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Items: 46

1.

Gut microbiota modulates adoptive cell therapy via CD8α dendritic cells and IL-12.

Uribe-Herranz M, Bittinger K, Rafail S, Guedan S, Pierini S, Tanes C, Ganetsky A, Morgan MA, Gill S, Tanyi JL, Bushman FD, June CH, Facciabene A.

JCI Insight. 2018 Feb 22;3(4). pii: 94952. doi: 10.1172/jci.insight.94952. [Epub ahead of print]

PMID:
29467322
2.

A Pilot Characterization of the Human Chronobiome.

Skarke C, Lahens NF, Rhoades SD, Campbell A, Bittinger K, Bailey A, Hoffmann C, Olson RS, Chen L, Yang G, Price TS, Moore JH, Bushman FD, Greene CS, Grant GR, Weljie AM, FitzGerald GA.

Sci Rep. 2017 Dec 7;7(1):17141. doi: 10.1038/s41598-017-17362-6.

3.

A role for bacterial urease in gut dysbiosis and Crohn's disease.

Ni J, Shen TD, Chen EZ, Bittinger K, Bailey A, Roggiani M, Sirota-Madi A, Friedman ES, Chau L, Lin A, Nissim I, Scott J, Lauder A, Hoffmann C, Rivas G, Albenberg L, Baldassano RN, Braun J, Xavier RJ, Clish CB, Yudkoff M, Li H, Goulian M, Bushman FD, Lewis JD, Wu GD.

Sci Transl Med. 2017 Nov 15;9(416). pii: eaah6888. doi: 10.1126/scitranslmed.aah6888.

4.

Microbial Lineages in Sarcoidosis. A Metagenomic Analysis Tailored for Low-Microbial Content Samples.

Clarke EL, Lauder AP, Hofstaedter CE, Hwang Y, Fitzgerald AS, Imai I, Biernat W, Rękawiecki B, Majewska H, Dubaniewicz A, Litzky LA, Feldman MD, Bittinger K, Rossman MD, Patterson KC, Bushman FD, Collman RG.

Am J Respir Crit Care Med. 2018 Jan 15;197(2):225-234. doi: 10.1164/rccm.201705-0891OC.

PMID:
28846439
5.

Protective major histocompatibility complex allele prevents type 1 diabetes by shaping the intestinal microbiota early in ontogeny.

Silverman M, Kua L, Tanca A, Pala M, Palomba A, Tanes C, Bittinger K, Uzzau S, Benoist C, Mathis D.

Proc Natl Acad Sci U S A. 2017 Sep 5;114(36):9671-9676. doi: 10.1073/pnas.1712280114. Epub 2017 Aug 22.

PMID:
28831005
6.

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease.

Lewis JD, Chen EZ, Baldassano RN, Otley AR, Griffiths AM, Lee D, Bittinger K, Bailey A, Friedman ES, Hoffmann C, Albenberg L, Sinha R, Compher C, Gilroy E, Nessel L, Grant A, Chehoud C, Li H, Wu GD, Bushman FD.

Cell Host Microbe. 2017 Aug 9;22(2):247. doi: 10.1016/j.chom.2017.07.011. No abstract available.

PMID:
28799909
7.

Diabetes Enhances IL-17 Expression and Alters the Oral Microbiome to Increase Its Pathogenicity.

Xiao E, Mattos M, Vieira GHA, Chen S, Corrêa JD, Wu Y, Albiero ML, Bittinger K, Graves DT.

Cell Host Microbe. 2017 Jul 12;22(1):120-128.e4. doi: 10.1016/j.chom.2017.06.014.

PMID:
28704648
8.

Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome.

Pannaraj PS, Li F, Cerini C, Bender JM, Yang S, Rollie A, Adisetiyo H, Zabih S, Lincez PJ, Bittinger K, Bailey A, Bushman FD, Sleasman JW, Aldrovandi GM.

JAMA Pediatr. 2017 Jul 1;171(7):647-654. doi: 10.1001/jamapediatrics.2017.0378.

PMID:
28492938
9.

Optimizing methods and dodging pitfalls in microbiome research.

Kim D, Hofstaedter CE, Zhao C, Mattei L, Tanes C, Clarke E, Lauder A, Sherrill-Mix S, Chehoud C, Kelsen J, Conrad M, Collman RG, Baldassano R, Bushman FD, Bittinger K.

Microbiome. 2017 May 5;5(1):52. doi: 10.1186/s40168-017-0267-5. Review.

10.

INSPIIRED: A Pipeline for Quantitative Analysis of Sites of New DNA Integration in Cellular Genomes.

Sherman E, Nobles C, Berry CC, Six E, Wu Y, Dryga A, Malani N, Male F, Reddy S, Bailey A, Bittinger K, Everett JK, Caccavelli L, Drake MJ, Bates P, Hacein-Bey-Abina S, Cavazzana M, Bushman FD.

Mol Ther Methods Clin Dev. 2016 Dec 18;4:39-49. doi: 10.1016/j.omtm.2016.11.002. eCollection 2017 Mar 17.

11.

INSPIIRED: Quantification and Visualization Tools for Analyzing Integration Site Distributions.

Berry CC, Nobles C, Six E, Wu Y, Malani N, Sherman E, Dryga A, Everett JK, Male F, Bailey A, Bittinger K, Drake MJ, Caccavelli L, Bates P, Hacein-Bey-Abina S, Cavazzana M, Bushman FD.

Mol Ther Methods Clin Dev. 2016 Dec 18;4:17-26. doi: 10.1016/j.omtm.2016.11.003. eCollection 2017 Mar 17.

