Yooseph S - Search Results

1

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. Edlund A, et al. Among authors: yooseph s. Microbiome. 2013 Oct 2;1(1):25. doi: 10.1186/2049-2618-1-25. Microbiome. 2013. PMID: 24451062 Free PMC article.

2

Uncovering complex microbiome activities via metatranscriptomics during 24 hours of oral biofilm assembly and maturation.

Edlund A, Yang Y, Yooseph S, He X, Shi W, McLean JS. Edlund A, et al. Among authors: yooseph s. Microbiome. 2018 Dec 6;6(1):217. doi: 10.1186/s40168-018-0591-4. Microbiome. 2018. PMID: 30522530 Free PMC article.

3

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. McLean JS, et al. Among authors: yooseph s. Proc Natl Acad Sci U S A. 2013 Jun 25;110(26):E2390-9. doi: 10.1073/pnas.1219809110. Epub 2013 Jun 10. Proc Natl Acad Sci U S A. 2013. PMID: 23754396 Free PMC article.

4

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle.

He X, McLean JS, Edlund A, Yooseph S, Hall AP, Liu SY, Dorrestein PC, Esquenazi E, Hunter RC, Cheng G, Nelson KE, Lux R, Shi W. He X, et al. Among authors: yooseph s. Proc Natl Acad Sci U S A. 2015 Jan 6;112(1):244-9. doi: 10.1073/pnas.1419038112. Epub 2014 Dec 22. Proc Natl Acad Sci U S A. 2015. PMID: 25535390 Free PMC article.

5

Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism.

Edlund A, Yang Y, Yooseph S, Hall AP, Nguyen DD, Dorrestein PC, Nelson KE, He X, Lux R, Shi W, McLean JS. Edlund A, et al. Among authors: yooseph s. ISME J. 2015 Dec;9(12):2605-19. doi: 10.1038/ismej.2015.72. Epub 2015 May 29. ISME J. 2015. PMID: 26023872 Free PMC article.

6

Microbial diversity in individuals and their household contacts following typical antibiotic courses.

Abeles SR, Jones MB, Santiago-Rodriguez TM, Ly M, Klitgord N, Yooseph S, Nelson KE, Pride DT. Abeles SR, et al. Among authors: yooseph s. Microbiome. 2016 Jul 30;4(1):39. doi: 10.1186/s40168-016-0187-9. Microbiome. 2016. PMID: 27473422 Free PMC article.

7

Metagenome and Metatranscriptome Analyses Using Protein Family Profiles.

Zhong C, Edlund A, Yang Y, McLean JS, Yooseph S. Zhong C, et al. Among authors: yooseph s. PLoS Comput Biol. 2016 Jul 11;12(7):e1004991. doi: 10.1371/journal.pcbi.1004991. eCollection 2016 Jul. PLoS Comput Biol. 2016. PMID: 27400380 Free PMC article.

8

SPA: a short peptide assembler for metagenomic data.

Yang Y, Yooseph S. Yang Y, et al. Among authors: yooseph s. Nucleic Acids Res. 2013 Apr;41(8):e91. doi: 10.1093/nar/gkt118. Epub 2013 Feb 23. Nucleic Acids Res. 2013. PMID: 23435317 Free PMC article.

9

SFA-SPA: a suffix array based short peptide assembler for metagenomic data.

Yang Y, Zhong C, Yooseph S. Yang Y, et al. Among authors: yooseph s. Bioinformatics. 2015 Jun 1;31(11):1833-5. doi: 10.1093/bioinformatics/btv052. Epub 2015 Jan 30. Bioinformatics. 2015. PMID: 25637561

10

GRASPx: efficient homolog-search of short peptide metagenome database through simultaneous alignment and assembly.

Zhong C, Yang Y, Yooseph S. Zhong C, et al. Among authors: yooseph s. BMC Bioinformatics. 2016 Aug 31;17 Suppl 8(Suppl 8):283. doi: 10.1186/s12859-016-1119-1. BMC Bioinformatics. 2016. PMID: 27585568 Free PMC article.

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