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Items: 1 to 20 of 92

1.

Accurate and universal delineation of prokaryotic species.

Mende DR, Sunagawa S, Zeller G, Bork P.

Nat Methods. 2013 Sep;10(9):881-4. doi: 10.1038/nmeth.2575. Epub 2013 Jul 28.

PMID:
23892899
2.

Metagenomic species profiling using universal phylogenetic marker genes.

Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P.

Nat Methods. 2013 Dec;10(12):1196-9. doi: 10.1038/nmeth.2693. Epub 2013 Oct 20.

PMID:
24141494
3.
4.

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.

Mende DR, Letunic I, Huerta-Cepas J, Li SS, Forslund K, Sunagawa S, Bork P.

Nucleic Acids Res. 2017 Jan 4;45(D1):D529-D534. doi: 10.1093/nar/gkw989. Epub 2016 Oct 24.

5.

Predicting prokaryotic ecological niches using genome sequence analysis.

Suen G, Goldman BS, Welch RD.

PLoS One. 2007 Aug 15;2(8):e743.

6.

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences.

Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M.

BMC Genomics. 2011;12 Suppl 2:S4. doi: 10.1186/1471-2164-12-S2-S4. Epub 2011 Jul 27.

7.

Prokaryotic phylogenies inferred from whole-genome sequence and annotation data.

Du W, Cao Z, Wang Y, Sun Y, Blanzieri E, Liang Y.

Biomed Res Int. 2013;2013:409062. doi: 10.1155/2013/409062. Epub 2013 Aug 29.

8.

DNA barcoding and phylogenetic analysis of Pectinidae (Mollusca: Bivalvia) based on mitochondrial COI and 16S rRNA genes.

Feng Y, Li Q, Kong L, Zheng X.

Mol Biol Rep. 2011 Jan;38(1):291-9. doi: 10.1007/s11033-010-0107-1. Epub 2010 Mar 25.

PMID:
20336381
9.

Phylogenomics of prokaryotic ribosomal proteins.

Yutin N, Puigbò P, Koonin EV, Wolf YI.

PLoS One. 2012;7(5):e36972. doi: 10.1371/journal.pone.0036972. Epub 2012 May 16.

10.

Whole genome phylogeny of Prochlorococcus marinus group of cyanobacteria: genome alignment and overlapping gene approach.

Prabha R, Singh DP, Gupta SK, Rai A.

Interdiscip Sci. 2014 Jun;6(2):149-57. doi: 10.1007/s12539-013-0024-9. Epub 2014 Jun 17.

PMID:
25172453
11.

The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains.

Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, Ludwig W, Glöckner FO, Rosselló-Móra R.

Syst Appl Microbiol. 2008 Sep;31(4):241-50. doi: 10.1016/j.syapm.2008.07.001. Epub 2008 Aug 9.

PMID:
18692976
12.

Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus) in China with multiple gene markers.

Dai QY, Gao Q, Wu CS, Chesters D, Zhu CD, Zhang AB.

PLoS One. 2012;7(4):e32544. doi: 10.1371/journal.pone.0032544. Epub 2012 Apr 3.

13.

DNA barcode sequence identification incorporating taxonomic hierarchy and within taxon variability.

Little DP.

PLoS One. 2011;6(8):e20552. doi: 10.1371/journal.pone.0020552. Epub 2011 Aug 16.

14.

Phylogenetic reconstruction in the order Nymphaeales: ITS2 secondary structure analysis and in silico testing of maturase k (matK) as a potential marker for DNA bar coding.

Biswal DK, Debnath M, Kumar S, Tandon P.

BMC Bioinformatics. 2012;13 Suppl 17:S26. doi: 10.1186/1471-2105-13-S17-S26. Epub 2012 Dec 13.

15.

Identifying the true oysters (Bivalvia: Ostreidae) with mitochondrial phylogeny and distance-based DNA barcoding.

Liu J, Li Q, Kong L, Yu H, Zheng X.

Mol Ecol Resour. 2011 Sep;11(5):820-30. doi: 10.1111/j.1755-0998.2011.03025.x. Epub 2011 May 19.

PMID:
21592313
16.

Performance comparison of genetic markers for high-throughput sequencing-based biodiversity assessment in complex communities.

Zhan A, Bailey SA, Heath DD, Macisaac HJ.

Mol Ecol Resour. 2014 Sep;14(5):1049-59. doi: 10.1111/1755-0998.12254. Epub 2014 Apr 12.

PMID:
24655333
17.

Gene order phylogeny of the genus Prochlorococcus.

Luo H, Shi J, Arndt W, Tang J, Friedman R.

PLoS One. 2008;3(12):e3837. doi: 10.1371/journal.pone.0003837. Epub 2008 Dec 3.

18.

COI is better than 16S rRNA for DNA barcoding Asiatic salamanders (Amphibia: Caudata: Hynobiidae).

Xia Y, Gu HF, Peng R, Chen Q, Zheng YC, Murphy RW, Zeng XM.

Mol Ecol Resour. 2012 Jan;12(1):48-56. doi: 10.1111/j.1755-0998.2011.03055.x. Epub 2011 Aug 8.

PMID:
21824335
19.

Universal COI primers for DNA barcoding amphibians.

Che J, Chen HM, Yang JX, Jin JQ, Jiang K, Yuan ZY, Murphy RW, Zhang YP.

Mol Ecol Resour. 2012 Mar;12(2):247-58. doi: 10.1111/j.1755-0998.2011.03090.x. Epub 2011 Dec 7.

PMID:
22145866
20.

Studying long 16S rDNA sequences with ultrafast-metagenomic sequence classification using exact alignments (Kraken).

Valenzuela-González F, Martínez-Porchas M, Villalpando-Canchola E, Vargas-Albores F.

J Microbiol Methods. 2016 Mar;122:38-42. doi: 10.1016/j.mimet.2016.01.011. Epub 2016 Jan 23.

PMID:
26812576

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