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Results: 1 to 20 of 227

1.

Resources and costs for microbial sequence analysis evaluated using virtual machines and cloud computing.

Angiuoli SV, White JR, Matalka M, White O, Fricke WF.

PLoS One. 2011;6(10):e26624. doi: 10.1371/journal.pone.0026624. Epub 2011 Oct 19.

PMID:
22028928
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing.

Angiuoli SV, Matalka M, Gussman A, Galens K, Vangala M, Riley DR, Arze C, White JR, White O, Fricke WF.

BMC Bioinformatics. 2011 Aug 30;12:356. doi: 10.1186/1471-2105-12-356.

PMID:
21878105
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Rainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computing.

Zhao S, Prenger K, Smith L, Messina T, Fan H, Jaeger E, Stephens S.

BMC Genomics. 2013 Jun 27;14:425. doi: 10.1186/1471-2164-14-425.

PMID:
23802613
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community.

Krampis K, Booth T, Chapman B, Tiwari B, Bicak M, Field D, Nelson KE.

BMC Bioinformatics. 2012 Mar 19;13:42. doi: 10.1186/1471-2105-13-42.

PMID:
22429538
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Tavaxy: integrating Taverna and Galaxy workflows with cloud computing support.

Abouelhoda M, Issa SA, Ghanem M.

BMC Bioinformatics. 2012 May 4;13:77. doi: 10.1186/1471-2105-13-77.

PMID:
22559942
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

[A review on the bioinformatics pipelines for metagenomic research].

Ye DD, Fan MM, Guan Q, Chen HJ, Ma ZS.

Dongwuxue Yanjiu. 2012 Dec;33(6):574-85. doi: 10.3724/SP.J.1141.2012.06574. Review. Chinese.

PMID:
23266976
[PubMed - indexed for MEDLINE]
Free Article
7.

Phoenix 2: a locally installable large-scale 16S rRNA gene sequence analysis pipeline with Web interface.

Soh J, Dong X, Caffrey SM, Voordouw G, Sensen CW.

J Biotechnol. 2013 Sep 20;167(4):393-403. doi: 10.1016/j.jbiotec.2013.07.004. Epub 2013 Jul 16.

PMID:
23871656
[PubMed - indexed for MEDLINE]
Free Article
8.

Virtual metagenome reconstruction from 16S rRNA gene sequences.

Okuda S, Tsuchiya Y, Kiriyama C, Itoh M, Morisaki H.

Nat Commun. 2012;3:1203. doi: 10.1038/ncomms2203.

PMID:
23149747
[PubMed - indexed for MEDLINE]
9.

Analysis of 16S rRNA amplicon sequencing options on the Roche/454 next-generation titanium sequencing platform.

Tamaki H, Wright CL, Li X, Lin Q, Hwang C, Wang S, Thimmapuram J, Kamagata Y, Liu WT.

PLoS One. 2011;6(9):e25263. doi: 10.1371/journal.pone.0025263. Epub 2011 Sep 23.

PMID:
21966473
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Galaxy CloudMan: delivering cloud compute clusters.

Afgan E, Baker D, Coraor N, Chapman B, Nekrutenko A, Taylor J.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S4. doi: 10.1186/1471-2105-11-S12-S4.

PMID:
21210983
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Atlas2 Cloud: a framework for personal genome analysis in the cloud.

Evani US, Challis D, Yu J, Jackson AR, Paithankar S, Bainbridge MN, Jakkamsetti A, Pham P, Coarfa C, Milosavljevic A, Yu F.

BMC Genomics. 2012;13 Suppl 6:S19. doi: 10.1186/1471-2164-13-S6-S19. Epub 2012 Oct 26.

PMID:
23134663
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Metagenomic pyrosequencing and microbial identification.

Petrosino JF, Highlander S, Luna RA, Gibbs RA, Versalovic J.

Clin Chem. 2009 May;55(5):856-66. doi: 10.1373/clinchem.2008.107565. Epub 2009 Mar 5. Review.

PMID:
19264858
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

From genomics to metagenomics.

Desai N, Antonopoulos D, Gilbert JA, Glass EM, Meyer F.

Curr Opin Biotechnol. 2012 Feb;23(1):72-6. doi: 10.1016/j.copbio.2011.12.017. Epub 2012 Jan 5. Review.

PMID:
22227326
[PubMed - indexed for MEDLINE]
14.

Use of whole genome shotgun metagenomics: a practical guide for the microbiome-minded physician scientist.

Ma J, Prince A, Aagaard KM.

Semin Reprod Med. 2014 Jan;32(1):5-13. doi: 10.1055/s-0033-1361817. Epub 2014 Jan 3. Review.

PMID:
24390915
[PubMed - indexed for MEDLINE]
15.

Cost-effective cloud computing: a case study using the comparative genomics tool, roundup.

Kudtarkar P, Deluca TF, Fusaro VA, Tonellato PJ, Wall DP.

Evol Bioinform Online. 2010 Dec 22;6:197-203. doi: 10.4137/EBO.S6259.

PMID:
21258651
[PubMed]
Free PMC Article
16.

Computational methods for the analysis of tag sequences in metagenomics studies.

Chang Q, Luan Y, Chen T, Fuhrman JA, Sun F.

Front Biosci (Schol Ed). 2012 Jun 1;4:1333-43. Review.

PMID:
22652875
[PubMed - indexed for MEDLINE]
17.

Microbase2.0: a generic framework for computationally intensive bioinformatics workflows in the cloud.

Flanagan K, Nakjang S, Hallinan J, Harwood C, Hirt RP, Pocock MR, Wipat A.

J Integr Bioinform. 2012 Sep 24;9(2):212. doi: 10.2390/biecoll-jib-2012-212.

PMID:
23001322
[PubMed - indexed for MEDLINE]
18.

Exploiting parallel R in the cloud with SPRINT.

Piotrowski M, McGilvary GA, Sloan TM, Mewissen M, Lloyd AD, Forster T, Mitchell L, Ghazal P, Hill J.

Methods Inf Med. 2013;52(1):80-90. doi: 10.3414/ME11-02-0039. Epub 2012 Dec 7.

PMID:
23223611
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Parallel-META: efficient metagenomic data analysis based on high-performance computation.

Su X, Xu J, Ning K.

BMC Syst Biol. 2012 Jul 16;6 Suppl 1:S16. doi: 10.1186/1752-0509-6-S1-S16. Epub 2012 Jul 16.

PMID:
23046922
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads.

Bartram AK, Lynch MD, Stearns JC, Moreno-Hagelsieb G, Neufeld JD.

Appl Environ Microbiol. 2011 Jun;77(11):3846-52. doi: 10.1128/AEM.02772-10. Epub 2011 Apr 1. Erratum in: Appl Environ Microbiol. 2011 Aug;77(15):5569.

PMID:
21460107
[PubMed - indexed for MEDLINE]
Free PMC Article

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