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Results: 1 to 20 of 41

1.

Picocyanobacteria containing a novel pigment gene cluster dominate the brackish water Baltic Sea.

Larsson J, Celepli N, Ininbergs K, Dupont CL, Yooseph S, Bergman B, Ekman M.

ISME J. 2014 Mar 13. doi: 10.1038/ismej.2014.35. [Epub ahead of print]

PMID:
24621524
[PubMed - as supplied by publisher]
2.

Functional tradeoffs underpin salinity-driven divergence in microbial community composition.

Dupont CL, Larsson J, Yooseph S, Ininbergs K, Goll J, Asplund-Samuelsson J, McCrow JP, Celepli N, Allen LZ, Ekman M, Lucas AJ, Hagström Å, Thiagarajan M, Brindefalk B, Richter AR, Andersson AF, Tenney A, Lundin D, Tovchigrechko A, Nylander JA, Brami D, Badger JH, Allen AE, Rusch DB, Hoffman J, Norrby E, Friedman R, Pinhassi J, Venter JC, Bergman B.

PLoS One. 2014 Feb 27;9(2):e89549. doi: 10.1371/journal.pone.0089549. eCollection 2014.

PMID:
24586863
[PubMed - in process]
Free PMC Article
3.

Human papillomavirus community in healthy persons, defined by metagenomics analysis of human microbiome project shotgun sequencing data sets.

Ma Y, Madupu R, Karaoz U, Nossa CW, Yang L, Yooseph S, Yachimski PS, Brodie EL, Nelson KE, Pei Z.

J Virol. 2014 May;88(9):4786-97. doi: 10.1128/JVI.00093-14. Epub 2014 Feb 12.

PMID:
24522917
[PubMed - indexed for MEDLINE]
4.

An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome.

Edlund A, Yang Y, Hall AP, Guo L, Lux R, He X, Nelson KE, Nealson KH, Yooseph S, Shi W, McLean JS.

Microbiome. 2013 Oct 2;1(1):25. doi: 10.1186/2049-2618-1-25.

PMID:
24451062
[PubMed]
Free PMC Article
5.

Microbiome analysis of stool samples from African Americans with colon polyps.

Brim H, Yooseph S, Zoetendal EG, Lee E, Torralbo M, Laiyemo AO, Shokrani B, Nelson K, Ashktorab H.

PLoS One. 2013 Dec 20;8(12):e81352. doi: 10.1371/journal.pone.0081352. eCollection 2013.

PMID:
24376500
[PubMed - in process]
Free PMC Article
6.

A metagenomic framework for the study of airborne microbial communities.

Yooseph S, Andrews-Pfannkoch C, Tenney A, McQuaid J, Williamson S, Thiagarajan M, Brami D, Zeigler-Allen L, Hoffman J, Goll JB, Fadrosh D, Glass J, Adams MD, Friedman R, Venter JC.

PLoS One. 2013 Dec 11;8(12):e81862. doi: 10.1371/journal.pone.0081862. eCollection 2013.

PMID:
24349140
[PubMed - in process]
Free PMC Article
7.

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum.

McLean JS, Lombardo MJ, Badger JH, Edlund A, Novotny M, Yee-Greenbaum J, Vyahhi N, Hall AP, Yang Y, Dupont CL, Ziegler MG, Chitsaz H, Allen AE, Yooseph S, Tesler G, Pevzner PA, Friedman RM, Nealson KH, Venter JC, Lasken RS.

Proc Natl Acad Sci U S A. 2013 Jun 25;110(26):E2390-9. doi: 10.1073/pnas.1219809110. Epub 2013 Jun 10.

PMID:
23754396
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

SPA: a short peptide assembler for metagenomic data.

Yang Y, Yooseph S.

Nucleic Acids Res. 2013 Apr;41(8):e91. doi: 10.1093/nar/gkt118. Epub 2013 Feb 23.

PMID:
23435317
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Metagenomic investigation of microbes and viruses in patients with jaw osteonecrosis associated with bisphosphonate therapy.

Sedghizadeh PP, Yooseph S, Fadrosh DW, Zeigler-Allen L, Thiagarajan M, Salek H, Farahnik F, Williamson SJ.

