Publications

Found 145 results
Filters: Author is Shoshana J Wodak  [Clear All Filters]
2011
Rajendram, R., J. Carlos Ferreira, D. Grafodatskaya, S. Choufani, T. Chiang, S. Pu, D. T. Butcher, S. J. Wodak, and R. Weksberg, "Assessment of methylation level prediction accuracy in methyl-DNA immunoprecipitation and sodium bisulfite based microarray platforms.", Epigenetics, vol. 6, issue 4, pp. 410-5, 2011 Apr.
Fleishman, S. J., T. A. Whitehead, E-M. Strauch, J. E. Corn, S. Qin, H-X. Zhou, J. C. Mitchell, O. N. A. Demerdash, M. Takeda-Shitaka, G. Terashi, et al., "Community-wide assessment of protein-interface modeling suggests improvements to design methodology.", J Mol Biol, vol. 414, issue 2, pp. 289-302, 2011 Nov 25.
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.
Babu, M., J. J Díaz-Mejía, J. Vlasblom, A. Gagarinova, S. Phanse, C. Graham, F. Yousif, H. Ding, X. Xiong, A. Nazarians-Armavil, et al., "Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways.", PLoS Genet, vol. 7, issue 11, pp. e1002377, 2011 Nov.
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.
Malevanets, A., and S. J. Wodak, "Multiple replica repulsion technique for efficient conformational sampling of biological systems.", Biophys J, vol. 101, issue 4, pp. 951-60, 2011 Aug 17.
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.
Pu, S., A. L. Turinsky, J. Vlasblom, T. On, X. Xiong, A. Emili, Z. Zhang, J. Greenblatt, J. Parkinson, and S. J. Wodak, "Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human.", PLoS One, vol. 5, issue 11, pp. e14122, 2010.
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.
Ogata, K., T. Isomura, S. Kawata, H. Yamashita, H. Kubodera, and S. J. Wodak, "Lead generation and optimization based on protein-ligand complementarity.", Molecules, vol. 15, issue 6, pp. 4382-400, 2010 Jun.
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.
Santos, M. A., A. L. Turinsky, S. Ong, J. Tsai, M. F. Berger, G. Badis, S. Talukder, A. R. Gehrke, M. L. Bulyk, T. R. Hughes, et al., "Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences.", Nucleic Acids Res, vol. 38, issue 22, pp. 7927-42, 2010 Dec.
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.

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