2012

Antiviral effects of autologous CD4 T cells genetically modified with a conditionally replicating lentiviral vector expressing long antisense to HIV.
Tebas P, Stein D, Binder-Scholl G, Mukherjee R, Brady T, Rebello T, Humeau L, Kalos M, Papasavvas E, Montaner LJ, Schullery D, Shaheen F, Brennan AL, Zheng Z, Cotte J, Slepushkin V, Veloso E, Mackley A, Hwang WT, Aberra F, Zhan J, Boyer J, Collman RG,Bushman FD, Levine BL, June CH. Blood. 2013 Feb 28;121(9):1524-33. doi: 10.1182/blood-2012-07-447250. Epub 2012 Dec 20. Erratum in: Blood. 2014 Jul 24;124(4):663.

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.

Structure-constrained sparse canonical correlation analysis with an application to microbiome data analysis.
Chen J, Bushman FD, Lewis JD, Wu GD, Li H. Biostatistics. 2013 Apr;14(2):244-58. doi: 10.1093/biostatistics/kxs038. Epub 2012 Oct 15.

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.

Conservation of gene cassettes among diverse viruses of the human gut.
Minot S, Wu GD, Lewis JD, Bushman FD. PLoS One. 2012;7(8):e42342. doi: 10.1371/journal.pone.0042342. Epub 2012 Aug 10.

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.

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.

Innate lymphoid cells promote anatomical containment of lymphoid-resident commensal bacteria.
Sonnenberg GF, Monticelli LA, Alenghat T, Fung TC, Hutnick NA, Kunisawa J, Shibata N, Grunberg S, Sinha R, Zahm AM, Tardif MR, Sathaliyawala T, Kubota M, Farber DL, Collman RG, Shaked A, Fouser LA, Weiner DB, Tessier PA, Friedman JR, Kiyono H,Bushman FD, Chang KM, Artis D. Science. 2012 Jun 8;336(6086):1321-5. doi: 10.1126/science.1222551. Epub 2012 Jun 6.

Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis.
Kong HH, Oh J, Deming C, Conlan S, Grice EA, Beatson MA, Nomicos E, Polley EC, Komarow HD; NISC Comparative Sequence Program, Murray PR, Turner ML, Segre JA. Genome Res. 2012 May;22(5):850-9. doi: 10.1101/gr.131029.111. Epub 2012 Feb 6.

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