1 1

Proje Grubu: EEEAG Sayfa Sayısı: 84 Proje No: 112E137 Proje Bitiş Tarihi: 01.01.2015 Metin Dili: Türkçe İndeks Tarihi: 29-07-2022

Bionetaling: biyokimyasal ağlarda fonksiyonel ortoloji çıkarımı amaçlı global hizalamalar

Öz:
-
Anahtar Kelime:

Erişim Türü: Erişime Açık
  • [1] http://biotech.matcmadison.edu/resources/proteins/labManual/ images/220_04_113.png.
  • [2] Gamze Abaka, Turker Biyikoglu, and Cesim Erten. Campways: constrained alignment framework for the comparative analysis of a pair of metabolic path-ways. Bioinformatics, 29(13):i145–i153, 2013.
  • [3] R Aebersold and M Mann. Mass spectrometry-based proteomics. Nature, 422(6928):198–207, 2003.
  • [4] Rasmus Agren, Sergio Bordel, Adil Mardinoglu, Natapol Pornputtapong, Intawat Nookaew, and Jens Nielsen. Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using init. PLoS Compu-tational Biology, 8(5), 2012.
  • [5] A. E. Aladag˘ and C. Erten. Spinal: Scalable protein interaction network align-ment. Bioinformatics, 29(7):917–924, 2013.
  • [6] Ferhat Alkan and Cesim Erten. Beams: backbone extraction and merge strategy for the global many-to-many alignment of multiple ppi networks. Bioinformatics, 30(4):531–539, 2014.
  • [7] B. Aranda, P. Achuthan, Y. Alam-Faruque, I. Armean, A. Bridge, C. Derow, and et al. The intact molecular interaction database in 2010. Nucleic Acids Research, 38(Database-Issue):525–531, 2010.
  • [8] Michael Ashburner, Catherine A. Ball, Judith A. Blake, and et al. Gene Ontology: tool for the unification of biology. Nat Genet, 25(1):25–29, 2000.
  • [9] Ferhat Ay, Manolis Kellis, and Tamer Kahveci. Submap: aligning metabolic pathways with subnetwork mappings. Journal of Computational Biology, 18(13):219–235, 2011.
  • [10] Eric Banks, Elena Nabieva, Ryan Peterson, and Mona Singh. NetGrep: fast network schema searches in interactomes. Genome Biology, 9(9):R138+, 2008.
  • [11] Mohsen Bayati, Christian Borgs, Jennifer T. Chayes, and Riccardo Zecchina. Belief propagation for weighted b-matchings on arbitrary graphs and its relation to linear programs with integer solutions. SIAM J. Discrete Math., 25(2):989– 1011, 2011.
  • [12] Piotr Berman. A d/2 approximation for maximum weight independent set in d-claw free graphs. In Proceedings of the 7th Scandinavian Workshop on Algorithm Theory, SWAT ’00, pages 214–219, 2000.
  • [13] Judith A. Blake, Joel E. Richardson, Carol J. Bult, James A. Kadin, and Janan T. Eppig. The mouse genome database (mgd): the model organism database for the laboratory mouse. Nucleic Acids Research, 30(1):113–115, 2002.
  • [14] Ravi Boppana and Magnus´ M. Halldorsson´. Approximating maximum indepen-dent sets by excluding subgraphs. BIT, 32(2):180–196, May 1992.
  • [15] B.J. Breitkreutz, C. Stark, T. Reguly, L. Boucher, A. Breitkreutz, M. Livstone, R. Oughtred, D.H. Lackner, J. Bahler, V. Wood, and et al. The biogrid interaction database: 2008 update. Nucleic Acids Research, 36(Database-Issue):637–640, 2008.
  • [16] Carlo Vittorio Cannistraci, Gregorio Alanis-Lobato, and Timothy Ravasi. Min-imum curvilinearity to enhance topological prediction of protein interactions by network embedding. Bioinformatics, 29(13):i199–i209, 2013.
