APPAGATO: An APproximate PArallel and stochastic GrAph querying TOol for biological networks

Bioinformatics

Volumn 32, Issue 14, 2016, Pages 2159-2166

  Bonnici, Vincenzo ^a   Busato, Federico ^a   Micale, Giovanni ^b   Bombieri, Nicola ^a   Pulvirenti, Alfredo ^c   Giugno, Rosalba ^a,c  

^a UNIVERSITY OF VERONA   (Italy)

^b UNIVERSITY OF CATANIA   (Italy)

^c UNIVERSITY OF CATANIA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANIMAL; BIOLOGY; GENE ONTOLOGY; HUMAN; PROCEDURES; PROTEIN PROTEIN INTERACTION; SOFTWARE;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; GENE ONTOLOGY; HUMANS; PROTEIN INTERACTION MAPS; SOFTWARE;

EID: 84992406259     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw223     Document Type: Article

References (43)

1. Barabasi, A.L. and Oltvai, Z.N. (2004) Network biology: understanding the cell's functional organization. Nat. Rev. Genet., 5, 101-113.
2. Billeter, M. et al. (2009) Efficient stream compaction on wide SIMD manycore architectures. In Proceedings of the Conference on High Performance Graphics 2009, pp. 159-166. New Orleans, Louisiana, USA.
3. Blin, G. et al. (2010) Querying graphs in protein-protein interactions networks using feedback vertex set. IEEE/ACM Trans. Comput. Biol. Bioinform., 7, 628-635.
4. Bonnici, V. and Giugno, R. (2016) On the variable ordering in subgraph isomorphism algorithms. IEEE/ACM Trans. Comput. Biol. Bioinform., PP(99), 1545-5963.
5. Bonnici, V. et al. (2013) A subgraph isomorphism algorithm and its application to biochemical data. BMC Bioinformatics, 14(Suppl. 7), S13.
6. Bruckner, S. et al. (2010) Topology-free querying of protein interaction networks. J. Comput. Biol., 17, 237-252.
7. Busato, F. and Bombieri, N. (2015) BFS-4K: an efficient implementation of BFS for kepler GPU architectures. IEEE Trans. Parallel Distrib. Syst., 26, 1826-1838.
8. Ciriello, G. et al. (2012) Mutual exclusivity analysis identifies oncogenic network modules. Genome Res., 22, 398-406.
9. Cordella, L.P. et al. (2004) A (sub) graph isomorphism algorithm for matching large graphs. IEEE Trans. Pattern Anal. Mach. Intell., 26, 1367-1372.
10. Cormen, T. et al. (2009) Introduction to Algorithms. MIT Press, Cambridge, Massachusetts.
11. Creixell, P. et al. (2015) Pathway and network analysis of cancer genomes. Nat. Methods, 12, 615-621.
12. Dematte, L. and Prandi, D. (2010) Gpu computing for systems biology. Brief. Bioinform., 11, 323-333. cited By 56.
13. Dost, B. et al. (2008) Qnet: a tool for querying protein interaction networks. J. Comput. Biol., 15, 913-925.
14. Fortney, K. et al. (2010). Method inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging. Genom Biol., 13.
15. Gulsoy, G. and Kahveci, T. (2011) RINQ: reference-based indexing for network queries. Bioinformatics, 27, i149-i158.
16. Harris, M. et al. (2008). GPU Gems 3: Parallel Prefix Sum (Scan) with CUDA. Addison Wesley Professional, chapter 3.
17. Hong, L. et al. (2015) Subgraph matching with set similarity in a large graph database. IEEE Trans. Knowl. Data Eng., 27, 2507-2521.
18. Ideker, T. et al. (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics, 18(Suppl. 1), S233-S240.
19. Jiang, X. et al. (2011) Network-based auto-probit modeling for protein function prediction. Biometrics, 67, 958-966.
20. Kelley, B. et al. (2003) Conserved pathways within bacteria and yeast as revealed by global protein network alignment. PNAS, 100, 11394-11399.
21. Kelley, B. et al. (2004) PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Res., 1, W83-W88.
22. Khan, A. et al. (2013). NeMa: fast graph search with label similarity. In Proceedings of the 39th International Conference on Very Large Data Bases, PVLDB'13. VLDB Endowment, pp. 181-192. Riva del Garda, Trento, Italy.
23. Lawrence, C. et al. (1993) Detecting subtle sequence signals: a gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
24. Lim, J. et al. (2006) A protein-protein interaction network for human inherited ataxias and disorders of purkinje cell degeneration. Cell, 125, 801-814.
25. Ma, X. and Gao, L. (2012) Biological network analysis: insights into structure and functions. Brief. Funct. Genomics, 11, 434-442.
26. Malod-Dognin, N. and Przulj, N. (2015) L-GRAAL: Lagrangian graphletbased network aligner. Bioinformatics, 31, 2182-2189.
27. Micale, G. et al. (2014) GASOLINE: a greedy and stochastic algorithm for optimal local multiple alignment of interaction networks. PLoS ONE, 9, e98750.
28. Panni, S. and Rombo, S.E. (2015) Searching for repetitions in biological networks: methods, resources and tools. Brief. Bioinform., 16, 118-136.
29. Pienta, R. et al. (2014). MAGE: matching approximate patterns in richlyattributed graphs. In 2014 IEEE International Conference on Big Data, Big Data 2014, Washington, DC, October 27-30, pp. 585-590.
30. Pinter, R.Y. et al. (2005) Alignment of metabolic pathways. Bioinformatics, 21, 3401-3408.
31. Ruepp, A. et al. (2010) CORUM: the comprehensive resource of mammalian protein complexes. Nucleic Acids Res., 38(Suppl. 1), D497-D501.
32. Sahraeian, S.M.E. and Yoon, B.J. (2012) RESQUE: Network reduction using semi-Markov random walk scores for efficient querying of biological networks. Bioinformatics, 28, 2129-2136.
33. Shlomi, T. et al. (2006) QPath: a method for querying pathways in a proteinprotein interaction network. BMC Bioinformatics, 10, 199.
34. Sun, Z. et al. (2012) Efficient subgraph matching on billion node graphs. Proc. VLDB Endow., 5, 788-799.
35. Szklarczyk, D. et al. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res., 39, D561-D568.
36. Tian, Y. et al. (2007) SAGA: a subgraph matching tool for biological graphs. Bioinformatics, 15, 232-239.
37. Tian, Y. et al. (2008) Periscope/gq: a graph querying toolkit. Proc. VLDB Endow., 1, 1404-1407.
38. Vouzis, P.D. and Sahinidis, N.V. (2011) GPU-BLAST: using graphics processors to accelerate protein sequence alignment. Bioinformatics, 27, 182-188.
39. Wang, H. et al. (2013) Function-function correlated multi-label protein function prediction over interaction networks. J. Comput. Biol., 20, 322-343.
40. Yu, D. et al. (2013) Review of biological network data and its applications. Genomics Inform, 11, 200-210.
41. Yuanyuan, T. and Patel, J. (2008). Tale: a tool for approximate large graph matching. In Data IEEE 24th International Conference on Engineering, 2008, ICDE 2008, pp. 963-972. Cancun, Mexico.
42. Zhang, S. et al. (2009). Gaddi: distance index based subgraph matching in biological networks. In Proceedings of the 12th International Conference on Extending Database Technology: Advances in Database Technology, EDBT '09, pp. 192-203. ACM, New York, NY.
43. Zhao, K. and Chu, X. (2014) G-BLASTN: accelerating nucleotide alignment by graphics processors. Bioinformatics, 30, 1384-1391.