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Items: 1 to 50 of 70

1.

Co-occurrence of Anaerobes in Human Chronic Wounds.

Choi Y, Banerjee A, McNish S, Couch KS, Torralba MG, Lucas S, Tovchigrechko A, Madupu R, Yooseph S, Nelson KE, Shanmugam VK, Chan AP.

Microb Ecol. 2018 Aug 23. doi: 10.1007/s00248-018-1231-z. [Epub ahead of print]

PMID:
30141127
2.

Papio spp. Colon microbiome and its link to obesity in pregnancy.

Li X, Rensing C, Taylor WL, Costelle C, Brejnrod AD, Ferry RJ Jr, Higgins PB, Folli F, Kottapalli KR, Hubbard GB, Dick EJ Jr, Yooseph S, Nelson KE, Schlabritz-Loutsevitch N.

J Med Primatol. 2018 Jul 24. doi: 10.1111/jmp.12366. [Epub ahead of print]

PMID:
30039863
3.

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2018 Jul 6;36(7):660. doi: 10.1038/nbt0718-660a. No abstract available.

PMID:
29979671
4.

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2018 Feb 6;36(2):196. doi: 10.1038/nbt0218-196a. No abstract available.

5.

Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease.

Moustafa A, Li W, Anderson EL, Wong EHM, Dulai PS, Sandborn WJ, Biggs W, Yooseph S, Jones MB, Venter JC, Nelson KE, Chang JT, Telenti A, Boland BS.

Clin Transl Gastroenterol. 2018 Jan 18;9(1):e132. doi: 10.1038/ctg.2017.58.

6.

A Microbiomic Analysis in African Americans with Colonic Lesions Reveals Streptococcus sp.VT162 as a Marker of Neoplastic Transformation.

Brim H, Yooseph S, Lee E, Sherif ZA, Abbas M, Laiyemo AO, Varma S, Torralba M, Dowd SE, Nelson KE, Pathmasiri W, Sumner S, de Vos W, Liang Q, Yu J, Zoetendal E, Ashktorab H.

Genes (Basel). 2017 Nov 9;8(11). pii: E314. doi: 10.3390/genes8110314.

7.

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2017 Aug 8;35(8):725-731. doi: 10.1038/nbt.3893.

PMID:
28787424
8.

Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease.

Loomba R, Seguritan V, Li W, Long T, Klitgord N, Bhatt A, Dulai PS, Caussy C, Bettencourt R, Highlander SK, Jones MB, Sirlin CB, Schnabl B, Brinkac L, Schork N, Chen CH, Brenner DA, Biggs W, Yooseph S, Venter JC, Nelson KE.

Cell Metab. 2017 May 2;25(5):1054-1062.e5. doi: 10.1016/j.cmet.2017.04.001.

9.

Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies.

Greenwald WW, Klitgord N, Seguritan V, Yooseph S, Venter JC, Garner C, Nelson KE, Li W.

BMC Genomics. 2017 Apr 13;18(1):296. doi: 10.1186/s12864-017-3679-5.

10.

Differences in the Nasopharyngeal Microbiome During Acute Respiratory Tract Infection With Human Rhinovirus and Respiratory Syncytial Virus in Infancy.

Rosas-Salazar C, Shilts MH, Tovchigrechko A, Schobel S, Chappell JD, Larkin EK, Shankar J, Yooseph S, Nelson KE, Halpin RA, Moore ML, Anderson LJ, Peebles RS Jr, Das SR, Hartert TV.

J Infect Dis. 2016 Dec 15;214(12):1924-1928.

11.

Meta-omic analyses of Baltic Sea cyanobacteria: diversity, community structure and salt acclimation.

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

Environ Microbiol. 2017 Feb;19(2):673-686. doi: 10.1111/1462-2920.13592. Epub 2017 Jan 27.

PMID:
27871145
12.

Effect of Macondo Prospect 252 Oil on Microbiota Associated with Pelagic Sargassum in the Northern Gulf of Mexico.

Torralba MG, Franks JS, Gomez A, Yooseph S, Nelson KE, Grimes DJ.

Microb Ecol. 2017 Jan;73(1):91-100. doi: 10.1007/s00248-016-0857-y. Epub 2016 Nov 4.