12.

Normalization and microbial differential abundance strategies depend upon data characteristics.

Weiss S, Xu ZZ, Peddada S, Amir A, Bittinger K, Gonzalez A, Lozupone C, Zaneveld JR, Vázquez-Baeza Y, Birmingham A, Hyde ER, Knight R.

Microbiome. 2017 Mar 3;5(1):27. doi: 10.1186/s40168-017-0237-y.

13.

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota.

Lauder AP, Roche AM, Sherrill-Mix S, Bailey A, Laughlin AL, Bittinger K, Leite R, Elovitz MA, Parry S, Bushman FD.

Microbiome. 2016 Jun 23;4(1):29. doi: 10.1186/s40168-016-0172-3.

14.

Dietary Regulation of the Gut Microbiota Engineered by a Minimal Defined Bacterial Consortium.

Shen TC, Chehoud C, Ni J, Hsu E, Chen YY, Bailey A, Laughlin A, Bittinger K, Bushman FD, Wu GD.

PLoS One. 2016 May 13;11(5):e0155620. doi: 10.1371/journal.pone.0155620. eCollection 2016.

15.

A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms.

Indugu N, Bittinger K, Kumar S, Vecchiarelli B, Pitta D.

PeerJ. 2016 Feb 4;4:e1599. doi: 10.7717/peerj.1599. eCollection 2016.

16.

Composition and dynamics of the respiratory tract microbiome in intubated patients.

Kelly BJ, Imai I, Bittinger K, Laughlin A, Fuchs BD, Bushman FD, Collman RG.

Microbiome. 2016 Feb 11;4:7. doi: 10.1186/s40168-016-0151-8.

17.

Bidirectional interactions between indomethacin and the murine intestinal microbiota.

Liang X, Bittinger K, Li X, Abernethy DR, Bushman FD, FitzGerald GA.

Elife. 2015 Dec 23;4:e08973. doi: 10.7554/eLife.08973.

18.

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease.

Lewis JD, Chen EZ, Baldassano RN, Otley AR, Griffiths AM, Lee D, Bittinger K, Bailey A, Friedman ES, Hoffmann C, Albenberg L, Sinha R, Compher C, Gilroy E, Nessel L, Grant A, Chehoud C, Li H, Wu GD, Bushman FD.

Cell Host Microbe. 2015 Oct 14;18(4):489-500. doi: 10.1016/j.chom.2015.09.008. Erratum in: Cell Host Microbe. 2017 Aug 9;22(2):247.

19.

Alterations of the Subgingival Microbiota in Pediatric Crohn's Disease Studied Longitudinally in Discovery and Validation Cohorts.

Kelsen J, Bittinger K, Pauly-Hubbard H, Posivak L, Grunberg S, Baldassano R, Lewis JD, Wu GD, Bushman FD.

Inflamm Bowel Dis. 2015 Dec;21(12):2797-805. doi: 10.1097/MIB.0000000000000557.

20.

Engineering the gut microbiota to treat hyperammonemia.

Shen TC, Albenberg L, Bittinger K, Chehoud C, Chen YY, Judge CA, Chau L, Ni J, Sheng M, Lin A, Wilkins BJ, Buza EL, Lewis JD, Daikhin Y, Nissim I, Yudkoff M, Bushman FD, Wu GD.

J Clin Invest. 2015 Jul 1;125(7):2841-50. doi: 10.1172/JCI79214. Epub 2015 Jun 22.

21.

Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease.

Chehoud C, Albenberg LG, Judge C, Hoffmann C, Grunberg S, Bittinger K, Baldassano RN, Lewis JD, Bushman FD, Wu GD.

Inflamm Bowel Dis. 2015 Aug;21(8):1948-56. doi: 10.1097/MIB.0000000000000454.

22.

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 Aug 1;31(15):2461-8. doi: 10.1093/bioinformatics/btv183. Epub 2015 Mar 29.

23.

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. 2016 Jan;65(1):63-72. doi: 10.1136/gutjnl-2014-308209. Epub 2014 Nov 26.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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
29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

Spectral signatures of inter-system crossing mediated by energetically distant doorway levels: examples from the acetylene S1 state.

Bittinger KL, Virgo WL, Field RW.

J Phys Chem A. 2011 Nov 3;115(43):11921-43. doi: 10.1021/jp2037894. Epub 2011 Sep 29.

PMID:
21913705
37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

42.

Deconvolution of spectral data using a doorway-coupling model Hamiltonian.

Bittinger KL, Field RW.

J Chem Phys. 2010 Apr 7;132(13):134302. doi: 10.1063/1.3357311.

PMID:
20387928
43.

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.

44.

PyNAST: a flexible tool for aligning sequences to a template alignment.

Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R.

Bioinformatics. 2010 Jan 15;26(2):266-7. doi: 10.1093/bioinformatics/btp636. Epub 2009 Nov 13.

45.

Contrasting singlet-triplet dynamical behavior of two vibrational levels of the acetylene S1 2(1)3(1)B2 polyad.

Virgo WL, Bittinger KL, Steeves AH, Field RW.

J Phys Chem A. 2007 Dec 13;111(49):12534-7. Epub 2007 Oct 6.

PMID:
17918920
46.

Angle-energy distributions of Penning ions in crossed molecular beams. IV. He*(21 S,2 3S)+H2-->He+H2+ +e-.

Gulati K, Longley EJ, Dorko MJ, Bittinger KL, Siska PE.

J Chem Phys. 2004 May 8;120(18):8485-93.

PMID:
15267774

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