  • [17] R. Caspi, H. Foerster, C.A. Fulcher, P. Kaipa, M. Krummenacker, M. Laten-dresse, S. Paley, S.Y. Rhee, A.G. Shearer, C. Tissier, T.C. Walk, P. Zhang, and P.D. Karp. The metacyc database of metabolic pathways and enzymes and the biocyc collection of pathway/genome databases. Nucleic Acids Res, 36(Database issue):D623–31, 2008.
  • [18] A. Ceol, A. Chatr Aryamontri, L. Licata, D. Peluso, L. Briganti, L. Perfetto, L. Castagnoli, and G. Cesareni. Mint, the molecular interaction database: 2009 update. Nucleic Acids Research, 38(Database-Issue):532–539, 2010.
  • [19] J. M. Cherry, C. Adler, C. Ball, S. A. Chervitz, S. S. Dwight, E. T. Hester, Y. Jia, G. Juvik, T. Roe, M. Schroeder, S. Weng, and D. Botstein. SGD: Saccharomyces Genome Database. Nucleic acids research, 26(1):73–79, January 1998.
  • [20] Leonid Chindelevitch, Chung-Shou Liao, and Bonnie Berger. Local optimization for global alignment of protein interaction networks. In Pacific Symposium on Biocomputing, pages 123–132, 2010.
  • [21] Connor Clark and Jugal Kalita. A comparison of algorithms for the pairwise alignment of biological networks. Bioinformatics, 30(16):2351–2359, 2014.
  • [22] Jose C. Clemente, Kenji Satou, and Gabriel Valiente. Phylogenetic reconstruction from non-genomic data. Bioinformatics, 23(2):e110–e115, January 2007.
  • [23] Konrad Dabrowski, Vadim V. Lozin, Haiko Muller,¨ and Dieter Rautenbach. Pa-rameterized complexity of the weighted independent set problem beyond graphs of bounded clique number. J. Discrete Algorithms, 14:207–213, 2012.
  • [24] Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, and Roded Sharan. Qnet: A tool for querying protein interaction networks. Journal of Computational Biology, 15(7):913–925, 2008.
  • [25] Rodney G. Downey and Michael R. Fellows. Parameterized Complexity. Springer-Verlag, 1999.
  • [26] Jack Edmonds. Maximum matching and a polyhedron with 0, 1-vertices. Journal of Research of the National Bureau of Standards B, 69:125–130, 1965.
  • [27] Isabelle Fagnot, Gaelle¨ Lelandais, and Stephane´ Vialette. Bounded list injective homomorphism for comparative analysis of protein-protein interaction graphs. J. of Discrete Algorithms, 6(2):178–191, June 2008.
  • [28] Yi Fang, William Benjamin, Mengtian Sun, and Karthik Ramani. Global geo-metric affinity for revealing high fidelity protein interaction network. PLoS ONE, 6(5):e19349, 2013.
  • [29] Guillaume Fertin, Romeo Rizzi, and Stephane´ Vialette. Finding occurrences of protein complexes in protein–protein interaction graphs. Journal of Discrete Al-gorithms, 7(1):90 – 101, 2009.
  • [30] Jason Flannick, Antal Novak, Balaji S. Srinivasan, Harley H. McAdams, and Serafim Batzoglou. Graemlin: general and robust alignment of multiple large interaction networks. Genome Research, 16(9):1169–1181, 2006.
  • [31] Jason Flannick, Antal F. Novak, Chuong B. Do, Balaji S. Srinivasan, and Serafim Batzoglou. Automatic parameter learning for multiple local network alignment. Journal of Computational Biology, 16(8):1001–1022, 2009.
  • [32] Francois Fouss, Alain Pirotte, Jean-Michel Renders, and Marco Saerens. Random-walk computation of similarities between nodes of a graph with appli-cation to collaborative recommendation. IEEE Trans. on Knowl. and Data Eng., 19(3):355–369, March 2007.
  • [33] Andrew D. Fox, Benjamin J. Hescott, Anselm C. Blumer, and Donna K. Slonim. Connectedness of PPI network neighborhoods identifies regulatory hub proteins. Bioinformatics, 27(8):1135–1142, 2011.
