Inferring Regulatory Networks from Expression Data Using Tree-Based Methods
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Summary
This article presents GENIE3, a new algorithm for the inference of GRNs that was best performer in the DREAM4 In Silico Multifactorial challenge and compares favorably with existing algorithms to decipher the genetic regulatory network of Escherichia coli.
- Type
- article
- Published
- 2010-09-28
- Cited by
- 2,030
- References
- 51
- Access
- Open access
- OpenAlex
- https://openalex.org/W2076513103
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:10420934
Keywords
Gene regulatory network, Inference, In silico, Computer science, Computational biology
References
- Computational Modeling of Gene Regulatory Networks - A Primer
- Discovering biomarkers from gene expression data for predicting cancer subgroups using neural networks and relational fuzzy clustering
- Lessons from the DREAM2 Challenges
- Reverse Engineering Molecular Regulatory Networks from Microarray Data with qp-Graphs
- A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics
- Reverse-engineering transcription control networks.
- High-dimensional graphs and variable selection with the Lasso
- Generating Realistic In Silico Gene Networks for Performance Assessment of Reverse Engineering Methods
- Supervised learning with decision tree-based methods in computational and systems biology.
- Evolutionary approaches for the reverse-engineering of gene regulatory networks: A study on a biologically realistic dataset
- From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data
- Inferring gene regulatory networks from time series data using the minimum description length principle
- Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles
- Reverse engineering cellular networks
- Extremely randomized trees
- Classification and regression trees
- Identification of Yeast Transcriptional Regulation Networks Using Multivariate Random Forests
- Inferring Genetic Networks and Identifying Compound Mode of Action via Expression Profiling
- Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements.
- Inferring sparse Gaussian graphical models with latent structure
Cited by
- Simulation and identification of gene regulatory networks
- Big Data Analytics in Healthcare
- Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize
- MICRAT: a novel algorithm for inferring gene regulatory networks using time series gene expression data
- Integrated Inference and Analysis of Regulatory Networks from Multi-Level Measurements
- Constructing Mathematical Models of Gene Regulatory Networks for the Yeast Cell Cycle and Other Periodic Processes
- Predicting the Behavior of the Supreme Court of the United States: A General Approach
- Inferring Gene Regulatory Networks from Expression Data using Ensemble Methods
- Computational Evaluation and Derivation of biological Networks in cancer and STEM cells
- A Probabilistic Model for Dirty Multi-task Feature Selection
- Estimation de modèles autorégressifs vectoriels à noyaux à valeur opérateur: application à l'inférence de réseaux. (Estimation of operator-valued kernel-based vector autoregressive models. Application to network inference)
- Machine learning for translational medicine
- Strategies for increasing the applicability of biological network inference
- The Lotus japonicus Genome
- Reconstructing gene regulatory networks from knock-out data using Gaussian Noise Model and Pearson Correlation Coefficient
- Data-driven integration of genome-scale regulatory and metabolic network models
- Practical Approaches to Biological Network Discovery
- Fast convex optimization for connectivity enforcement in gene regulatory network inference
- Gene Regulatory Network Inference from Multifactorial Perturbation Data Using both Regression and Correlation Analyses
- A Regulatory Role for the Insulin- and BDNF-Linked RORA in the Hippocampus: Implications for Alzheimer's Disease
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