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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.

ISME J. 2015 May 29. doi: 10.1038/ismej.2015.72. [Epub ahead of print]


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

Yang Y, Zhong C, Yooseph S.

Bioinformatics. 2015 Jun 1;31(11):1833-5. doi: 10.1093/bioinformatics/btv052. Epub 2015 Jan 30.


Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics.

Llorens-Marès T, Yooseph S, Goll J, Hoffman J, Vila-Costa M, Borrego CM, Dupont CL, Casamayor EO.

ISME J. 2015 Jul;9(7):1648-61. doi: 10.1038/ismej.2014.254. Epub 2015 Jan 9.


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.

Proc Natl Acad Sci U S A. 2015 Jan 6;112(1):244-9. doi: 10.1073/pnas.1419038112. Epub 2014 Dec 22.


Diet and feeding pattern affect the diurnal dynamics of the gut microbiome.

Zarrinpar A, Chaix A, Yooseph S, Panda S.

Cell Metab. 2014 Dec 2;20(6):1006-17. doi: 10.1016/j.cmet.2014.11.008.


GRASP: guided reference-based assembly of short peptides.

Zhong C, Yang Y, Yooseph S.

Nucleic Acids Res. 2015 Feb 18;43(3):e18. doi: 10.1093/nar/gku1210. Epub 2014 Nov 20.


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 Sep;8(9):1892-903. doi: 10.1038/ismej.2014.35. Epub 2014 Mar 13.


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.


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.


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.


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.


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.


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.


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.


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.


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.


Evaluation of 16S rDNA-based community profiling for human microbiome research.

Jumpstart Consortium Human Microbiome Project Data Generation Working Group.

PLoS One. 2012;7(6):e39315. doi: 10.1371/journal.pone.0039315. Epub 2012 Jun 13.


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.


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.


A framework for human microbiome research.

Human Microbiome Project Consortium.

Nature. 2012 Jun 13;486(7402):215-21. doi: 10.1038/nature11209.

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