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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). pii: e01578-15. doi: 10.1128/mBio.01578-15.


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.


Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats.

Sherrill-Mix S, Ocwieja KE, Bushman FD.

Retrovirology. 2015 Sep 17;12(1):79. doi: 10.1186/s12977-015-0205-1.


BIRC2/cIAP1 Is a Negative Regulator of HIV-1 Transcription and Can Be Targeted by Smac Mimetics to Promote Reversal of Viral Latency.

Pache L, Dutra MS, Spivak AM, Marlett JM, Murry JP, Hwang Y, Maestre AM, Manganaro L, Vamos M, Teriete P, Martins LJ, König R, Simon V, Bosque A, Fernandez-Sesma A, Cosford ND, Bushman FD, Young JA, Planelles V, Chanda SK.

Cell Host Microbe. 2015 Sep 9;18(3):345-53. doi: 10.1016/j.chom.2015.08.009.


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.


Multi-center Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals.

Beck JM, Schloss PD, Venkataraman A, Twigg Iii H, 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 Aug 6. [Epub ahead of print]


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.


Host Factors in Retroviral Integration and the Selection of Integration Target Sites.

Craigie R, Bushman FD.

Microbiol Spectr. 2014 Dec;2(6). doi: 10.1128/microbiolspec.MDNA3-0026-2014.


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.


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.


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):e00648. doi: 10.1128/mBio.00648-15.


Inflammation-associated microbiota in pediatric eosinophilic esophagitis.

Benitez AJ, Hoffmann C, Muir AB, Dods KK, Spergel JM, Bushman FD, Wang ML.

Microbiome. 2015 Jun 1;3:23. doi: 10.1186/s40168-015-0085-6. eCollection 2015.


Coherence analysis discriminates between retroviral integration patterns in CD34(+) cells transduced under differing clinical trial conditions.

Hallwirth CV, Garg G, Peters TJ, Kramer BA, Malani NV, Hyman J, Ruan X, Ginn SL, Hetherington NA, Veeravalli L, Shahab A, Ranganathan S, Wei CL, Liddle C, Thrasher AJ, Bushman FD, Buckley MJ, Alexander IE.

Mol Ther Methods Clin Dev. 2015 Apr 29;2:15015. doi: 10.1038/mtm.2015.15. eCollection 2015.


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 Aug;21(8):1786-93. doi: 10.1097/MIB.0000000000000426.


Structural and sequencing analysis of local target DNA recognition by MLV integrase.

Aiyer S, Rossi P, Malani N, Schneider WM, Chandar A, Bushman FD, Montelione GT, Roth MJ.

Nucleic Acids Res. 2015 Jun 23;43(11):5647-63. doi: 10.1093/nar/gkv410. Epub 2015 May 12.


Genome editing technologies: defining a path to clinic.

Corrigan-Curay J, O'Reilly M, Kohn DB, Cannon PM, Bao G, Bushman FD, Carroll D, Cathomen T, Joung JK, Roth D, Sadelain M, Scharenberg AM, von Kalle C, Zhang F, Jambou R, Rosenthal E, Hassani M, Singh A, Porteus MH.

Mol Ther. 2015 May;23(5):796-806. doi: 10.1038/mt.2015.54. No abstract available.


Outcomes following gene therapy in patients with severe Wiskott-Aldrich syndrome.

Hacein-Bey Abina S, Gaspar HB, Blondeau J, Caccavelli L, Charrier S, Buckland K, Picard C, Six E, Himoudi N, Gilmour K, McNicol AM, Hara H, Xu-Bayford J, Rivat C, Touzot F, Mavilio F, Lim A, Treluyer JM, Héritier S, Lefrère F, Magalon J, Pengue-Koyi I, Honnet G, Blanche S, Sherman EA, Male F, Berry C, Malani N, Bushman FD, Fischer A, Thrasher AJ, Galy A, Cavazzana M.

JAMA. 2015 Apr 21;313(15):1550-63. doi: 10.1001/jama.2015.3253.


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.


A reverse transcription loop-mediated isothermal amplification assay optimized to detect multiple HIV subtypes.

Ocwieja KE, Sherrill-Mix S, Liu C, Song J, Bau H, Bushman FD.

PLoS One. 2015 Feb 12;10(2):e0117852. doi: 10.1371/journal.pone.0117852. eCollection 2015.


Nuclemeter: a reaction-diffusion based method for quantifying nucleic acids undergoing enzymatic amplification.

Liu C, Sadik MM, Mauk MG, Edelstein PH, Bushman FD, Gross R, Bau HH.

Sci Rep. 2014 Dec 5;4:7335. doi: 10.1038/srep07335.

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