Inference of genetic regulatory networks with regulatory hubs using vector autoregressions and automatic relevance determination with model selections

GREMA: modelling of emulated gene regulatory networks with confidence levels based on evolutionary intelligence to cope with the underdetermined problem

(2020) Ming-Ju Tsai et al.   BIOINFORMATICS

PFBNet: a priori-fused boosting method for gene regulatory network inference

(2020) Dandan Che et al.   BMC BIOINFORMATICS

Gene regulatory network inference from sparsely sampled noisy data

(2020) Atte Aalto et al.   Nature Communications

dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression data

(2018) Vân Anh Huynh-Thu et al.   Scientific Reports

Inferring gene expression networks with hubs using a degree weighted Lasso approach

(2018) Nurgazy Sulaimanov et al.   BIOINFORMATICS

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond

(2015) Socorro Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

Learning Bayesian Networks with thebnlearnRPackage

(2015) Marco Scutari   Journal of Statistical Software

SANTA: Quantifying the Functional Content of Molecular Networks

(2014) Alex J. Cornish et al.   PLoS Computational Biology

Autoregressive models for gene regulatory network inference: Sparsity, stability and causality issues

(2013) George Michailidis et al.   MATHEMATICAL BIOSCIENCES

Integrating external biological knowledge in the construction of regulatory networks from time-series expression data

(2012) Kenneth Lo et al.   BMC Systems Biology

Hub-Centered Gene Network Reconstruction Using Automatic Relevance Determination

(2012) Matthias Böck et al.   PLoS One

How to infer gene networks from expression profiles, revisited

(2011) C. A. Penfold et al.   Interface Focus

Inferring gene regression networks with model trees

(2010) Isabel A Nepomuceno-Chamorro et al.   BMC BIOINFORMATICS

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

Weighted-LASSO for Structured Network Inference from Time Course Data

(2010) Camille Charbonnier et al.   Statistical Applications in Genetics and Molecular Biology

Regularized estimation of large-scale gene association networks using graphical Gaussian models

(2009) Nicole Krämer et al.   BMC BIOINFORMATICS

Recursive regularization for inferring gene networks from time-course gene expression profiles

(2009) Teppei Shimamura et al.   BMC Systems Biology

Generating Realistic In Silico Gene Networks for Performance Assessment of Reverse Engineering Methods

(2009) Daniel Marbach et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Gene regulatory network inference: Data integration in dynamic models—A review

(2008) Michael Hecker et al.   BIOSYSTEMS

minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information

(2008) Patrick E Meyer et al.   BMC BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Rank-based edge reconstruction for scale-free genetic regulatory networks

(2008) Guanrao Chen et al.   BMC BIOINFORMATICS