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

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

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

PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli

(2018) Ming-Ju Tsai et al.   Scientific Reports

TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments

(2016) S.M. Minhaz Ud-Dean et al.   BMC BIOINFORMATICS

GeNOSA: inferring and experimentally supporting quantitative gene regulatory networks in prokaryotes

(2015) Yi-Hsiung Chen et al.   BIOINFORMATICS

Optimal design of gene knockout experiments for gene regulatory network inference

(2015) S. M. Minhaz Ud-Dean et al.   BIOINFORMATICS

Combining tree-based and dynamical systems for the inference of gene regulatory networks

(2015) Vân Anh Huynh-Thu et al.   BIOINFORMATICS

Quantitative and logic modelling of molecular and gene networks

(2015) Nicolas Le Novère   NATURE REVIEWS GENETICS

Assessment of Network Inference Methods: How to Cope with an Underdetermined Problem

(2014) Caroline Siegenthaler et al.   PLoS One

Ensemble Inference and Inferability of Gene Regulatory Networks

(2014) S. M. Minhaz Ud-Dean et al.   PLoS One

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

(2013) Néhémy Lim et al.   BIOINFORMATICS

Incorporating time-delays in S-System model for reverse engineering genetic networks

(2013) Ahsan Chowdhury et al.   BMC BIOINFORMATICS

Improved Inference of Gene Regulatory Networks through Integrated Bayesian Clustering and Dynamic Modeling of Time-Course Expression Data

(2013) Brian Godsey   PLoS One

Experimental assessment of static and dynamic algorithms for gene regulation inference from time series expression data

(2013) Miguel Lopes et al.   Frontiers in Genetics

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Studying and modelling dynamic biological processes using time-series gene expression data

(2012) Ziv Bar-Joseph et al.   NATURE REVIEWS GENETICS

GlobalMIT: learning globally optimal dynamic bayesian network with the mutual information test criterion

(2011) N. X. Vinh et al.   BIOINFORMATICS

TRANSWESD: inferring cellular networks with transitive reduction

(2010) Steffen Klamt et al.   BIOINFORMATICS

Advantages and limitations of current network inference methods

(2010) Riet De Smet et al.   NATURE REVIEWS MICROBIOLOGY

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

Genetic network inference as a series of discrimination tasks

(2009) Shuhei Kimura et al.   BIOINFORMATICS

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

(2009) Tarmo Äijö 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

Inferring Dynamic Genetic Networks with Low Order Independencies

(2009) Sophie Lèbre   Statistical Applications in Genetics and Molecular Biology

Function approximation approach to the inference of reduced NGnet models of genetic networks

(2008) Shuhei Kimura et al.   BMC BIOINFORMATICS

Parameter optimization in S-system models

(2008) Marco Vilela et al.   BMC Systems Biology

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

(2008) D. S. Johnson et al.   GENOME RESEARCH