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Items: 1 to 20 of 95

1.

A network-based approach for predicting missing pathway interactions.

Navlakha S, Gitter A, Bar-Joseph Z.

PLoS Comput Biol. 2012;8(8):e1002640. doi: 10.1371/journal.pcbi.1002640. Epub 2012 Aug 16.

2.

Refinement and expansion of signaling pathways: the osmotic response network in yeast.

Gat-Viks I, Shamir R.

Genome Res. 2007 Mar;17(3):358-67. Epub 2007 Jan 31.

3.
4.

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
5.

Finding friends and enemies in an enemies-only network: a graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions.

Qi Y, Suhail Y, Lin YY, Boeke JD, Bader JS.

Genome Res. 2008 Dec;18(12):1991-2004. doi: 10.1101/gr.077693.108. Epub 2008 Oct 2.

6.

Linking the signaling cascades and dynamic regulatory networks controlling stress responses.

Gitter A, Carmi M, Barkai N, Bar-Joseph Z.

Genome Res. 2013 Feb;23(2):365-76. doi: 10.1101/gr.138628.112. Epub 2012 Oct 11.

7.

Unveiling protein functions through the dynamics of the interaction network.

Sendiña-Nadal I, Ofran Y, Almendral JA, Buldú JM, Leyva I, Li D, Havlin S, Boccaletti S.

PLoS One. 2011 Mar 9;6(3):e17679. doi: 10.1371/journal.pone.0017679.

8.

Quantitative inference of dynamic regulatory pathways via microarray data.

Chang WC, Li CW, Chen BS.

BMC Bioinformatics. 2005 Mar 7;6:44.

9.

Efficient algorithms for detecting signaling pathways in protein interaction networks.

Scott J, Ideker T, Karp RM, Sharan R.

J Comput Biol. 2006 Mar;13(2):133-44.

PMID:
16597231
10.
11.

Conserved network motifs allow protein-protein interaction prediction.

Albert I, Albert R.

Bioinformatics. 2004 Dec 12;20(18):3346-52. Epub 2004 Jul 9.

PMID:
15247093
12.

Functional clustering of yeast proteins from the protein-protein interaction network.

Sen TZ, Kloczkowski A, Jernigan RL.

BMC Bioinformatics. 2006 Jul 24;7:355.

13.
14.

Inferring transcriptional compensation interactions in yeast via stepwise structure equation modeling.

Shieh GS, Chen CM, Yu CY, Huang J, Wang WF, Lo YC.

BMC Bioinformatics. 2008 Mar 3;9:134. doi: 10.1186/1471-2105-9-134.

15.

Towards an integrated protein-protein interaction network: a relational Markov network approach.

Jaimovich A, Elidan G, Margalit H, Friedman N.

J Comput Biol. 2006 Mar;13(2):145-64.

PMID:
16597232
16.

The high osmotic response and cell wall integrity pathways cooperate to regulate transcriptional responses to zymolyase-induced cell wall stress in Saccharomyces cerevisiae.

García R, Rodríguez-Peña JM, Bermejo C, Nombela C, Arroyo J.

J Biol Chem. 2009 Apr 17;284(16):10901-11. doi: 10.1074/jbc.M808693200. Epub 2009 Feb 20.

17.

Distance-wise pathway discovery from protein-protein interaction networks weighted by semantic similarity.

Jaromerska S, Praus P, Cho YR.

J Bioinform Comput Biol. 2014 Feb;12(1):1450004. doi: 10.1142/S0219720014500048. Epub 2014 Jan 7.

PMID:
24467762
18.

Inferring the effective TOR-dependent network: a computational study in yeast.

Mohammadi S, Subramaniam S, Grama A.

BMC Syst Biol. 2013 Aug 30;7:84. doi: 10.1186/1752-0509-7-84.

19.

From START to FINISH: the influence of osmotic stress on the cell cycle.

Radmaneshfar E, Kaloriti D, Gustin MC, Gow NA, Brown AJ, Grebogi C, Romano MC, Thiel M.

PLoS One. 2013 Jul 10;8(7):e68067. doi: 10.1371/journal.pone.0068067. Print 2013.

20.

Discovering pathways by orienting edges in protein interaction networks.

Gitter A, Klein-Seetharaman J, Gupta A, Bar-Joseph Z.

Nucleic Acids Res. 2011 Mar;39(4):e22. doi: 10.1093/nar/gkq1207. Epub 2010 Nov 24.

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