Identification of novel type III effectors using latent dirichlet allocation

Computational and Mathematical Methods in Medicine

Volumn 2012, Issue , 2012, Pages

  Yang, Yang ^a  

^a SHANGHAI MARITIME UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; SEMANTICS; STATISTICS;

AMINO ACID SEQUENCE; DISEASE DEVELOPMENT; GRAM-NEGATIVE BACTERIA; LATENT DIRICHLET ALLOCATION; MACHINE LEARNING METHODS; PSEUDOMONAS SYRINGAE; RESEARCH INTERESTS; TYPE III SECRETION SYSTEM;

LEARNING SYSTEMS;

AMINO ACID; BACTERIAL PROTEIN; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; DIRICHLET ALLOCATION MODEL; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; NONHUMAN; PSEUDOMONAS SYRINGAE; TYPE III SECRETION SYSTEM; ALGORITHM; ARTIFICIAL INTELLIGENCE; BACTERIAL GENOME; BIOLOGICAL MODEL; BIOLOGY; CHEMISTRY; COMPUTER SIMULATION; GRAM NEGATIVE BACTERIUM; METABOLISM; METHODOLOGY; NATURAL LANGUAGE PROCESSING; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; THEORETICAL MODEL;

ALGORITHMS; AMINO ACIDS; ARTIFICIAL INTELLIGENCE; BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; GENOME, BACTERIAL; GRAM-NEGATIVE BACTERIA; MODELS, BIOLOGICAL; MODELS, THEORETICAL; NATURAL LANGUAGE PROCESSING; PROTEINS; PSEUDOMONAS SYRINGAE; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY;

EID: 84867288210     PISSN: 1748670X     EISSN: 17486718     Source Type: Journal    
DOI: 10.1155/2012/696190     Document Type: Article

References (21)

1. Galán J. E., Collmer A., Type III secretion machines: bacterial devices for protein delivery into host cells. Science 1999 284 5418 1322 1328 2-s2.0-0033591446 10.1126/science.284.5418.1322 (Pubitemid 29289652)
2. He S. Y., Nomura K., Whittam T. S., Type III protein secretion mechanism in mammalian and plant pathogens. Biochimica et Biophysica Acta 2004 1694 13 181 206 2-s2.0-8844275498 10.1016/j.bbamcr.2004.03.011 (Pubitemid 39535069)
3. Arnold R., Brandmaier S., Kleine F., Tischler P., Heinz E., Behrens S., Niinikoski A., Mewes H. W., Horn M., Rattei T., Sequence-based prediction of type III secreted proteins. PLoS Pathogens 2009 5 4 e1000376 2-s2.0-66349124179 10.1371/journal.ppat.1000376
4. Yang Y., A comparative study on sequence feature extraction for type III secreted effector prediction. Proceedings of the 8th International Conference on Fuzzy Systems and Knowledge Discovery (FSKD '11) July 2011
5. Wang Y., Zhang Q., Sun M. A., Guo D., High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles. Bioinformatics 2011 27 6 777 784 2-s2.0-79952594050 10.1093/bioinformatics/btr021
6. Ferreira A. O., Myers C. R., Gordon J. S., Martin G. B., Vencato M., Collmer A., Wehling M. D., Alfano J. R., Moreno-Hagelsieb G., Lamboy W. F., DeClerck G., Schneider D. J., Cartinhour S. W., Whole-genome expression profiling defines the HrpL regulon of Pseudomonas syringae pv. tomato DC3000, allows de novo reconstruction of the Hrp cis clement, and identifies novel coregulated genes. Molecular Plant-Microbe Interactions 2006 19 11 1167 1179 2-s2.0-33750204881 10.1094/MPMI-19-1167 (Pubitemid 44607329)
7. Panina E. M., Mattoo S., Griffith N., Kozak N. A., Yuk M. H., Miller J. F., A genome-wide screen identifies a Bordetella type III secretion effector and candidate effectors in other species. Molecular Microbiology 2005 58 1 267 279 2-s2.0-26244460966 10.1111/j.1365-2958.2005.04823.x (Pubitemid 41415046)
8. Sato Y., Takaya A., Yamamoto T., Meta-analytic approach to the accurate prediction of secreted virulence effectors in gram-negative bacteria. BMC Bioinformatics 2011 12 1, article 442
9. Yang Y., Zhao J., Morgan R. L., Ma W., Jiang T., Computational prediction of type III secreted proteins from gram-negative bacteria. BMC Bioinformatics 2010 11 supplement 1, article S47 2-s2.0-75149124497 10.1186/1471-2105-11-S1-S47
10. Guttman D. S., Vinatzer B. A., Sarkar S. F., Ranall M. V., Kettler G., Greenberg J. T., A functional screen for the type III (Hrp) secretome of the plant pathogen Pseudomonas syringae. Science 2002 295 5560 1722 1726 2-s2.0-0036500995 10.1126/science.295.5560.1722 (Pubitemid 34202909)
11. Blei D. M., Ng A. Y., Jordan M. I., Latent dirichlet allocation. Journal of Machine Learning Research 2003 3 4-5 993 1022 2-s2.0-0141607824
12. Wang C., Blei D., Fei-Fei L., Simultaneous image classification and annotation. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops (CVPR '09) June 2009 1903 1910 2-s2.0-70450178502 10.1109/CVPRW.2009.5206800
13. Zhang H., Qiu B., Giles C., Foley H., Yen J., An LDA-based community structure discovery approach for large-scale social networks. Proceedings of the IEEE Intelligence and Security Informatics (ISI '07) May 2007 200 207
14. Neal R. M., Markov chain sampling methods for dirichiet process mixture models. Journal of Computational and Graphical Statistics 2000 9 2 249 265 2-s2.0-77950032550
15. Blei D., Jordan M., Variational inference for dirichlet process mixtures. Bayesian Analysis 2006 1 1 121 144
16. Yang Y., Lu B. L., Extracting features from protein sequences using Chinese segmentation techniques for subcellular localization. Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB '05) November 2005 288 295 2-s2.0-33847242222
17. Chang C. C., Lin C. J.,. 2001, LIBSVM: a library for support vector machines, software
18. Steyvers M., Griffiths T.,. 2011, Matlab Topic Modeling Toolbox 1.4, software
19. Casper-Lindley C., Dahlbeck D., Clark E. T., Staskawicz B. J., Direct biochemical evidence for type III secretion-dependent translocation of the AvrBs2 effector protein into plant cells. Proceedings of the National Academy of Sciences of the United States of America 2002 99 12 8336 8341 2-s2.0-0037062493 10.1073/pnas.122220299 (Pubitemid 34651053)
20. Petnicki-Ocwieja T., Schneider D. J., Tam V. C., Chancey S. T., Shan L., Jamir Y., Schechter L. M., Janes M. D., Robin Buell C., Tang X., Collmer A., Alfano J. R., Genomewide identification of proteins secreted by the Hrp type III protein secretion system of Pseudomonas syringae pv. tomato DC3000. Proceedings of the National Academy of Sciences of the United States of America 2002 99 11 7652 7657 2-s2.0-0037188539 10.1073/pnas.112183899 (Pubitemid 34568746)
21. Schechter L. M., Roberts K. A., Jamir Y., Alfano J. R., Collmer A., Pseudomonas syringae type III secretion system targeting signals and novel effectors studied with a Cya translocation reporter. Journal of Bacteriology 2004 186 2 543 555 2-s2.0-0347915662 10.1128/JB.186.2.543-555.2004 (Pubitemid 38076444)