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Number of citations per year for the bioinformatics software tool GRNInfer

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This map represents all the scientific publications referring to GRNInfer per scientific context
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GRNInfer specifications


Unique identifier OMICS_24034
Name GRNInfer
Alternative names Gene Regulatory Network Inference, GNR
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes




No version available


  • person_outline Luonan Chen
  • person_outline Dong Xu
  • person_outline Xiang-Sun Zhang

Publication for Gene Regulatory Network Inference

GRNInfer citations


Application of network construction to estimate functional changes to insulin receptor substrates 1 and 2 in Huh7 cells following infection with the hepatitis C virus

PMCID: 4991679
PMID: 27432476
DOI: 10.3892/mmr.2016.5527

[…] The gene networks of the top 50 significantly differentially expressed genes between Huh7 and HCV-Huh7 cells were constructed using GRNInfer ( and GVedit version 2.38 ( tools. GRNInfer () is a linear programming and decomposition algorithm for calculating gene networks from […]


Pathway mapping and development of disease specific biomarkers: protein based network biomarkers

J Cell Mol Med
PMCID: 4407592
PMID: 25560835
DOI: 10.1111/jcmm.12447

[…] d algorithms ,. Computational programs were developed to integrate selected genes or proteins into the knowledge-based networks via the combination of genomics, proteomics and bioinformatics, such as GRNInfer , MDCinfer , TRNInfer , Samo , MNAligner , PTG , PRNA , NOA , differential dependency network (DDN) , WGCNA , SurvNet or DiME , each of them has its own advantages and strength on basis of s […]


Data Mining in Networks of Differentially Expressed Genes during Sow Pregnancy

PMCID: 3334670
PMID: 22532788
DOI: 10.7150/ijbs.4071

[…] clopedia of Genes and Genomes (KEGG). Fisher's exact test was used to select each significant pathway, and the significance threshold was defined by the p value . Networks were reconstructed by using GRNInfer , . GRNInfer is a method based on linear programming and a decomposition procedure to combine multiple time-course microarray datasets from different conditions for inferring gene regulatory […]


Role of clinical bioinformatics in the development of network based Biomarkers

J Clin Bioinforma
PMCID: 3221619
PMID: 22024468
DOI: 10.1186/2043-9113-1-28

[…] ed to integrate selected proteins into the knowledge-based networks via the combination of genomics, proteomics and bioinformatics. Those methodologies include gene regulatory network inference tool (GRNInfer), gene regulatory network reconstruction tool with compound targets (nGNTInfer), inferring transcriptional regulatory networks from high-throughput data (nTRNInfer), inferring protein-protein […]


Inferring gene regulatory networks from asynchronous microarray data with AIRnet

BMC Genomics
PMCID: 2975420
PMID: 21047387
DOI: 10.1186/1471-2164-11-S2-S6

[…] s instead of correlation of absolute values. (1) (2)The Dialogue for Reverse Engineering Assessments and Methods (DREAM) organization creates benchmark data and metrics for evaluating the accuracy of gene regulatory network inference algorithms []. Table shows example data for generating influence vectors. The columns represent different microarray samples for the DREAM knockout experiment. In th […]


Integrative Decomposition Procedure and Kappa Statistics for the Distinguished Single Molecular Network Construction and Analysis

PMCID: 2668912
PMID: 19390583
DOI: 10.1155/2009/726728

[…] We, respectively, constructed the interaction network of the above 51 genes in healthy tissues and that in tumor using GRNInfer [] and GVedit tools and selected the ATF2-centered downstream subnetworks. With comparison of these ATF2-centered subnetworks, we can get a more clear perception of the notable differences be […]

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GRNInfer institution(s)
Department of Electrical Engineering and Electronics, Osaka Sangyo University, Osaka, Japan; Academy of Mathematics and Systems Science, CAS, Beijing, China; Computer Science Department and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Institute of Systems Biology, Shanghai University, Shanghai, China
GRNInfer funding source(s)
Supported by project Bioinformatics, Bureau of Basic Science, CAS and by a USDA grant CSREES 2004–25,604-14,708.

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