TY - JOUR AU - von Mering, C. AU - Krause, R. AU - Snel, B. AU - Cornell, M. AU - Oliver, S. G. AU - Fields, S. AU - Bork, P. PY - 2002 DA - 2002// TI - Comparative assessment of large-scale data sets of protein-protein interactions JO - Nature VL - 417 UR - https://doi.org/10.1038/nature750 DO - 10.1038/nature750 ID - von Mering2002 ER - TY - JOUR AU - Ito, T. AU - Chiba, T. AU - Ozawa, R. AU - Yoshida, M. AU - Hattori, M. AU - Sakaki, Y. PY - 2001 DA - 2001// TI - A comprehensive two-hybrid analysis to explore the yeast protein interactome JO - Proc Natl Acad Sci VL - 98 UR - https://doi.org/10.1073/pnas.061034498 DO - 10.1073/pnas.061034498 ID - Ito2001 ER - TY - JOUR AU - Uetz, P. AU - Cagney, G. AU - Mansfield, T. A. AU - Judson, R. AU - Knight, J. R. AU - Lockshon, D. AU - Narayan, V. AU - Srinivasan, M. AU - Pochart, P. PY - 2000 DA - 2000// TI - A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae JO - Nature VL - 403 UR - https://doi.org/10.1038/35001009 DO - 10.1038/35001009 ID - Uetz2000 ER - TY - JOUR AU - Gavin, A. C. AU - Bosche, M. AU - Krause, R. AU - Grandi, P. AU - Marzioch, M. AU - Bauer, A. AU - Schultz, J. AU - Rick, J. M. AU - Michon, A. M. AU - Cruciat, C. M. PY - 2002 DA - 2002// TI - Functional organization of the yeast proteome by systematic analysis of protein complexes JO - Nature VL - 415 UR - https://doi.org/10.1038/415141a DO - 10.1038/415141a ID - Gavin2002 ER - TY - JOUR AU - Ho, Y. AU - Gruhler, A. AU - Heilbut, A. AU - Bader, G. D. AU - Moore, L. AU - Adams, S. L. AU - Millar, A. AU - Taylor, P. AU - Bennett, K. AU - Boutilier, K. PY - 2002 DA - 2002// TI - Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry JO - Nature VL - 415 UR - https://doi.org/10.1038/415180a DO - 10.1038/415180a ID - Ho2002 ER - TY - JOUR AU - Bowers, P. M. AU - Pellegrini, M. AU - Thompson, M. J. AU - Fierro, J. AU - Yeates, T. O. AU - Eisenberg, D. PY - 2004 DA - 2004// TI - Prolinks: a database of protein functional linkages derived from coevolution JO - Genome Biology VL - 5 UR - https://doi.org/10.1186/gb-2004-5-5-r35 DO - 10.1186/gb-2004-5-5-r35 ID - Bowers2004 ER - TY - JOUR AU - Jansen, R. AU - Yu, H. AU - Greenbaum, D. AU - Kluger, Y. AU - Krogan, N. J. AU - Chung, S. AU - Emili, A. AU - Snyder, M. AU - Greenblatt, J. F. AU - Gerstein, M. PY - 2003 DA - 2003// TI - A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data JO - Science VL - 302 UR - https://doi.org/10.1126/science.1087361 DO - 10.1126/science.1087361 ID - Jansen2003 ER - TY - JOUR AU - Lee, I. AU - Date, S. V. AU - Adai, A. T. AU - Marcotte, E. M. PY - 2004 DA - 2004// TI - A Probabilistic Functional Network of Yeast Genes JO - Science VL - 306 UR - https://doi.org/10.1126/science.1099511 DO - 10.1126/science.1099511 ID - Lee2004 ER - TY - JOUR AU - von Mering, C. AU - Jensen, L. J. AU - Snel, B. AU - Hooper, S. D. AU - Krupp, M. AU - Foglierini, M. AU - Jouffre, N. AU - Huynen, M. A. AU - Bork, P. PY - 2005 DA - 2005// TI - STRING: known and predicted protein-protein associations, integrated and transferred across organisms JO - Nucleic Acids Research VL - 33 UR - https://doi.org/10.1093/nar/gki005 DO - 10.1093/nar/gki005 ID - von Mering2005 ER - TY - JOUR AU - Arnau, V. AU - Mars, S. AU - Marin, I. PY - 2005 DA - 2005// TI - Iterative cluster analysis of protein interaction data JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti021 DO - 10.1093/bioinformatics/bti021 ID - Arnau2005 ER - TY - JOUR AU - Bader, J. S. PY - 2003 DA - 2003// TI - Greedily building protein networks with confidence JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg358 DO - 10.1093/bioinformatics/btg358 ID - Bader2003 ER - TY - JOUR AU - Hu, H. AU - Yan, X. AU - Huang, Y. AU - Han, J. AU - Zhou, X. J. PY - 2005 DA - 2005// TI - Mining coherent dense subgraphs