Parallelized preprocessing algorithms for high-density oligonucleotide arrays

IPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM

Volumn , Issue , 2008, Pages

  Schmidberger, Markus ^a   Mansmann, Ulrich ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOASSAY; COMMUNICATION; COMPUTER NETWORKS; DATA STORAGE EQUIPMENT; DISTRIBUTED PARAMETER NETWORKS; GENE EXPRESSION; LINGUISTICS; MESSAGE PASSING; MICROARRAYS; OLIGONUCLEOTIDES; PARALLEL PROCESSING SYSTEMS;

HIGH-DENSITY; PARALLEL AND DISTRIBUTED PROCESSING; PARALLELIZATION;

PARALLEL ALGORITHMS;

EID: 51049117012     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IPDPS.2008.4536175     Document Type: Conference Paper

References (16)

1. B. M. Bolstad. Low-level Analysis of High-density Oligonucleotide Array Data: Background, Normalization and Summarization. PhD thesis, University of California, Berkeley, 2004.
2. L. Dagum and R. Menon. Openmp: an industry standard api for shared-memory programming. IEEE Computational Science and Engineering, 5(1):46-55, Jan.-March 1998.
3. E. Gabriel, G. E. Fagg, G. Bosilca, T. Angskun, J. J. Dongarra, J. M. Squyres, V. Sahay, P. Kambadur, B. Barrett, A. Lumsdaine, R. H. Castain, D. J. Daniel, R. L. Graham, and T. S. Woodall. Open MPI: Goals, concept, and design of a next generation MPI implementation. In Proceedings, 11th European PVM/MPI Users' Group Meeting, pages 97-104, Budapest, Hungary, September 2004.
4. R. Gentleman, V. J. Carey, W. Huber, R. Irizarry, and S. Dudoit. Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Statistics for Biology and Health. Springer, 2005.
5. R. C. Gentleman, V. J. Carey, D. M. Bates, B. Bolstad, M. Dettling, S. Dudoit, B. Ellis, L. Gautier, Y. Ge, J. Gentry, K. Hornik, T. Hothorn, W. Huber, S. Iacus, R. Irizarry, F. Leisch, C. Li, M. Maechler, A. J. Rossini, G. Sawitzki, C. Smith, G. Smyth, L. Tierney, J. Y. H. Yang, and J. Zhang. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biology, 5:R80, 2004.
6. S. Hochreiter, D.-A. Clevert, and K. Obermayer. A new summarization method for affymetrix probe level data. Bioinformatics, 22(8):943-949, Apr 2006.
7. W. Huber, A. von Heydebreck, H. Sltmann, A. Poustka, and M. Vingron. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics, 18 Suppl 1:S96-104, 2002.
8. R. Irizarry, L. Gautier, and L. Cope. An r package for analyses of affymetrix oligonucleotide arrays. In G. Parmigiani, E. Garrett, R. Irizarry, and S. Zeger, editors, The Analysis of Gene Expression Data: Methods and Software. Springer, New York, 2002.
9. R. A. Irizarry, B. Hobbs, F. Collin, Y. D. Beazer-Barclay, K. J. Antonellis, U. Scherf, and T. P. Speed. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4(2):249-264, Apr 2003.
10. U. E. B. A. Lukk M, Nikkila J. Application of text mining to create human gene expression atlas from public data. (Submitted), 2007.
11. H. Parkinson, M. Kapushesky, M. Shojatalab, N. Abeygunawardena, R. Coulson, A. Farne, E. Holloway, N. Kolesnykov, P. Lilja, M. Lukk, R. Mani, T. Rayner, A. Sharma, E. William, U. Sarkans, and A. Brazma. Arrayexpress-a public database of microarray experiments and gene expression profiles. Nucleic Acids Res, 35(Database issue):D747-D750, Jan 2007.
12. A. Rossini. Simple parallel statistical computing in r. UW Biostatistics Working Paper Series, 193, 2003.
13. H. Sevcikova. Statistical simulations on parallel computers. Journal of Computational and Graphical Statistics, 13(4):886-906, 2003.
14. J. M. Squyres and A. Lumsdaine. A component architecture for lam/mpi. In Proceedings, 10th European PVM/MPI Users' Group Meeting, number 2840 in Lecture Notes in Computer Science, pages 379-387, Venice, Italy, September / October 2003. Springer-Verlag.
15. R. D. C. Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria, 2007. ISBN 3-900051-07-0.
16. H. Yu. The Rmpi Package. Department of Statistical and Actuarial Sciences; University of Western Ontario, London, Ontario N6A 5B7, 04 2004.