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Results: 1 to 20 of 21

1.

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA.

Kelly BJ, Gross R, Bittinger K, Sherrill-Mix S, Lewis JD, Collman RG, Bushman FD, Li H.

Bioinformatics. 2015 Mar 29. pii: btv183. [Epub ahead of print]

PMID:
25819674
2.

Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production.

Wu GD, Compher C, Chen EZ, Smith SA, Shah RD, Bittinger K, Chehoud C, Albenberg LG, Nessel L, Gilroy E, Star J, Weljie AM, Flint HJ, Metz DC, Bennett MJ, Li H, Bushman FD, Lewis JD.

Gut. 2014 Nov 26. pii: gutjnl-2014-308209. doi: 10.1136/gutjnl-2014-308209. [Epub ahead of print]

PMID:
25431456
3.

Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients.

Young JC, Chehoud C, Bittinger K, Bailey A, Diamond JM, Cantu E, Haas AR, Abbas A, Frye L, Christie JD, Bushman FD, Collman RG.

Am J Transplant. 2015 Jan;15(1):200-9. doi: 10.1111/ajt.13031. Epub 2014 Nov 17.

PMID:
25403800
4.

Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing.

Bittinger K, Charlson ES, Loy E, Shirley DJ, Haas AR, Laughlin A, Yi Y, Wu GD, Lewis JD, Frank I, Cantu E, Diamond JM, Christie JD, Collman RG, Bushman FD.

Genome Biol. 2014;15(10):487.

5.

Coinfection. Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation.

Osborne LC, Monticelli LA, Nice TJ, Sutherland TE, Siracusa MC, Hepworth MR, Tomov VT, Kobuley D, Tran SV, Bittinger K, Bailey AG, Laughlin AL, Boucher JL, Wherry EJ, Bushman FD, Allen JE, Virgin HW, Artis D.

Science. 2014 Aug 1;345(6196):578-82. doi: 10.1126/science.1256942. Epub 2014 Jul 17.

PMID:
25082704
6.

Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota.

Albenberg L, Esipova TV, Judge CP, Bittinger K, Chen J, Laughlin A, Grunberg S, Baldassano RN, Lewis JD, Li H, Thom SR, Bushman FD, Vinogradov SA, Wu GD.

Gastroenterology. 2014 Nov;147(5):1055-63.e8. doi: 10.1053/j.gastro.2014.07.020. Epub 2014 Jul 18.

PMID:
25046162
7.

Temporal dynamics in the ruminal microbiome of dairy cows during the transition period.

Pitta DW, Kumar S, Vecchiarelli B, Shirley DJ, Bittinger K, Baker LD, Ferguson JD, Thomsen N.

J Anim Sci. 2014 Sep;92(9):4014-22. doi: 10.2527/jas.2014-7621. Epub 2014 Jul 14.

PMID:
25023800
8.

Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment.

Dollive S, Chen YY, Grunberg S, Bittinger K, Hoffmann C, Vandivier L, Cuff C, Lewis JD, Wu GD, Bushman FD.

PLoS One. 2013 Aug 19;8(8):e71806. doi: 10.1371/journal.pone.0071806. eCollection 2013.

9.

Dendritic cell expression of the signaling molecule TRAF6 is critical for gut microbiota-dependent immune tolerance.

Han D, Walsh MC, Cejas PJ, Dang NN, Kim YF, Kim J, Charrier-Hisamuddin L, Chau L, Zhang Q, Bittinger K, Bushman FD, Turka LA, Shen H, Reizis B, Defranco AL, Wu GD, Choi Y.

Immunity. 2013 Jun 27;38(6):1211-22. doi: 10.1016/j.immuni.2013.05.012. Epub 2013 Jun 20.

10.

Plasmodium falciparum-like parasites infecting wild apes in southern Cameroon do not represent a recurrent source of human malaria.

Sundararaman SA, Liu W, Keele BF, Learn GH, Bittinger K, Mouacha F, Ahuka-Mundeke S, Manske M, Sherrill-Mix S, Li Y, Malenke JA, Delaporte E, Laurent C, Mpoudi Ngole E, Kwiatkowski DP, Shaw GM, Rayner JC, Peeters M, Sharp PM, Bushman FD, Hahn BH.

Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):7020-5. doi: 10.1073/pnas.1305201110. Epub 2013 Apr 8.

11.

Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts.

Charlson ES, Bittinger K, Chen J, Diamond JM, Li H, Collman RG, Bushman FD.

PLoS One. 2012;7(9):e42786. doi: 10.1371/journal.pone.0042786. Epub 2012 Sep 6.

12.

Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota after lung transplant.

Charlson ES, Diamond JM, Bittinger K, Fitzgerald AS, Yadav A, Haas AR, Bushman FD, Collman RG.

Am J Respir Crit Care Med. 2012 Sep 15;186(6):536-45. doi: 10.1164/rccm.201204-0693OC. Epub 2012 Jul 12.

13.

A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples.

Dollive S, Peterfreund GL, Sherrill-Mix S, Bittinger K, Sinha R, Hoffmann C, Nabel CS, Hill DA, Artis D, Bachman MA, Custers-Allen R, Grunberg S, Wu GD, Lewis JD, Bushman FD.

Genome Biol. 2012 Jul 3;13(7):R60. doi: 10.1186/gb-2012-13-7-r60.

14.

Associating microbiome composition with environmental covariates using generalized UniFrac distances.

Chen J, Bittinger K, Charlson ES, Hoffmann C, Lewis J, Wu GD, Collman RG, Bushman FD, Li H.

Bioinformatics. 2012 Aug 15;28(16):2106-13. doi: 10.1093/bioinformatics/bts342. Epub 2012 Jun 17.

15.

Linking long-term dietary patterns with gut microbial enterotypes.

Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD.

Science. 2011 Oct 7;334(6052):105-8. doi: 10.1126/science.1208344. Epub 2011 Sep 1.

16.

Switching between raltegravir resistance pathways analyzed by deep sequencing.

Mukherjee R, Jensen ST, Male F, Bittinger K, Hodinka RL, Miller MD, Bushman FD.

AIDS. 2011 Oct 23;25(16):1951-9. doi: 10.1097/QAD.0b013e32834b34de.

17.

Topographical continuity of bacterial populations in the healthy human respiratory tract.

Charlson ES, Bittinger K, Haas AR, Fitzgerald AS, Frank I, Yadav A, Bushman FD, Collman RG.

Am J Respir Crit Care Med. 2011 Oct 15;184(8):957-63. doi: 10.1164/rccm.201104-0655OC. Epub 2011 Jun 16.

18.

Disordered microbial communities in the upper respiratory tract of cigarette smokers.

Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD, Collman RG.

PLoS One. 2010 Dec 20;5(12):e15216. doi: 10.1371/journal.pone.0015216.

19.

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags.

Wu GD, Lewis JD, Hoffmann C, Chen YY, Knight R, Bittinger K, Hwang J, Chen J, Berkowsky R, Nessel L, Li H, Bushman FD.

BMC Microbiol. 2010 Jul 30;10:206. doi: 10.1186/1471-2180-10-206.

20.

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.

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