Category Title Journal Year
Reports of Original Research Modeling HIV-1 integrase complexes based on their hydrodynamic properties.
A. A. Podtelezhnikov, K. Gao, F. D. Bushman, A. McCammon. (2003) Modeling HIV-1 Integrase Complexes Based on Their Hydrodynamic Structure. Biopolymers, 68, 110-121. PMID 12579583.
Biopolymers. 2003
Reports of Original Research Poly(ADP-ribose) polymerase 1 is not strictly required for infection of murine cells by retroviruses.
A. C. Siva and F. D. Bushman. (2002) PARP-1 is not strictly required for infection of murine cells by retroviruses. J. Virol., 76, p. 11904-11910. PMID 12414932.
J Virol. 2002
Review Articles Retroviral DNA integration: HIV and the role of LEDGF/p75.
A. Ciuffi and F. D. Bushman. (2006) Retroviral DNA integration: HIV and the role of LEDGF/p75. Trends Genet. Epub. PMID 16730094.
Trends Genet. 2006
Reports of Original Research A role for LEDGF/p75 in targeting HIV DNA integration.
A. Ciuffi, M. Llano, E. Poeschla, H. Marshall, C. Hoffmann, J. Leipzig, P. Shinn, J. Ecker, F. Bushman. (2005) A role for LEDGF/p75 in targeting HIV DNA integration. Nat. Med. 11, 1287-1289. PMID 16311605.
Nat Med. 2005
Reports of Original Research Integration site selection by HIV-based vectors in dividing and growth-arrested IMR-90 lung fibroblasts.
A. Ciuffi, R. S. Mitchell, C. Hoffmann, J. Leipzig, P. Shinn, J. R. Ecker, F. D. Bushman. (2005) Integration site selecetion by HIV-based vectors in dividing and growth-arrested IMR-90 lung fibroblasts. Mol. Therapy 13, 366-73. PMID 16325473.
Mol Ther. 2006
Reports of Original Research Modulating target site selection during human immunodeficiency virus DNA integration in vitro with an engineered tethering factor.
A. Ciuffi, T. Diamond, Y. Hwang, H. M. Marshall, and F. D. Bushman. Fusions of LEDGF/p75 to lambda repressor promote HIV DNA integration near lambda operators in vitro. Hum. Gene Ther. 2006 Sept 17(9): 960-7. PMID 16972764.
Hum Gene Ther. 2006
Reports of Original Research Identification of discrete functional domains of HIV-1 integrase and their organization within an active multimeric complex.
A. Engelman, F.D. Bushman and R. Craigie. (1993) Identification of discrete functional domains of HIV-1 integrase and their organization within an active multimeric complex. EMBO J. 12: 3269-3276. PMID 8344264.
EMBO J. 1993
Reports of Original Research HIV-1 integration in the human genome favors active genes and local hotspots.
A. R. W. Schröder, P. Shinn, H. Chen, C. Berry, J. R. Ecker, and F. D. Bushman. (2002) HIV-1 Integration in the Human Genome Favors Active Genes and Local Hotspots. Cell 110, 521-529. PMID 12202041. (see also cover)
Cell. 2002
Reports of Original Research Construction and analysis of cells lacking the HMGA gene family.
B. Beitzel and F. D. Bushman. (2003) Construction and analysis of cells lacking the HMGA gene family. Nuc. Acids Res. 31, 5025-5032. PMID 12930952.
Nucleic Acids Res. 2003
Reports of Original Research Cell cycle arrest in G2/M promotes early steps of infection by human immunodeficiency virus.
B. Groschel and F. D. Bushman. (2005) Cell cycle arrest in G/M promotes early steps of infection by human immunodeficiency virus. J. Virol. 79, 5695-5704. PMID 15827184.
J Virol. 2005
Reports of Original Research Gene transfer in humans using a conditionally replicating lentiviral vector.
B. L. Levine, L. M. Humeau, J. Boyer, R.-R. MacGregor, T. Rebello, X. Lu, G. K. Binder, V. Slepushkin, J. R. Mascola, F. D. Bushman, B. Dropulic, and C. H. June. Sustained gene transfer in humans using lentiviral vectors. Proc Natl Acad Sci USA. 2006 Nov 14;103(46):17372-7. PMID 17090675.
Proc Natl Acad Sci U S A. 2006
Reports of Original Research The interferon response inhibits HIV particle production by induction of TRIM22.
Barr SD, Smiley JR, Bushman FD. The interferon response inhibits HIV particle production by induction of TRIM22. PLoS Pathog. 2008 Feb 29;4(2):e1000007. PMID: 18389079.
PLoS Pathog. 2008
Reports of Original Research Estimating abundances of retroviral insertion sites from DNA fragment length data.
