2015

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. PubMed PMID: 28846439; PubMed Central PMCID: PMC5768903.

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. PMID: 26701907.

Destabilization of the gut microbiome marks the end-stage of simian immunodeficiency virus infection in wild chimpanzees.
Barbian HJ, Li Y, Ramirez M, Klase Z, Lipende I, Mjungu D, Moeller AH, Wilson ML, Pusey AE, Lonsdorf EV, Bushman FD, Hahn BH. Am J Primatol. 2015 Dec 16. doi: 10.1002/ajp.22515. PMID: 26676710.

Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals.
Beck JM, Schloss PD, Venkataraman A, Twigg H 3rd, Jablonski KA, Bushman FD, Campbell TB, Charlson ES, Collman RG, Crothers K, Curtis JL, Drews KL, Flores SC, Fontenot AP, Foulkes MA, Frank I, Ghedin E, Huang L, Lynch SV, Morris A, Palmer BE, Schmidt TM, Sodergren E, Weinstock GM, Young VB; Lung HIV Microbiome Project. Am J Respir Crit Care Med. 2015 Dec 1;192(11):1335-44. doi: 10.1164/rccm.201501-0128OC. PMID: 26247840.

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. PMID: 26288001.

Microbiota-Dependent Priming of Antiviral Intestinal Immunity in Drosophila.
Sansone CL, Cohen J, Yasunaga A, Xu J, Osborn G, Subramanian H, Gold B, Buchon N, Cherry S. Cell Host Microbe. 2015 Nov 11;18(5):571-81. doi: 10.1016/j.chom.2015.10.010.
PMID: 26567510.

The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome.
Hannigan GD, Meisel JS, Tyldsley AS, Zheng Q, Hodkinson BP, SanMiguel AJ, Minot S, Bushman FD, Grice EA. MBio. 2015 Oct 20;6(5):e01578-15. doi: 10.1128/mBio.01578-15. PMID: 26489866.

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. PubMed PMID: 26468751.

Rationale and Design of the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) Study. Sarcoidosis Protocol.
Moller DR, Koth LL, Maier LA, Morris A, Drake W, Rossman M, Leader JK, Collman RG, Hamzeh N, Sweiss NJ, Zhang Y, O’Neal S, Senior RM, Becich M, Hochheiser HS, Kaminski N, Wisniewski SR, Gibson KF; GRADS Sarcoidosis Study Group. Ann Am Thorac Soc. 2015 Oct;12(10):1561-71. doi: 10.1513/AnnalsATS.201503-172OT.  PMID: 26193069.

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 Aug 17. [Epub ahead of print] PubMed PMID: 26288001.

Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock.
Liang X, Bushman FD, FitzGerald GA. Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):10479-84. doi: 10.1073/pnas.1501305112. Epub 2015 Aug 3. PMID: 26240359.

Engineering the gut microbiota to treat hyperammonemia.
Shen TD, 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 Jun 22. pii: 79214. doi: 10.1172/JCI79214.

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. Des. 2015 Jun 16.

Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9.
Bryson AL, Hwang Y, Sherrill-Mix S, Wu GD, Lewis JD, Black L, Clark TA, Bushman FD. MBio. 2015 Jun 16;6(3). pii: e00648-15. doi: 10.1128/mBio.00648-15

Comparative Effectiveness of Nutritional and Biological Therapy in North American Children with Active Crohn’s Disease.
Lee D, Baldassano RN, Otley AR, Albenberg L, Griffiths AM, Compher C, Chen EZ, Li H, Gilroy E, Nessel L, Grant A, Chehoud C, Bushman FD, Wu GD, Lewis JD. Inflamm Bowel Dis. 2015 May 12. [Epub ahead of print]

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.

The shared microbiota of humans and companion animals as evaluated from Staphylococcus carriage sites.
Misic AM, Davis MF, Tyldsley AS, Hodkinson BP, Tolomeo P, Hu B, Nachamkin I, Lautenbach E, Morris DO, Grice EA. Microbiome. 2015 Jan 23;3:2. doi: 10.1186/s40168-014-0052-7. eCollection 2015.

Current Concepts and Ongoing Research in the Prevention and Treatment of Open Fracture Infections.
Hannigan GD, Pulos N, Grice EA, Mehta S. Adv Wound Care (New Rochelle). 2015 Jan 1;4(1):59-74. Review.

Next-Generation Sequencing: A Review of Technologies and Tools for Wound Microbiome Research.
Hodkinson BP, Grice EA. Adv Wound Care (New Rochelle). 2015 Jan 1;4(1):50-58. Review.

Ethnic/racial and genetic influences on cerumen odorant profiles.
Prokop-Prigge KA, Mansfield CJ, Parker MR, Thaler E, Grice EA, Wysocki CJ, Preti G. J Chem Ecol. 2015 Jan;41(1):67-74. doi: 10.1007/s10886-014-0533-y. Epub 2014 Dec 13.

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