across massive biological networks for functional discovery JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti1049 DO - 10.1093/bioinformatics/bti1049 ID - Hu2005 ER - TY - JOUR AU - Scholtens, D. AU - Vidal, M. AU - Gentleman, R. PY - 2005 DA - 2005// TI - Local modeling of global interactome networks JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti567 DO - 10.1093/bioinformatics/bti567 ID - Scholtens2005 ER - TY - CHAP AU - Scott, J. AU - Ideker, T. AU - Karp, R. M. AU - Sharan, R. PY - 2005 DA - 2005// TI - Efficient algorithms for detecting signaling pathways in protein interaction networks BT - Proceedings of RECOMB ID - Scott2005 ER - TY - JOUR AU - Yamanishi, Y. AU - Vert, J. P. AU - Kanehisa, M. PY - 2004 DA - 2004// TI - Protein network inference from multiple genomic data: a supervised approach JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth910 DO - 10.1093/bioinformatics/bth910 ID - Yamanishi2004 ER - TY - CHAP AU - Lanckriet, G. R. G. AU - Deng, M. AU - Cristianini, N. AU - Jordan, M. I. AU - Noble, W. S. PY - 2004 DA - 2004// TI - Kernel-based data fusion and its application to protein function prediction in yeast BT - Pac Symp Biocomput ID - Lanckriet2004 ER - TY - JOUR AU - Letovsky, S. AU - Kasif, S. PY - 2003 DA - 2003// TI - Predicting protein function from protein/protein interaction data: a probabilistic approach JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg1026 DO - 10.1093/bioinformatics/btg1026 ID - Letovsky2003 ER - TY - JOUR AU - Tsuda, K. AU - Noble, W. S. PY - 2004 DA - 2004// TI - Learning kernels from biological networks by maximizing entropy JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth906 DO - 10.1093/bioinformatics/bth906 ID - Tsuda2004 ER - TY - JOUR AU - Asthana, S. AU - King, O. D. AU - Gibbons, F. D. AU - Roth, F. P. PY - 2004 DA - 2004// TI - Predicting Protein Complex Membership Using Probabilistic Network Reliability JO - Genome Research VL - 14 UR - https://doi.org/10.1101/gr.2203804 DO - 10.1101/gr.2203804 ID - Asthana2004 ER - TY - CHAP AU - Can, T. AU - Çamoğlu, O. AU - Singh, A. K. PY - 2005 DA - 2005// TI - Analysis of protein-protein interaction networks using random walks BT - Proceedings of the 5th ACM SIGKDD Workshop on Data Mining in Bioinformatics, Chicago ID - Can2005 ER - TY - JOUR AU - Bader, G. D. AU - Hogue, C. W. V. PY - 2003 DA - 2003// TI - An automated method for finding molecular complexes in large protein interaction networks JO - BMC Bioinformatics VL - 4 UR - https://doi.org/10.1186/1471-2105-4-2 DO - 10.1186/1471-2105-4-2 ID - Bader2003 ER - TY - JOUR AU - Spirin, V. AU - Mirny, L. A. PY - 2003 DA - 2003// TI - Protein complexes and functional modules in molecular networks JO - Proceedings of the National Academy of Sciences (PNAS) VL - 100 UR - https://doi.org/10.1073/pnas.2032324100 DO - 10.1073/pnas.2032324100 ID - Spirin2003 ER - TY - JOUR AU - Enright, A. AU - Dongen, S. V. AU - Ouzounis, C. PY - 2002 DA - 2002// TI - An efficient algorithm for large-scale detection of protein families JO - Nucleic Acids Research VL - 30 UR - https://doi.org/10.1093/nar/30.7.1575 DO - 10.1093/nar/30.7.1575 ID - Enright2002 ER - TY - JOUR AU - Adamcsek, B. AU - Palla, G. AU - Farkas, I. AU - Derényi, I. AU - Viscek, T. PY - 2006 DA - 2006// TI - CFinder: locating cliques and overlapping modules in biological networks JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl039 DO - 10.1093/bioinformatics/btl039 ID - Adamcsek2006 ER - TY - JOUR AU - Asur, S. AU - Ucar, D. AU - Parthasarathy, S. PY - 2007 DA - 2007// TI - An ensemble framework for clustering protein-protein interaction networks JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm212 DO - 10.1093/bioinformatics/btm212 ID - Asur2007 ER - TY - JOUR AU - Lovasz, L. PY - 1996 