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Items: 50

1.

VOLARE: visual analysis of disease-associated microbiome-immune system interplay.

Siebert JC, Neff CP, Schneider JM, Regner EH, Ohri N, Kuhn KA, Palmer BE, Lozupone CA, Görg C.

BMC Bioinformatics. 2019 Aug 20;20(1):432. doi: 10.1186/s12859-019-3021-0.

2.

Gut microbiota phenotypes of obesity.

Stanislawski MA, Dabelea D, Lange LA, Wagner BD, Lozupone CA.

NPJ Biofilms Microbiomes. 2019 Jul 1;5:18. doi: 10.1038/s41522-019-0091-8. eCollection 2019.

3.

Gut microbiota from high-risk men who have sex with men drive immune activation in gnotobiotic mice and in vitro HIV infection.

Li SX, Sen S, Schneider JM, Xiong KN, Nusbacher NM, Moreno-Huizar N, Shaffer M, Armstrong AJS, Severs E, Kuhn K, Neff CP, McCarter M, Campbell T, Lozupone CA, Palmer BE.

PLoS Pathog. 2019 Apr 4;15(4):e1007611. doi: 10.1371/journal.ppat.1007611. eCollection 2019 Apr.

4.

Reply to Moossavi and Azad, "Quantifying and Interpreting the Association between Early-Life Gut Microbiota Composition and Childhood Obesity".

Stanislawski MA, Dabelea D, Wagner BD, Iszatt N, Dahl C, Sontag MK, Knight R, Lozupone CA, Eggesbø M.

MBio. 2019 Feb 12;10(1). pii: e00047-19. doi: 10.1128/mBio.00047-19. No abstract available.

5.

Functional Microbiomics in Liver Transplantation: Identifying Novel Targets for Improving Allograft Outcomes.

Kriss M, Verna EC, Rosen HR, Lozupone CA.

Transplantation. 2019 Apr;103(4):668-678. doi: 10.1097/TP.0000000000002568. Review.

PMID:
30507741
6.

An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men.

Armstrong AJS, Shaffer M, Nusbacher NM, Griesmer C, Fiorillo S, Schneider JM, Preston Neff C, Li SX, Fontenot AP, Campbell T, Palmer BE, Lozupone CA.

Microbiome. 2018 Nov 5;6(1):198. doi: 10.1186/s40168-018-0580-7.

7.

Gut Microbiota in the First 2 Years of Life and the Association with Body Mass Index at Age 12 in a Norwegian Birth Cohort.

Stanislawski MA, Dabelea D, Wagner BD, Iszatt N, Dahl C, Sontag MK, Knight R, Lozupone CA, Eggesbø M.

MBio. 2018 Oct 23;9(5). pii: e01751-18. doi: 10.1128/mBio.01751-18.

8.

Subversion of Systemic Glucose Metabolism as a Mechanism to Support the Growth of Leukemia Cells.

Ye H, Adane B, Khan N, Alexeev E, Nusbacher N, Minhajuddin M, Stevens BM, Winters AC, Lin X, Ashton JM, Purev E, Xing L, Pollyea DA, Lozupone CA, Serkova NJ, Colgan SP, Jordan CT.

Cancer Cell. 2018 Oct 8;34(4):659-673.e6. doi: 10.1016/j.ccell.2018.08.016. Epub 2018 Sep 27.

PMID:
30270124
9.

Low diversity gut microbiota dysbiosis: drivers, functional implications and recovery.

Kriss M, Hazleton KZ, Nusbacher NM, Martin CG, Lozupone CA.

Curr Opin Microbiol. 2018 Aug;44:34-40. doi: 10.1016/j.mib.2018.07.003. Epub 2018 Jul 20. Review.

10.

Fecal Microbiota Composition Drives Immune Activation in HIV-infected Individuals.

Neff CP, Krueger O, Xiong K, Arif S, Nusbacher N, Schneider JM, Cunningham AW, Armstrong A, Li S, McCarter MD, Campbell TB, Lozupone CA, Palmer BE.