Berry CC, Gillet NA, Melamed A, Gormley N, Bangham CR, Bushman FD. (2012) Estimating abundances of retroviral insertion sites from DNA fragment length data. Bioinformatics. 2012 Mar 15;28(6):755-62. Epub 2012 Jan 11. PMID 22238265.
Bioinformatics. 2012
Reports of Original Research HIV integration site distributions in resting and activated CD4+ T cells infected in culture.
Brady T, Agosto LM, Malani N, Berry CC, O'Doherty U, Bushman F . HIV integration site distributions in resting and activated CD4+ T cells infected in culture. AIDS. 2009 Jul 31;23(12):1461-71. PMID: 19550285
AIDS. 2009
Reports of Original Research Nondividing cells: a safer bet for integrating vectors?
Brady T, Bushman FD. (2011) Nondividing cells: a safer bet for integrating vectors? Mol Ther. 2011 Apr;19(4):640-1. No abstract available. PMID 21455211.
Mol Ther. 2011
Reports of Original Research Integration target site selection by a resurrected human endogenous retrovirus.
Brady T, Lee YN, Ronen K, Malani N, Berry CC, Bieniasz PD, Bushman FD. Integration target site selection by a resurrected human endogenous retrovirus. Genes Dev. 2009 Mar 1;23(5):633-42. PMID: 19270161.
Genes Dev. 2009
Reports of Original Research A method to sequence and quantify DNA integration for monitoring outcome in gene therapy.
Brady T, Roth SL, Malani N, Wang GP, Berry CC, Leboulch P, Hacein-Bey-Abina S, Cavazzana-Calvo M, Papapetrou EP, Sadelain M, Savilahti H, Bushman FD. A method to sequence and quantify DNA integration for monitoring outcome in gene therapy.Nucleic Acids Res 2011 Mar 16. PMID: 21415009
Nucleic Acids Res. 2011
Reports of Original Research Dodging the genes.
Bushman F. (1993) Dodging the genes. Curr Biol. 1993 Aug 1;3(8):533-5. No abstract available. PMID 15335696.
Curr Biol. 1993
Reports of Original Research Measuring covert HIV replication during HAART: the abundance of 2-LTR circles is not a reliable marker.
Bushman F. (2003) Measuring covert HIV replication during HAART: the abundance of 2-LTR circles is not a reliable marker. AIDS. 2003 Mar 28;17(5):749-50. No abstract available. PMID 12646799.
AIDS. 2003
Reports of Original Research RNA interference: applications in vertebrates.
Bushman F. (2003) RNA interference: applications in vertebrates. Mol Ther. 2003 Jan;7(1):9-10. No abstract available. PMID 12573612.
Mol Ther. 2003
Reports of Original Research Gene regulation: selfish elements make a mark.
Bushman F. (2004) Gene regulation: selfish elements make a mark. Nature. 2004 May 20;429(6989):253-5. No abstract available. PMID 15152235.
Nature. 2004
Review Articles Massively parallel pyrosequencing in HIV research.
Bushman FD, Hoffmann C, Ronen K, Malani N, Minkah N, Rose HM, Tebas P, Wang GP. Massively parallel pyrosequencing in HIV research. AIDS. 2008 Jul 31;22(12):1411-5. Review. PMID: 18614863.
AIDS. 2008
Review Articles Host cell factors in HIV replication: meta-analysis of genome-wide studies.
Bushman FD, Malani N, Fernandes J, D'Orso I, Cagney G, Diamond TL, Zhou H, Hazuda DJ, Espeseth AS, König R, Bandyopadhyay S, Ideker T, Goff SP, Krogan NJ, Frankel AD, Young JA, Chanda SK. Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathog. 2009 May;5(5):e1000437. Epub 2009 May 29. PMID: 19478882.
PLoS Pathog. 2009
Reports of Original Research Selection of target sites for mobile DNA integration in the human genome.
C. Berry, S. Hannenhalli, J. Leipzig, and F.D. Bushman. Selection of target sites for mobile DNA integration in the human genome. PLoS Comput Biol. 2006 Nov 24; 2(11):e157. PMID 17166054.
PLoS Comput Biol. 2006
Reports of Original Research DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations.
C. Hoffmann, N. Minkah, J. Leipzig, P. Tebas, and F.D. Bushman. DNA bar coding and pyrophosphate sequencing to identify rare HIV drug resistance mutations. Nucleic Acids Res. 2007 Jun 18; 35(13): e91. PMID: 17576693.
Nucleic Acids Res. 2007
Review Articles HIV cDNA integration: molecular biology and inhibitor development.
C. M. Farnet and F. D. Bushman. (1996) HIV cDNA integration: molecular biology and inhibitor development. AIDS 10 (supplement A): 3-11.
AIDS. 1996
Reports of Original Research Human immunodeficiency virus type 1 cDNA integration: new aromatic hydroxylated inhibitors and studies of the inhibition mechanism.
