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Results: 1 to 20 of 24

1.

Performance of two Southern California benthic community condition indices using species abundance and presence-only data: relevance to DNA barcoding.

Ranasinghe JA, Stein ED, Miller PE, Weisberg SB.

PLoS One. 2012;7(8):e40875. doi: 10.1371/journal.pone.0040875. Epub 2012 Aug 7.

PMID:
22879881
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing.

Baird DJ, Hajibabaei M.

Mol Ecol. 2012 Apr;21(8):2039-44.

PMID:
22590728
[PubMed - indexed for MEDLINE]
3.

Next-generation sequencing technologies for environmental DNA research.

Shokralla S, Spall JL, Gibson JF, Hajibabaei M.

Mol Ecol. 2012 Apr;21(8):1794-805. doi: 10.1111/j.1365-294X.2012.05538.x. Review.

PMID:
22486820
[PubMed - indexed for MEDLINE]
4.

Environmental DNA.

Taberlet P, Coissac E, Hajibabaei M, Rieseberg LH.

Mol Ecol. 2012 Apr;21(8):1789-93. doi: 10.1111/j.1365-294X.2012.05542.x. No abstract available.

PMID:
22486819
[PubMed - indexed for MEDLINE]
5.

Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies.

Taberlet P, Prud'Homme SM, Campione E, Roy J, Miquel C, Shehzad W, Gielly L, Rioux D, Choler P, Clément JC, Melodelima C, Pompanon F, Coissac E.

Mol Ecol. 2012 Apr;21(8):1816-20. doi: 10.1111/j.1365-294X.2011.05317.x. Epub 2012 Feb 2.

PMID:
22300434
[PubMed - indexed for MEDLINE]
6.

MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S.

Mol Biol Evol. 2011 Oct;28(10):2731-9. doi: 10.1093/molbev/msr121. Epub 2011 May 4.

PMID:
21546353
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos.

Hajibabaei M, Shokralla S, Zhou X, Singer GA, Baird DJ.

PLoS One. 2011 Apr 13;6(4):e17497. doi: 10.1371/journal.pone.0017497.

PMID:
21533287
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.

Goecks J, Nekrutenko A, Taylor J; Galaxy Team.

Genome Biol. 2010;11(8):R86. doi: 10.1186/gb-2010-11-8-r86. Epub 2010 Aug 25.

PMID:
20738864
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Search and clustering orders of magnitude faster than BLAST.

Edgar RC.

Bioinformatics. 2010 Oct 1;26(19):2460-1. doi: 10.1093/bioinformatics/btq461. Epub 2010 Aug 12.

PMID:
20709691
[PubMed - indexed for MEDLINE]
Free Article
10.

Direct PCR amplification and sequencing of specimens' DNA from preservative ethanol.

Shokralla S, Singer GA, Hajibabaei M.

Biotechniques. 2010 Mar;48(3):233-4. doi: 10.2144/000113362.

PMID:
20359306
[PubMed - indexed for MEDLINE]
Free Article
11.

Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises.

Creer S, Fonseca VG, Porazinska DL, Giblin-Davis RM, Sung W, Power DM, Packer M, Carvalho GR, Blaxter ML, Lambshead PJ, Thomas WK.

Mol Ecol. 2010 Mar;19 Suppl 1:4-20. doi: 10.1111/j.1365-294X.2009.04473.x. Review.

PMID:
20331766
[PubMed - indexed for MEDLINE]
12.

Galaxy: a web-based genome analysis tool for experimentalists.

Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J.

Curr Protoc Mol Biol. 2010 Jan;Chapter 19:Unit 19.10.1-21. doi: 10.1002/0471142727.mb1910s89.

PMID:
20069535
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

bold: The Barcode of Life Data System (http://www.barcodinglife.org).

Ratnasingham S, Hebert PD.

Mol Ecol Notes. 2007 May 1;7(3):355-364.

PMID:
18784790
[PubMed]
Free PMC Article
14.

Database indexing for production MegaBLAST searches.

Morgulis A, Coulouris G, Raytselis Y, Madden TL, Agarwala R, Schäffer AA.

Bioinformatics. 2008 Aug 15;24(16):1757-64. doi: 10.1093/bioinformatics/btn322. Epub 2008 Jun 21. Erratum in: Bioinformatics. 2008 Dec 15;24(24):2942.

PMID:
18567917
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Species detection using environmental DNA from water samples.

Ficetola GF, Miaud C, Pompanon F, Taberlet P.

Biol Lett. 2008 Aug 23;4(4):423-5. doi: 10.1098/rsbl.2008.0118.

PMID:
18400683
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Microbial diversity in the deep sea and the underexplored "rare biosphere".

Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, Arrieta JM, Herndl GJ.

Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12115-20. Epub 2006 Jul 31.

PMID:
16880384
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Developments in aquatic insect biomonitoring: a comparative analysis of recent approaches.

Bonada N, Prat N, Resh VH, Statzner B.

Annu Rev Entomol. 2006;51:495-523.

PMID:
16332221
[PubMed - indexed for MEDLINE]
18.

Critical factors for assembling a high volume of DNA barcodes.

Hajibabaei M, deWaard JR, Ivanova NV, Ratnasingham S, Dooh RT, Kirk SL, Mackie PM, Hebert PD.

Philos Trans R Soc Lond B Biol Sci. 2005 Oct 29;360(1462):1959-67.

PMID:
16214753
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Galaxy: a platform for interactive large-scale genome analysis.

Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A.

Genome Res. 2005 Oct;15(10):1451-5. Epub 2005 Sep 16.

PMID:
16169926
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Genome sequencing in microfabricated high-density picolitre reactors.

Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM.

Nature. 2005 Sep 15;437(7057):376-80. Epub 2005 Jul 31. Erratum in: Nature. 2006 May 4;441(7089):120. Ho, Chun He [corrected to Ho, Chun Heen].

PMID:
16056220
[PubMed - indexed for MEDLINE]
Free PMC Article

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