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

TRANSWESD: inferring cellular networks with transitive reduction

(2010) Steffen Klamt et al.   BIOINFORMATICS

Time lagged information theoretic approaches to the reverse engineering of gene regulatory networks

(2010) Vijender Chaitankar et al.   BMC BIOINFORMATICS

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

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

From Knockouts to Networks: Establishing Direct Cause-Effect Relationships through Graph Analysis

(2010) Andrea Pinna et al.   PLoS One

Gene Regulatory Networks from Multifactorial Perturbations Using Graphical Lasso: Application to the DREAM4 Challenge

(2010) Patricia Menéndez 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

Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics

(2009) Tarmo Äijö et al.   BIOINFORMATICS

Systems Biology Strikes Gold

(2009) Diogo M. Camacho et al.   CELL

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

(2009) Irene Cantone et al.   CELL

ReTRN: A retriever of real transcriptional regulatory network and expression data for evaluating structure learning algorithm

(2009) Yong Li et al.   GENOMICS

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

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS