driven reverse engineering of signaling pathways using ensembles of dynamic models.PLoS computational biology · 2017Article
- Exploring candidate biological functions by Boolean Function Networks for Saccharomyces cerevisiae.PloS one · 2017Article
- Inference of Gene Regulatory Network Based on Local Bayesian Networks.PLoS computational biology · 2016Article
- Article
- Gene Regulatory Network Inferences Using a Maximum-Relevance and Maximum-Significance Strategy.PloS one · 2016Article
- Enabling network inference methods to handle missing data and outliers.BMC bioinformatics · 2015Article
- Kickoff to conflict: a sequence analysis of intra-state conflict-preceding event structures.PloS one · 2015Article
- Reverse engineering and identification in systems biology: strategies, perspectives and challenges.Journal of the Royal Society, Interface · 2014Review
- Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Building mathematical models of cellular networks lies at the core of systems biology. It involves, among other tasks, the reconstruction of the structure of interactions between molecular components, which is known as network inference or reverse engineering. Information theory can help in the goal of extracting as much information as possible from the available data. A large number of methods founded on these concepts have been proposed in the literature, not only in biology journals, but in a wide range of areas. Their critical comparison is difficult due to the different focuses and the adoption of different terminologies. Here we attempt to review some of the existing information theoretic methodologies for network inference, and clarify their differences. While some of these methods have achieved notable success, many challenges remain, among which we can mention dealing with incomplete measurements, noisy data, counterintuitive behaviour emerging from nonlinear relations or feedback loops, and computational burden of dealing with large data sets.
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Registered trials
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