NSRGRN: a network structure refinement method for gene regulatory network inference

Predicting lncRNA–disease associations based on combining selective similarity matrix fusion and bidirectional linear neighborhood label propagation

(2023) Guo-Bo Xie et al.   BRIEFINGS IN BIOINFORMATICS

EnANNDeep: An Ensemble-based lncRNA–protein Interaction Prediction Framework with Adaptive k-Nearest Neighbor Classifier and Deep Models

(2022) Lihong Peng et al.   Interdisciplinary Sciences-Computational Life Sciences

Fast and accurate inference of gene regulatory networks through robust precision matrix estimation

(2022) Antoine Passemiers et al.   BIOINFORMATICS

NSCGRN: a network structure control method for gene regulatory network inference

(2022) Wei Liu et al.   BRIEFINGS IN BIOINFORMATICS

Identification of miRNA–disease associations via deep forest ensemble learning based on autoencoder

(2022) Wei Liu et al.   BRIEFINGS IN BIOINFORMATICS

Cell–cell communication inference and analysis in the tumour microenvironments from single-cell transcriptomics: data resources and computational strategies

(2022) Lihong Peng et al.   BRIEFINGS IN BIOINFORMATICS

Inference of gene regulatory networks using pseudo-time series data

(2021) Yuelei Zhang et al.   BIOINFORMATICS

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

(2021) Mengyuan Zhao et al.   BRIEFINGS IN BIOINFORMATICS

Prioritizing antiviral drugs against SARS-CoV-2 by integrating viral complete genome sequences and drug chemical structures

(2021) Lihong Peng et al.   Scientific Reports

Using high-throughput multi-omics data to investigate structural balance in elementary gene regulatory network motifs

(2021) Alberto Zenere et al.   BIOINFORMATICS

A novel lncRNA–protein interaction prediction method based on deep forest with cascade forest structure

(2021) Xiongfei Tian et al.   Scientific Reports

Inferring Gene Regulatory Networks Using the Improved Markov Blanket Discovery Algorithm

(2021) Wei Liu et al.   Interdisciplinary Sciences-Computational Life Sciences

LPI-HyADBS: a hybrid framework for lncRNA-protein interaction prediction integrating feature selection and classification

(2021) Liqian Zhou et al.   BMC BIOINFORMATICS

LPI-deepGBDT: a multiple-layer deep framework based on gradient boosting decision trees for lncRNA–protein interaction identification

(2021) Liqian Zhou et al.   BMC BIOINFORMATICS

A hybrid deep learning framework for gene regulatory network inference from single-cell transcriptomic data

(2021) Mengyuan Zhao et al.   BRIEFINGS IN BIOINFORMATICS

LPI-EnEDT: an ensemble framework with extra tree and decision tree classifiers for imbalanced lncRNA-protein interaction data classification

(2021) Lihong Peng et al.   BioData Mining

WBNPMD: weighted bipartite network projection for microRNA-disease association prediction

(2019) Guobo Xie et al.   Journal of Translational Medicine

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

D3GRN: a data driven dynamic network construction method to infer gene regulatory networks

(2019) Xiang Chen et al.   BMC GENOMICS

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

(2018) Vân Anh Huynh-Thu 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

Gene regulatory network inference using PLS-based methods

(2016) Shun Guo et al.   BMC BIOINFORMATICS

Application of Euclidean distance measurement and principal component analysis for gene identification

(2016) Antara Ghosh et al.   GENE

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

Optimal design of gene knockout experiments for gene regulatory network inference

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

Reconstructing gene regulatory networks from knock-out data using Gaussian Noise Model and Pearson Correlation Coefficient

(2015) Faridah Hani Mohamed Salleh et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Next generation sequencing technology: Advances and applications

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

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

(2014) Xiujun Zhang et al.   NUCLEIC ACIDS RESEARCH

NIMEFI: Gene Regulatory Network Inference using Multiple Ensemble Feature Importance Algorithms

(2014) Joeri Ruyssinck et al.   PLoS One

Network cleanup

(2013) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Network link prediction by global silencing of indirect correlations

(2013) Baruch Barzel et al.   NATURE BIOTECHNOLOGY

Network deconvolution as a general method to distinguish direct dependencies in networks

(2013) Soheil Feizi et al.   NATURE BIOTECHNOLOGY

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

(2011) Xiujun Zhang et al.   BIOINFORMATICS

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

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

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

Genome-wide identification of post-translational modulators of transcription factor activity in human B cells

(2009) Kai Wang et al.   NATURE BIOTECHNOLOGY

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

(2008) Patrick E Meyer et al.   BMC BIOINFORMATICS

Properties of developmental gene regulatory networks

(2008) E. H. Davidson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA