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NARROMI specifications

Information


Unique identifier OMICS_16688
Name NARROMI
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No

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Publication for NARROMI

NARROMI in publications

 (6)
PMCID: 5655205
PMID: 29113310
DOI: 10.18632/oncotarget.21268

[…] shows the main results of the three algorithms and the dbncs algorithm to infer grns., the fpr of the dbncs algorithm is 9.9% lower than genie3 and aracne algorithm, which is 3.7% lower than that of narromi algorithm. the ppv is 45.2% higher than genie3 algorithm and 25.3% higher than narromi algorithm. the acc is 10% higher than genie3 algorithm and 4.5% higher than narromi algorithm. matthew's […]

PMCID: 5471331
PMID: 28663756
DOI: 10.3389/fpls.2017.01044

[…] two major network construction and analysis methods as described below., we constructed another template tf network using a state-of-the-art gene-expression-based tf network construction method, narromi (zhang et al., ). using 1,893 microarray data sets, narromi produced 6,213,143 tf-target gene edges (p < 0.05). edges of strong association (|pcc| > 0.67) in eight mrna-seq data sets […]

PMCID: 5260093
PMID: 28155657
DOI: 10.1186/s12864-016-3317-7

[…] method (tigress [] with two different parameter settings, see tableĀ  for the details), and one method with both of ordinary differential equation based recursive optimization and mutual information (narromi []). the set of 14 algorithms includes several high-performance algorithms, ie, genie3 is the winner of both of dream4 (dream, dialogue on reverse engineering assessment and methods) […]

PMCID: 4460612
PMID: 26044212
DOI: 10.1186/1755-8794-8-S2-S10

[…] therefore, grn is used for the purpose of discarding non-significant genes, as grn is a very effective method that can consider complex relationships of many genes [] (in here, candidate genes). narromi [] was used for grn construction. details of grn construction are described in methods section. using the topology information created by narromi, we discarded those candidates that have weak […]

PMCID: 4373852
PMID: 25807392
DOI: 10.1371/journal.pone.0119294

[…] correlation based estimation methods [], model-based methods [, , ], and mutual information(mi)-based methods, such as cmi [], mi-cmi [], mi3 [] and pca-cmi [] and ipca-cmi []. furthermore, narromi [] combined regression-based optimization and information theory- based mi to achieve improved accuracy., however, the above approaches suffer from two limitations when handling networks […]


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NARROMI institution(s)
Institute of Systems Biology, Shanghai University, Shanghai, China; School of Communication and Information Engineering, Shanghai University, Shanghai, China; LERIA, University of Angers, Angers, France; Key Laboratory of Systems Biology, SIBS-Novo Nordisk Translational Research Centre for PreDiabetes, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; Department of Computer Science, School of Electronics and Information Engineering, Tongji University, Shanghai, China
NARROMI funding source(s)
Supported by Sino-French Cai Yuanpei Program from CSC (20106050), NSFC (91029301, 61134013, 61072149, 91130032, 61103075, 31100949), Innovation Program of Shanghai Municipal Education Commission (13ZZ072), Shanghai Pujiang Program, Chief Scientist Program of SIBS from CAS (2009CSP002), Knowledge Innovation Program of SIBS of CAS (2011KIP203), the Knowledge Innovation Program of CAS (KSCX2-EW-R-01), National Center for Mathematics and Interdisciplinary Sciences of CAS, and the FIRST Program initiated by CSTP, Radapop and LigeRO Projects (2009-2013, Pays de La Loire Region, France).

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