  • [34] Andrea Franceschini, Damian Szklarczyk, Sune Frankild, Michael Kuhn, Mi-lan Simonovic, Alexander Roth, Jianyi Lin, Pablo Minguez, Peer Bork, Chris-tian von Mering, and Lars Juhl Jensen. STRING v9.1: protein-protein interac-tion networks, with increased coverage and integration. Nucleic Acids Research, 41(Database-Issue):808–815, 2013.
  • [35] Harold N. Gabow. Scaling algorithms for network problems. In Proceedings of the 24th Annual Symposium on Foundations of Computer Science, SFCS ’83, pages 248–258, Washington, DC, USA, 1983. IEEE Computer Society.
  • [36] M. R. Garey and David S. Johnson. Computers and Intractability: A Guide to the Theory of NP-Completeness. W. H. Freeman, 1979. [37] C. S. Goh and F. E. Cohen. Co-evolutionary analysis reveals insights into protein-protein interactions. Journal of molecular biology, 324(1):177–192, 2002.
  • [38] R. Guimera,` M. Sales-Pardo, and L.A.N. Amaral. A network-based method for target selection in metabolic networks. Bioinformatics, 23(13):1616–1622, July 2007.
  • [39] M. M. Halldorsson´. Approximations of weighted independent set and heredi-tary subset problems. Journal of Graph Algorithms and Applications, 4(1):1–16, 2000.
  • [40] V. Helms. Principles of Computational Cell Biology. Wiley-VCH, 2008.
  • [41] M. Heymans and A. Singh. Deriving phylogenetic trees from the similarity anal-ysis of metabolic pathways. Bioinformatics, 19:138–146, 2003.
  • [42] H.D. Holtje,¨ G. Folkers, and T. Beier. Molecular modeling: basic principles and applications. Methods and principles in medicinal chemistry. VCH, 1997.
  • [43] Hailiang Huang, Bruno Jedynak, and Joel S. Bader. Where have all the inter-actions gone? estimating the coverage of two-hybrid protein interaction maps. PLoS Computational Biology, 3(11), 2007.
  • [44] T.J. Hubbard, B.L. Aken, S. Ayling, B. Ballester, K. Beal, E. Bragin, S. Brent, Y. Chen, P. Clapham, L. Clarke, and et al. Ensembl 2009. Nucleic Acids Research, 37(Database-Issue):690–697, 2009.
  • [45] Jose MG Izarzugaza, David Juan, Carles Pons, Florencio Pazos, and Alfonso Va-lencia. Enhancing the prediction of protein pairings between interacting families using orthology information. BMC Bioinformatics, 9(35), 2008.
  • [46] B. Junker and F. Schreiber. Analysis of Biological Networks. Wiley-Interscience, 2008.
  • [47] Minoru Kanehisa, Susumu Goto, Yoko Sato, Miho Furumichi, and Mao Tanabe. Kegg for integration and interpretation of large-scale molecular data sets. Nucleic Acids Research, 40(Database-Issue):109–114, 2012.
  • [48] Brian P. Kelley, Roded Sharan, Richard M. Karp, Taylor Sittler, David E. Root, Brent R. Stockwell, and Trey Ideker. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proceedings of the Na-tional Academy of Sciences, 100(20):11394–11399, 2003.
  • [49] Brian P. Kelley, Bingbing Yuan, Fran Lewitter, Roded Sharan, Brent R. Stock-well, and Trey Ideker. Pathblast: a tool for alignment of protein interaction net-works. Nucleic Acids Research, 32(Web-Server-Issue):83–88, 2004.
  • [50] T.S. Keshava Prasad, R. Goel, K. Kandasamy, S. Keerthikumar, S. Kumar, S. Mathivanan, D. Telikicherla, R. Raju, B. Shafreen, A. Venugopal, and et al. Human protein reference database-2009 update. Nucleic Acids Research, 37(Database-Issue):767–772, 2009.
  • [51] Mehmet Koyuturk,¨ Yohan Kim, Umut Topkara, Shankar Subramaniam, Wojciech Szpankowski, and Ananth Grama. Pairwise alignment of protein interaction net-works. Journal of Computational Biology, 13(2):182–199, 2006.
