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Items: 1 to 20 of 118

1.

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.

Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PS, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, Detter JC, De Vos P, Donohue TJ, Dong XZ, Ehrlich DS, Fraser C, Gibbs R, Gilbert J, Gilna P, Glöckner FO, Jansson JK, Keasling JD, Knight R, Labeda D, Lapidus A, Lee JS, Li WJ, Ma J, Markowitz V, Moore ER, Morrison M, Meyer F, Nelson KE, Ohkuma M, Ouzounis CA, Pace N, Parkhill J, Qin N, Rossello-Mora R, Sikorski J, Smith D, Sogin M, Stevens R, Stingl U, Suzuki K, Taylor D, Tiedje JM, Tindall B, Wagner M, Weinstock G, Weissenbach J, White O, Wang J, Zhang L, Zhou YG, Field D, Whitman WB, Garrity GM, Klenk HP.

PLoS Biol. 2014 Aug 5;12(8):e1001920. doi: 10.1371/journal.pbio.1001920. eCollection 2014 Aug.

2.

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.

Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA.

Nature. 2009 Dec 24;462(7276):1056-60. doi: 10.1038/nature08656.

3.

Adding genomic 'foliage' to the tree of life.

Walker A.

Nat Rev Microbiol. 2014 Feb;12(2):78. doi: 10.1038/nrmicro3203. No abstract available.

PMID:
24429416
4.

Past and future species definitions for Bacteria and Archaea.

Rosselló-Móra R, Amann R.

Syst Appl Microbiol. 2015 Jun;38(4):209-16. doi: 10.1016/j.syapm.2015.02.001. Epub 2015 Feb 20. Review.

PMID:
25747618
5.

TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy.

Meier-Kolthoff JP, Göker M.

Nat Commun. 2019 May 16;10(1):2182. doi: 10.1038/s41467-019-10210-3.

6.

Insights into the phylogeny and coding potential of microbial dark matter.

Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T.

Nature. 2013 Jul 25;499(7459):431-7. doi: 10.1038/nature12352. Epub 2013 Jul 14.

PMID:
23851394
7.

Towards a systematic understanding of differences between archaeal and bacterial diversity.

Spang A, Offre P.

Environ Microbiol Rep. 2019 Feb;11(1):9-12. doi: 10.1111/1758-2229.12701. Epub 2018 Nov 5.

PMID:
30394664
8.

En route to a genome-based classification of Archaea and Bacteria?

Klenk HP, Göker M.

Syst Appl Microbiol. 2010 Jun;33(4):175-82. doi: 10.1016/j.syapm.2010.03.003. Epub 2010 Apr 20. Review.

PMID:
20409658
9.

Flexible genomic islands as drivers of genome evolution.

Rodriguez-Valera F, Martin-Cuadrado AB, López-Pérez M.

Curr Opin Microbiol. 2016 Jun;31:154-160. doi: 10.1016/j.mib.2016.03.014. Epub 2016 Apr 14. Review.

PMID:
27085300
10.

Illuminating microbial diversity.

Forster SC.

Nat Rev Microbiol. 2017 Oct;15(10):578. doi: 10.1038/nrmicro.2017.106. Epub 2017 Aug 30. No abstract available.

PMID:
28852214
11.

Microbial taxonomy in the era of OMICS: application of DNA sequences, computational tools and techniques.

Mahato NK, Gupta V, Singh P, Kumari R, Verma H, Tripathi C, Rani P, Sharma A, Singhvi N, Sood U, Hira P, Kohli P, Nayyar N, Puri A, Bajaj A, Kumar R, Negi V, Talwar C, Khurana H, Nagar S, Sharma M, Mishra H, Singh AK, Dhingra G, Negi RK, Shakarad M, Singh Y, Lal R.

Antonie Van Leeuwenhoek. 2017 Oct;110(10):1357-1371. doi: 10.1007/s10482-017-0928-1. Epub 2017 Aug 22. Review.

PMID:
28831610
12.

Metagenomics: genomic analysis of microbial communities.

Riesenfeld CS, Schloss PD, Handelsman J.

Annu Rev Genet. 2004;38:525-52. Review.

PMID:
15568985
13.

Status of genome projects for nonpathogenic bacteria and archaea.

Nelson KE, Paulsen IT, Heidelberg JF, Fraser CM.

Nat Biotechnol. 2000 Oct;18(10):1049-54. Review.

PMID:
11017041
14.

Microbial Ecology and Evolution in the Acid Mine Drainage Model System.

Huang LN, Kuang JL, Shu WS.

Trends Microbiol. 2016 Jul;24(7):581-593. doi: 10.1016/j.tim.2016.03.004. Epub 2016 Apr 2. Review.

PMID:
27050827
15.
16.

Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life.

Spang A, Caceres EF, Ettema TJG.

Science. 2017 Aug 11;357(6351). pii: eaaf3883. doi: 10.1126/science.aaf3883. Review.

PMID:
28798101
17.

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.

Parks DH, Rinke C, Chuvochina M, Chaumeil PA, Woodcroft BJ, Evans PN, Hugenholtz P, Tyson GW.

Nat Microbiol. 2017 Nov;2(11):1533-1542. doi: 10.1038/s41564-017-0012-7. Epub 2017 Sep 11. Erratum in: Nat Microbiol. 2017 Dec 12;:.

PMID:
28894102
18.

Microbial species delineation using whole genome sequences.

Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K, Kyrpides NC, Pati A.

Nucleic Acids Res. 2015 Aug 18;43(14):6761-71. doi: 10.1093/nar/gkv657. Epub 2015 Jul 6.

19.

Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes.

Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR.

Genome Biol. 2010;11(3):R31. doi: 10.1186/gb-2010-11-3-r31. Epub 2010 Mar 15.

20.

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.

Mukherjee S, Seshadri R, Varghese NJ, Eloe-Fadrosh EA, Meier-Kolthoff JP, Göker M, Coates RC, Hadjithomas M, Pavlopoulos GA, Paez-Espino D, Yoshikuni Y, Visel A, Whitman WB, Garrity GM, Eisen JA, Hugenholtz P, Pati A, Ivanova NN, Woyke T, Klenk HP, Kyrpides NC.

Nat Biotechnol. 2017 Jul;35(7):676-683. doi: 10.1038/nbt.3886. Epub 2017 Jun 12.

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