2016

Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches
Sartor RB, Wu GD.  Gastroenterology. 2017 Feb;152(2):327-339.e4. doi: 10.1053/j.gastro.2016.10.012. Epub 2016 Oct 18. Review. PubMed PMID: 27769810; PubMed Central PMCID: PMC5511756.

Commensal Microbes Induce Serum IgA Responses that Protect against Polymicrobial Sepsis.
Cell Host. Wilmore JR, Gaudette BT, Gomez Atria D, Hashemi T, Jones DD, Gardner CA, Cole SD, Misic AM, Beiting DP, Allman D.  Microbe. 2018 Feb 7. pii: S1931-3128(18)30040-4. doi: 10.1016/j.chom.2018.01.005. [Epub ahead of print] PubMed PMID: 29478774.

East Meets West: The Increasing Incidence of Inflammatory Bowel Disease in Asia as a Paradigm for Environmental Effects on the Pathogenesis of Immune-Mediated Disease
Yang Y, Owyang C, Wu GD. Gastroenterology. 2016 Dec;151(6):e1-e5. doi: 10.1053/j.gastro.2016.10.034. Epub 2016 Nov 1. PubMed PMID: 27810482; PubMed Central PMCID: PMC5439349.

Health Disparities and the Microbiome
Findley K, Williams DR, Grice EA, Bonham VL. Trends Microbiol. 2016 Nov;24(11):847-850. doi: 10.1016/j.tim.2016.08.001. Epub 2016 Oct 3. PubMed PMID: 27712950; PubMed Central PMCID: PMC5695575.

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework
Zheng Q, Grice EA.  PLoS Comput Biol. 2016 Oct 5;12(10):e1005096. doi: 10.1371/journal.pcbi.1005096. eCollection 2016 Oct. PubMed PMID: 27706155; PubMed Central PMCID: PMC5051939.

Redefining the Chronic-Wound Microbiome: Fungal Communities Are Prevalent, Dynamic, and Associated with Delayed Healing
Kalan L, Loesche M, Hodkinson BP, Heilmann K, Ruthel G, Gardner SE, Grice EA.  MBio. 2016 Sep 6;7(5). pii: e01058-16. doi: 10.1128/mBio.01058-16. PubMed PMID: 27601572; PubMed Central PMCID: PMC5013295.

Glial-cell-derived neuroregulators control type 3 innate lymphoid cells and gut defence
Ibiza S, García-Cassani B, Ribeiro H, Carvalho T, Almeida L, Marques R, Misic AM, Bartow-McKenney C, Larson DM, Pavan WJ, Eberl G, Grice EA, Veiga-Fernandes H.  Nature. 2016 Jul 21;535(7612):440-443. doi: 10.1038/nature18644. Epub 2016 Jul 13. PubMed PMID: 27409807; PubMed Central PMCID: PMC4962913.

A Summary of the First HIV Microbiome Workshop 2015.
Williams B, Mirmonsef P, Boucher CA, Bushman F, Carrington-Lawrence S, Collman RG, Dandekar S, Dang Q, Malaspina A, Paredes R, Stone A, Landay A. AIDS Res Hum Retroviruses. 2016 Jul 14.  PMID: 27267576.

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. PMID: 27338728.

A Model-Based Approach For Species Abundance Quantification Based On Shotgun Metagenomic Data.
Chen EZ, Bushman FD, Li H. Stat Biosci. 2017 Jun;9(1):13-27. doi: 10.1007/s12561-016-9148-x. Epub 2016 May 16. PubMed PMID: 28959368; PubMed Central PMCID: PMC5612490.

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. PMID: 27176607.

Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation.
Chehoud C, Dryga A, Hwang Y, Nagy-Szakal D, Hollister EB, Luna RA, Versalovic J, Kellermayer R, Bushman FD. MBio. 2016 Mar 29;7(2):e00322. doi: 10.1128/mBio.00322-16. PMID: 27025251.

Genomes of cryptic chimpanzee Plasmodium species reveal key evolutionary events leading to human malaria.
Sundararaman SA, Plenderleith LJ, Liu W, Loy DE, Learn GH, Li Y, Shaw KS, Ayouba A, Peeters M, Speede S, Shaw GM, Bushman FD, Brisson D, Rayner JC, Sharp PM, Hahn BH. Nat Commun. 2016 Mar 22;7:11078. doi: 10.1038/ncomms11078. PMID: 27002652.

Peptidoglycan from the gut microbiota governs the lifespan of circulating phagocytes at homeostasis.
Hergott CB, Roche AM, Tamashiro E, Clarke TB, Bailey AG, Laughlin A, Bushman FD, Weiser JN. Blood. 2016 May 19;127(20):2460-71. doi: 10.1182/blood-2015-10-675173. Epub 2016 Mar 17. PMID: 26989200.

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. PMID: 26865050.

Differential Thiol-Based Switches Jump-Start Vibrio cholerae Pathogenesis.
Liu Z, Wang H, Zhou Z, Naseer N, Xiang F, Kan B, Goulian M, Zhu J. Cell Rep. 2016 Jan 12;14(2):347-54. doi: 10.1016/j.celrep.2015.12.038. Epub 2015 Dec 31. PubMed PMID: 26748713; PubMed Central PMCID: PMC4715633.

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