Joint stage recognition and anatomical annotation of drosophila gene expression patterns

Bioinformatics

Volumn 28, Issue 12, 2012, Pages

  Cai, Xiao ^a   Wang, Hua ^a   Huang, Heng ^a   Ding, Chris ^a  

^a The University of Texas at Arlington   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DROSOPHILA MELANOGASTER;

ALGORITHM; ANIMAL; ARTICLE; ARTIFICIAL INTELLIGENCE; BIOLOGY; DROSOPHILA MELANOGASTER; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GENOME; HISTOLOGY; IMAGE PROCESSING; METHODOLOGY; THEORETICAL MODEL;

ALGORITHMS; ANIMALS; ARTIFICIAL INTELLIGENCE; COMPUTATIONAL BIOLOGY; DROSOPHILA MELANOGASTER; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENOME, INSECT; IMAGE PROCESSING, COMPUTER-ASSISTED; MODELS, THEORETICAL;

EID: 84863533180     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts220     Document Type: Article

References (29)

1. Brin, S. and Page, L. (1998) The anatomy of a large-scale hypertextual web search engine. In International Conference on World Wide Web (WWW), Elsevier Science Publishers, 107-117.
2. Chang, C. and Lin, C. (2011) LIBSVM: a library for support vector machines. ACM Transactions on Intelligent Systems and Technology, 2, 1-27.
3. Fowlkes, C. et al. (2008) A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell, 133, 364-374.
4. Grumbling, G. et al. (2006) FlyBase: anatomical data, images and queries. Nucleic Acids Res., 34, D484-D488.
5. Hendriks, C. L. et al. (2006) Three dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline. Genome Biol., 7, R123
6. Ji, S. et al. (2008) Extracting shared subspace for multi-label classification. In ACM SIGKDD International Conference on Knowledge Discovery and Data Mining 2009, 381-389.
7. Ji, S. et al. (2009) Drosophila gene expression pattern annotation using sparse features and term-term interactions. In ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 407-416.
8. Ji, S. et al. (2010) A shared-subspace learning framework for multi-label classification. ACM Transactions on Knowledge Discovery from Data (TKDD), 4, 1-29.
9. Kang, F. et al. (2006) Correlated label propagation with application to multi-label learning. In IEEE International Conference on Computer Vision and Pattern Recognition (CVPR), 1719-1726.
10. Kumar, S. et al. (2002) BEST: A novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development. Genetics, 162, 2037-2047.
11. L'ecuyer, E. et al. (2007) Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell, 131, 174-187.
12. Li, Y. et al. (2009) Drosophila gene expression pattern annotation through multi-instance multi-label learning. In Proceedings of the 21st International Joint Conference on Artificial Intelligence, AAAI press, 1445-1450.
13. Lowe, D. (2004) Distinctive image features from scale-invariant keypoints. Int. J. Comput. Vis., 60, 91-110.
14. Lyne, R. et al. (2007) FlyMine: an integrated database for Drosophila and anopheles genomics. Genome Biol., 8, R129.
15. Megason, S. and Fraser, S. (2007) Imaging in systems biology. Cell, 130, 784-795.
16. Peng, H. and Myers, E.W. (2004) Comparing in situ mRNA expression patterns of drosophila embryos. In International Conference on Research in Computational Molecular Biology (RECOMB), ACM, 157-166.
17. Peng, H. et al. (2007) Automatic image analysis for gene expression patterns of fly embryos. BMC Cell Biol., 8(Suppl. 1), S7.
18. Puniyani, K. et al. (2010) SPEX2: Automated Concise Extraction of Spatial Gene Expression Patterns from Fly Embryo ISH Images. Intell. Sys. Mol. Biol., 26, i47-i56.
19. Shuiwang, J. et al. (2009) A bag-of-words approach for Drosophila gene expression pattern annotation. BMC Bioinformatics, 10, 119.
20. Tomancak, P. et al. (2002) Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol., 3, 88.
21. Tomancak, P. et al. (2007) Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol., 8, R145.
22. Tong, H. et al. (2006) Fast random walk with restart and its applications. In IEEE International Conference on Data Mining (ICDM), 613-622.
23. Tsoumakas, G. and Vlahavas, I.P. (2007) Random k-labelsets: An ensemble method for multilabel classification. In European conference on Machine Learning, Springer-Verlag, 406-417.
24. Wang, H. et al. (2009) Image annotation using multi-label correlated Green's function. In IEEE International Conference on Computer Vision, 2029-2034.
25. Weigmann, K. et al. (2003) FlyMove - a new way to look at development of Drosophila. Trends Genet. 19, 310-311.
26. Zelnik-Manor, L. and Perona, P. (2004) Self-tuning spectral clustering. Advances in neural information processing systems, 17, 16.
27. Zha, Z. et al. (2008) Graph-based semi-supervised learning with multi-label. In IEEE International Conference on Multimedia and Expo (ICME), 1321-1324.
28. Zhou, D. and Schölkopf, B. (2004) Learning from labeled and unlabeled data using random walks. In Annual Symposium of the German Association for Pattern Recognition (DAGM), Springer, 237-244.
29. Zhu, X. et al. (2003) Semi-supervised learning using gaussian fields and harmonic functions. In International Conference on Machine Learning (ICML), ACM press, 912-919.