A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series

Algorithms for Molecular Biology

Volumn 4, Issue 1, 2009, Pages

  Madeira, Sara C ^a,b,c   Oliveira, Arlindo L ^a,b  

^a INESC ID   (Portugal)

^b INSTITUTO SUPERIOR TÉCNICO   (Portugal)

^c UNIVERSITY OF BEIRA INTERIOR   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

SACCHAROMYCES CEREVISIAE;

EID: 67651018681     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-4-8     Document Type: Article

References (32)

1. Bar-Joseph Z Analyzing time series gene expression data Bioinformatics 2004, 20(16)2493-2503. 15130923
2. Androulakis IP Yang E Almon RR Analysis of Time-Series Gene Expression Data: Methods, Challenges and Opportunities Annual Review of Biomedical Engineering 2007, 9:205-228. 17341157
3. McLachlan GJ Do K Ambroise C Analysing microarray gene expression data Wiley Series in Probability and Statistics 2004
4. Cheng Y Church GM Biclustering of Expression Data In Proc of the 8th International Conference on Intelligent Systems for Molecular Biology 2000:93-103.
5. Mechelen IV Bock HH Boeck PD Two-mode clustering methods: A structured overview Stat Methods Med Res. 2004, 13(5):363-394. 15516031
6. Madeira SC Oliveira AL Biclustering algorithms for biological data analysis: A survey IEEE/ACM Trans Comput Biol Bioinform 2004, 1(1):24-45. 17048406
7. Tanay A Sharan R Shamir R Discovering statistically significant biclusters in gene expression data Bioinformatics. 2002, 18(Suppl 1):S136-S144. 12169541
8. Ben-Dor A Chor B Karp R Yakhini Z Discovering Local Structure in Gene Expression Data: The Order-Preserving Submatrix Problem J Comput Biol 2002, 10(3-4):373-384.
9. Madeira SC Teixeira MC Sá-Correia I Oliveira AL Identification of Regulatory Modules in Time Series Gene Expression Data using a Linear Time Biclustering Algorithm IEEE/ACM Transactions on Computational Biology and Bioinformatics, 21 Mar. 2008 IEEE Computer Society Digital Library. IEEE Computer Society 10.1109/TCBB.2008.34
10. Peeters R The maximum edge biclique problem is NP-complete Discrete Applied Mathematics 2003, 131(3):651-654.
11. Yang E Foteinou PT King K Yarmush ML Androulakis I A novel non-overlapping bi-clustering algorithm for network generation using living cell array data Bioinformatics 2007, 23(17):2306-2313. 17827207
12. Murali TM Kasif S Extracting conserved gene expression motifs from gene expression data Pac Symp Biocomput 2003:77-88. 12603019
13. Koyuturk M Szpankowski W Grama A Biclustering Gene-Feature Matrices for Statistically Significant Dense Patterns In Proc of the 8th International Conference on Research in Computational Molecular Biology 2004:480-484.
14. Liu J Wang W Yang J Biclustering in gene expression data by tendency In Proc of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference 2004:182-193.
15. Liu J Wang W Yang J A framework for ontology-driven subspace clustering In Proc of the 10th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining 2004:623-628.
16. Liu J Wang W Yang J Gene ontology friendly biclustering of expression profiles In Proc of the 3rd IEEE Computational Systems Bioinformatics Conference 2004:436-447.
17. Liu J Wang W Yang J Mining Sequential Patterns from Large Data Sets Kluwer 2005:18.
18. Lonardi S Szpankowski W Yang Q Finding Biclusters by Random Projections In Proc of the 15th Annual Symposium on Combinatorial Pattern Matching 2004:102-116.
19. Sheng Q Moreau Y Moor BD Biclustering microarray data by Gibbs sampling Bioinformatics 2003, 19(Suppl 2):iI196-ii205. 14534190
20. Ji L Tan K Identifying time-lagged gene clusters using gene expression data Bioinformatics 2005, 21(4):509-516. 15374868
21. Wu C Fu Y Murali TM Kasif S Gene expression module discovery using Gibbs sampling Genome Informatics 2004, 15:239-248. 15712126
22. Madeira SC Oliveira AL A Linear Time Biclustering Algorithm for Time Series Gene Expression Data Proc of the 5th Workshop on Algorithms in Bioinformatics Springer Verlag, LNCS/LNBI 3692 2005:39-52.
23. Prelic A Bleuler S Zimmermann P Wille A Buhlmann P Gruissem W Hennig L Thiele L Zitzler E A systematic comparison and evaluation of biclustering methods for gene expression data Bioinformatics 2006, 22(10):1282-1283. 16551664
24. Zhang Y Zha H Chu CH A Time-Series Biclustering Algorithm for Revealing Co-Regulated Genes In Proc of the 5th IEEE International Conference on Information Technology: Coding and Computing 2005:32-37.
25. Gusfield D Algorithms on strings, trees, and sequences Computer Science and Computational Biology Series, Cambridge University Press 1997
26. Sagot MF Spelling approximate repeated or common motifs using a suffix tree Proc of Latin'98 Springer Verlag, LNCS 1380 1998:111-127.
27. Madeira SC Efficient Biclustering Algorithms for Time Series Gene Expression Data Analysis PhD thesis Instituto Superior Técnico, Technical University of Lisbon 2008
28. Martin D Brun C Remy E Mouren P Thieffry D Jacq B GOToolBox: Functional investigation of gene datasets based on Gene Ontology Genome Biology 2004, 5(12)R101. http://burgundy.cmmt.ubc.ca/GOToolBox/ 545796 15575967
29. Teixeira MC Monteiro P Jain P Tenreiro S Fernandes AR Mira NP Alenquer M Freitas AT Oliveira AL Sa-Correia I The YEASTRACT database: A tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae Nucleic Acids Research 2006, 34:D446-D451. http://www.yeastract.com/ 1347376 16381908
30. Gasch AP Spellman PT Kao CM Carmel-Harel O Eisen MB Storz G Botstein D Brown PO Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes Molecular Biology of the Cell 2000, 11:4241-4257. 15070 11102521
31. Ji L Tan K Mining gene expression data for positive and negative co-regulated gene clusters Bioinformatics 2004, 20(16):2711-2718. 15145808
32. Madeira SC Oliveira AL An Efficient Biclustering Algorithm for finding Genes with Similar Patterns in Time-Series Expression Data Proc of the 5th Asia Pacific Bioinformatics Conference, Series in Advances in Bioinformatics and Computational Biology Imperial College Press 2007, 5:67-80.