Gene regulatory networks inference using a multi-GPU exhaustive search algorithm

BMC Bioinformatics

Volumn 14, Issue , 2013, Pages

  Borelli, Fabrizio F ^a   de Camargo, Raphael Y ^a   Martins, David C ^a   Rozante, Luiz C S ^a  

^a UNIVERSIDADE FEDERAL DO ABC   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEX NETWORKS; COST BENEFIT ANALYSIS; FEATURE EXTRACTION; GENE EXPRESSION; GENES; GRAPHICS PROCESSING UNIT; LEARNING ALGORITHMS; PARALLEL PROGRAMMING; PROBLEM SOLVING; PROGRAM PROCESSORS;

COMBINATORIAL PROBLEM; CRITERION FUNCTIONS; EXHAUSTIVE SEARCH ALGORITHMS; FEATURE SELECTION METHODS; GENE EXPRESSION DATA; GENE REGULATORY NETWORKS; PROOF OF PRINCIPLES; SELECTION TECHNIQUES;

INFERENCE ENGINES;

COST BENEFIT ANALYSIS; GENE REGULATORY NETWORK; ALGORITHM; ARTICLE; BIOLOGY; METHODOLOGY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; GENE REGULATORY NETWORKS;

EID: 84899674471     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-S18-S5     Document Type: Article

References (34)

1. Maniatis T, Reed R: An extensive network of coupling among gene expression machines. Nature 2002, 416:499-560
2. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P: Molecular biology of the cell. 4 edition. New York: Taylor & Francis Books, Inc.; 2002
3. DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM: Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet 1996, 14(4):457-460
4. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW: Serial analysis of gene expression. Science 1995, 270:484-487
5. Wang Z, Gerstein M, Snyder M: RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10:57-63
6. Friedman N, Linial M, Nachman I, Pe'er D: Using Bayesian networks to analyze expression data. Journal of Computational Biology 2000, 7:601-620
7. Chen M, Ning K: BNArray: an R package for constructing gene regulatory networks from microarray data by using Bayesian network. Bioinformatics Application Notes 2006, 22:2952-2954
8. Butte AJ, Kohane IS: Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Symp Biocomput 2000, 418-429
9. Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A: ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 2006, 7(Suppl 1):S7
10. Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS: Large-scale mapping and validation of escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol 2007, 5:e8
11. Barrera J, Cesar-Jr RM, Martins-Jr DC, Vencio RZN, Merino EF, Yamamoto MM, Leonardi FG, Pereira CAB, del Portillo HA: Constructing probabilistic genetic networks of Plasmodium falciparum from dynamical expression signals of the intraerythrocytic development cycle. Methods of Microarray Data Analysis V Springer; 2007, 11-26
12. Lopes FM, Martins DC Jr, Cesar RM Jr: Feature selection environment for genomic applications. BMC Bioinformatics 2008, 9:451
13. Lopes FM, Martins-Jr DC, Cesar-Jr RM: Comparative study of GRN's inference methods based on feature selection by mutual information. IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) Minneapolis, MN, USA; 2009
14. D'haeseleer P, Liang S, Somogyi R: Genetic Network Inference: From Co-Expression Clustering to Reverse Engineering. Bioinformatics 2000, 16:707-726
15. de Jong H: Modeling and Simulation of Genetic Regulatory Systems: A Literature Review. Journal of Computational Biology 2002, 9:67-103
16. Styczynski MP, Stephanopoulos G: Overview of computational methods for the inference of gene regulatory networks. Computers & Chemical Engineering 2005, 29(3):519-534
17. Schlitt T, Brazma A: Current approaches to gene regulatory network modelling. BMC Bioinformatics 2007, 8:S9
18. Karlebach G, Shamir R: Modelling and analysis of gene regulatory networks. Nat Rev Mol Cell Biol 2008, 9(10):770-780
19. Hecker M, Lambeck S, Susanne Toepfer EvS, Guthke R: Gene regulatory network inference: Data integration in dynamic models-A review. Biosystems 2009, 96:86-103
20. Owens JD, Houston M, Luebke D, Green S, Stone JE, Phillips JC: GPU computing. Proceedings of the IEEE 2008, 96(5):879-899
21. Che S, Boyer M, Meng J, Tarjan D, Sheaffer JW, Skadron K: A performance study of general-purpose applications on graphics processors using CUDA. Journal of Parallel Distributed Computing 2008, 68(10):1370-1380
22. Shi H, Schmidt B, Liu W, Muller-Wittig W: Parallel mutual information estimation for inferring gene regulatory networks on GPUs. BMC Research Notes 2011, 4:189
23. Borelli FF, Camargo RY, Martins-Jr DC, Stransky B, Rozante LCS: Accelerating Gene Regulatory Networks Inference through GPU/CUDA Programming. 2nd IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) Las Vegas, NV; 2012
24. Pluim JPW, Maints JBA, Viergever MA: Mutual-information-based registration of medical images: a survey. IEEE Transactions on Medical Imaging 2003, 22:986-1004
25. Martins-Jr DC, Cesar-Jr RM, Barrera J: W-operator window design by minimization of mean conditional entropy. Pattern Analysis & Applications 2006, 9:139-153
26. Fraser AM, Swinney HL: Independent coordinates for strange attractors from mutual information. Phys Rev A 1986, 33:1134-1140
27. Zhou X, Wang X, Dougherty ER, Russ D, Suh E: Gene Clustering Based on Clusterwide Mutual Information. Journal of Computational Biology 2004, 11:147-161
28. Zhou X, Wang X, Dougherty ER: Nonlinear-Probit Gene Classification Using Mutual-Information and Wavelet Based Feature Selection. Biological Systems 2004, 12(3):371-386
29. Martins-Jr DC, Braga-Neto U, Hashimoto RF, Dougherty ER, Bittner ML: Intrinsically Multivariate Predictive Genes. IEEE Journal of Selected Topics in Signal Processing 2008, 2(3):424-439
30. Shannon CE, Weaver W: The mathematical theory of communication Univ. of Illinois Press; 1963
31. Nvidia1: NVIDIA CUDA C Programming Guide 2010 [http://www.nvidia.com/]
32. Kauffman SA: The Origins of Order New York: Oxford University Press; 1993
33. Lopes FM, Cesar-Jr RM, Costa LF: Gene expression complex networks: synthesis, identification and analysis. Journal of Computational Biology 2011, 18:1353-1367
34. Bozdech Z, Llinás M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. Plos Biol 2003, 1:E5