Gene regulatory network inference using fused LASSO on multiple data sets

Inferring Networks from Multiple Samples with Consensus LASSO

(2016) Nathalie Villa-Vialaneix et al.   Quality Technology and Quantitative Management

Inferring gene regulatory networks by integrating ChIP-seq/chip and transcriptome data via LASSO-type regularization methods

(2014) Jing Qin et al.   METHODS

Ensemble-Based Network Aggregation Improves the Accuracy of Gene Network Reconstruction

(2014) Rui Zhong et al.   PLoS One

Analysis on a superlinearly convergent augmented Lagrangian method

(2013) Ya Xiang Yuan   ACTA MATHEMATICA SINICA-ENGLISH SERIES

A categorical network approach for discovering differentially expressed regulations in cancer

(2013) Nikolay Balov   BMC Medical Genomics

The Mycobacterium tuberculosis regulatory network and hypoxia

(2013) James E. Galagan et al.   NATURE

Network link prediction by global silencing of indirect correlations

(2013) Baruch Barzel et al.   NATURE BIOTECHNOLOGY

Network deconvolution as a general method to distinguish direct dependencies in networks

(2013) Soheil Feizi et al.   NATURE BIOTECHNOLOGY

Inference of Gene Regulatory Networks with Sparse Structural Equation Models Exploiting Genetic Perturbations

(2013) Xiaodong Cai et al.   PLoS Computational Biology

Harnessing Diversity towards the Reconstructing of Large Scale Gene Regulatory Networks

(2013) Takeshi Hase et al.   PLoS Computational Biology

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

(2013) Franck Rapaport et al.   GENOME BIOLOGY

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection

(2012) Anne-Claire Haury et al.   BMC Systems Biology

Learning Sparse Causal Gaussian Networks With Experimental Intervention: Regularization and Coordinate Descent

(2012) Fei Fu et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Unraveling gene regulatory networks from time-resolved gene expression data -- a measures comparison study

(2011) Sabrina Hempel et al.   BMC BIOINFORMATICS

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

Dynamic Bayesian networks in molecular plant science: inferring gene regulatory networks from multiple gene expression time series

(2011) Frank Dondelinger et al.   EUPHYTICA

Brief review of regression-based and machine learning methods in genetic epidemiology: the Genetic Analysis Workshop 17 experience

(2011) Abhijit Dasgupta et al.   GENETIC EPIDEMIOLOGY

Directed Partial Correlation: Inferring Large-Scale Gene Regulatory Network through Induced Topology Disruptions

(2011) Yinyin Yuan et al.   PLoS One

TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach

(2010) Pietro Zoppoli et al.   BMC BIOINFORMATICS

Metabolomic and transcriptomic stress response of Escherichia coli

(2010) Szymon Jozefczuk et al.   Molecular Systems Biology

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

(2010) S. Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

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

Analysis and Computational Dissection of Molecular Signature Multiplicity

(2010) Alexander Statnikov et al.   PLoS Computational Biology

Simulation-based model selection for dynamical systems in systems and population biology

(2009) Tina Toni et al.   BIOINFORMATICS

Inference of Gene Regulatory Networks Using Time-Series Data: A Survey

(2009) Chao Sima et al.   CURRENT GENOMICS

Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes

(2009) B. J. Blencowe et al.   GENES & DEVELOPMENT

Partial Correlation Estimation by Joint Sparse Regression Models

(2009) Jie Peng et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

AGRONOMICS1: A New Resource for Arabidopsis Transcriptome Profiling

(2009) H. Rehrauer et al.   PLANT PHYSIOLOGY

Reconstruction of genetic association networks from microarray data: a partial least squares approach

(2008) V. Pihur et al.   BIOINFORMATICS

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

(2008) Patrick E Meyer et al.   BMC BIOINFORMATICS

Modelling and analysis of gene regulatory networks

(2008) Guy Karlebach et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Using matrix of thresholding partial correlation coefficients to infer regulatory network

(2007) Lide Han et al.   BIOSYSTEMS