C. M. Farnet, B. Wang, M. Hansen, J. R. Lipford, L. Zalkow, W. E. Robinson Jr., J. Siegel, and F. Bushman (1998) HIV-1 cDNA integration: new aromatic hydroxylated inhibitors and studies of inhibitor mechanism. Antimicro. Agents and Chemo. 42, 2245-2253. PMID 9736543.
Antimicrob Agents Chemother. 1998
Reports of Original Research Total synthesis and evaluation of lamellarin alpha 20-Sulfate analogues.
C. P. Ridley, M. Venkata Rami Reddy, G. Rocha, F. D. Bushman, D. J. Faulkner. (2002) Total synthesis and evaluation of lamellarin alpha-20 sulfate analogs. Bioorg. & Med. Chem. 10, 3285-3290. PMID 12150874.
Bioorg Med Chem. 2002
Reports of Original Research HIV-1 cDNA integration: requirement of HMG I(Y) protein for function of preintegration complexes in vitro.
C.M. Farnet and F.D. Bushman. (1997) HIV-1 cDNA integration: Requirements of HMG I(Y) Protein for function of preintegration complexes in vitro. Cell 88, 483-492. PMID 9038339.
Cell. 1997
Reports of Original Research Differential inhibition of HIV-1 preintegration complexes and purified integrase protein by small molecules.
C.M. Farnet, B. Wang, J.R. Lipford, and F.D. Bushman. (1996) Differential inhibition of HIV-1 preintegration complexes and purified integrase protein by small molecules. Proc. Natl. Acad. Sci. USA 93,9742-9747. PMID 8790401.
Proc Natl Acad Sci U S A. 1996
Reports of Original Research PyNAST: a flexible tool for aligning sequences to a template alignment.
Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. PyNAST: A flexible tool for aligning sequences to a template alignment. Bioinformatics. 2010 Jan 15;26(2):266-7. PMID: 19914921
Bioinformatics. 2010
Reports of Original Research 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. QIIME allows analysis of high-throughput community sequencing data.Nat Methods. 2010 May;7(5):335-6. PMID: 20383131
Nat Methods. 2010
Reports of Original Research High-definition mapping of retroviral integration sites defines the fate of allogeneic T cells after donor lymphocyte infusion.
Cattoglio C, Maruggi G, Bartholomae C, Malani N, Pellin D, Cocchiarella F, Magnani Z, Ciceri F, Ambrosi A, von Kalle C, Bushman FD, Bonini C, Schmidt M, Mavilio F, Recchia A. High-definition mapping of retroviral integration sites defines the fate of allogeneic T cells after donor lymphocyte infusion.PLoS One 2010 Dec 22;5(12):e15688. PMID: 21203516
PLoS One. 2010
Reports of Original Research Is normal hematopoiesis maintained solely by long-term multipotent stem cells?
Cavazzana-Calvo M, Fischer A, Bushman FD, Payen E, Hacein-Bey-Abina S, Leboulch P. Is normal hematopoiesis maintained solely by long-term multipotent stem cells? Blood 2011 Feb 8. PMID: 21304104
Blood. 2011
Reports of Original Research Transfusion independence and HMGA2 activation after gene therapy of human β-thalassaemia.
Cavazzana-Calvo M, Payen E, Negre O, Wang G, Hehir K, Fusil F, Down J, Denaro M, Brady T, Westerman K, Cavallesco R, Gillet-Legrand B, Caccavelli L, Sgarra R, Maouche-Chrétien L, Bernaudin F, Girot R, Dorazio R, Mulder GJ, Polack A, Bank A, Soulier J, Larghero J, Kabbara N, Dalle B, Gourmel B, Socie G, Chrétien S, Cartier N, Aubourg P, Fischer A, Cornetta K, Galacteros F, Beuzard Y, Gluckman E, Bushman F, Hacein-Bey-Abina S, Leboulch P. Transfusion independence and HMGA2 activation after gene therapy of human β-thalassaemia. Nature 2010 Sep 16;467(7313):318-22. PMID: 20844535
Nature. 2010
Reports of Original Research 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. (2011) Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med. 2011 Oct 15;184(8):957-63. Epub 2011 Jun 16. PMID 21680950.
Am J Respir Crit Care Med. 2011
Reports of Original Research 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. Disordered microbial communities in the upper respiratory tract of cigarette smokers.PLoS One 2010 Dec 20;5(12):e15216. PMID: 21188149
PLoS One. 2010
Reports of Original Research Methods for integration site distribution analyses in animal cell genomes.
Ciuffi A, Ronen K, Brady T, Malani N, Wang G, Berry CC, Bushman FD. Methods for integration site distribution analyses in animal cell genomes. Methods. 2009 Apr;47(4):261-8. Epub 2008 Nov 25. PMID: 19038346.
Methods. 2009
Reports of Original Research Challenges in vector and trial design using retroviral vectors for long-term gene correction in hematopoietic stem cell gene therapy.