EBioMedicine. 2018 Apr;30:192-202. doi: 10.1016/j.ebiom.2018.03.024. Epub 2018 Mar 26.

11.

Unraveling Interactions between the Microbiome and the Host Immune System To Decipher Mechanisms of Disease.

Lozupone CA.

mSystems. 2018 Mar 6;3(2). pii: e00183-17. doi: 10.1128/mSystems.00183-17. eCollection 2018 Mar-Apr.

12.

Gut microbiota in adolescents and the association with fatty liver: the EPOCH study.

Stanislawski MA, Lozupone CA, Wagner BD, Eggesbø M, Sontag MK, Nusbacher NM, Martinez M, Dabelea D.

Pediatr Res. 2018 Aug;84(2):219-227. doi: 10.1038/pr.2018.32. Epub 2018 Apr 18.

13.

Differences in fecal microbial metabolites and microbiota of children with autism spectrum disorders.

Kang DW, Ilhan ZE, Isern NG, Hoyt DW, Howsmon DP, Shaffer M, Lozupone CA, Hahn J, Adams JB, Krajmalnik-Brown R.

Anaerobe. 2018 Feb;49:121-131. doi: 10.1016/j.anaerobe.2017.12.007. Epub 2017 Dec 22.

PMID:
29274915
14.

Associations between acute gastrointestinal GvHD and the baseline gut microbiota of allogeneic hematopoietic stem cell transplant recipients and donors.

Liu C, Frank DN, Horch M, Chau S, Ir D, Horch EA, Tretina K, van Besien K, Lozupone CA, Nguyen VH.

Bone Marrow Transplant. 2017 Dec;52(12):1643-1650. doi: 10.1038/bmt.2017.200. Epub 2017 Oct 2.

PMID:
28967895
15.

Pre-pregnancy weight, gestational weight gain, and the gut microbiota of mothers and their infants.

Stanislawski MA, Dabelea D, Wagner BD, Sontag MK, Lozupone CA, Eggesbø M.

Microbiome. 2017 Sep 4;5(1):113. doi: 10.1186/s40168-017-0332-0.

16.

Microbiome and metabolome data integration provides insight into health and disease.

Shaffer M, Armstrong AJS, Phelan VV, Reisdorph N, Lozupone CA.

Transl Res. 2017 Nov;189:51-64. doi: 10.1016/j.trsl.2017.07.001. Epub 2017 Jul 14. Review.

17.

The environment, epigenome, and asthma.

Yang IV, Lozupone CA, Schwartz DA.

J Allergy Clin Immunol. 2017 Jul;140(1):14-23. doi: 10.1016/j.jaci.2017.05.011. Review.

18.

Striking a Balance with Help from our Little Friends - How the Gut Microbiota Contributes to Immune Homeostasis.

Arnolds KL, Lozupone CA.

Yale J Biol Med. 2016 Sep 30;89(3):389-395. eCollection 2016 Sep. Review.

19.

Diverse Intestinal Bacteria Contain Putative Zwitterionic Capsular Polysaccharides with Anti-inflammatory Properties.

Neff CP, Rhodes ME, Arnolds KL, Collins CB, Donnelly J, Nusbacher N, Jedlicka P, Schneider JM, McCarter MD, Shaffer M, Mazmanian SK, Palmer BE, Lozupone CA.

Cell Host Microbe. 2016 Oct 12;20(4):535-547. doi: 10.1016/j.chom.2016.09.002. Epub 2016 Sep 29.

20.

Getting to know the microbiome.

Lozupone CA.

Nat Microbiol. 2016 Mar 14;1:16030. doi: 10.1038/nmicrobiol.2016.30. No abstract available.

PMID:
27572447
21.

The HIV-Associated Enteric Microbiome Has Gone Viral.

Palmer BE, Li SX, Lozupone CA.

Cell Host Microbe. 2016 Mar 9;19(3):270-2. doi: 10.1016/j.chom.2016.02.014.

