TY - JOUR AU - Gavin, A. C. AU - Bösche, M. AU - Krause, R. AU - Grandi, P. AU - Marzioch, M. AU - Bauer, A. AU - Schultz, J. AU - Rick, M. AU - Michon, A. M. AU - Cruciat, C. M. AU - Remor, M. AU - Höfert, C. AU - Schelder, M. AU - Brajenovic, M. AU - Ruffner, H. AU - Merino, A. AU - Klein, K. AU - Hudak, M. AU - Dickson, D. AU - Rudi, T. AU - Gnau, V. AU - Bauch, A. AU - Bastuck, S. AU - Huhse, B. AU - Leutwein, C. AU - Heurtier, M. A. AU - Copley, R. R. AU - Edelmann, A. AU - Querfurth, E. AU - Rybin, V. AU - Drewes, G. AU - Raida, M. AU - Bouwmeester, T. AU - Bork, P. AU - Seraphin, B. AU - Kuster, B. AU - Neubauer, G. AU - Superti-Furga, G. 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 - STD TI - Kazemipour A, Goliaei B, Pezeshk H. Protein complex discovery by interaction filtering from protein interaction networks using mutual rank Coexpression and sequence similarity. Biomed Res Int. 2015;2015. Article ID 165186:1–7. ID - ref2 ER - TY - JOUR AU - Lage, K. AU - Karlberg, E. O. AU - Størling, Z. M. AU - Ólason, P. Í. AU - Pedersen, A. G. AU - Rigina, O. AU - Hinsby, A. M. AU - Tümer, Z. AU - Pociot, F. AU - Tommerup, N. AU - Moreau, Y. AU - Brunak, S. PY - 2007 DA - 2007// TI - A human phenome-interactome network of protein complexes implicated in genetic disorders JO - Nat Biotechnol VL - 25 UR - https://doi.org/10.1038/nbt1295 DO - 10.1038/nbt1295 ID - Lage2007 ER - TY - JOUR AU - Yang, Z. H. AU - Yu, F. Y. AU - Lin, H. F. AU - Wang, J. PY - 2014 DA - 2014// TI - Integrating PPI datasets with the PPI data from biomedical literature for protein complex detection JO - BMC Med Genet VL - 7 ID - Yang2014 ER - TY - JOUR AU - Srihari, S. AU - Leong, H. W. PY - 2012 DA - 2012// TI - Temporal dynamics of protein complexes in PPI networks: a case study using yeast cell cycle dynamics JO - BMC Bioinform. VL - 13 ID - Srihari2012 ER - TY - JOUR AU - Li, M. AU - Zheng, R. Q. AU - Zhang, H. H. AU - Wang, J. X. AU - Pan, Y. PY - 2014 DA - 2014// TI - Effective identification of essential proteins based on priori knowledge, network topology and gene expressions JO - Methods VL - 67 UR - https://doi.org/10.1016/j.ymeth.2014.02.016 DO - 10.1016/j.ymeth.2014.02.016 ID - Li2014 ER - TY - BOOK AU - Kaufman, L. AU - Rousseeuw, P. J. PY - 1990 DA - 1990// TI - Finding Groups in Data: An Introduction to Cluster Analysis UR - https://doi.org/10.1002/9780470316801 DO - 10.1002/9780470316801 ID - Kaufman1990 ER - TY - JOUR AU - Pilevar, A. H. AU - Sukumar, M. PY - 2005 DA - 2005// TI - A grid-clustering algorithm for high-dimensional very large spatial data bases JO - Pattern Recogn Lett VL - 26 UR - https://doi.org/10.1016/j.patrec.2004.09.052 DO - 10.1016/j.patrec.2004.09.052 ID - Pilevar2005 ER - TY - STD TI - Ester M, Kriegel HP, Sander J, Xu XW. A density-based algorithm for discovering clusters in large spatial databases with noise. In: Proceedings of the 2nd international conference on knowledge discovery and data mining. Menlo Park: The AAAI Press; 1996. p. 226–31. ID - ref9 ER - TY - JOUR AU - Ankerst, M. AU - Breunig, M. AU - Kriegel, H. AU - Sander, J. PY - 1999 DA - 1999// TI - OPTICS: ordering points to identify the clustering structure JO - ACM SIGMOD Rec VL - 28 UR - https://doi.org/10.1145/304181.304187 DO - 10.1145/304181.304187 ID - Ankerst1999 ER - TY - STD TI - Holland JH. Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control, and Artificial Intelligence. Quarterly Review of Biology. 