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atBioNet specifications


Unique identifier OMICS_18851
Name atBioNet
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 1.1.10
Stability No
Maintained No




No version available



This tool is not available anymore.

Publication for atBioNet

atBioNet citations


Protein protein interaction analysis to identify biomarker networks for endometriosis

PMCID: 5704338
PMID: 29201163
DOI: 10.3892/etm.2017.5185

[…] Endometriosis-associated genes were submitted to atBioNet ( and PPIs were obtained. atBioNet is a network analysis tool that provides a systematic insight into gene interactions b […]


In silico identification of potential key regulatory factors in smoking induced lung cancer

BMC Med Genomics
PMCID: 5463402
PMID: 28592245
DOI: 10.1186/s12920-017-0284-z

[…] The data set is publicly available at Gene Expression Omnibus (GEO) (, under data source access GSE4115. GEO2R, atBioNet, and Enrichr are online tools. Soft was created by Ma’ayan Laboratory, Icahn school of medicine at Mount Sinai. Spira’s panel of an 80-gene biomarker is available at (https://drive. […]


From protein protein interactions to protein co expression networks: a new perspective to evaluate large scale proteomic data

EURASIP J Bioinform Syst Biol
PMCID: 5359264
PMID: 28477207
DOI: 10.1186/s13637-017-0059-z

[…] biology studies, like the production of accurate -omics data and the collection of reliable molecular interactions. The most broadly adopted softwares include Cytoscape and its plugins [], VisANT [], atBioNet [], PINA [], and Ingenuity [] which represents a commercial solution. On the contrary, Cytoscape is a software now developed by an international consortium of open-source developers. Figure […]


Biological Networks for Cancer Candidate Biomarkers Discovery

Cancer Inform
PMCID: 5012434
PMID: 27625573
DOI: 10.4137/CIN.S39458

[…] as a biomarker from urinary for recurrence in bladder cancer, and identifying noninvasive blood-based diagnosis markers for pancreatic cancer. Ding et al. developed a web-based PPI network tool named atBioNet, which was created by integrating seven public PPI databases for biomarker discovery using a fast network-clustering algorithm called structural clustering algorithm for networks, to find dis […]


Applications of systems approaches in the study of rheumatic diseases

PMCID: 4351319
PMID: 25750554
DOI: 10.3904/kjim.2015.30.2.148

[…] se-related candidate genes such as SOCS3, PDGRFA, NFKBIA, and NCF2, consistent with previous reports [,,,]. However, much follow up is necessary to validate these findings. In another study using the atBioNet database system, two major modules were generated from seed genes using a fast-network-clustering algorithm: inflammatory process and immune activity []. The major signaling pathway involved […]


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atBioNet institution(s)
ICF International at FDA's National Center for Toxicological Research, Jefferson, AR, USA; Divisions of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA; Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA; State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China; Department of Information Science, University of Arkansas at Little Rock, Little Rock, AR, USA
atBioNet funding source(s)
Supported by the National Center for Toxicological Research (NCTR) of the U.S. Food and Drug Administration (FDA) for postdoctoral and faculty support through the Oak Ridge Institute for Science and Education (ORISE).

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