Publications

Found 145 results
Filters: Author is Shoshana J Wodak  [Clear All Filters]
2007
Wodak, S. J., "From the Mediterranean coast to the shores of Lake Ontario: CAPRI's premiere on the American continent.", Proteins, vol. 69, issue 4, pp. 697-8, 2007 Dec 1.
Pu, S., J. Vlasblom, A. Emili, J. Greenblatt, and S. J. Wodak, "Identifying functional modules in the physical interactome of Saccharomyces cerevisiae.", Proteomics, vol. 7, issue 6, pp. 944-60, 2007 Mar.
Dessailly, B. H., M. F. Lensink, and S. J. Wodak, "Relating destabilizing regions to known functional sites in proteins.", BMC Bioinformatics, vol. 8, pp. 141, 2007.
2006
Vlasblom, J., S. Wu, S. Pu, M. Superina, G. Liu, C. Orsi, and S. J. Wodak, "GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks.", Bioinformatics, vol. 22, issue 17, pp. 2178-9, 2006 Sep 1.
Krogan, N. J., G. Cagney, H. Yu, G. Zhong, X. Guo, A. Ignatchenko, J. Li, S. Pu, N. Datta, A. P. Tikuisis, et al., "Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.", Nature, vol. 440, issue 7084, pp. 637-43, 2006 Mar 30.
Croes, D., F. Couche, S. J. Wodak, and J. van Helden, "Inferring meaningful pathways in weighted metabolic networks.", J Mol Biol, vol. 356, issue 1, pp. 222-36, 2006 Feb 10.
Simonis, N., D. Gonze, C. Orsi, J. van Helden, and S. J. Wodak, "Modularity of the transcriptional response of protein complexes in yeast.", J Mol Biol, vol. 363, issue 2, pp. 589-610, 2006 Oct 20.
2005
Méndez, R., R. Leplae, M. F. Lensink, and S. J. Wodak, "Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures.", Proteins, vol. 60, issue 2, pp. 150-69, 2005 Aug 1.
Jaramillo, A., and S. J. Wodak, "Computational protein design is a challenge for implicit solvation models.", Biophys J, vol. 88, issue 1, pp. 156-71, 2005 Jan.
Güldener, U., M. Münsterkötter, G. Kastenmüller, N. Strack, J. van Helden, C. Lemer, J. Richelles, S. J. Wodak, J. García-Martínez, J. E. Pérez-Ortín, et al., "CYGD: the Comprehensive Yeast Genome Database.", Nucleic Acids Res, vol. 33, issue Database issue, pp. D364-8, 2005 Jan 1.
Croes, D., F. Couche, S. J. Wodak, and J. van Helden, "Metabolic PathFinding: inferring relevant pathways in biochemical networks.", Nucleic Acids Res, vol. 33, issue Web Server issue, pp. W326-30, 2005 Jul 1.
2004
Leplae, R., A. Hebrant, S. J. Wodak, and A. Toussaint, "ACLAME: a CLAssification of Mobile genetic Elements.", Nucleic Acids Res, vol. 32, issue Database issue, pp. D45-9, 2004 Jan 1.
Lemer, C., E. Antezana, F. Couche, F. Fays, X. Santolaria, R's. Janky, Y. Deville, J. Richelle, and S. J. Wodak, "The aMAZE LightBench: a web interface to a relational database of cellular processes.", Nucleic Acids Res, vol. 32, issue Database issue, pp. D443-8, 2004 Jan 1.
Simonis, N., S. J. Wodak, G. N. Cohen, and J. van Helden, "Combining pattern discovery and discriminant analysis to predict gene co-regulation.", Bioinformatics, vol. 20, issue 15, pp. 2370-9, 2004 Oct 12.
Wodak, S. J., and R. Méndez, "Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications.", Curr Opin Struct Biol, vol. 14, issue 2, pp. 242-9, 2004 Apr.
Giraldo, J., L. De Maria, and S. J. Wodak, "Shift in nucleotide conformational equilibrium contributes to increased rate of catalysis of GpAp versus GpA in barnase.", Proteins, vol. 56, issue 2, pp. 261-76, 2004 Aug 1.
Simonis, N., J. van Helden, G. N. Cohen, and S. J. Wodak, "Transcriptional regulation of protein complexes in yeast.", Genome Biol, vol. 5, issue 5, pp. R33, 2004.
2003
Govaerts, C., A. Bondue, J-Y. Springael, M. Olivella, X. Deupi, E. Le Poul, S. J. Wodak, M. Parmentier, L. Pardo, and C. Blanpain, "Activation of CCR5 by chemokines involves an aromatic cluster between transmembrane helices 2 and 3.", J Biol Chem, vol. 278, issue 3, pp. 1892-903, 2003 Jan 17.
Méndez, R., R. Leplae, L. De Maria, and S. J. Wodak, "Assessment of blind predictions of protein-protein interactions: current status of docking methods.", Proteins, vol. 52, issue 1, pp. 51-67, 2003 Jul 1.
Ogata, K., A. Jaramillo, W. Cohen, J-P. Briand, F. Connan, J. Choppin, S. Muller, and S. J. Wodak, "Automatic sequence design of major histocompatibility complex class I binding peptides impairing CD8+ T cell recognition.", J Biol Chem, vol. 278, issue 2, pp. 1281-90, 2003 Jan 10.
Janin, J., K. Henrick, J. Moult, L. Ten Eyck, M. J. E. Sternberg, S. Vajda, I. Vakser, and S. J. Wodak, "CAPRI: a Critical Assessment of PRedicted Interactions.", Proteins, vol. 52, issue 1, pp. 2-9, 2003 Jul 1.
Wernisch, L., and S. J. Wodak, "Identifying structural domains in proteins.", Methods Biochem Anal, vol. 44, pp. 365-85, 2003.
Deville, Y., D. Gilbert, J. van Helden, and S. J. Wodak, "An overview of data models for the analysis of biochemical pathways.", Brief Bioinform, vol. 4, issue 3, pp. 246-59, 2003 Sep.
2002
Ochagavia, M. Elena, J. Richelle, and S. J. Wodak, "Advanced pairwise structure alignments of proteins and analysis of conformational changes.", Bioinformatics, vol. 18, issue 4, pp. 637-40, 2002 Apr.
Ogata, K., and S. J. Wodak, "Conserved water molecules in MHC class-I molecules and their putative structural and functional roles.", Protein Eng, vol. 15, issue 8, pp. 697-705, 2002 Aug.

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