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Searching for SNPs with cloud computing
Ben Langmead, Michael C Schatz, Jimmy Lin, Mihai Pop, Steven L Salzberg
Genome Biol. 2009; 10(11): R134. Published online 2009 November 20. doi: 10.1186/gb-2009-10-11-r134
PMCID:
PMC3091327
Abstract Full Text PDF–598K Supplementary Material
 Is Cited by the Following 21 Articles in this Archive:
Resources and Costs for Microbial Sequence Analysis Evaluated Using Virtual Machines and Cloud Computing
Samuel V. Angiuoli, James R. White, Malcolm Matalka, Owen White, W. Florian Fricke
PLoS One. 2011; 6(10): e26624. Published online 2011 October 19. doi: 10.1371/journal.pone.0026624
PMCID:
PMC3197577
Abstract Full Text PDF–556K Supplementary Material
CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing
Samuel V Angiuoli, Malcolm Matalka, Aaron Gussman, Kevin Galens, Mahesh Vangala, David R Riley, Cesar Arze, James R White, Owen White, W Florian Fricke
BMC Bioinformatics. 2011; 12: 356. Published online 2011 August 30. doi: 10.1186/1471-2105-12-356
PMCID:
PMC3228541
Abstract Full Text PDF–2.3M Supplementary Material
Biomedical Cloud Computing With Amazon Web Services
Vincent A. Fusaro, Prasad Patil, Erik Gafni, Dennis P. Wall, Peter J. Tonellato
PLoS Comput Biol. 2011 August; 7(8): e1002147. Published online 2011 August 25. doi: 10.1371/journal.pcbi.1002147
PMCID:
PMC3161908
Full Text PDF–283K
Applications of the pipeline environment for visual informatics and genomics computations
Ivo D Dinov, Federica Torri, Fabio Macciardi, Petros Petrosyan, Zhizhong Liu, Alen Zamanyan, Paul Eggert, Jonathan Pierce, Alex Genco, James A Knowles, Andrew P Clark, John D Van Horn, Joseph Ames, Carl Kesselman, Arthur W Toga
BMC Bioinformatics. 2011; 12: 304. Published online 2011 July 26. doi: 10.1186/1471-2105-12-304
PMCID:
PMC3199760
Abstract Full Text PDF–6.9M
CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping
Tung Nguyen, Weisong Shi, Douglas Ruden
BMC Res Notes. 2011; 4: 171. Published online 2011 June 6. doi: 10.1186/1756-0500-4-171
PMCID:
PMC3127959
Abstract Full Text PDF–393K Supplementary Material
A framework for variation discovery and genotyping using next-generation DNA sequencing data
M.A. DePristo, E. Banks, R.E. Poplin, K.V. Garimella, J.R. Maguire, C. Hartl, A.A. Philippakis, G. del Angel, M.A Rivas, M. Hanna, A. McKenna, T.J. Fennell, A.M. Kernytsky, A.Y. Sivachenko, K. Cibulskis, S.B. Gabriel, D. Altshuler, M.J. Daly
Nat Genet. Author manuscript; available in PMC 2011 November 1.
Published in final edited form as: Nat Genet. 2011 May; 43(5): 491–498. Published online 2011 April 10. doi: 10.1038/ng.806
PMCID:
PMC3083463
Abstract Full Text PDF–1.9M Supplementary Material
The impact of next-generation sequencing on genomics
Jun Zhang, Rod Chiodini, Ahmed Badr, Genfa Zhang
J Genet Genomics. Author manuscript; available in PMC 2011 April 13.
