Accurate multiple network alignment through context-sensitive random walk

BMC Systems Biology

Volumn 9, Issue , 2015, Pages

  Jeong, Hyundoo ^a   Yoon, Byung Jun ^a,b  

^a TEXAS A AND M UNIVERSITY   (United States)

^b HAMAD BIN KHALIFA UNIVERSITY   (Qatar)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BIOLOGY; PROCEDURES; PROTEIN ANALYSIS; STATISTICS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; PROTEIN INTERACTION MAPPING; STOCHASTIC PROCESSES;

EID: 84928739036     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-9-S1-S7     Document Type: Article

References (35)

1. Sharan R, Ideker T: Modeling cellular machinery through biological network comparison. Nature Biotechnology 2006, 24(4):427-433.
2. Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, Uetz P, Sittler T, Karp RM, Ideker T: Conserved patterns of protein interaction in multiple species. Proceedings of the National Academy of Sciences of the United States of America 2005, 102(6):1974-1979.
3. Dost B, Shlomi T, Gupta N, Ruppin E, Bafna V, Sharan R: QNet: a tool for querying protein interaction networks. Journal of Computational Biology 2008, 15(7):913-925.
4. Sahraeian SME, Yoon BJ: RESQUE: Network reduction using semi-Markov random walk scores for efficient querying of biological networks. Bioinformatics 2012, 28(16):2129-2136.
5. Huang Q, Wu LY, Zhang XS: An efficient network querying method based on conditional random fields. Bioinformatics 2011, 27(22):3173-3178.
6. Singh R, Xu J, Berger B: Global alignment of multiple protein interaction networks with application to functional orthology detection. Proceedings of the National Academy of Sciences of the United States of America 2008, 105(35):12763-12768.
7. Liao CS, Lu K, Baym M, Singh R, Berger B: IsoRankN: spectral methods for global alignment of multiple protein networks. Bioinformatics 2009, 25(12):i253-i258.
8. Flannick J, Novak A, Srinivasan BS, McAdams HH, Batzoglou S: Graemlin: general and robust alignment of multiple large interaction networks. Genome Research 2006, 16(9):1169-1181.
9. Kuchaiev O, Milenković T, Memišević V, Hayes W, Pržulj N: Topological network alignment uncovers biological function and phylogeny. Journal of the Royal Society Interface 2010, 7(50):1341-1354.
10. Kuchaiev O, Pržulj N: Integrative network alignment reveals large regions of global network similarity in yeast and human. Bioinformatics 2011, 27(10):1390-1396.
11. Phan HT, Sternberg MJ: PINALOG: a novel approach to align protein interaction networks-implications for complex detection and function prediction. Bioinformatics 2012, 28(9):1239-1245.
12. Sahraeian SME, Yoon BJ: SMETANA: accurate and scalable algorithm for probabilistic alignment of large-scale biological networks. PLoS ONE 2013, 8(7):e67995.
13. Hu J, Kehr B, Reinert K: NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks. Bioinformatics 2013, 30(4):540-548.
14. Alkan F, Erten C: BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks. Bioinformatics 2014, 30(4):531-539.
15. Yoon BJ, Qian X, Sahraeian SME: Comparative analysis of biological networks: Hidden markov model and markov chain-based approach. IEEE Signal Processing Magazine 2012, 29:22-34.
16. Panni S, Rombo SE: Searching for repetitions in biological networks: methods, resources and tools. Briefings in Bioinformatics 2013, 30(10):1343-1352.
17. Do CB, Mahabhashyam MS, Brudno M, Batzoglou S : ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Research 2005, 15(2):330-340.
18. Hamada M, Asai K: A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA). Journal of Computational Biology 2012, 19(5):532-549.
19. Roshan U, Livesay DR: Probalign: multiple sequence alignment using partition function posterior probabilities. Bioinformatics 2006, 22(22):2715-2721.
20. Sahraeian SME, Yoon BJ: PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences. Nucleic Acids Research 2010, 38(15):4917-4928.
21. Sahraeian SME, Yoon BJ: PicXAA-R: efficient structural alignment of multiple RNA sequences using a greedy approach. BMC Bioinformatics 2011, 12(Suppl 1):S38.
22. Sahraeian SME, Yoon BJ: PicXAA-Web: a web-based platform for nonprogressive maximum expected accuracy alignment of multiple biological sequences. Nucleic Acids Research 2011, 39 Web Server: 8-12.
23. Durbin R: Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge University Press; 1998.
24. Jeong H, Yoon BJ: Effective estimation of node-to-node correspondence between different graphs. IEEE Signal Processing Letters.
25. Sahraeian SME, Yoon BJ: A network synthesis model for generating protein interaction network families. PLoS ONE 2012, 7(8):e41474.
26. Park D, Singh R, Baym M, Liao CS, Berger B: IsoBase: a database of functionally related proteins across PPI networks. Nucleic Acids Research 2011, 39(suppl 1):D295-D300.
27. Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, Oughtred R, Lackner DH, Bähler J, Wood V, et al: The BioGRID interaction database: 2008 update. Nucleic Acids Research 2008, 36(suppl 1):D637-D640.
28. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D: The database of interacting proteins: 2004 update. Nucleic Acids Research 2004, 32(suppl 1):D449-D451.
29. Prasad TK, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, et al: Human protein reference database: 2009 update. Nucleic Acids Research 2009, 37(suppl 1): D767-D772.
30. Ceol A, Aryamontri AC, Licata L, Peluso D, Briganti L, Perfetto L, Castagnoli L, Cesareni G: MINT, the molecular interaction database: 2009 update. Nucleic Acids Research 2009, D532-D539.
31. Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian A, Kerrien S, Khadake J, et al: The IntAct molecular interaction database in 2010. Nucleic Acids Research 2010, 38(suppl 1):D525-D531.
32. Kanehisa M, Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Research 2000, 28:27-30.
33. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y: KEGG for linking genomes to life and the environment. Nucleic Acids Research 2008, 36(suppl 1):D480-D484.
34. Hakes L, Pinney JW, Robertson DL, Lovell SC: Protein-protein interaction networks and biology-what's the connection? Nature Biotechnology 2008, 26:69-72.
35. Kuchaiev O, Rašajski M, Higham DJ, Pržulj N: Geometric de-noising of protein-protein interaction networks. PLoS Computational Biology 2009, 5(8):e1000454.