References

Here you find a list of all published work used in ProCope in alphabetical order:

[1] P. Aloy, B. Böttcher, H. Ceulemans, C. Leutwein, C. Mellwig, S. Fischer, A. C. Gavin, P. Bork, G. Superti-Furga, L. Serrano, and R. B. Russell. Structure-based assembly of protein complexes in yeast. Science, 303(5666):2026-2029, March 2004. [ Web | PubMed ]
[2] Sylvain Brohée and Jacques van Helden. Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics, 7:488, 2006. [ Web | PubMed ]
[3] Caroline Friedel, Jan Krumsiek, Ralf Zimmer. Bootstrapping the interactome: Unsupervised identification of protein complexes in yeast. RECOMB 2008, LNBI 4955:3-16, 2008. [ Web ]
[4] Sean R Collins, Patrick Kemmeren, Xue-Chu Zhao, Jack F Greenblatt, Forrest Spencer, Frank C P Holstege, Jonathan S Weissman, and Nevan J Krogan. Toward a comprehensive atlas of the physical interactome of saccharomyces cerevisiae. Mol Cell Proteomics, 6(3):439-450, Mar 2007. [ Web | PubMed ]
[5] Tom Fawcett. An introduction to roc analysis. Pattern Recognition Letters, 27(8):861-874, June 2006. [ DOI | Web ]
[6] Anne-Claude Gavin, Patrick Aloy, Paola Grandi, Roland Krause, Markus Boesche, Martina Marzioch, Christina Rau, Lars Juhl Jensen, Sonja Bastuck, Birgit Dümpelfeld, Angela Edelmann, Marie-Anne Heurtier, Verena Hoffman, Christian Hoefert, Karin Klein, Manuela Hudak, Anne-Marie Michon, Malgorzata Schelder, Markus Schirle, Marita Remor, Tatjana Rudi, Sean Hooper, Andreas Bauer, Tewis Bouwmeester, Georg Casari, Gerard Drewes, Gitte Neubauer, Jens M Rick, Bernhard Kuster, Peer Bork, Robert B Russell, and Giulio Superti-Furga. Proteome survey reveals modularity of the yeast cell machinery. Nature, 440(7084):631-636, Mar 2006. [ Web | PubMed ]
[7] G. Traver Hart, Insuk Lee, and Edward R Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. BMC Bioinformatics, 8:236, 2007. [ Web | PubMed ]
[8] Y. Ho, A. Gruhler, A. Heilbut, G. D. Bader, L. Moore, S. L. Adams, A. Millar, P. Taylor, K. Bennett, K. Boutilier, L. Yang, C. Wolting, I. Donaldson, S. Schandorff, J. Shewnarane, M. Vo, J. Taggart, M. Goudreault, B. Muskat, C. Alfarano, D. Dewar, Z. Lin, K. Michalickova, A. R. Willems, H. Sassi, P. A. Nielsen, K. J. Rasmussen, J. R. Andersen, L. E. Johansen, L. H. Hansen, H. Jespersen, A. Podtelejnikov, E. Nielsen, J. Crawford, V. Poulsen, B. D. Sörensen, J. Matthiesen, R. C. Hendrickson, F. Gleeson, T. Pawson, M. F. Moran, D. Durocher, M. Mann, C. W. Hogue, D. Figeys, and M. Tyers. Systematic identification of protein complexes in saccharomyces cerevisiae by mass spectrometry. Nature, 415(6868):180-183, January 2002. [ Web | PubMed ]
[9] W. K. Huh, J. V. Falvo, L. C. Gerke, A. S. Carroll, R. W. Howson, J. S. Weissman, and E. K. O'Shea. Global analysis of protein localization in budding yeast. Nature, 425(6959):686-691, October 2003. [ Web | PubMed ]
[10] Nevan J Krogan, Gerard Cagney, Haiyuan Yu, Gouqing Zhong, Xinghua Guo, Alexandr Ignatchenko, Joyce Li, Shuye Pu, Nira Datta, Aaron P Tikuisis, Thanuja Punna, José M Peregrín-Alvarez, Michael Shales, Xin Zhang, Michael Davey, Mark D Robinson, Alberto Paccanaro, James E Bray, Anthony Sheung, Bryan Beattie, Dawn P Richards, Veronica Canadien, Atanas Lalev, Frank Mena, Peter Wong, Andrei Starostine, Myra M Canete, James Vlasblom, Samuel Wu, Chris Orsi, Sean R Collins, Shamanta Chandran, Robin Haw, Jennifer J Rilstone, Kiran Gandi, Natalie J Thompson, Gabe Musso, Peter St Onge, Shaun Ghanny, Mandy H Y Lam, Gareth Butland, Amin M Altaf-Ul, Shigehiko Kanaya, Ali Shilatifard, Erin O'Shea, Jonathan S Weissman, C. James Ingles, Timothy R Hughes, John Parkinson, Mark Gerstein, Shoshana J Wodak, Andrew Emili, and Jack F Greenblatt. Global landscape of protein complexes in the yeast saccharomyces cerevisiae. Nature, 440(7084):637-643, Mar 2006. [ Web | PubMed ]
[11] Anuj Kumar, Seema Agarwal, John A. Heyman, Sandra Matson, Matthew Heidtman, Stacy Piccirillo, Lara Umansky, Amar Drawid, Ronald Jansen, Yang Liu, Kei-Hoi Cheung, Perry Miller, Mark Gerstein, Shirleen G. Roeder, and Michael Snyder. Subcellular localization of the yeast proteome. Genes Dev., 16(6):707-719, March 2002. [ Web | PubMed ]
[12] H. W. Mewes, C. Amid, R. Arnold, D. Frishman, U. Güldener, G. Mannhaupt, M. Münsterkötter, P. Pagel, N. Strack, V. Stümpflen, J. Warfsmann, and A. Ruepp. Mips: analysis and annotation of proteins from whole genomes. Nucleic Acids Res, 32 Database issue, January 2004. [ Web | PubMed ]
[13] Shuye Pu, Jim Vlasblom, Andrew Emili, Jack Greenblatt, and Shoshana J Wodak. Identifying functional modules in the physical interactome of saccharomyces cerevisiae. Proteomics, 7(6):944-960, Mar 2007. [ DOI | Web | PubMed ]
[14] Andreas Schlicker, Francisco S Domingues, Jörg Rahnenführer, and Thomas Lengauer. A new measure for functional similarity of gene products based on gene ontology. BMC Bioinformatics, 7:302, 2006. [ Web | PubMed ]
[15] Stijn van Dongen. Graph Clustering by Flow Simulation. PhD thesis, University of Utrecht, 2000. [ Web ]
[16] Haiyuan Yu, Nicholas M Luscombe, Hao Xin Lu, Xiaowei Zhu, Yu Xia, Jing-Dong J Han, Nicolas Bertin, Sambath Chung, Marc Vidal, and Mark Gerstein. Annotation transfer between genomes: protein-protein interologs and protein-dna regulogs. Genome Res, 14(6):1107-1118, Jun 2004. [ DOI | Web ]
[17] Bing Zhang, Byung-Hoon Park, Tatiana Karpinets, and Nagiza F Samatova. From pull-down data to protein interaction networks and complexes with biological relevance. Bioinformatics 24, 979-986, 2008. [ DOI | PubMed ]

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