1975;6(2):126–137. ID - ref11 ER - TY - CHAP AU - Kennedy, J. AU - Eberhart, R. PY - 1995 DA - 1995// TI - Particle swarm optimization BT - Proceeding of the IEEE international conference on neural networks UR - https://doi.org/10.1109/ICNN.1995.488968 DO - 10.1109/ICNN.1995.488968 ID - Kennedy1995 ER - TY - BOOK AU - Krishnanand, K. N. AU - Ghose, D. PY - 2005 DA - 2005// TI - Detection of multiple source locations using a glowworm metaphor with applications to collective robotics PB - IEEE Swarm Intelligence Sysposium CY - Pasadena ID - Krishnanand2005 ER - TY - JOUR AU - Adamcsek, B. AU - Palla, G. AU - Farkas, I. J. AU - Derényi, I. AU - Vicsek, 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 - Bader, G. D. AU - Hogue, C. W. PY - 2003 DA - 2003// TI - An automated method for finding molecular complexes in large protein interaction networks JO - BMC Bioinform. 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 - Liu, G. AU - Wong, L. AU - Chua, H. PY - 2009 DA - 2009// TI - Complex discovery from weighted PPI networks JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp311 DO - 10.1093/bioinformatics/btp311 ID - Liu2009 ER - TY - JOUR AU - Wu, M. AU - Li, X. AU - Kwoh, C. AU - Ng, S. K. PY - 2009 DA - 2009// TI - A core-attachment based method to detect protein complexes in PPI networks JO - BMC Bioinform. VL - 10 UR - https://doi.org/10.1186/1471-2105-10-1 DO - 10.1186/1471-2105-10-1 ID - Wu2009 ER - TY - JOUR AU - Nepusz, T. AU - Yu, H. AU - Paccanaro, H. PY - 2012 DA - 2012// TI - Detecting overlapping protein complexes in protein-protein interaction networks JO - Nat Methods VL - 9 UR - https://doi.org/10.1038/nmeth.1938 DO - 10.1038/nmeth.1938 ID - Nepusz2012 ER - TY - STD TI - Dongen BSV. Graph clustering by flow simulation. Dissertation for doctoral degree, Center for Math and Computer Science (CWI). Utrecht: University of Utrecht; 2000. ID - ref19 ER - TY - STD TI - Lei XJ, Li H, Wu Fang-Xiang. Detecting Protein Complexes from DPINs by OPTICS Based on Particle Swarm Optimization. 2016 IEEE International Conference on Bioinformatics andBiomedicine. Shenzhen, China. 2016;1814–21. ID - ref20 ER - TY - STD TI - Shi BY, Eberhart R. A modified particle swarm optimizer. Proceedings of the IEEE Congress on Evolutionary Computation. Anchorage: IEEE; 1998:303–8. ID - ref21 ER - TY - JOUR AU - Yedidia, J. AU - Freeman, W. T. AU - Weiss, Y. PY - 2001 DA - 2001// TI - Understanding belief Propa- gation and its generalizations JO - Int Joint Conf Artif Intell (IJCAI) VL - 54 ID - Yedidia2001 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 - BMC Bioinform. VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg1026 DO - 10.1093/bioinformatics/btg1026 ID - Letovsky2003 ER - TY - JOUR AU - Xenarios, I. AU - Salwnski, L. AU - Duan, X. J. AU - Higney, P. AU - Kim, S. M. AU - Eisenberg, D. PY - 2002 DA - 2002// TI - DIP, the database of interacting proteins: a research tool for studying cellular networks of protein interactions JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.1.303 DO - 10.1093/nar/30.1.303 ID - Xenarios2002 ER - TY - JOUR AU - Krogan, N. J. AU - Cagney, G. AU - Yu, H. AU - Zhong, G. AU - Guo, X. AU - Ignatchenko, A. AU - Li, J. AU - Pu, S. AU - Datta, N. AU - Tikuisis, A. P. PY - 2006 DA - 2006// TI - Global landscape of protein complexes in the yeast Saccharomyces Cerevisiae JO - Nature VL - 440 UR - https://doi.org/10.1038/nature04670 DO - 10.1038/nature04670 ID - Krogan2006 ER - TY - JOUR AU - Güldener, U. AU - Münsterkötter, M. AU - Oesterheld, M. AU - Pagel, P. AU - Ruepp, A. AU - Mewes, H. W. AU - Stümpflen, V. PY - 2006 DA - 2006// TI - MPact: the MIPS protein interaction resource on yeast JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkj003 DO - 10.1093/nar/gkj003 ID - Güldener2006 ER - TY - JOUR AU - Gavin, A. C. AU - Aloy, P. AU - Grandi, P. AU - Krause, R. AU - Boesche, M. AU - Marzioch, M. AU - Rau, C. AU - Jensen, L. J. AU - Bastuck, S. AU - Dümpelfeld, B. AU - Edelmann, A. AU - Heurtier, M. A. AU - Hoffman, V. AU - Hoefert, C. AU - Klein, K. AU - Hudak, M. AU - Michon, A. M. AU - Schelder, M. AU - Schirle, M. AU - Remor, M. AU - Rudi, T. AU - Hooper, S. AU - Bauer, A. AU - Bouwmeester, T. AU - Casari, G. AU - Drewes, G. AU - Neubauer, G. AU - Rick, J. M. AU - Kuster, B. AU - Bork, P. AU - Russell, R. B. AU - Furga, G. S. PY - 2006 DA - 2006// TI - Proteome survey reveals modularity of the yeast cell machinery JO - Nature VL - 440 UR - https://doi.org/10.1038/nature04532 DO - 10.1038/nature04532 ID - Gavin2006 ER - TY - JOUR AU - Pu, S. AU - Wong, J. AU - Turner, B. AU - Cho, E. AU - Wodak, S. J. PY - 2009 DA - 2009// TI - Up-to-date catalogues of yeast protein complexes JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn1005 DO - 10.1093/nar/gkn1005 ID - Pu2009 ER - TY - JOUR AU - Lei, X. J. AU - Wang, F. AU - Wu, F. X. AU - Zhang, A. D. AU - Pedrycz, W. PY - 2016 DA - 2016// TI - Protein complex identification through Markov clustering with firefly algorithm on dynamic protein-protein interaction networks JO - Inf Sci VL - 329 UR - https://doi.org/10.1016/j.ins.2015.09.028 DO - 10.1016/j.ins.2015.09.028 ID - Lei2016 ER - TY - JOUR AU - Tu, B. P. AU - Kudlicki, A. AU - Rowicka, M. AU - McKnight, S. L. PY - 2005 DA - 2005// TI - Logic of the yeast metabolic cycle: temporal compart mentalization of cellular processes JO - Science VL - 310 UR - https://doi.org/10.1126/science.1120499 DO - 10.1126/science.1120499 ID - Tu2005 ER - TY - BOOK AU - Zhang, A. D. PY - 2009 DA - 2009// TI - Protein interaction networks: computational analysis PB - Cambridge University Press CY - New York UR - https://doi.org/10.1017/CBO9780511626593 DO - 10.1017/CBO9780511626593 ID - Zhang2009 ER - TY - JOUR AU - Brohée, S. AU - Helden, J. V. PY - 2006 DA - 2006// TI - Evaluation of clustering algorithms for protein–protein interaction network JO - BMC Bioinform VL - 7 UR - https://doi.org/10.1186/1471-2105-7-488 DO - 10.1186/1471-2105-7-488 ID - Brohée2006 ER - TY - CHAP AU - Friedel, C. C. AU - Krumsiek, J. AU - Zimmer, R. ED - Vingron, M. ED - Wong, L. PY - 2008 DA - 2008// TI - Bootstrapping the interactome: unsupervised identification of protein complexes in yeast. In BT - Proceedings of the 12th annual conference on research in computational molecular biology (RECOMB) UR - https://doi.org/10.1007/978-3-540-78839-3_2 DO - 10.1007/978-3-540-78839-3_2 ID - Friedel2008 ER - TY - JOUR AU - Sadeque, A. AU - Serão, N. V. AU - Southey, B. R. AU - Delfino, K. R. AU - Rodriguez-Zas, S. L. PY - 2012 DA - 2012// TI - Identification and characterization of alternative exon usage linked glioblastoma multiforme survival JO - BMC Med Genet VL - 5 ID - Sadeque2012 ER - TY - JOUR AU - Altaf-Ul-Amin, M. AU - Shinbo, Y. AU - Mihara, K. AU - Kurokawa, K. AU - Kanaya, S. PY - 2006 DA - 2006// TI - Development and implementation of an algorithm for detection ofprotein complexes in large interaction networks JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-207 DO - 10.1186/1471-2105-7-207 ID - Altaf-Ul-Amin2006 ER -