A comprehensive overview and critical evaluation of gene regulatory network inference technologies

Inference of Gene Regulatory Networks Based on Nonlinear Ordinary Differential Equations

(2020) Baoshan Ma et al.   BIOINFORMATICS

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

(2020) Ming-Ju Tsai et al.   BIOINFORMATICS

Gene Regulatory Network Inference: Connecting Plant Biology and Mathematical Modeling

(2020) Lisa Van den Broeck et al.   Frontiers in Genetics

PFBNet: a priori-fused boosting method for gene regulatory network inference

(2020) Dandan Che et al.   BMC BIOINFORMATICS

Network inference in systems biology: recent developments, challenges, and applications

(2020) Michael M Saint-Antoine et al.   CURRENT OPINION IN BIOTECHNOLOGY

Computational Analysis of the Global Effects of Ly6E in the Immune Response to Coronavirus Infection Using Gene Networks

(2020) Fernando M. Delgado-Chaves et al.   Genes

Supervised learning of gene-regulatory networks based on graph distance profiles of transcriptomics data

(2020) Zahra Razaghi-Moghadam et al.   npj Systems Biology and Applications

Network inference performance complexity: a consequence of topological, experimental, and algorithmic determinants

(2019) Joseph J Muldoon et al.   BIOINFORMATICS

Predicting gene regulatory interactions based on spatial gene expression data and deep learning

(2019) Yang Yang et al.   PLoS Computational Biology

Gene regulatory network inference resources: A practical overview

(2019) Daniele Mercatelli et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

LiPLike: towards gene regulatory network predictions of high certainty

(2019) Rasmus Magnusson et al.   BIOINFORMATICS

Deep learning for inferring gene relationships from single-cell expression data

(2019) Ye Yuan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring Gene Regulatory Networks of Metabolic Enzymes Using Gradient Boosted Trees

(2019) Yi Zhang et al.   IEEE Journal of Biomedical and Health Informatics

Next-Generation Machine Learning for Biological Networks

(2018) Diogo M. Camacho et al.   CELL

Inferring large-scale gene regulatory networks using a randomized algorithm based on singular value decomposition

(2018) Anjing Fan et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

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

BiXGBoost: a scalable, flexible boosting-based method for reconstructing gene regulatory networks

(2018) Ruiqing Zheng et al.   BIOINFORMATICS

GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks

(2018) Thomas Moerman et al.   BIOINFORMATICS

MICRAT: a novel algorithm for inferring gene regulatory networks using time series gene expression data

(2018) Bei Yang et al.   BMC Systems Biology

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Part mutual information for quantifying direct associations in networks

(2016) Juan Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inference of Gene Regulatory Network Based on Local Bayesian Networks

(2016) Fei Liu et al.   PLoS Computational Biology

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

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

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond

(2015) Socorro Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

Next generation sequencing technology: Advances and applications

(2014) H.P.J. Buermans et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Next-generation Bioinformatics: connecting bases to genes, networks and disease

(2014) P. Horton   BRIEFINGS IN BIOINFORMATICS

A review on the computational approaches for gene regulatory network construction

(2014) Lian En Chai et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks

(2014) Xiujun Zhang et al.   NUCLEIC ACIDS RESEARCH

Hybrid regulatory models: a statistically tractable approach to model regulatory network dynamics

(2013) Andrea Ocone et al.   BIOINFORMATICS

Supervised, semi-supervised and unsupervised inference of gene regulatory networks

(2013) S. R. Maetschke et al.   BRIEFINGS IN BIOINFORMATICS

Reverse engineering and identification in systems biology: strategies, perspectives and challenges

(2013) A. F. Villaverde et al.   Journal of the Royal Society Interface

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

(2012) Xiujun Zhang et al.   BIOINFORMATICS

Comparison of co-expression measures: mutual information, correlation, and model based indices

(2012) Lin Song et al.   BMC BIOINFORMATICS

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection

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

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Gene regulatory network inference: evaluation and application to ovarian cancer allows the prioritization of drug targets

(2012) Piyush B Madhamshettiwar et al.   Genome Medicine

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

(2011) Thomas Schaffter 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

Validation of gene regulatory networks: scientific and inferential

(2010) E. R. Dougherty   BRIEFINGS IN BIOINFORMATICS

Stability selection

(2010) Nicolai Meinshausen et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Metabolomic and transcriptomic stress response of Escherichia coli

(2010) Szymon Jozefczuk et al.   Molecular Systems Biology

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

Lessons from the DREAM2 Challenges

(2009) Gustavo Stolovitzky et al.   Annals of the New York Academy of Sciences

A Tutorial on Analysis and Simulation of Boolean Gene Regulatory Network Models

(2009) Yufei Xiao   CURRENT GENOMICS

Challenges for modeling global gene regulatory networks during development: Insights from Drosophila

(2009) Bartek Wilczynski et al.   DEVELOPMENTAL BIOLOGY

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

SIRENE: supervised inference of regulatory networks

(2008) F. Mordelet et al.   BIOINFORMATICS

Inference of Noisy Nonlinear Differential Equation Models for Gene Regulatory Networks Using Genetic Programming and Kalman Filtering

(2008) Lijun Qian et al.   IEEE TRANSACTIONS ON SIGNAL PROCESSING

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS