ENNET: inferring large gene regulatory networks from expression data using gradient boosting

OKVAR-Boost: a novel boosting algorithm to infer nonlinear dynamics and interactions in gene regulatory networks

(2013) Néhémy Lim et al.   BIOINFORMATICS

Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks

(2013) Alex Greenfield et al.   BIOINFORMATICS

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

(2012) Xiujun Zhang et al.   BIOINFORMATICS

Context-specific transcriptional regulatory network inference from global gene expression maps using double two-way t-tests

(2012) Jianlong Qi et al.   BIOINFORMATICS

Inferring gene regulatory networks by ANOVA

(2012) Robert Küffner et al.   BIOINFORMATICS

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection

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

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

(2011) Thomas Schaffter et al.   BIOINFORMATICS

Inferring the conservative causal core of gene regulatory networks

(2010) Gökmen Altay et al.   BMC Systems Biology

Improved Reconstruction of In Silico Gene Regulatory Networks by Integrating Knockout and Perturbation Data

(2010) Kevin Y. Yip et al.   PLoS One

Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges

(2010) Robert J. Prill et al.   PLoS One

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

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

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

A Gene Network Simulator to Assess Reverse Engineering Algorithms

(2009) Barbara Di Camillo et al.   Annals of the New York Academy of Sciences

Benchmarking regulatory network reconstruction with GRENDEL

(2009) B. C. Haynes et al.   BIOINFORMATICS

GeNGe: systematic generation of gene regulatory networks

(2009) Hendrik Hache et al.   BIOINFORMATICS

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

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

A system for generating transcription regulatory networks with combinatorial control of transcription

(2008) Sushmita Roy et al.   BIOINFORMATICS

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

(2008) Patrick E Meyer et al.   BMC BIOINFORMATICS