22.

Complexities of Gut Microbiome Dysbiosis in the Context of HIV Infection and Antiretroviral Therapy.

Li SX, Armstrong A, Neff CP, Shaffer M, Lozupone CA, Palmer BE.

Clin Pharmacol Ther. 2016 Jun;99(6):600-11. doi: 10.1002/cpt.363. Epub 2016 Apr 16. Review.

23.

The UniFrac significance test is sensitive to tree topology.

Lozupone CA, Knight R.

BMC Bioinformatics. 2015 Jul 7;16:211. doi: 10.1186/s12859-015-0640-y.

24.

HIV-induced alteration in gut microbiota: driving factors, consequences, and effects of antiretroviral therapy.

Lozupone CA, Rhodes ME, Neff CP, Fontenot AP, Campbell TB, Palmer BE.

Gut Microbes. 2014 Jul 1;5(4):562-70. doi: 10.4161/gmic.32132. Epub 2014 Jul 31. Review.

PMID:
25078714
25.

Muc5b is required for airway defence.

Roy MG, Livraghi-Butrico A, Fletcher AA, McElwee MM, Evans SE, Boerner RM, Alexander SN, Bellinghausen LK, Song AS, Petrova YM, Tuvim MJ, Adachi R, Romo I, Bordt AS, Bowden MG, Sisson JH, Woodruff PG, Thornton DJ, Rousseau K, De la Garza MM, Moghaddam SJ, Karmouty-Quintana H, Blackburn MR, Drouin SM, Davis CW, Terrell KA, Grubb BR, O'Neal WK, Flores SC, Cota-Gomez A, Lozupone CA, Donnelly JM, Watson AM, Hennessy CE, Keith RC, Yang IV, Barthel L, Henson PM, Janssen WJ, Schwartz DA, Boucher RC, Dickey BF, Evans CM.

Nature. 2014 Jan 16;505(7483):412-6. doi: 10.1038/nature12807. Epub 2013 Dec 8.

26.

Alterations in the gut microbiota associated with HIV-1 infection.

Lozupone CA, Li M, Campbell TB, Flores SC, Linderman D, Gebert MJ, Knight R, Fontenot AP, Palmer BE.

Cell Host Microbe. 2013 Sep 11;14(3):329-39. doi: 10.1016/j.chom.2013.08.006.

27.

Meta-analyses of studies of the human microbiota.

Lozupone CA, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, Vázquez-Baeza Y, Jansson JK, Gordon JI, Knight R.

Genome Res. 2013 Oct;23(10):1704-14. doi: 10.1101/gr.151803.112. Epub 2013 Jul 16.

28.

Cohabiting family members share microbiota with one another and with their dogs.

Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, Berg-Lyons D, Caporaso JG, Knights D, Clemente JC, Nakielny S, Gordon JI, Fierer N, Knight R.

Elife. 2013 Apr 16;2:e00458. doi: 10.7554/eLife.00458.

29.

Diversity, stability and resilience of the human gut microbiota.

Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R.

Nature. 2012 Sep 13;489(7415):220-30. doi: 10.1038/nature11550. Review.

30.

Human gut microbiome viewed across age and geography.

Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI.

Nature. 2012 May 9;486(7402):222-7. doi: 10.1038/nature11053.

31.

RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs.

Widmann J, Stombaugh J, McDonald D, Chocholousova J, Gardner P, Iyer MK, Liu Z, Lozupone CA, Quinn J, Smit S, Wikman S, Zaneveld JR, Knight R.

RNA. 2012 Jul;18(7):1319-27. doi: 10.1261/rna.032052.111. Epub 2012 May 29.

32.

Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis.

Sullam KE, Essinger SD, Lozupone CA, O'Connor MP, Rosen GL, Knight R, Kilham SS, Russell JA.

Mol Ecol. 2012 Jul;21(13):3363-78. doi: 10.1111/j.1365-294X.2012.05552.x. Epub 2012 Apr 4.

33.

