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Items: 1 to 20 of 263

1.

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
2.

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
3.

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
4.

Prediction of missing enzyme genes in a bacterial metabolic network. Reconstruction of the lysine-degradation pathway of Pseudomonas aeruginosa.

Yamanishi Y, Mihara H, Osaki M, Muramatsu H, Esaki N, Sato T, Hizukuri Y, Goto S, Kanehisa M.

FEBS J. 2007 May;274(9):2262-73. Epub 2007 Mar 27.

5.

Biological network mapping and source signal deduction.

Brynildsen MP, Wu TY, Jang SS, Liao JC.

Bioinformatics. 2007 Jul 15;23(14):1783-91. Epub 2007 May 11.

PMID:
17495996
6.

Simultaneous inference of biological networks of multiple species from genome-wide data and evolutionary information: a semi-supervised approach.

Kashima H, Yamanishi Y, Kato T, Sugiyama M, Tsuda K.

Bioinformatics. 2009 Nov 15;25(22):2962-8. doi: 10.1093/bioinformatics/btp494. Epub 2009 Aug 17.

PMID:
19689962
7.

Inferring network interactions within a cell.

Carter GW.

Brief Bioinform. 2005 Dec;6(4):380-9. Review.

PMID:
16420736
8.

Prediction of drug-target interaction networks from the integration of chemical and genomic spaces.

Yamanishi Y, Araki M, Gutteridge A, Honda W, Kanehisa M.

Bioinformatics. 2008 Jul 1;24(13):i232-40. doi: 10.1093/bioinformatics/btn162.

9.

A lock-and-key model for protein-protein interactions.

Morrison JL, Breitling R, Higham DJ, Gilbert DR.

Bioinformatics. 2006 Aug 15;22(16):2012-9. Epub 2006 Jun 20.

PMID:
16787977
10.

Enzyme kinetics and computational modeling for systems biology.

Mendes P, Messiha H, Malys N, Hoops S.

Methods Enzymol. 2009;467:583-99. doi: 10.1016/S0076-6879(09)67022-1.

PMID:
19897108
11.

Understanding signaling in yeast: Insights from network analysis.

Arga KY, Onsan ZI, Kirdar B, Ulgen KO, Nielsen J.

Biotechnol Bioeng. 2007 Aug 1;97(5):1246-58.

PMID:
17252576
12.

Combining multisource information through functional-annotation-based weighting: gene function prediction in yeast.

Ray SS, Bandyopadhyay S, Pal SK.

IEEE Trans Biomed Eng. 2009 Feb;56(2):229-36. doi: 10.1109/TBME.2008.2005955. Epub 2008 Sep 30.

PMID:
19272921
13.

An analysis pipeline for the inference of protein-protein interaction networks.

Taylor RC, Singhal M, Daly DS, Gilmore J, Cannon WR, Domico K, White AM, Auberry DL, Auberry KJ, Hooker BS, Hurst G, McDermott JE, McDonald WH, Pelletier DA, Schmoyer D, Wiley HS.

Int J Data Min Bioinform. 2009;3(4):409-30.

PMID:
20052905
14.

Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data.

Boyer F, Morgat A, Labarre L, Pothier J, Viari A.

Bioinformatics. 2005 Dec 1;21(23):4209-15. Epub 2005 Oct 10.

PMID:
16216829
15.

A probabilistic graph-theoretic approach to integrate multiple predictions for the protein-protein subnetwork prediction challenge.

Chua HN, Hugo W, Liu G, Li X, Wong L, Ng SK.

Ann N Y Acad Sci. 2009 Mar;1158:224-33. doi: 10.1111/j.1749-6632.2008.03760.x.

PMID:
19348644
16.

Modelling dynamic processes in yeast.

Klipp E.

Yeast. 2007 Nov;24(11):943-59.

17.

Context-sensitive data integration and prediction of biological networks.

Myers CL, Troyanskaya OG.

Bioinformatics. 2007 Sep 1;23(17):2322-30. Epub 2007 Jun 28.

PMID:
17599939
18.

An improved prediction of catalytic residues in enzyme structures.

Tang YR, Sheng ZY, Chen YZ, Zhang Z.

Protein Eng Des Sel. 2008 May;21(5):295-302. doi: 10.1093/protein/gzn003. Epub 2008 Feb 20.

PMID:
18287176
19.

Fitting a geometric graph to a protein-protein interaction network.

Higham DJ, Rasajski M, Przulj N.

Bioinformatics. 2008 Apr 15;24(8):1093-9. doi: 10.1093/bioinformatics/btn079. Epub 2008 Mar 14.

PMID:
18344248
20.

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