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Items: 1 to 20 of 116

1.

GENIES: gene network inference engine based on supervised analysis.

Kotera M, Yamanishi Y, Moriya Y, Kanehisa M, Goto S.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W162-7. doi: 10.1093/nar/gks459. Epub 2012 May 18.

2.

DINIES: drug-target interaction network inference engine based on supervised analysis.

Yamanishi Y, Kotera M, Moriya Y, Sawada R, Kanehisa M, Goto S.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W39-45. doi: 10.1093/nar/gku337. Epub 2014 May 16.

3.

MetaPath Online: a web server implementation of the network expansion algorithm.

Handorf T, Ebenhöh O.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W613-8. Epub 2007 May 5.

4.

Selective integration of multiple biological data for supervised network inference.

Kato T, Tsuda K, Asai K.

Bioinformatics. 2005 May 15;21(10):2488-95. Epub 2005 Feb 22.

PMID:
15728114
5.

Supervised enzyme network inference from the integration of genomic data and chemical information.

Yamanishi Y, Vert JP, Kanehisa M.

Bioinformatics. 2005 Jun;21 Suppl 1:i468-77.

PMID:
15961492
6.

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.

PMID:
19381531
7.
8.

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function.

Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, Maitland A, Mostafavi S, Montojo J, Shao Q, Wright G, Bader GD, Morris Q.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W214-20. doi: 10.1093/nar/gkq537.

9.

ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks.

Klein J, Leupold S, Münch R, Pommerenke C, Johl T, Kärst U, Jänsch L, Jahn D, Retter I.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W460-4. doi: 10.1093/nar/gkn217. Epub 2008 Apr 25.

10.

metaSHARK: a WWW platform for interactive exploration of metabolic networks.

Hyland C, Pinney JW, McConkey GA, Westhead DR.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W725-8.

11.

Computational tools for the modern andrologist.

Niederberger C.

J Androl. 1996 Sep-Oct;17(5):462-6. Review.

12.

ViaComplex: software for landscape analysis of gene expression networks in genomic context.

Castro MA, Filho JL, Dalmolin RJ, Sinigaglia M, Moreira JC, Mombach JC, de Almeida RM.

Bioinformatics. 2009 Jun 1;25(11):1468-9. doi: 10.1093/bioinformatics/btp246. Epub 2009 Apr 15.

PMID:
19369498
13.

BiologicalNetworks: visualization and analysis tool for systems biology.

Baitaluk M, Sedova M, Ray A, Gupta A.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W466-71.

14.
15.

The KEGG databases at GenomeNet.

Kanehisa M, Goto S, Kawashima S, Nakaya A.

Nucleic Acids Res. 2002 Jan 1;30(1):42-6.

16.

PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways.

Mlecnik B, Scheideler M, Hackl H, Hartler J, Sanchez-Cabo F, Trajanoski Z.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W633-7.

17.

GEM-TREND: a web tool for gene expression data mining toward relevant network discovery.

Feng C, Araki M, Kunimoto R, Tamon A, Makiguchi H, Niijima S, Tsujimoto G, Okuno Y.

BMC Genomics. 2009 Sep 3;10:411. doi: 10.1186/1471-2164-10-411.

18.

ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis.

Pitkänen E, Akerlund A, Rantanen A, Jouhten P, Ukkonen E.

J Integr Bioinform. 2008 Aug 25;5(2). doi: 10.2390/biecoll-jib-2008-102.

PMID:
20134058
19.

Protein network inference from multiple genomic data: a supervised approach.

Yamanishi Y, Vert JP, Kanehisa M.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i363-70.

PMID:
15262821
20.

A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm.

Podell S, Gaasterland T, Allen EE.

BMC Bioinformatics. 2008 Oct 7;9:419. doi: 10.1186/1471-2105-9-419.

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