PMID:
27815589
13.

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

Zhong C, Yang Y, Yooseph S.

BMC Bioinformatics. 2016 Aug 31;17 Suppl 8:283. doi: 10.1186/s12859-016-1119-1.

14.

A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome.

Anderson EL, Li W, Klitgord N, Highlander SK, Dayrit M, Seguritan V, Yooseph S, Biggs W, Venter JC, Nelson KE, Jones MB.

Sci Rep. 2016 Aug 25;6:31731. doi: 10.1038/srep31731.

15.

Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis.

Rajagopala SV, Yooseph S, Harkins DM, Moncera KJ, Zabokrtsky KB, Torralba MG, Tovchigrechko A, Highlander SK, Pieper R, Sender L, Nelson KE.

BMC Genomics. 2016 Aug 15;17(1):635. doi: 10.1186/s12864-016-2965-y.

16.

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.

Microbiome. 2016 Jul 30;4(1):39. doi: 10.1186/s40168-016-0187-9.

17.

Metagenome and Metatranscriptome Analyses Using Protein Family Profiles.

Zhong C, Edlund A, Yang Y, McLean JS, Yooseph S.

PLoS Comput Biol. 2016 Jul 11;12(7):e1004991. doi: 10.1371/journal.pcbi.1004991. eCollection 2016 Jul.

18.

Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters.

Brindefalk B, Ekman M, Ininbergs K, Dupont CL, Yooseph S, Pinhassi J, Bergman B.

Environ Microbiol. 2016 Dec;18(12):4442-4455. doi: 10.1111/1462-2920.13407. Epub 2016 Jul 14.

PMID:
27306515
19.

Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.

Díez B, Nylander JA, Ininbergs K, Dupont CL, Allen AE, Yooseph S, Rusch DB, Bergman B.

PLoS One. 2016 May 19;11(5):e0155757. doi: 10.1371/journal.pone.0155757. eCollection 2016.

20.

Global biogeography of Prochlorococcus genome diversity in the surface ocean.

Kent AG, Dupont CL, Yooseph S, Martiny AC.

ISME J. 2016 Aug;10(8):1856-65. doi: 10.1038/ismej.2015.265. Epub 2016 Feb 2.

21.

Geomicrobiology of sublacustrine thermal vents in Yellowstone Lake: geochemical controls on microbial community structure and function.

Inskeep WP, Jay ZJ, Macur RE, Clingenpeel S, Tenney A, Lovalvo D, Beam JP, Kozubal MA, Shanks WC, Morgan LA, Kan J, Gorby Y, Yooseph S, Nealson K.

Front Microbiol. 2015 Oct 26;6:1044. doi: 10.3389/fmicb.2015.01044. eCollection 2015.

22.

Library preparation methodology can influence genomic and functional predictions in human microbiome research.

Jones MB, Highlander SK, Anderson EL, Li W, Dayrit M, Klitgord N, Fabani MM, Seguritan V, Green J, Pride DT, Yooseph S, Biggs W, Nelson KE, Venter JC.

Proc Natl Acad Sci U S A. 2015 Nov 10;112(45):14024-9. doi: 10.1073/pnas.1519288112. Epub 2015 Oct 28.

23.

Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection.

Yooseph S, Kirkness EF, Tran TM, Harkins DM, Jones MB, Torralba MG, O'Connell E, Nutman TB, Doumbo S, Doumbo OK, Traore B, Crompton PD, Nelson KE.

BMC Genomics. 2015 Aug 22;16:631. doi: 10.1186/s12864-015-1819-3.

24.

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 Dec;9(12):2605-19. doi: 10.1038/ismej.2015.72. Epub 2015 May 29.

25.

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.

PMID:
25637561
26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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.

44.

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
45.

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.

46.

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.

47.

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.

48.

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
49.

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.

50.

METAREP: JCVI metagenomics reports--an open source tool for high-performance comparative metagenomics.

Goll J, Rusch DB, Tanenbaum DM, Thiagarajan M, Li K, Methé BA, Yooseph S.

Bioinformatics. 2010 Oct 15;26(20):2631-2. doi: 10.1093/bioinformatics/btq455. Epub 2010 Aug 26.

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