ArticleBMC bioinformatics2016
Gene regulatory network inference using PLS-based methods.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- BCTI: a Bayesian network-based method for revealing critical transitions in complex biological systems.PeerJ · 2026Article
- SPREd: a simulation-supervised neural network tool for gene regulatory network reconstruction.Bioinformatics advances · 2024Article
- SPREd: A simulation-supervised neural network tool for gene regulatory network reconstruction.bioRxiv : the preprint server for biology · 2023Article
- Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection.PLoS computational biology · 2023Article
- Article
- Comparison of hepatic responses to glucose perturbation between healthy and obese mice based on the edge type of network structures.Scientific reports · 2023Article
- Article
- Network-based approaches for modeling disease regulation and progression.Computational and structural biotechnology journal · 2023Review
- Knowledge of the perturbation design is essential for accurate gene regulatory network inference.Scientific reports · 2022Article
- Article
- Fast and accurate inference of gene regulatory networks through robust precision matrix estimation.Bioinformatics (Oxford, England) · 2022Article
- KBoost: a new method to infer gene regulatory networks from gene expression data.Scientific reports · 2021Article
- Biomarker Prioritisation and Power Estimation Using Ensemble Gene Regulatory Network Inference.International journal of molecular sciences · 2020Article
- PFBNet: a priori-fused boosting method for gene regulatory network inference.BMC bioinformatics · 2020Article
- Specific functions for Mediator complex subunits from different modules in the transcriptional response of Arabidopsis thaliana to abiotic stress.Scientific reports · 2020Article
- D3GRN: a data driven dynamic network construction method to infer gene regulatory networks.BMC genomics · 2019Article
- CONFIGURE: A pipeline for identifying context specific regulatory modules from gene expression data and its application to breast cancer.BMC medical genomics · 2019Article
- Markov chain Monte Carlo simulation of a Bayesian mixture model for gene network inference.Genes & genomics · 2019Article
- Semi-supervised network inference using simulated gene expression dynamics.Bioinformatics (Oxford, England) · 2018Article
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4 authors.
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Abstract
backgroundInferring the topology of gene regulatory networks (GRNs) from microarray gene expression data has many potential applications, such as identifying candidate drug targets and providing valuable insights into the biological processes. It remains a challenge due to the fact that the data is noisy and high dimensional, and there exists a large number of potential interactions.
resultsWe introduce an ensemble gene regulatory network inference method PLSNET, which decomposes the GRN inference problem with p genes into p subproblems and solves each of the subproblems by using Partial least squares (PLS) based feature selection algorithm. Then, a statistical technique is used to refine the predictions in our method. The proposed method was evaluated on the DREAM4 and DREAM5 benchmark datasets and achieved higher accuracy than the winners of those competitions and other state-of-the-art GRN inference methods.
conclusionsSuperior accuracy achieved on different benchmark datasets, including both in silico and in vivo networks, shows that PLSNET reaches state-of-the-art performance.
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