Oral Surg Oral Med Oral Pathol Oral Radiol. 2012 Dec;114(6):764-70. doi: 10.1016/j.oooo.2012.08.444.

PMID:
23159114
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Metagenomic exploration of viruses throughout the Indian Ocean.

Williamson SJ, Allen LZ, Lorenzi HA, Fadrosh DW, Brami D, Thiagarajan M, McCrow JP, Tovchigrechko A, Yooseph S, Venter JC.

PLoS One. 2012;7(10):e42047. doi: 10.1371/journal.pone.0042047. Epub 2012 Oct 17.

PMID:
23082107
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Analyses of the microbial diversity across the human microbiome.

Li K, Bihan M, Yooseph S, Methé BA.

PLoS One. 2012;7(6):e32118. doi: 10.1371/journal.pone.0032118. Epub 2012 Jun 13.

PMID:
22719823
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).

Goll J, Thiagarajan M, Abubucker S, Huttenhower C, Yooseph S, Methé BA.

PLoS One. 2012;7(6):e29044. doi: 10.1371/journal.pone.0029044. Epub 2012 Jun 13.

PMID:
22719821
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Comparative genome analysis of 19 Ureaplasma urealyticum and Ureaplasma parvum strains.

Paralanov V, Lu J, Duffy LB, Crabb DM, Shrivastava S, Methé BA, Inman J, Yooseph S, Xiao L, Cassell GH, Waites KB, Glass JI.

BMC Microbiol. 2012 May 30;12:88. doi: 10.1186/1471-2180-12-88.

PMID:
22646228
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage.

Dupont CL, Rusch DB, Yooseph S, Lombardo MJ, Richter RA, Valas R, Novotny M, Yee-Greenbaum J, Selengut JD, Haft DH, Halpern AL, Lasken RS, Nealson K, Friedman R, Venter JC.

ISME J. 2012 Jun;6(6):1186-99. doi: 10.1038/ismej.2011.189. Epub 2011 Dec 15.

PMID:
22170421
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

From bacterial to microbial ecosystems (metagenomics).

Williamson SJ, Yooseph S.

Methods Mol Biol. 2012;804:35-55. doi: 10.1007/978-1-61779-361-5_3. Review.

PMID:
22144147
[PubMed - indexed for MEDLINE]
16.

Going deeper: metagenome of a hadopelagic microbial community.

Eloe EA, Fadrosh DW, Novotny M, Zeigler Allen L, Kim M, Lombardo MJ, Yee-Greenbaum J, Yooseph S, Allen EE, Lasken R, Williamson SJ, Bartlett DH.

PLoS One. 2011;6(5):e20388. doi: 10.1371/journal.pone.0020388. Epub 2011 May 24.

PMID:
21629664
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees.

Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA.

PLoS One. 2011 Mar 18;6(3):e18011. doi: 10.1371/journal.pone.0018011.

PMID:
21437252
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data.

Tanenbaum DM, Goll J, Murphy S, Kumar P, Zafar N, Thiagarajan M, Madupu R, Davidsen T, Kagan L, Kravitz S, Rusch DB, Yooseph S.

Stand Genomic Sci. 2010 Mar 30;2(2):229-37. doi: 10.4056/sigs.651139.

PMID:
21304707
[PubMed]
Free PMC Article
19.

Genomic and functional adaptation in surface ocean planktonic prokaryotes.

Yooseph S, Nealson KH, Rusch DB, McCrow JP, Dupont CL, Kim M, Johnson J, Montgomery R, Ferriera S, Beeson K, Williamson SJ, Tovchigrechko A, Allen AE, Zeigler LA, Sutton G, Eisenstadt E, Rogers YH, Friedman R, Frazier M, Venter JC.

Nature. 2010 Nov 4;468(7320):60-6. doi: 10.1038/nature09530.

PMID:
21048761
[PubMed - indexed for MEDLINE]
20.

Using DGGE profiling to develop a novel culture medium suitable for oral microbial communities.

Tian Y, He X, Torralba M, Yooseph S, Nelson KE, Lux R, McLean JS, Yu G, Shi W.

Mol Oral Microbiol. 2010 Oct;25(5):357-67. doi: 10.1111/j.2041-1014.2010.00585.x.

PMID:
20883224
[PubMed - indexed for MEDLINE]
Free PMC Article

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