  • [52] Oleksii Kuchaiev, Tijana Milenkovic,´ Vesna Memiseviˇc,´ Wayne Hayes, and Natasaˇ Przuljˇ. Topological network alignment uncovers biological function and phylogeny. Journal of The Royal Society Interface, 7(50):1341–1354, 2010.
  • [53] Oleksii Kuchaiev and Natasa Przuljˇ. Integrative network alignment reveals large regions of global network similarity in yeast and human. Bioinformatics, 27(10):1390–1396, 2011.
  • [54] Oleksii Kuchaiev, Marija Rasajski, Desmond J. Higham, and Natasa Przulj. Ge-ometric de-noising of protein-protein interaction networks. PLoS Computational Biology, 5(8):e1000454, 2009.
  • [55] Sheng-An Lee, Cheng hsiung Chan, Chi-Hung Tsai, Jin-Mei Lai, Feng-Sheng Wang, Cheng-Yan Kao, and Chi-Ying F Huang. Ortholog-based protein-protein interaction prediction and its application to inter-species interactions. BMC Bioinformatics, 9:S11, 2008.
  • [56] Chengwei Lei and Jianhua Ruan. A novel link prediction algorithm for recon-structing protein-protein interaction networks by topological similarity. Bioinfor-matics, 29(3):355–364, 2013.
  • [57] Chung-Shou Liao, Kanghao Lu, Michael Baym, Rohit Singh, and Bonnie Berger. Isorankn: spectral methods for global alignment of multiple protein networks. Bioinformatics, 25(12):i253–i258, 2009.
  • [58] Brenton Louie, Roger Higdon, and Eugene Kolker. A statistical model of pro-tein sequence similarity and function similarity reveals overly-specific function predictions. PLoS One, 4(10):e7546, 2009.
  • [59] J. March. Advanced Organic Chemistry: Reactions, Mechanisms, and Structure. Wiley, New York, 1985.
  • [60] Edward M. Marcotte, Matteo Pellegrini, Ho-Leung Ng, Danny W. Rice, Todd O. Yeates, and David Eisenberg. Detecting protein function and protein-protein in-teractions from genome sequences. Science (New York, N.Y.), 285(5428):751– 753, 1999.
  • [61] Kurt Mehlhorn and Stefan Naher. Leda: A Platform for Combinatorial and Ge-ometric Computing. Cambridge University Press, 1999.
  • [62] V. Memiseviˇc´ and N. Przuljˇ. C-graal: Common-neighbors-based global graph alignment of biological networks. Integr Biol (Camb), 4(7):734–43, 2012.
  • [63] Tijana Milenkovic,´ Weng Leong Ng, Wayne Hayes, and Natasaˇ Przuljˇ. Optimal network alignment with graphlet degree vectors. Cancer Inform., 9:121–137, 2010.
  • [64] Aziz Mithani, Jotun Hein, and Gail M. Preston. Comparative analysis of metabolic networks provides insight into the evolution of plant pathogenic and non-pathogenic lifestyles in Pseudomonas. Mol Biol Evol, 28(1):483–499, 2011.
  • [65] Manikandan Narayanan and Richard M. Karp. Comparing Protein Interaction Networks via a Graph Match-and-Split Algorithm. Journal of Computational Biology, 14(7):892–907, 2007.
  • [66] RA Pache and P Aloy. Increasing the precision of orthology-based complex pre-diction through network alignment. PeerJ., 2:e413, 2014.
  • [67] Daniel Park, Rohit Singh, Michael Baym, Chung-Shou Liao, and Bonnie Berger. Isobase: a database of functionally related proteins across ppi networks. Nucleic Acids Research, 39(Database-Issue):295–300, 2011.
  • [68] Ron Y. Pinter, Oleg Rokhlenko, Esti Yeger Lotem, and Michal Ziv-Ukelson. Alignment of metabolic pathways. Bioinformatics, 21(16):3401–3408, 2005.
  • [69] Venkatesh Raman and Saket Saurabh. Triangles, 4-cycles and parameterized (in-)tractability. In Proceedings of the 10th Scandinavian Conference on Algorithm Theory, SWAT’06, pages 304–315, 2006.
