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Items: 1 to 20 of 263


atBioNet--an integrated network analysis tool for genomics and biomarker discovery.

Ding Y, Chen M, Liu Z, Ding D, Ye Y, Zhang M, Kelly R, Guo L, Su Z, Harris SC, Qian F, Ge W, Fang H, Xu X, Tong W.

BMC Genomics. 2012 Jul 20;13:325. doi: 10.1186/1471-2164-13-325.


Constructing a robust protein-protein interaction network by integrating multiple public databases.

Martha VS, Liu Z, Guo L, Su Z, Ye Y, Fang H, Ding D, Tong W, Xu X.

BMC Bioinformatics. 2011 Oct 18;12 Suppl 10:S7. doi: 10.1186/1471-2105-12-S10-S7.


IIIDB: a database for isoform-isoform interactions and isoform network modules.

Tseng YT, Li W, Chen CH, Zhang S, Chen JJ, Zhou X, Liu CC.

BMC Genomics. 2015;16 Suppl 2:S10. doi: 10.1186/1471-2164-16-S2-S10. Epub 2015 Jan 21.


Analyzing and interpreting genome data at the network level with ConsensusPathDB.

Herwig R, Hardt C, Lienhard M, Kamburov A.

Nat Protoc. 2016 Oct;11(10):1889-907. doi: 10.1038/nprot.2016.117. Epub 2016 Sep 8.


Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data.

Li M, Wu X, Wang J, Pan Y.

BMC Bioinformatics. 2012 May 23;13:109. doi: 10.1186/1471-2105-13-109.


A comparison of the functional modules identified from time course and static PPI network data.

Tang X, Wang J, Liu B, Li M, Chen G, Pan Y.

BMC Bioinformatics. 2011 Aug 15;12:339. doi: 10.1186/1471-2105-12-339.


ModuLand plug-in for Cytoscape: determination of hierarchical layers of overlapping network modules and community centrality.

Szalay-Beko M, Palotai R, Szappanos B, Kovács IA, Papp B, Csermely P.

Bioinformatics. 2012 Aug 15;28(16):2202-4. doi: 10.1093/bioinformatics/bts352. Epub 2012 Jun 19.


MOfinder: a novel algorithm for detecting overlapping modules from protein-protein interaction network.

Yu Q, Li GH, Huang JF.

J Biomed Biotechnol. 2012;2012:103702. doi: 10.1155/2012/103702. Epub 2012 Feb 8.


A structural approach for finding functional modules from large biological networks.

Mete M, Tang F, Xu X, Yuruk N.

BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S19. doi: 10.1186/1471-2105-9-S9-S19.


Growing functional modules from a seed protein via integration of protein interaction and gene expression data.

Maraziotis IA, Dimitrakopoulou K, Bezerianos A.

BMC Bioinformatics. 2007 Oct 23;8:408.


Biological Network Inference and analysis using SEBINI and CABIN.

Taylor R, Singhal M.

Methods Mol Biol. 2009;541:551-76. doi: 10.1007/978-1-59745-243-4_24. Review.


ModuleRole: a tool for modulization, role determination and visualization in protein-protein interaction networks.

Li G, Li M, Zhang Y, Wang D, Li R, GuimerĂ  R, Gao JT, Zhang MQ.

PLoS One. 2014 May 1;9(5):e94608. doi: 10.1371/journal.pone.0094608. eCollection 2014.


IIS--Integrated Interactome System: a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools.

Carazzolle MF, de Carvalho LM, Slepicka HH, Vidal RO, Pereira GA, Kobarg J, Meirelles GV.

PLoS One. 2014 Jun 20;9(6):e100385. doi: 10.1371/journal.pone.0100385. eCollection 2014. Erratum in: PLoS One. 2014;9(9):e108101.


Functional analysis of OMICs data and small molecule compounds in an integrated "knowledge-based" platform.

Nikolsky Y, Kirillov E, Zuev R, Rakhmatulin E, Nikolskaya T.

Methods Mol Biol. 2009;563:177-96. doi: 10.1007/978-1-60761-175-2_10.


SPICi: a fast clustering algorithm for large biological networks.

Jiang P, Singh M.

Bioinformatics. 2010 Apr 15;26(8):1105-11. doi: 10.1093/bioinformatics/btq078. Epub 2010 Feb 24.


Genomics Portals: integrative web-platform for mining genomics data.

Shinde K, Phatak M, Johannes FM, Chen J, Li Q, Vineet JK, Hu Z, Ghosh K, Meller J, Medvedovic M.

BMC Genomics. 2010 Jan 13;11:27. doi: 10.1186/1471-2164-11-27.


HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery.

Leung A, Bader GD, Reimand J.

Bioinformatics. 2014 Aug 1;30(15):2230-2. doi: 10.1093/bioinformatics/btu172. Epub 2014 Apr 8.


Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis.

Lysenko A, Defoin-Platel M, Hassani-Pak K, Taubert J, Hodgman C, Rawlings CJ, Saqi M.

BMC Bioinformatics. 2011 May 25;12:203. doi: 10.1186/1471-2105-12-203.


Improving protein complex prediction by reconstructing a high-confidence protein-protein interaction network of Escherichia coli from different physical interaction data sources.

Taghipour S, Zarrineh P, Ganjtabesh M, Nowzari-Dalini A.

BMC Bioinformatics. 2017 Jan 3;18(1):10. doi: 10.1186/s12859-016-1422-x.

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