Corrigan-Curay J, Cohen-Haguenauer O, O'Reilly M, Ross SR, Fan H, Rosenberg N, Somia N, King N, Friedmann T, Dunbar C, Aiuti A, Naldini L, Baum C, von Kalle C, Kiem HP, Montini E, Bushman F, Sorrentino BP, Carrondo M, Malech H, Gahrton G, Shapiro R, et al. (2012) Challenges in vector and trial design using retroviral vectors for long-term gene correction in hematopoietic stem cell gene therapy. Mol Ther. 2012 Jun;20(6):1084-94. doi: 10.1038/mt.2012.93. No abstract available. PMID 22652996.
Mol Ther. 2012
Reports of Original Research Bulged DNA substrates for identifying poxvirus resolvase inhibitors.
Culyba M, Hwang Y, Attar S, Madrid PB, Bupp J, Huryn D, Sanchez L, Grobler J, Miller MD, Bushman FD. (2012) Bulged DNA substrates for identifying poxvirus resolvase inhibitors. Nucleic Acids Res. 2012 May 11. [Epub ahead of print] PMID 22581770.
Nucleic Acids Res. 2012
Reports of Original Research Metal cofactors in the structure and activity of the fowlpox resolvase.
Culyba MJ, Hwang Y, Hu JY, Minkah N, Ocwieja KE, Bushman FD. Metal cofactors in the structure and activity of the fowlpox resolvase.J Mol Bio. 2010 May 28;399(1):182-95. PMID: 20380839
J Mol Biol. 2010
Reports of Original Research DNA binding and cleavage by the fowlpox virus resolvase.
Culyba MJ, Hwang Y, Minkah N, Bushman FD. DNA binding and cleavage by the fowlpox virus resolvase. J Biol Chem. 2009 Jan 9;284(2):1190-201. Epub 2008 Nov 12. PMID: 19004818.
J Biol Chem. 2009
Review Articles Molecular mechanisms of HIV-1 proviral latency.
D. Bisgrove, M. Lewinski, F. D. Bushman, and E. Verdin. (2005) Molecular mechanisms of human immunodeficiency virus-1 proviral latency. Expert Review of Anti Infect Ther. 3, 805-814. PMID 16207172.
Expert Rev Anti Infect Ther. 2005
Reports of Original Research Thalassiolins A-C: new marine-derived inhibitors of HIV cDNA integrase.
D. C. Rowley, M. S. T. Hansen, D. Rhodes, C. A. Sotriffer, H. Ni, J. A. McCammon, F. D. Bushman, and W. Fenical. (2002) Thalassiolins A-C: New Marine-Derived Antiviral Agents that Inhibit HIV cDNA Integration. Bioorg. & Med. Chem. 10, 3619. PMID 12213478.
Bioorg Med Chem. 2002
Reports of Original Research Isolation and characterization of novel human immunodeficiency virus integrase inhibitors from fungal metabolites.
D. Hazuda, C. U. Blau, P. Felock, J. Hastings, B. Pramanik, A. Wolfe, F. Bushman, C. Farnet, M. Goetz, M. Williams, K. Silverman, R. Lingham, and S. Singh (1999) Isolation and characterization of novel human immunodeficiency virus integrase inhibitors from fungal metabolites. Antimicro. Agents and Chemo. 10, 63-70. PMID 10335400.
Antivir Chem Chemother. 1999
Reports of Original Research Human immunodeficiency virus integrase directs integration to sites of severe DNA distortion within the nucleosome core.
D. Pruss, F.D. Bushman and A.P. Wolffe. (1994) HIV integrase directs integration to sites of severe DNA distortion within the nucleosome core. Proc. Natl. Acad. Sci. USA 91: 5913-5917. PMID 8016088.
Proc Natl Acad Sci U S A. 1994
Reports of Original Research The influence of DNA and nucleosome structure on integration events directed by HIV integrase.
D. Pruss, R. Reeves, F.D. Bushman and A.P. Wolffe. (1994) The influence of DNA and nucleosome structure on integration events directed by HIV integrase. J. Biol. Chem. 269: 25031-25041. PMID 7929189.
J Biol Chem. 1994
Reports of Original Research Paired DNA three-way junctions as scaffolds for assembling integrase complexes.
E. P. Johnson and F. D. Bushman. Paired DNA Three-Way Junctions as Scaffolds for Assembling Integrase Complexes. (2001) Virology 286(2):304-16. PMID 11485398.
Virology. 2001
Review Articles Genome-wide analysis of retroviral DNA integration.
F. D. Bushman, M. Lewinski, A. Ciuffi, S. Barr, J. Leipzig, S. Hannenhalli, C. Hoffmann. (2005)Genome-wide analysis of retroviral DNA integration.Nature Reviews Microbiology 3, 848-858.
Nat Rev Microbiol. 2005
Reports of Original Research New devleopments in the biology and treatment of AIDS.