  • [70] M. Remm, C. E. Storm, and E. L. Sonnhammer. Automatic clustering of or-thologs and in-paralogs from pairwise species comparisons. Journal of molecular biology, 314(5):1041–1052, 2001.
  • [71] Sayed M. Sahraeian and Byung-Jun Yoon. A Network Synthesis Model for Gen-erating Protein Interaction Network Families. PLoS ONE, 7(8):e41474+, August 2012.
  • [72] Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon. Smetana: Accu-rate and scalable algorithm for probabilistic alignment of large-scale biological networks. PLoS ONE, 8(7):e67995, 07 2013.
  • [73] Shuichi Sakai, Mitsunori Togasaki, and Koichi Yamazaki. A note on greedy algorithms for the maximum weighted independent set problem. Discrete Appl. Math., 126(2-3):313–322, March 2003.
  • [74] L. Salwinski, C.S. Miller, A.J. Smith, F.K. Pettit, J.U. Bowie, and D. Eisen-berg. The database of interacting proteins: 2004 update. Nucleic Acids Research, 32:449–451, 2004.
  • [75] Roded Sharan and Trey Ideker. Modeling cellular machinery through biological network comparison. Nature Biotechnology, 24(4):427–433, 2006.
  • [76] Roded Sharan, Silpa Suthram, Ryan M. Kelley, Tanja Kuhn, Scott McCuine, Peter Uetz, Taylor Sittler, Richard M. Karp, and Trey Ideker. Conserved patterns of protein interaction in multiple species. Proceedings of the National Academy of Sciences of the United States of America, 102(6):1974–1979, 2005.
  • [77] Roded Sharan, Igor Ulitsky, and Ron Shamir. Network-based prediction of pro-tein function. Molecular systems biology, 3(1), 2007.
  • [78] TL Shi, YX Li, YD Cai, and KC Chou. Computational methods for protein-protein interaction and their application. Curr Protein Pept Sci., 6:443–449, 2005.
  • [79] Tomer Shlomi, Daniel Segal, Eytan Ruppin, and Roded Sharan. QPath: a method for querying pathways in a protein-protein interaction network. BMC Bioinfor-matics, 7:199+, 2006.
  • [80] Rohit Singh, Jinbo Xu, and Bonnie Berger. Global alignment of multiple protein interaction networks. In Pacific Symposium on Biocomputing, pages 303–314, 2008.
  • [81] Lucy Skrabanek, Harpreet K. Saini, Gary D. Bader, and Anton J. Enright. Com-putational prediction of protein-protein interactions. Molecular Biotechnology, 38(1):1–17, 2008.
  • [82] Yukako Tohsato, Hideo Matsuda, and Akihiro Hashimoto. A multiple alignment algorithm for metabolic pathway analysis using enzyme hierarchy. In Proceed-ings of the Eighth International Conference on Intelligent Systems for Molecular Biology, pages 376–383. AAAI, 2000.
  • [83] Hanghang Tong, Christos Faloutsos, and Jia-Yu Pan. Fast random walk with restart and its applications. In Proceedings of the Sixth International Conference on Data Mining, ICDM ’06, pages 613–622, 2006.
  • [84] Susan Tweedie, Michael Ashburner, Kathleen Falls, Paul Leyland, Peter Mc-quilton, Steven Marygold, Gillian Millburn, David Osumi-Sutherland, Andrew Schroeder, Ruth Seal, Haiyan Zhang, and The FlyBase Consortium. Fly-Base: enhancing Drosophila Gene Ontology annotations. Nucl. Acids Res., 37(suppl 1):D555–559, January 2009.
  • [85] A Valencia and F Pazos. Computational methods for the prediction of protein interactions. Curr Opin Struct Biol., 3:368–373, 2002.
  • [86] Christian von Mering, Lars Juhl Jensen, Berend Snel, Sean D. Hooper, Markus Krupp, Mathilde Foglierini, Nelly Jouffre, Martijn A. Huynen, and Peer Bork. String: known and predicted protein-protein associations, integrated and trans-ferred across organisms. Nucleic Acids Research, 33(Database-Issue):433–437, 2005.
