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Items: 1 to 20 of 93

1.

Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method.

Duhaime MB, Deng L, Poulos BT, Sullivan MB.

Environ Microbiol. 2012 Sep;14(9):2526-37. doi: 10.1111/j.1462-2920.2012.02791.x. Epub 2012 Jun 20.

2.

Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses.

Kim KH, Bae JW.

Appl Environ Microbiol. 2011 Nov;77(21):7663-8. doi: 10.1128/AEM.00289-11. Epub 2011 Sep 16.

3.

Assessment of REPLI-g Multiple Displacement Whole Genome Amplification (WGA) Techniques for Metagenomic Applications.

Ahsanuddin S, Afshinnekoo E, Gandara J, Hakyemezoğlu M, Bezdan D, Minot S, Greenfield N, Mason CE.

J Biomol Tech. 2017 Apr;28(1):46-55. doi: 10.7171/jbt.17-2801-008. Epub 2017 Mar 21. Erratum in: J Biomol Tech. 2017 Jul;28(2):96.

4.

Metagenomics.

Gilbert JA, Laverock B, Temperton B, Thomas S, Muhling M, Hughes M.

Methods Mol Biol. 2011;733:173-83. doi: 10.1007/978-1-61779-089-8_12.

PMID:
21431770
5.

Preparation of metagenomic libraries from naturally occurring marine viruses.

Solonenko SA, Sullivan MB.

Methods Enzymol. 2013;531:143-65. doi: 10.1016/B978-0-12-407863-5.00008-3.

PMID:
24060120
6.

Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes.

Oyola SO, Otto TD, Gu Y, Maslen G, Manske M, Campino S, Turner DJ, Macinnis B, Kwiatkowski DP, Swerdlow HP, Quail MA.

BMC Genomics. 2012 Jan 3;13:1. doi: 10.1186/1471-2164-13-1.

7.

Exploring the diversity of plant DNA viruses and their satellites using vector-enabled metagenomics on whiteflies.

Ng TF, Duffy S, Polston JE, Bixby E, Vallad GE, Breitbart M.

PLoS One. 2011 Apr 22;6(4):e19050. doi: 10.1371/journal.pone.0019050.

8.

Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA.

Marine R, Polson SW, Ravel J, Hatfull G, Russell D, Sullivan M, Syed F, Dumas M, Wommack KE.

Appl Environ Microbiol. 2011 Nov;77(22):8071-9. doi: 10.1128/AEM.05610-11. Epub 2011 Sep 23.

9.

Optimization of whole-transcriptome amplification from low cell density deep-sea microbial samples for metatranscriptomic analysis.

Wu J, Gao W, Zhang W, Meldrum DR.

J Microbiol Methods. 2011 Jan;84(1):88-93. doi: 10.1016/j.mimet.2010.10.018. Epub 2010 Oct 31.

PMID:
21044647
10.

Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis.

Hammond M, Homa F, Andersson-Svahn H, Ettema TJ, Joensson HN.

Microbiome. 2016 Oct 6;4(1):52.

11.

Comparing viral metagenomics methods using a highly multiplexed human viral pathogens reagent.

Li L, Deng X, Mee ET, Collot-Teixeira S, Anderson R, Schepelmann S, Minor PD, Delwart E.

J Virol Methods. 2015 Mar;213:139-46. doi: 10.1016/j.jviromet.2014.12.002. Epub 2014 Dec 11.

12.

Laboratory procedures to generate viral metagenomes.

Thurber RV, Haynes M, Breitbart M, Wegley L, Rohwer F.

Nat Protoc. 2009;4(4):470-83. doi: 10.1038/nprot.2009.10.

PMID:
19300441
13.

Virus Hunting: Discovery of New Episomal Circular Viruses by Rolling Circle Techniques.

Vanmechelen B, Rector A, Maes P.

Curr Protoc Microbiol. 2017 Feb 6;44:1E.12.1-1E.12.18. doi: 10.1002/cpmc.23.

PMID:
28166385
14.

Novel Degenerate PCR Method for Whole-Genome Amplification Applied to Peru Margin (ODP Leg 201) Subsurface Samples.

Martino AJ, Rhodes ME, Biddle JF, Brandt LD, Tomsho LP, House CH.

Front Microbiol. 2012 Jan 23;3:17. doi: 10.3389/fmicb.2012.00017. eCollection 2012.

15.

Whole-genome amplification (WGA) of marine photosynthetic eukaryote populations.

Lepere C, Demura M, Kawachi M, Romac S, Probert I, Vaulot D.

FEMS Microbiol Ecol. 2011 Jun;76(3):513-23. doi: 10.1111/j.1574-6941.2011.01072.x. Epub 2011 Mar 16.

16.

Metagenomics using next-generation sequencing.

Bragg L, Tyson GW.

Methods Mol Biol. 2014;1096:183-201. doi: 10.1007/978-1-62703-712-9_15.

PMID:
24515370
17.

Towards quantitative viromics for both double-stranded and single-stranded DNA viruses.

Roux S, Solonenko NE, Dang VT, Poulos BT, Schwenck SM, Goldsmith DB, Coleman ML, Breitbart M, Sullivan MB.

PeerJ. 2016 Dec 8;4:e2777. doi: 10.7717/peerj.2777. eCollection 2016.

18.

Sequencing platform and library preparation choices impact viral metagenomes.

Solonenko SA, Ignacio-Espinoza JC, Alberti A, Cruaud C, Hallam S, Konstantinidis K, Tyson G, Wincker P, Sullivan MB.

BMC Genomics. 2013 May 10;14:320. doi: 10.1186/1471-2164-14-320.

19.

Linear amplification for deep sequencing.

Hoeijmakers WA, Bártfai R, Françoijs KJ, Stunnenberg HG.

Nat Protoc. 2011 Jun 23;6(7):1026-36. doi: 10.1038/nprot.2011.345.

PMID:
21720315
20.

Multiply primed rolling-circle amplification method for the amplification of circular DNA viruses.

Stevens H, Rector A, Van Ranst M.

Cold Spring Harb Protoc. 2010 Apr;2010(4):pdb.prot5415. doi: 10.1101/pdb.prot5415.

PMID:
20360369

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