F. D. Bushman, N. R. Landau, and E. A. Emini. (1998) New devleopments in the biology and treatment of AIDS. Proc. Natl. Acad. Sci. 1998; USA 95,11041-11042. PMID .
Proc. Natl. Acad. Sci. 1998
Review Articles New developments in the biology and treatment of HIV.
F. D. Bushman, N. R. Landau, and E. A. Emini. (1998) New devleopments in the biology and treatment of AIDS. Proc. Natl. Acad. Sci. USA 95,11041-11042.
Proc Natl Acad Sci U S A. 1998
Review Articles Activators, deactivators and deactivated activators.
F. D. Bushman. (1992) Activators, deactivators, and deactivated activators. Current Biology 2: 673-675.
Curr Biol. 1992
Review Articles Retroelement transposition: Dodging the genes.
F. D. Bushman. (1993) Retroelement transposition: Dodging the genes. Current Biology 3: 533-535.
Current Biology 1993
Review Articles Targeting retroviral integration.
F. D. Bushman. (1995) Targeting retroviral integration. Science 267: 1443-1444.
Science. 1995
Review Articles Host proteins in retroviral cDNA integration.
F. D. Bushman. (1999) Host proteins in retroviral cDNA integration. Advances in Virus Research, 301-317. PMID 10384239.
Adv Virus Res. 1999
Review Articles A new cellular system opposing HIV infection: implications for gene transfer?
F. D. Bushman. (2002) A new cellular system opposing HIV infection: implications for gene transfer? Mol. Therapy 6, 441.
Mol Ther. 2002
Book Chapters Integration site selection by lentiviruses: biology and possible control.
F. D. Bushman. (2002) Integration site selection by lentiviruses: biology and possible control. In "Lentiviral Vectors". Curr. Top. Microbiol. Immunol. (D. Trono, ed).
Curr Top Microbiol Immunol. 2002
Review Articles Targeting retroviral integration?
F. D. Bushman. (2002) Targeting retroviral integration? Mol. Therapy 6, 570-571.
Mol Ther. 2002
Reports of Original Research Retroviral integration and human gene therapy.
F. D. Bushman. (2007) Retroviral integration and human gene therapy. J Clin Invest. 117 (8): 2083-6. PMID 17671645.
J Clin Invest. 2007
Reports of Original Research Rous sarcoma virus integrase protein: mapping functions for catalysis and substrate binding.
F.D. Bushman and B. Wang. (1994) Rous Sarcoma Virus Integrase Protein: Mapping Functions for Catalysis and Substrate Binding. J. Virol. 68:2215-2223. PMID 8139006.
J Virol. 1994
Reports of Original Research Activation of transcription by the bacteriophage 434 repressor.
F.D. Bushman and M. Ptashne. (1986) Activation of transcription by the bacteriophage 434 repressor. Proc. Natl. Acad. Sci. USA 83: 9353-9357. PMID 3467310.
Proc Natl Acad Sci U S A. 1986
Reports of Original Research Turning lambda Cro into a transcriptional activator.
F.D. Bushman and M. Ptashne. (1988) Turning lambda Cro into a transcriptional activator. Cell 58: 1163-1171. PMID 2968842.
Cell. 1988
Reports of Original Research Tethering human immunodeficiency virus type 1 preintegration complexes to target DNA promotes integration at nearby sites.
F.D. Bushman and M.D. Miller. (1997) Tethering HIV-1 preintegration complexes to target DNA promotes integration at nearby sites. J. Virol. 71: 458-464. PMID 8985371.
J Virol. 1997
Reports of Original Research Sequence requirements for integration of Moloney murine leukemia virus DNA in vitro.
F.D. Bushman and R. Craigie. (1990) Sequences at the ends of Moloney murine leukemia virus DNA required for integration in vitro. J. Virol. 64: 5645-5648. PMID 2214030.
J Virol. 1990
Reports of Original Research Activities of human immunodeficiency virus (HIV) integration protein in vitro: specific cleavage and integration of HIV DNA.
F.D. Bushman and R. Craigie. (1991) Activities of human immunodeficiency virus (HIV) integration protein in vitro: Specific cleavage and integration of HIV DNA. Proc. Natl. Acad. Sci. USA 88: 1339-1343. PMID 1847518.
Proc Natl Acad Sci U S A. 1991
Reports of Original Research Integration of human immunodeficiency virus DNA: adduct interference analysis of required DNA sites.
F.D. Bushman and R. Craigie. (1992) Integration of human immunodeficiency virus DNA: adduct interference analysis of required sites. Proc. Natl. Acad. Sci. USA 89: 3458-3462. PMID 1533044.
Proc Natl Acad Sci U S A. 1992
Reports of Original Research Conserved pattern of embryonic actin gene expression in several sea urchins and a sand dollar.