Published in final edited form as: J Genet Genomics. 2011 March 20; 38(3): 95–109. Published online 2011 March 15. doi: 10.1016/j.jgg.2011.02.003
PMCID:
PMC3076108
Abstract Full Text PDF–132K
SOLiDzipper: A High Speed Encoding Method for the Next-Generation Sequencing Data
Young Jun Jeon, Sang Hyun Park, Sung Min Ahn, Hee Joung Hwang
Evol Bioinform Online. 2011; 7: 1–6. Published online 2011 March 10. doi: 10.4137/EBO.S6618
PMCID:
PMC3072624
Abstract Full Text PDF–582K
Next-Generation Sequencing of Coccidioides immitis Isolated during Cluster Investigation
David M. Engelthaler, Tom Chiller, James A. Schupp, Joshua Colvin, Stephen M. Beckstrom-Sternberg, Elizabeth M. Driebe, Tracy Moses, Waibhav Tembe, Shripad Sinari, James S. Beckstrom-Sternberg, Alexis Christoforides, John V. Pearson, John Carpten, Paul Keim, Ashley Peterson, Dawn Terashita, S. Arunmozhi Balajee
Emerg Infect Dis. 2011 February; 17(2): 227–232. doi: 10.3201/eid1702.100620
PMCID:
PMC3204756
Abstract Full Text PDF–704K
An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics
Ronald C Taylor
BMC Bioinformatics. 2010; 11(Suppl 12): S1. Published online 2010 December 21. doi: 10.1186/1471-2105-11-S12-S1
PMCID:
PMC3040523
Abstract Full Text PDF–191K
SeqWare Query Engine: storing and searching sequence data in the cloud
Brian D O’Connor, Barry Merriman, Stanley F Nelson
BMC Bioinformatics. 2010; 11(Suppl 12): S2. Published online 2010 December 21. doi: 10.1186/1471-2105-11-S12-S2
PMCID:
PMC3040528
Abstract Full Text PDF–469K
Galaxy CloudMan: delivering cloud compute clusters
Enis Afgan, Dannon Baker, Nate Coraor, Brad Chapman, Anton Nekrutenko, James Taylor
BMC Bioinformatics. 2010; 11(Suppl 12): S4. Published online 2010 December 21. doi: 10.1186/1471-2105-11-S12-S4
PMCID:
PMC3040530
Abstract Full Text PDF–545K
Current Trends and New Challenges of Databases and Web Applications for Systems Driven Biological Research
Pradeep Kumar Sreenivasaiah, Do Han Kim
Front Physiol. 2010; 1: 147. Prepublished online 2010 September 28. Published online 2010 December 3. doi: 10.3389/fphys.2010.00147
PMCID:
PMC3059952
Abstract Full Text PDF–468K
Challenges of sequencing human genomes
Daniel C. Koboldt, Li Ding, Elaine R. Mardis, Richard K. Wilson
Brief Bioinform. 2010 September; 11(5): 484–498. Published online 2010 September 20. doi: 10.1093/bib/bbq016
PMCID:
PMC2980933
Abstract Full Text PDF–822K
Computational solutions to large-scale data management and analysis
Eric E. Schadt, Michael D. Linderman, Jon Sorenson, Lawrence Lee, Garry P. Nolan
Nat Rev Genet. Author manuscript; available in PMC 2011 June 28.
Published in final edited form as: Nat Rev Genet. 2010 September; 11(9): 647–657. doi: 10.1038/nrg2857
PMCID:
PMC3124937
Abstract Full Text PDF–206K
Cloud-scale RNA-sequencing differential expression analysis with Myrna
Ben Langmead, Kasper D Hansen, Jeffrey T Leek
Genome Biol. 2010; 11(8): R83. Published online 2010 August 11. doi: 10.1186/gb-2010-11-8-r83
PMCID:
PMC2945785
Abstract Full Text PDF–1.2M
The application of massively parallel sequencing technologies in diagnostics
Andreas Dahl, Florian Mertes, Bernd Timmermann, Hans Lehrach
F1000 Biol Rep. 2010; 2: 59. Published online 2010 August 9. doi: 10.3410/B2-59
PMCID:
PMC2990631
Abstract Full Text PDF–113K
Cloud Computing and the DNA Data Race
Michael C. Schatz, Ben Langmead, Steven L. Salzberg
Nat Biotechnol. Author manuscript; available in PMC 2011 January 1.
Published in final edited form as: Nat Biotechnol. 2010 July; 28(7): 691–693. doi: 10.1038/nbt0710-691
PMCID:
PMC2904649
Full Text PDF–187K
A Quick Guide to Large-Scale Genomic Data Mining
Curtis Huttenhower, Oliver Hofmann
PLoS Comput Biol. 2010 May; 6(5): e1000779. Published online 2010 May 27. doi: 10.1371/journal.pcbi.1000779
PMCID:
PMC2877728
Full Text PDF–882K Supplementary Material
Cloud computing for comparative genomics
Dennis P Wall, Parul Kudtarkar, Vincent A Fusaro, Rimma Pivovarov, Prasad Patil, Peter J Tonellato
BMC Bioinformatics. 2010; 11: 259. Published online 2010 May 18. doi: 10.1186/1471-2105-11-259
PMCID:
PMC3098063
Abstract Full Text PDF–657K Supplementary Material
A survey of sequence alignment algorithms for next-generation sequencing
Heng Li, Nils Homer
Brief Bioinform. 2010 September; 11(5): 473–483. Published online 2010 May 11. doi: 10.1093/bib/bbq015
PMCID:
PMC2943993
Abstract Full Text PDF–334K
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