  • [87] JF Xia, SL Wang, and YK Lei. Computational methods for the prediction of protein-protein interactions. Protein Pept Lett., 9:1069–1078, 2010.
  • [88] Qingwu Yang and Sing-Hoi Sze. Path matching and graph matching in biological networks. Journal of Computational Biology, 14(1):56–67, 2007.
  • [89] Mikhail Zaslavskiy, Francis R. Bach, and Jean-Philippe Vert. Global alignment of protein-protein interaction networks by graph matching methods. Bioinformatics, 25(12):259–267, 2009.
  • [90] Li Zhenping, Shihua Zhang, Yong Wang, Xiang-Sun Zhang, and Luonan Chen. Alignment of molecular networks by integer quadratic programming. Bioinfor-matics, 23(13):1631–1639, July 2007.
APA ERTEN C, BIYIKOĞLU T, HALİLOĞLU T (2015). Bionetaling: biyokimyasal ağlarda fonksiyonel ortoloji çıkarımı amaçlı global hizalamalar. , 1 - 84.
Chicago ERTEN Cesim,BIYIKOĞLU Türker,HALİLOĞLU Türkan Bionetaling: biyokimyasal ağlarda fonksiyonel ortoloji çıkarımı amaçlı global hizalamalar. (2015): 1 - 84.
MLA ERTEN Cesim,BIYIKOĞLU Türker,HALİLOĞLU Türkan Bionetaling: biyokimyasal ağlarda fonksiyonel ortoloji çıkarımı amaçlı global hizalamalar. , 2015, ss.1 - 84.
AMA ERTEN C,BIYIKOĞLU T,HALİLOĞLU T Bionetaling: biyokimyasal ağlarda fonksiyonel ortoloji çıkarımı amaçlı global hizalamalar. . 2015; 1 - 84.
Vancouver ERTEN C,BIYIKOĞLU T,HALİLOĞLU T Bionetaling: biyokimyasal ağlarda fonksiyonel ortoloji çıkarımı amaçlı global hizalamalar. . 2015; 1 - 84.
IEEE ERTEN C,BIYIKOĞLU T,HALİLOĞLU T "Bionetaling: biyokimyasal ağlarda fonksiyonel ortoloji çıkarımı amaçlı global hizalamalar." , ss.1 - 84, 2015.
ISNAD ERTEN, Cesim vd. "Bionetaling: biyokimyasal ağlarda fonksiyonel ortoloji çıkarımı amaçlı global hizalamalar". (2015), 1-84.
APA ERTEN C, BIYIKOĞLU T, HALİLOĞLU T (2015). Bionetaling: biyokimyasal ağlarda fonksiyonel ortoloji çıkarımı amaçlı global hizalamalar. , 1 - 84.
Chicago ERTEN Cesim,BIYIKOĞLU Türker,HALİLOĞLU Türkan Bionetaling: biyokimyasal ağlarda fonksiyonel ortoloji çıkarımı amaçlı global hizalamalar. (2015): 1 - 84.
MLA ERTEN Cesim,BIYIKOĞLU Türker,HALİLOĞLU Türkan Bionetaling: biyokimyasal ağlarda fonksiyonel ortoloji çıkarımı amaçlı global hizalamalar. , 2015, ss.1 - 84.
AMA ERTEN C,BIYIKOĞLU T,HALİLOĞLU T Bionetaling: biyokimyasal ağlarda fonksiyonel ortoloji çıkarımı amaçlı global hizalamalar. . 2015; 1 - 84.
Vancouver ERTEN C,BIYIKOĞLU T,HALİLOĞLU T Bionetaling: biyokimyasal ağlarda fonksiyonel ortoloji çıkarımı amaçlı global hizalamalar. . 2015; 1 - 84.
IEEE ERTEN C,BIYIKOĞLU T,HALİLOĞLU T "Bionetaling: biyokimyasal ağlarda fonksiyonel ortoloji çıkarımı amaçlı global hizalamalar." , ss.1 - 84, 2015.
ISNAD ERTEN, Cesim vd. "Bionetaling: biyokimyasal ağlarda fonksiyonel ortoloji çıkarımı amaçlı global hizalamalar". (2015), 1-84.