Publications

Found 27 results
Filters: Keyword is Protein Interaction Mapping and Author is Shoshana J Wodak  [Clear All Filters]
2014
Lensink, M. F., I. H. Moal, P. A. Bates, P. L. Kastritis, A. S. J. Melquiond, E. Karaca, C. Schmitz, M. van Dijk, A. M. J. J. Bonvin, M. Eisenstein, et al., "Blind prediction of interfacial water positions in CAPRI.", Proteins, vol. 82, issue 4, pp. 620-32, 2014 Apr.
Turinsky, A. L., S. Razick, B. Turner, I. M. Donaldson, and S. J. Wodak, "Navigating the global protein-protein interaction landscape using iRefWeb.", Methods Mol Biol, vol. 1091, pp. 315-31, 2014.
Lensink, M. F., and S. J. Wodak, "Score_set: a CAPRI benchmark for scoring protein complexes.", Proteins, vol. 82, issue 11, pp. 3163-9, 2014 Nov.
2013
Moretti, R., S. J. Fleishman, R. Agius, M. Torchala, P. A. Bates, P. L. Kastritis, J. P. G. L. M. Rodrigues, M. Trellet, A. M. J. J. Bonvin, M. Cui, et al., "Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.", Proteins, vol. 81, issue 11, pp. 1980-7, 2013 Nov.
Lensink, M. F., and S. J. Wodak, "Docking, scoring, and affinity prediction in CAPRI.", Proteins, vol. 81, issue 12, pp. 2082-95, 2013 Dec.
Wodak, S. J., J. Vlasblom, A. L. Turinsky, and S. Pu, "Protein-protein interaction networks: the puzzling riches.", Curr Opin Struct Biol, vol. 23, issue 6, pp. 941-53, 2013 Dec.
2012
Babu, M., J. Vlasblom, S. Pu, X. Guo, C. Graham, B. D. M. Bean, H. E. Burston, F. J. Vizeacoumar, J. Snider, S. Phanse, et al., "Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae.", Nature, vol. 489, issue 7417, pp. 585-9, 2012 Sep 27.
2011
Turinsky, A. L., B. Turner, R. C. Borja, J. A. Gleeson, M. Heath, S. Pu, T. Switzer, D. Dong, Y. Gong, T. On, et al., "DAnCER: disease-annotated chromatin epigenetics resource.", Nucleic Acids Res, vol. 39, issue Database issue, pp. D889-94, 2011 Jan.
Wodak, S. J., J. Vlasblom, and S. Pu, "High-throughput analyses and curation of protein interactions in yeast.", Methods Mol Biol, vol. 759, pp. 381-406, 2011.
Turinsky, A. L., S. Razick, B. Turner, I. M. Donaldson, and S. J. Wodak, "Interaction databases on the same page.", Nat Biotechnol, vol. 29, issue 5, pp. 391-3, 2011 May.
Hao, Y., A. Merkoulovitch, J. Vlasblom, S. Pu, A. L. Turinsky, D. Roudeva, B. Turner, J. Greenblatt, and S. J. Wodak, "OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms.", Bioinformatics, vol. 27, issue 6, pp. 883-4, 2011 Mar 15.
2010
Lensink, M. F., and S. J. Wodak, "Blind predictions of protein interfaces by docking calculations in CAPRI.", Proteins, vol. 78, issue 15, pp. 3085-95, 2010 Nov 15.
Lensink, M. F., and S. J. Wodak, "Docking and scoring protein interactions: CAPRI 2009.", Proteins, vol. 78, issue 15, pp. 3073-84, 2010 Nov 15.
On, T., X. Xiong, S. Pu, A. Turinsky, Y. Gong, A. Emili, Z. Zhang, J. Greenblatt, S. J. Wodak, and J. Parkinson, "The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses.", Proteins, vol. 78, issue 9, pp. 2075-89, 2010 Jul.
Turner, B., S. Razick, A. L. Turinsky, J. Vlasblom, E. K. Crowdy, E. Cho, K. Morrison, I. M. Donaldson, and S. J. Wodak, "iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence.", Database (Oxford), vol. 2010, pp. baq023, 2010.
Turinsky, A. L., S. Razick, B. Turner, I. M. Donaldson, and S. J. Wodak, "Literature curation of protein interactions: measuring agreement across major public databases.", Database (Oxford), vol. 2010, pp. baq026, 2010.
2009
Wodak, S. J., S. Pu, J. Vlasblom, and B. Séraphin, "Challenges and rewards of interaction proteomics.", Mol Cell Proteomics, vol. 8, issue 1, pp. 3-18, 2009 Jan.
Vlasblom, J., and S. J. Wodak, "Markov clustering versus affinity propagation for the partitioning of protein interaction graphs.", BMC Bioinformatics, vol. 10, pp. 99, 2009.
Pu, S., J. Wong, B. Turner, E. Cho, and S. J. Wodak, "Up-to-date catalogues of yeast protein complexes.", Nucleic Acids Res, vol. 37, issue 3, pp. 825-31, 2009 Feb.
2007
Lensink, M. F., R. Méndez, and S. J. Wodak, "Docking and scoring protein complexes: CAPRI 3rd Edition.", Proteins, vol. 69, issue 4, pp. 704-18, 2007 Dec 1.
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.
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.
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.
2003
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.

Pages