The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins.

McNulty NP, Yatsunenko T, Hsiao A, Faith JJ, Muegge BD, Goodman AL, Henrissat B, Oozeer R, Cools-Portier S, Gobert G, Chervaux C, Knights D, Lozupone CA, Knight R, Duncan AE, Bain JR, Muehlbauer MJ, Newgard CB, Heath AC, Gordon JI.

Sci Transl Med. 2011 Oct 26;3(106):106ra106. doi: 10.1126/scitranslmed.3002701.

34.

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO.

Nat Biotechnol. 2011 May;29(5):415-20. doi: 10.1038/nbt.1823.

35.

Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins.

Hansen EE, Lozupone CA, Rey FE, Wu M, Guruge JL, Narra A, Goodfellow J, Zaneveld JR, McDonald DT, Goodrich JA, Heath AC, Knight R, Gordon JI.

Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4599-606. doi: 10.1073/pnas.1000071108. Epub 2011 Feb 11.

36.

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R.

Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4516-22. doi: 10.1073/pnas.1000080107. Epub 2010 Jun 3.

37.

QIIME allows analysis of high-throughput community sequencing data.

Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R.

Nat Methods. 2010 May;7(5):335-6. doi: 10.1038/nmeth.f.303. Epub 2010 Apr 11. No abstract available.

39.

Identifying genetic determinants needed to establish a human gut symbiont in its habitat.

Goodman AL, McNulty NP, Zhao Y, Leip D, Mitra RD, Lozupone CA, Knight R, Gordon JI.

Cell Host Microbe. 2009 Sep 17;6(3):279-89. doi: 10.1016/j.chom.2009.08.003.

40.

The convergence of carbohydrate active gene repertoires in human gut microbes.

Lozupone CA, Hamady M, Cantarel BL, Coutinho PM, Henrissat B, Gordon JI, Knight R.

Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):15076-81. doi: 10.1073/pnas.0807339105. Epub 2008 Sep 19.

41.

Worlds within worlds: evolution of the vertebrate gut microbiota.

Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI.

Nat Rev Microbiol. 2008 Oct;6(10):776-88. doi: 10.1038/nrmicro1978. Review.

42.

Species divergence and the measurement of microbial diversity.

Lozupone CA, Knight R.

FEMS Microbiol Rev. 2008 Jul;32(4):557-78. doi: 10.1111/j.1574-6976.2008.00111.x. Epub 2008 Apr 22. Review.

43.

The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis.

McKenna P, Hoffmann C, Minkah N, Aye PP, Lackner A, Liu Z, Lozupone CA, Hamady M, Knight R, Bushman FD.

PLoS Pathog. 2008 Feb 8;4(2):e20. doi: 10.1371/journal.ppat.0040020.

44.

Global patterns in bacterial diversity.

Lozupone CA, Knight R.

Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11436-40. Epub 2007 Jun 25.

45.

Evolution of symbiotic bacteria in the distal human intestine.

Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, Martens EC, Henrissat B, Coutinho PM, Minx P, Latreille P, Cordum H, Van Brunt A, Kim K, Fulton RS, Fulton LA, Clifton SW, Wilson RK, Knight RD, Gordon JI.

PLoS Biol. 2007 Jul;5(7):e156. Epub 2007 Jun 19.

46.

Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities.

Lozupone CA, Hamady M, Kelley ST, Knight R.

Appl Environ Microbiol. 2007 Mar;73(5):1576-85. Epub 2007 Jan 12.

47.

Obesity alters gut microbial ecology.

Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI.

Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):11070-5. Epub 2005 Jul 20.

49.

Molecular and cultural assessment of chytrid and Spizellomyces populations in grassland soils.

Lozupone CA, Klein DA.

Mycologia. 2002 May-Jun;94(3):411-20.

PMID:
21156512
50.

The molecular basis of nuclear genetic code change in ciliates.

Lozupone CA, Knight RD, Landweber LF.

Curr Biol. 2001 Jan 23;11(2):65-74.

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