F.D. Bushman and W.R. Crain. (1983) Conserved pattern of embryonic actin gene expression in several sea urchins and a sand dollar. Dev. Biol. 98: 429-436. PMID 6873462.
Dev Biol. 1983
Reports of Original Research Domains of the integrase protein of human immunodeficiency virus type 1 responsible for polynucleotidyl transfer and zinc binding.
F.D. Bushman, A. Engelman, I. Palmer, P. Wingfield and R. Craigie. (1993) Domains of the integrase protein of human immunodeficiency virus type 1 responsible for polynucleotidyl transfer and zinc binding. Proc. Natl. Acad. Sci. USA 90: 3428-3432. PMID 8386373.
Proc Natl Acad Sci U S A. 1993
Reports of Original Research A single glutamic acid residue plays a key role in the transcriptional activation function of lambda repressor.
F.D. Bushman, C. Shang and M. Ptashne. (1989) A single glutamic acid residue plays a key role in the transcriptional activation function of lambda repressor. Cell 58: 1163-1171. PMID 2570642.
Cell. 1989
Reports of Original Research Ethylation interference and X-ray crystallography identify similar interactions between 434 repressor and operator.
F.D. Bushman, J.E., Anderson, S.C. Harrison and M. Ptashne. (1985) Ethylation interference and X-ray crystallography identify similar interactions between 434 repressor and operator. Nature 316: 651-653. PMID 4033762.
Nature. 1985
Reports of Original Research Retroviral DNA integration directed by HIV integration protein in vitro.
F.D. Bushman, T. Fujiwara and R. Craigie. (1990) Retroviral DNA integration directed by HIV IN protein in vitro. Science 249: 1555-1558. PMID 2171144.
Science. 1990
Reports of Original Research The bacteriophage 434 right operator. Roles of O(R)1, O(R)2 and O(R)3.
F.D. Bushman. (1993) The bacteriophage 434 right operator: Roles of OR1, OR2, and OR3. J. Mol. Biol. 230: 28-40. PMID 8450541.
J Mol Biol. 1993
Reports of Original Research Tethering human immunodeficiency virus 1 integrase to a DNA site directs integration to nearby sequences.
F.D. Bushman. (1994) Tethering human immunodeficiency virus 1 integrase to a DNA site directs integration to nearby sequences. Proc. Natl. Acad. Sci. USA 91: 9233-9237. PMID 7937746.
Proc Natl Acad Sci U S A. 1994
Review Articles Constructing the vertebrate genome: evidence from eels that LINEs mobilize SINEs.
F.D. Bushman. (2002) Constructing the vertebrate genome: evidence from eels that LINEs mobilize SINEs. Mol. Cell. 10; 961-962.
Mol Cell. 2002
Review Articles Targeting survival: integration site selection by retroviruses and LTR-retrotransposons.
F.D. Bushman. (2003) Targeting survival: integration site selection by retroviruses and LTR-retrotransposons. Cell. 115; 135-138. PMID 14567911.
Cell. 2003
Review Articles Evolutionary Teamwork: Constructing eukaryotes through endosymbiosis.
F.D. Bushman. (2004) Evolutionary Teamwork: Constructing eukaryotes through endosymbiosis. The Scientist. 18: 33-34.
The Scientist. 2004
Review Articles Gene regulation: selfish elements make a mark.
F.D. Bushman. (2004) Gene regulation: Selfish elements make a mark. Nature. 429: 253-55.
Nature. 2004
Reports of Original Research Single-particle image reconstruction of a tetramer of HIV integrase bound to DNA.
G. Ren, K. Gao, F. D. Bushman, and M. Yeager. (2007) Single particle image reconstruction of a tetramer of HIV integrase bound to DNA. J Mol Biol. 366 (1): 286-94. PMID 17157316.
J Mol Biol. 2007
Reports of Original Research A statistical method for comparing viral growth curves.
G. Wang and F. D. Bushman. (2006) A statistical method for comparing viral growth curves. J. Virol. Meth. 135, 118-123. PMID 16564579.
J Virol Methods. 2006
Reports of Original Research HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications.
G.P. Wang, A. Ciuffi, J. Leipzig, C.C. Berry, and F.D. Bushman. HIV integration in the human genome: regulation by post-translational modification of histones. Genome Res. 2007 Jun 1. PMID 17545577.
Genome Res. 2007
Reports of Original Research LEDGF hybrids efficiently retarget lentiviral integration into heterochromatin.
Gijsbers R, Ronen K, Vets S, Malani N, De Rijck J, McNeely M, Bushman FD, Debyser Z. LEDGF hybrids efficiently retarget lentiviral integration into heterochromatin. Mol Ther. 2010 Mar;18(3):552-60. PMID: 20195265
Mol Ther. 2010
Reports of Original Research Role of the PWWP domain of lens epithelium-derived growth factor (LEDGF)/p75 cofactor in lentiviral integration targeting.
