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Original Articles

Multilevel approaches for large-scale proteomic networks

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Pages 683-695 | Received 30 Sep 2006, Accepted 08 Mar 2007, Published online: 02 Jul 2007

References

  • Oliveira , S. and Seok , S. C. A multilevel approach for identifying functional modules in protein–protein interaction networks . Proceedings of IWBRA 2006 . pp. 726 – 773 . Berlin : Springer-Verlag . Lecture Notes in Computer Science, 3992
  • Oliveira , S. and Seok , S. C. Triangular clique based multilevel approaches to identify functional modules . Paper presented at the Seventh International Meeting on High Performance Computing for Computational Science (VECPAR 2006) . July 10–13 2006 , Rio de Janeiro, Brazil.
  • Oliveira , S. and Seok , S. C. A matrix-based multilevel approach to identify functional protein models . International Journal of Bioinformatics Research and Applications , To appear
  • Abou-Rjeili , A. and Karypis , G. 2006 . Multilevel algorithms for partitioning power-law graphs . IEEE International Parallel & Distributed Processing Symposium (IPDPS) , In press
  • Spirin , V. and Mirny , L. A. 2003 . Protein complexes and functional modules in molecular networks . Proc. Natl. Acad. Sci. USA , 100 : 12123 – 12128 .
  • Zhang , C. , Liu , S. and Zhou , Y. Q. 2006 . Fast and accurate method for identifying high-quality protein-interaction modules by clique merging and its application to yeast . J. Proteome Res. , 5 : 801 – 807 .
  • Krogan , N. J. , Cagney , G. , Yu , H. Y. , Zhong , G. Q. , Guo , X. H. , Ignatchenko , A. , Li , J. , Pu , S. Y. , Datta , N. , Tikuisis , A. P. , Punna , T. , Peregrin-Alvarez , J. M. , Shales , M. , Zhang , X. , Davey , M. , Robinson , M. D. , Paccanaro , A. , Bray , J. E. , Sheung , A. , Beattie , B. , Richards , D. P. , Canadien , V. , Lalev , A. , Mena , F. , Wong , P. , Starostine , A. , Canete , M. M. , Vlasblom , J. , Wu , S. , Orsi , C. , Collins , S. R. , Chandran , S. , Haw , R. , Rilstone , J. J. , Gandi , K. , Thompson , N. J. , Musso , G. , St Onge , P. , Ghanny , S. , Lam , MH. Y. , Butland , G. , Altaf-Ui , A. M. , Kanaya , S. , Shilatifard , A. , O'Shea , E. , Weissman , J. S. , Ingles , C. J. , Hughes , T. R. , Parkinson , J. , Gerstein , M. , Wodak , S. J. , Emili , A. and Greenblatt , J. F. 2006 . “ Global landscape of protein complexes in the yeast saccharomyces cerevisiae ” . In Nature Vol. 440 , 637 – 643 .
  • Bornholdt , S. and Schuster , H. G. 2003 . Handbook of Graphs and Networks , Edited by: Bornholdt , S. and Schuster , H. G. Wilhelm : Wiley VCH .
  • Uetz , P. , Giot , L. , Cagney , G. , Mansfield , T. A. , Judson , R. S. , Knight , J. R. , Lockshon , D. , Narayan , V. , Srinivasan , M. , Pochart , P. , Qureshi-Emili , A. , Li , Y. , Godwin , B. , Conover , D. , Kalbfleisch , T. , Vijayadamodar , G. , Yang , M. J. , Johnston , M. , Fields , S. and Rothberg , J. M. 2000 . A comprehensive analysis of protein–protein interactions in saccharomyces cerevisiae . Nature , 403 : 623 – 627 .
  • Ito , T. , Chiba , T. , Ozawa , R. , Yoshida , M. , Hattori , M. and Sakaki , Y. 2001 . A comprehensive two-hybrid analysis to explore the yeast protein interactome . Proc. Natl. Acad. Sci. , 98 : 4277 – 4278 .
  • Gavin , A. C. , Bosche , M. , Krause , R. , Grandi , P. , Marzioch , M. , Bauer , A. , Schultz , J. , Rick , J. M. , Michon , A. M. , Cruciat , C. M. , Remor , M. , Hofert , C. , Schelder , M. , Brajenovic , M. , Ruffner , H. , Merino , A. , Klein , K. , Hudak , M. , Dickson , D. , Rudi , T. , Gnau , V. , Bauch , A. , Bastuck , S. , Huhse , B. , Leutwein , C. , Heurtier , M. A. , Copley , R. R. , Edelmann , A. , Querfurth , E. , Rybin , V. , Drewes , G. , Raida , M. , Bouwmeester , T. , Bork , P. , Seraphin , B. , Kuster , B. , Neubauer , G. and Superti-Furga , G. 2002 . Functional organization of the yeast proteome by systematic analysis of protein complexes . Nature , 415 : 141 – 147 .