DA - 1996// TI - Random walks on graphs: A survey JO - Combinatorics, Paul Erdos is Eighty VL - 2 ID - Lovasz1996 ER - TY - JOUR AU - Mewes, H. W. AU - Amid, C. AU - Arnold, R. AU - Frishman, D. AU - Guldener, U. AU - Mannhaupt, G. AU - Munsterkotter, M. AU - Pagel, P. AU - Strack, N. AU - Stumpflen, V. AU - Warfsmann, J. AU - Ruepp, A. PY - 2004 DA - 2004// TI - MIPS: analysis and annotation of proteins from whole genomes JO - Nucleic Acids Research VL - 32 UR - https://doi.org/10.1093/nar/gkh092 DO - 10.1093/nar/gkh092 ID - Mewes2004 ER - TY - CHAP AU - Tong, H. AU - Faloutsos, C. AU - Pan, J. Y. PY - 2006 DA - 2006// BT - Fast Random Walk With Restart and Its Applications ID - Tong2006 ER - TY - JOUR AU - Kiemer, L. AU - Costa, S. AU - Ueffing, M. AU - Cesareni, G. PY - 2007 DA - 2007// TI - WI-PHI: A weighted yeast interactome enriched for direct physical interactions JO - Proteomics VL - 7 UR - https://doi.org/10.1002/pmic.200600448 DO - 10.1002/pmic.200600448 ID - Kiemer2007 ER - TY - CHAP AU - Dongen, S. V. PY - 2000 DA - 2000// TI - Graph clustering by flow simulation BT - PhD thesis PB - University of Utrecht CY - The Netherlands ID - Dongen2000 ER - TY - JOUR AU - Brohee, S. AU - van Helden, J. PY - 2006 DA - 2006// TI - Evaluation of clustering algorithms for protein-protein interaction networks JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-488 DO - 10.1186/1471-2105-7-488 ID - Brohee2006 ER - TY - JOUR AU - Andreopoulos, B. AU - An, A. AU - Wang, X. AU - Schroeder, M. PY - 2009 DA - 2009// TI - A roadmap of clustering algorithms: finding a match for a biomedical application JO - Brief Bioinform VL - 10 ID - Andreopoulos2009 ER - TY - JOUR AU - Myers, C. AU - Barrett, D. AU - Hibbs, M. AU - Huttenhower, C. AU - Troyanskaya, O. PY - 2006 DA - 2006// TI - Finding function: evaluation methods for functional genomic data JO - BMC Genomics VL - 7 UR - https://doi.org/10.1186/1471-2164-7-187 DO - 10.1186/1471-2164-7-187 ID - Myers2006 ER - TY - JOUR AU - Ashburner, M. AU - Ball, C. A. AU - Blake, J. A. AU - Botstein, D. AU - Butler, H. AU - Cherry, J. M. AU - Davis, A. P. AU - Dolinski, K. AU - Dwight, S. S. AU - Eppig, J. T. AU - Harris, M. A. AU - Hill, D. P. AU - Issel-Tarver, L. AU - Kasarskis, A. AU - Lewis, S. AU - Matese, J. C. AU - Richardson, J. E. AU - Ringwald, M. AU - Rubin, G. M. AU - Sherlock, G. PY - 2000 DA - 2000// TI - Gene ontology: tool for the unification of biology. The Gene Ontology Consortium JO - Nat Genet VL - 25 UR - https://doi.org/10.1038/75556 DO - 10.1038/75556 ID - Ashburner2000 ER - TY - JOUR AU - Wang, Q. AU - Rymond, B. PY - 2003 DA - 2003// TI - Rds3p Is Required for Stable U2 snRNP Recruitment to the Splicing Apparatus JO - Molecular and Cellular Biology VL - 23 UR - https://doi.org/10.1128/MCB.23.20.7339-7349.2003 DO - 10.1128/MCB.23.20.7339-7349.2003 ID - Wang2003 ER - TY - JOUR AU - Freeman, L. AU - Aragon-Alcaide, L. AU - Strunnikov, A. PY - 2000 DA - 2000// TI - The Condensin Complex Governs Chromosome Condensation and Mitotic Transmission of rDNA JO - The Journal of Cell Biology VL - 149 UR - https://doi.org/10.1083/jcb.149.4.811 DO - 10.1083/jcb.149.4.811 ID - Freeman2000 ER - TY - JOUR AU - Kemp, H. AU - Sprague, G. PY - 2003 DA - 2003// TI - Far3 and Five Interacting Proteins Prevent Premature Recovery from Pheromone Arrest in the Budding Yeast Saccharomyces cerevisiae JO - Molecular and Cellular Biology VL - 23 UR - https://doi.org/10.1128/MCB.23.5.1750-1763.2003 DO - 10.1128/MCB.23.5.1750-1763.2003 ID - Kemp2003 ER - TY - JOUR AU - Corso, G. M. D. PY - 1997 DA - 1997// TI - Estimating an Eigenvector by the Power Method with a Random Start JO - SIAM J Matrix Anal Appl VL - 18 UR - https://doi.org/10.1137/S0895479895296689 DO - 10.1137/S0895479895296689 ID - Corso1997 ER -