Gijsbers R, Vets S, De Rijck J, Ocwieja KE, Ronen K, Malani N, Bushman FD, Debyser Z. (2011) Role of the PWWP domain of lens epithelium-derived growth factor (LEDGF)/p75 cofactor in lentiviral integration targeting. J Biol Chem. 2011 Dec 2;286(48):41812-25. Epub 2011 Oct 10. PMID 21987578.
J Biol Chem. 2011
Reports of Original Research The host genomic environment of the provirus determines the abundance of HTLV-1-infected T-cell clones.
Gillet NA, Malani N, Melamed A, Gormley N, Carter R, Bentley D, Berry C, Bushman FD, Taylor GP, Bangham CR. The host genomic environment of the provirus determines the abundance of HTLV-1-infected T-cell clones.Blood. 2011 Mar 17;117(11):3113-22. PMID: 21228324
Blood. 2011
Reports of Original Research Structural properties of HIV integrase. Lens epithelium-derived growth factor oligomers.
Gupta K, Diamond T, Hwang Y, Bushman F, Van Duyne GD. Structural properties of HIV integrase. Lens epithelium-derived growth factor oligomers.J Biol Chem. 2010 Jun 25;285(26):20303-15. PMID: 20406807
J Biol Chem. 2010
Reports of Original Research Developing a dynamic pharmacophore model for HIV-1 integrase.
H. A. Carlson, K. M. Masukawa, K. Rubins, F. D. Bushman, W. L. Jorgensen, R. Lins, J. M. Briggs, J. A. McCammon (2000) Developing a Dynamic Pharmacophore Model for HIV-1 Integrase. J. Med. Chem. 43, 2100-2114. PMID 10841789.
J Med Chem. 2000
Reports of Original Research Role of PSIP1/LEDGF/p75 in lentiviral infectivity and integration targeting.
H.M. Marshall, K. Ronen, C. Berry, M. Llano, H. Sutherland, D. Saenz, W. Bickmore, E. Poeschla, and F.D. Bushman. Role of PSIP1/LEDGF/p75 in Lentiviral Infectivity and Integration Targeting. PLoS ONE. 2007 Dec 19; 2(12): e1340. PMID: 18092005.
PLoS One. 2007
Reports of Original Research Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1.
Hacein-Bey-Abina S, Garrigue A, Wang GP, Soulier J, Lim A, Morillon E, Clappier E, Caccavelli L, Delabesse E, Beldjord K, Asnafi V, MacIntyre E, Dal Cortivo L, Radford I, Brousse N, Sigaux F, Moshous D, Hauer J, Borkhardt A, Belohradsky BH, Wintergerst U, Velez MC, Leiva L, Sorensen R, Wulffraat N, Blanche S, Bushman FD, Fischer A, Cavazzana-Calvo M. Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1. J Clin Invest. 2008 Sep;118(9):3132-42. PMID: 18688285.
J Clin Invest. 2008
Reports of Original Research Efficacy of gene therapy for X-linked severe combined immunodeficiency.
Hacein-Bey-Abina S, Hauer J, Lim A, Picard C, Wang GP, Berry CC, Martinache C, Rieux-Laucat F, Latour S, Belohradsky BH, Leiva L, Sorensen R, Debré M, Casanova JL, Blanche S, Durandy A, Bushman FD, Fischer A, Cavazzana-Calvo M. Efficacy of gene therapy for X-linked severe combined immunodeficiency.N Engl J Med. 2010 Jul 22;363(4):355-64. PMID: 20660403
N Engl J Med. 2010
Reports of Original Research High-fat diet determines the composition of the murine gut microbiome independently of obesity.
Hildebrandt MA, Hoffmann C, Sherrill-Mix SA, Keilbaugh SA, Hamady M, Chen YY, Knight R, Ahima RS, Bushman F, Wu GD (2009). High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology. 137(5):1716-24.e1-2. PMID: 19706296
Gastroenterology. 2009
Reports of Original Research Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis.
Hill DA, Hoffmann C, Abt MC, Du Y, Kobuley D, Kirn TJ, Bushman FD, Artis D. Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis. Mucosal Immunol. 2010 Mar;3(2):148-58. PMID: 19940845
Mucosal Immunol. 2010
Reports of Original Research Commensal bacteria-derived signals regulate basophil hematopoiesis and allergic inflammation.
Hill DA, Siracusa MC, Abt MC, Kim BS, Kobuley D, Kubo M, Kambayashi T, Larosa DF, Renner ED, Orange JS, Bushman FD, Artis D. (2012) Commensal bacteria-derived signals regulate basophil hematopoiesis and allergic inflammation. Nat Med. 2012 Mar 25;18(4):538-46. doi: 10.1038/nm.2657. PMID 22447074.
Nat Med. 2012
Reports of Original Research Community-wide response of the gut microbiota to enteropathogenic Citrobacter rodentium infection revealed by deep sequencing.
