Genomic annotation prediction based on integrated information

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 7548 LNBI, Issue , 2012, Pages 238-252

  Chicco, Davide ^a   Tagliasacchi, Marco ^a   Masseroli, Marco ^a  

^a POLITECNICO DI MILANO   (Italy)

Author keywords

Bioinformatics data integration; Biomolecular annotation prediction; Biomolecular databases; Data warehouse; Information integration; Software infrastructures

Indexed keywords

BIO-MOLECULAR; BIOINFORMATICS DATA; BIOMOLECULAR DATABASE; INFORMATION INTEGRATION; SOFTWARE INFRASTRUCTURE;

ARTIFICIAL INTELLIGENCE; DATA WAREHOUSES; GENES;

BIOINFORMATICS;

EID: 84871571727     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-35686-5_20     Document Type: Conference Paper

References (37)

1. Galperin, M.Y., Cochrane, G.R.: Nucleic Acids Research Annual Database Issue and the NAR Online Molecular Biology Database Collection in 2009. Nucleic Acids Res. 37(Database issue), D1-D4 (2009)
2. EMBL Nucleotide Sequence Database Statistics, http://www3.ebi.ac.uk/ Services/DBStats/
3. Huang, D.W., Sherman, B.T., Lempicki, R.A.: Bioinformatics Enrichment Tools: Paths toward the Comprehensive Functional Analysis of Large Gene Lists. Nucleic Acids Res. 37, 1-13 (2009)
4. Al-Shahrour, F., Minguez, P., Tárraga, J., Medina, I., Alloza, E., Montaner, D., Dopazo, J.: FatiGO+: A Functional Profiling Tool for Genomic Data. Integration of Functional Annotation, Regulatory Motifs and Interaction Data with Microarray Experiments. Nucleic Acids Res. 35(Web Server issue), W91-W96 (2007)
5. Huang, D.W., Sherman, B.T., Tan, Q., Kir, J., Liu, D., Bryant, D., Guo, Y., et al.: DAVID Bioinformatics Resources: Expanded Annotation Database and Novel Algorithms to Better Extract Biology from Large Gene Lists. Nucleic Acids Res. 35(Web Server issue), W169-W175 (2007)
6. Masseroli, M., Martucci, D., Pinciroli, F.: GFINDer: Genome Function INtegrated Discoverer through Dynamic Annotation, Statistical Analysis, and Mining. Nucleic Acids Res. 32, W293-W300 (2004)
7. Masseroli, M.: Management and Analysis of Genomic Functional and Phenotypic Controlled Annotations to Support Biomedical Investigation and Practice. IEEE Trans. Inf. Technol. Biomed. 11, 376-385 (2007)
8. Sujansky, W.: Heterogeneous Database Integration in Biomedicine. J. Biomed. Inform. 34, 285-298 (2001)
9. Hernandez, T., Kambhampati, S.: Integration of Biological Sources: Current Systems and Challenges ahead. SIGMOD Record 33, 51-60 (2004)
10. The Gene Ontology Consortium: Creating the Gene Ontology Resource: Design and Implementation. Genome Res. 11, 1425-1433 (2001)
11. Khatri, P., Done, B., Rao, A., Done, A., Draghici, S.: A Semantic Analysis of the Annotations of the Human Genome. Bioinformatics 21, 3416-3421 (2005)
12. Davidson, S.B., Overton, C., Tanen, V., Wong, L.: BioKleisli: A Digital Library for Biomedical Researchers. Int. J. Digit. Libr. 1, 36-53 (1997)
13. Davidson, S.B., Crabtree, J., Brunk, B., Schug, J., Tannen, V., Overton, C., Stoeckert, C.: K2/Kleisli and GUS: Experiments in Integrated Access to Genomic Data Sources. IBM System Journal 40, 512-531 (2001)
14. Etzold, T., Ulyanov, A., Argos, P.: SRS: Information Retrieval System for Molecular Biology Data Banks. Methods Enzymol. 266, 114-128 (1996)
15. Tatusova, T.A., Karsch-Mizrachi, I., Ostell, J.A.: Complete Genomes in WWW Entrez: Data Representation and Analysis. Bioinformatics 15, 536-543 (1999)
