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The case for cloud computing in genome informatics
Lincoln D Stein
Genome Biol. 2010; 11(5): 207. Published online 2010 May 5. doi: 10.1186/gb-2010-11-5-207
PMCID:
PMC2898083
Abstract Full Text PDF–648K

Is Cited by the Following 23 Articles in this Archive:

Efficient de novo assembly of large genomes using compressed data structures
Jared T. Simpson, Richard Durbin
Genome Res. 2012 March; 22(3): 549–556. doi: 10.1101/gr.126953.111
PMCID:
PMC3290790
Abstract Full Text PDF–256K
Opportunities and Challenges for the Life Sciences Community
Eugene Kolker, Elizabeth Stewart, Vural Ozdemir
OMICS. 2012 March; 16(3): 138–147. doi: 10.1089/omi.2011.0152
PMCID:
PMC3300061
Free in PMC on 2013/03/01
Transcriptome-Based Differentiation of Closely-Related Miscanthus Lines
Philippe Chouvarine, Amanda M. Cooksey, Fiona M. McCarthy, David A. Ray, Brian S. Baldwin, Shane C. Burgess, Daniel G. Peterson
PLoS One. 2012; 7(1): e29850. Published online 2012 January 10. doi: 10.1371/journal.pone.0029850
PMCID:
PMC3254643
Abstract Full Text PDF–374K
ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets
Alyssa C Frazee, Ben Langmead, Jeffrey T Leek
BMC Bioinformatics. 2011; 12: 449. Published online 2011 November 16. doi: 10.1186/1471-2105-12-449
PMCID:
PMC3229291
Abstract Full Text PDF–298K
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
Pybedtools: a flexible Python library for manipulating genomic datasets and annotations
Ryan K. Dale, Brent S. Pedersen, Aaron R. Quinlan
Bioinformatics. 2011 December 15; 27(24): 3423–3424. Published online 2011 September 23. doi: 10.1093/bioinformatics/btr539
PMCID:
PMC3232365
Abstract Full Text PDF–70K 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
The real cost of sequencing: higher than you think!
Andrea Sboner, Xinmeng Jasmine Mu, Dov Greenbaum, Raymond K Auerbach, Mark B Gerstein
Genome Biol. 2011; 12(8): 125. Published online 2011 August 25. doi: 10.1186/gb-2011-12-8-125
PMCID:
PMC3245608
Free in PMC on 2012/08/25
Cistrome: an integrative platform for transcriptional regulation studies
Tao Liu, Jorge A Ortiz, Len Taing, Clifford A Meyer, Bernett Lee, Yong Zhang, Hyunjin Shin, Swee S Wong, Jian Ma, Ying Lei, Utz J Pape, Michael Poidinger, Yiwen Chen, Kevin Yeung, Myles Brown, Yaron Turpaz, X Shirley Liu
Genome Biol. 2011; 12(8): R83. Published online 2011 August 22. doi: 10.1186/gb-2011-12-8-r83
PMCID:
PMC3245621
Abstract Full Text PDF–2.1M Supplementary Material
Menu-driven cloud computing and resource sharing for R and Bioconductor
Hamid Bolouri, Rajiv Dulepet, Michael Angerman
Bioinformatics. 2011 August 15; 27(16): 2309–2310. Published online 2011 June 17. doi: 10.1093/bioinformatics/btr364
PMCID:
PMC3150038
Free in PMC on 2012/08/15
Targeted Assembly of Short Sequence Reads
René L. Warren, Robert A. Holt
PLoS One. 2011; 6(5): e19816. Published online 2011 May 11. doi: 10.1371/journal.pone.0019816
PMCID:
PMC3092772
Abstract Full Text PDF–237K
PeakRanger: A cloud-enabled peak caller for ChIP-seq data
Xin Feng, Robert Grossman, Lincoln Stein
BMC Bioinformatics. 2011; 12: 139. Published online 2011 May 9. doi: 10.1186/1471-2105-12-139
PMCID:
PMC3103446
Abstract Full Text PDF–1.4M Supplementary Material
Efficient storage of high throughput DNA sequencing data using reference-based compression
Markus Hsi-Yang Fritz, Rasko Leinonen, Guy Cochrane, Ewan Birney
Genome Res. 2011 May; 21(5): 734–740. doi: 10.1101/gr.114819.110
PMCID:
PMC3083090
Abstract Full Text PDF–645K
KBWS: an EMBOSS associated package for accessing bioinformatics web services
Kazuki Oshita, Kazuharu Arakawa, Masaru Tomita
Source Code Biol Med. 2011; 6: 8. Published online 2011 April 29. doi: 10.1186/1751-0473-6-8
PMCID:
PMC3101651
Abstract Full Text PDF–240K
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
Genome Medicine: past, present and future
Charles Auffray, Timothy Caulfield, Muin J Khoury, James R Lupski, Matthias Schwab, Timothy Veenstra
Genome Med. 2011; 3(1): 6. Published online 2011 January 31. doi: 10.1186/gm220
PMCID:
PMC3092091
Full Text PDF–259K
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
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
SUPERFAMILY 1.75 including a domain-centric gene ontology method
David A. de Lima Morais, Hai Fang, Owen J. L. Rackham, Derek Wilson, Ralph Pethica, Cyrus Chothia, Julian Gough
Nucleic Acids Res. 2011 January; 39(Database issue): D427–D434. Published online 2010 November 8. doi: 10.1093/nar/gkq1130
PMCID:
PMC3013712
Abstract Full Text PDF–3.7M
The UCSC Genome Browser database: update 2011
Pauline A. Fujita, Brooke Rhead, Ann S. Zweig, Angie S. Hinrichs, Donna Karolchik, Melissa S. Cline, Mary Goldman, Galt P. Barber, Hiram Clawson, Antonio Coelho, Mark Diekhans, Timothy R. Dreszer, Belinda M. Giardine, Rachel A. Harte, Jennifer Hillman-Jackson, Fan Hsu, Vanessa Kirkup, Robert M. Kuhn, Katrina Learned, Chin H. Li, Laurence R. Meyer, Andy Pohl, Brian J. Raney, Kate R. Rosenbloom, Kayla E. Smith, David Haussler, W. James Kent
Nucleic Acids Res. 2011 January; 39(Database issue): D876–D882. Published online 2010 October 18. doi: 10.1093/nar/gkq963
PMCID:
PMC3242726
Abstract Full Text PDF–1.9M
Predictive, preventive, personalized and participatory medicine: back to the future
Charles Auffray, Dominique Charron, Leroy Hood
Genome Med. 2010; 2(8): 57. Published online 2010 August 26. doi: 10.1186/gm178
PMCID:
PMC2945014
Abstract Full Text PDF–234K
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
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
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