  • Ho , Y. , Gruhler , A. , Heilbut , A. , Bader , G. D. , Moore , L. , Adams , S. L. , Millar , A. , Taylor , P. , Bennett , K. , Boutilier , K. , Yang , L. Y. , Wolting , C. , Donaldson , I. , Schandorff , S. , Shewnarane , J. , Vo , M. , Taggart , J. , Goudreault , M. , Muskat , B. , Alfarano , C. , Dewar , D. , Lin , Z. , Michalickova , K. , Willems , A. R. , Sassi , H. , Nielsen , P. A. , Rasmussen , K. J. , Andersen , J. R. , Johansen , L. E. , Hansen , L. H. , Jespersen , H. , Podtelejnikov , A. , Nielsen , E. , Crawford , J. , Poulsen , V. , Sorensen , B. D. , Matthiesen , J. , Hendrickson , R. C. , Gleeson , F. , Pawson , T. , Moran , M. F. , Durocher , D. , Mann , M. , Hogue , C. W.V. , Figeys , D. and Tyers , M. 2002 . Systematic identification of protein complexes in saccharomyces cerevisiae by mass spectrometry . Nature , 415 : 123 – 124 .
  • Mewes , H. W. , Amid , C. , Arnold , R. , Frishman , D. , Guldener , U. , Mannhaupt , G. , Munsterkotter , M. , Pagel , P. , Strack , N. , Stumpflen , V. , Warfsmann , J. and Ruepp , A. 2004 . Mips: Analysis and annotation of proteins from whole genomes . Nucleic Acids Res. , 32 : D41 – 4 .
  • Von Mering , C. , Krause , R. , Snel , B. , Cornell , M. , Oliver , S. G. , Fields , S. and Bork , P. 2002 . Comparative assessment of large-scale data sets of protein–protein interactions . Nature , 417 : 399 – 403 .
  • Seok , S. C. 2007 . Multilevel Clustering Algorithms for Documents and Large-Scale Proteomic Networks , PhD thesis. In preparation
  • Guldener , U. , Munsterkotter , M. , Kastenmuller , G. , Strack , N. , van Helden , J. , Lemer , C. , Richelles , J. , Wodak , S. J. , Garcia-Martinez , J. , Perez-Ortin , J. E. , Michael , H. , Kaps , A. , Talla , E. , Dujon , B. , Andre , B. , Souciet , J. L. , De Montigny , J. , Bon , E. , Gaillardin , C. and Mewes , H. W. 2005 . Cygd: the comprehensive yeast genome database . Nucleic Acids Research , 33 : D364 – D368 . Database issue
  • Seidman , S. B. 1983 . Network structure and minimum degree . Social Networks , 5 : 269 – 287 .
  • Bader , G. D. and Hogue , C. W. 2003 . An automated method for finding molecular complexes in large protein interaction networks . BMC Bioinformatics , 4 article 2
  • Ramadan , E. , Osgood , C. and Pothen , A. 2005 . The architecture of a proteomic network in the yeast . Proceedings of CompLife 2005 , : 265 – 276 . Lecture Notes in Bioinformatics, 3695
  • Ding , C. , He , X. , Zha , H. , Gu , M. and Simon , H. A min-max cut algorithm for graph partitioning data clustering . ICDM 2001, Proceedings IEEE International Conference on Data Mining, 2001 . pp. 107 – 114 .
  • Ding , C. , He , X. , Meraz , R. F. and Holbrook , S. R. 2004 . A unified representation of multiprotein complex data for modeling interaction networks . Proteins: Structure, Function, and Bioinformatics , 57 : 99 – 108 .
  • Kernighan , B. W. and Lin , S. 1970 . An efficient heuristic procedure for partitioning graphs . The Bell System Technical Journal , 49 : 291 – 307 .
  • Fiduccia , C. M. and Mattheyses , R. M. A linear time heuristic for improving network partitions . 19th IEEE Design Automation Conference . pp. 175 – 181 .
  • Skiena , S. 1998 . The Algorithm Design Manual , New York : Springer-Verlag .
  • Watts , D. J. and Strogatz , S. H. 1998 . Collective dynamics of ‘small-world’ networks . Nature , 393 : 409 – 410 .
  • Goldberg , D. S. and Roth , F. P. Assessing experimentally derived interactions in a small world . Proceedings of the National Academy of Sciences . Vol. 100 , pp. 4372 – 4376 .
  • Barabasi , A. L. and Oltvai , Z. N. 2004 . Network biology: Understanding the cell's functional organization . Nature Reviews Genetics , 5 : 101 – 113 .
  • Bron , C. and Kerbosch , J. 1973 . Algorithm 457: Finding all cliques of an undirected graph . Communications of the ACM , 16 : 575 – 577 .

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