16. Safran, M., Solomon, I., Shmueli, O., Lapidot, M., Shen-Orr, S., Adato, A., et al.: GeneCards 2002: Towards a Complete, Object-Oriented, Human Gene Compendium. Bioinformatics 18, 1542-1543 (2002)
17. Diehn, M., Sherlock, G., Binkley, G., Jin, H., Matese, J.C., Hernandez-Boussard, T., et al.: SOURCE: A Unified Genomic Resource of Functional Annotations, Ontologies, and Gene Expression Data. Nucleic Acids Res. 31, 219-223 (2003)
18. Freier, A., Hofestädt, R., Lange, M., Scholz, U., Stephanik, A.: BioDataServer: A SQL-Based Service for the Online Integration of Life Science Data. Silico Biol. 2, 37-57 (2002)
19. Haas, L.M., Schwarz, P.M., Kodali, P., Kotlar, E., Rice, J.E., Swops, W.C.: DiscoveryLink: A System for Integrated Access to Life Sciences Data Sources. IBM Systems Journal 40, 489-511 (2001)
20. Kasprzyk, A., Keefe, D., Smedley, D., London, D., Spooner, W., Melsopp, C., et al.: EnsMart: A Generic System for Fast and Flexible Access to Biological Data. Genome Res. 14, 160-169 (2004)
21. Lee, T.J., Pouliot, Y., Wagner, V., Gupta, P., Stringer-Calvert, D.W., Tenenbaum, J.D., Karp, P.D.: BioWarehouse: A Bioinformatics Database Warehouse Toolkit. BMC Bioinformatics 7, 1-14 (2006)
22. Drineas, P.: Clustering large graphs via the singular value decomposition: Theoretical advances in data clustering. Machine Learning 56, 9-33 (2004)
23. Lin, D.: An Information-Theoretic Definition of Similarity. In: Shavlik, J.W. (ed.) Proceedings of the 15th International Conference on Machine Learning (ICML 1998), pp. 296-304. Morgan Kaufmann Publishers Inc., San Francisco (1998)
24. King, O.D., Foulger, R.E., Dwight, S.S., White, J.V., Roth, F.P.: Predicting Gene Function From Patterns of Annotation. Genome Res. 13, 896-904 (2003)
25. Tao, Y., Sam, L., Li, J., Friedman, C., Lussier, Y.A.: Information theory applied to the sparse gene ontology annotation network to predict novel gene function. Bioinformatics 23, 529-538 (2007)
26. AMD Core Math Library (ACML), http://developer.amd.com/cpu/libraries/ acml/
27. Rohde, D.: SVDLIBC, http://tedlab.mit.edu/~dr/SVDLIBC
28. Dagum, L., Menon, R.: OpenMP: an industry standard API for shared-memory programming. IEEE Computational Science & Engineering 5, 46-55 (1998)
29. Gordon, R.: Essential JNI: Java Native Interface. Prentice-Hall, Inc., NJ (1998)
30. Lawson, C.L., Hanson, R.J., Kincaid, D.R., Krogh, F.T.: Basic Linear Algebra Subprograms for Fortran Usage. ACM Transactions on Mathematical Software (TOMS) 5 (1979)
31. Berry, M., Do, T., O'Brien, G., Krishna, V., Varadhan, S.: SVDPACKC (Version 1.0) User's Guide. Citeseer (1993)
32. Angerson, B., Dongarra, G., McKenney, D.C., et al.: LAPACK: A portable linear algebra library for high-performance computers. In: Proceedings of the 1990 ACM/IEEE Conference on Supercomputing, pp. 2-11. IEEE Computer Society Press, Los Alamitos (1990)
33. Hofmann, T.: Probabilistic Latent Semantic Indexing. In: Proceedings of the 22nd Annual International SIGIR Conference on Research and Development in Information Retrieval (SIGIR 1999). ACM, New York (1999)
34. Egan, J.P.: Signal Detection Theory and ROC Analysis. Academic Press, New York (1975)
35. Search-Computing.org, http://www.search-computing.org
36. Ceri, S., Brambilla, M. (eds.): Search Computing. LNCS, vol. 5950. Springer, Heidelberg (2010)
37. Masseroli, M., Ghisalberti, G.: Bio-SeCo: Integration and Global Ranking of Biomedical Search Results. In: Ceri, S., Brambilla, M. (eds.) Search Computing II. LNCS, vol. 6585, pp. 203-214. Springer, Heidelberg (2011)