NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference

Inferring gene regulatory networks by ANOVA

(2012) Robert Küffner et al.   BIOINFORMATICS

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Robust Detection of Hierarchical Communities from Escherichia coli Gene Expression Data

(2012) Santiago Treviño et al.   PLoS Computational Biology

GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods

(2011) Thomas Schaffter et al.   BIOINFORMATICS

Large-scale dynamic gene regulatory network inference combining differential equation models with local dynamic Bayesian network analysis

(2011) Zheng Li et al.   BIOINFORMATICS

Identification of context-specific gene regulatory networks with GEMULA—gene expression modeling using LAsso

(2011) Geert Geeven et al.   BIOINFORMATICS

Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information

(2011) Xiujun Zhang et al.   BIOINFORMATICS

An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma

(2011) Pavel Sumazin et al.   CELL

Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression

(2011) L. T. MacNeil et al.   GENOME RESEARCH

Gene network inference and visualization tools for biologists: application to new human transcriptome datasets

(2011) Daniel Hurley et al.   NUCLEIC ACIDS RESEARCH

Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function

(2011) Vincenzo Belcastro et al.   NUCLEIC ACIDS RESEARCH

Functional characterization of bacterial sRNAs using a network biology approach

(2011) S. R. Modi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Construction of regulatory networks using expression time-series data of a genotyped population

(2011) K. Y. Yeung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting Novel Associations in Large Data Sets

(2011) D. N. Reshef et al.   SCIENCE

MISS: a non-linear methodology based on mutual information for genetic association studies in both population and sib-pairs analysis

(2010) Helena Brunel et al.   BIOINFORMATICS

Revealing differences in gene network inference algorithms on the network level by ensemble methods

(2010) Gökmen Altay et al.   BIOINFORMATICS

Multilevel support vector regression analysis to identify condition-specific regulatory networks

(2010) Li Chen et al.   BIOINFORMATICS

Discovery of Chemical Compound Groups with Common Structures by a Network Analysis Approach (Affinity Prediction Method)

(2010) Shigeru Saito et al.   Journal of Chemical Information and Modeling

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

Model-based method for transcription factor target identification with limited data

(2010) Antti Honkela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Revealing strengths and weaknesses of methods for gene network inference

(2010) D. Marbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli

(2009) Rui-Sheng Wang et al.   BMC BIOINFORMATICS

A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches

(2009) Irene Cantone et al.   CELL

Incorporating Existing Network Information into Gene Network Inference

(2009) Scott Christley et al.   PLoS One

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

(2008) Patrick E Meyer et al.   BMC BIOINFORMATICS