Hoffmann C, Hill DA, Minkah N, Kirn T, Troy A, Artis D, Bushman FD. Community-wide response of the gut microbiota to enteropathogenic Citrobacter rodentium infection revealed by deep sequencing. Infect Immun. 2009 Oct;77(10):4668-78. Epub 2009 Jul 27. PMID: 19635824.
Infect Immun. 2009
Reports of Original Research The mobility of an HIV-1 integrase active site loop is correlated with catalytic activity.
J. Greenwald, V. Le, S. L. Butler, F. D. Bushman, and S. Choe. (1999) Mobility of the HIV-1 integrase active site loop is important for catalytic activity. Biochemistry 38, 8892-8898. PMID 10413562.
Biochemistry. 1999
Reports of Original Research Roles of host cell factors in circularization of retroviral dna.
J. M. Kilzer, T. Straker, B. Beitzel, K. Meek, M. Weitzman, and F. D. Bushman. (2003) Roles of host cell factors in circularization onf retroviral DNA. Virology. 314, 460-467. PMID 14517098.
Virology. 2003
Reports of Original Research Global landscape of HIV-human protein complexes.
Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, et al. (2011) Global landscape of HIV-human protein complexes. Nature. 2011 Dec 21;481(7381):365-70. doi: 10.1038/nature10719. PMID 22190034.
Nature. 2011
Reports of Original Research Cofactors for human immunodeficiency virus type 1 cDNA integration in vitro.
K. Gao, R. J. Gorelick, D. G. Johnson, and F. D. Bushman. (2003) Cofactors for HIV-1 cDNA integration in vitro. J. Virol., 77, 1598-1603. PMID 12502875.
J Virol. 2003
Reports of Original Research Human immunodeficiency virus type 1 integrase: arrangement of protein domains in active cDNA complexes.
K. Gao, S. L. Butler, and F. D. Bushman. Human Immunodeficiency Virus Type-1 Integrase: Arrangement of Protein Domains in Active cDNA Complexes. (2001) EMBO J. 20, 3565-3576. PMID 11432843.
EMBO J. 2001
Reports of Original Research Metal binding by the D,DX35E motif of human immunodeficiency virus type 1 integrase: selective rescue of Cys substitutions by Mn2+ in vitro.
K. Gao, S. Wong, and F. D. Bushman. (2004) Metal binding by the D,DX35E motif of HIV-1 integrase: selective rescue of Cys substitutions by Mn2+ in vitro. J. Virol. 78, 6715-6722. PMID 15194746. (see also cover)
J Virol. 2004
Reports of Original Research Structural basis for specificity in the poxvirus topoisomerase.
K. Perry, Y. Hwang, F. D. Bushman, and G. D. Van Duyne. Structural basis for specificity in the poxvirus topoisomerase. Mol Cell. 2006 Aug 4;23(3):343-54. PMID 16885024.
Mol Cell. 2006
Reports of Original Research Repair of gaps in retroviral DNA integration intermediates.
K. Yoder and F.D. Bushman (2000) Repair of Gaps in Retroviral DNA Integration Intermediates. J. Virol. 74, 11191-11200. PMID 11070016.
J Virol. 2000
Reports of Original Research The DNA repair genes XPB and XPD defend cells from retroviral infection.
K. Yoder, A. Sarasin, K. Kraemer, M. McIhatton, F. D. Bushman, R. Fishel. (2006) The DNA repair genes XPB and XPD defend cells from retroviral infection. Proc. Natl. Acad. Sci. USA, 103: 4622-4627. PMID 1653783.
Proc Natl Acad Sci U S A. 2006
Reports of Original Research Bayesian community-wide culture-independent microbial source tracking.
Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelley ST. (2011) Bayesian community-wide culture-independent microbial source tracking. Nat Methods. 2011 Jul 17;8(9):761-3. doi: 10.1038/nmeth.1650. PMID 21765408.
Nat Methods. 2011
Reports of Original Research Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication.
König R, Zhou Y, Elleder D, Diamond TL, Bonamy GM, Irelan JT, Chiang CY, Tu BP, De Jesus PD, Lilley CE, Seidel S, Opaluch AM, Caldwell JS, Weitzman MD, Kuhen KL, Bandyopadhyay S, Ideker T, Orth AP, Miraglia LJ, Bushman FD, Young JA, Chanda SK. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell. 2008 Oct 3;135(1):49-60. PMID: 18854154.
Cell. 2008
Reports of Original Research Modulation of activity of Moloney murine leukemia virus preintegration complexes by host factors in vitro.
L. Li, C. M. Farnet, W. F. Anderson, and F. D. Bushman (1998) Modulation of activity of MoMuLV preintegration complexes by several host activities in vitro. J. Virol. 72, 2125-2131. PMID 9499068.
J Virol. 1998
Reports of Original Research Role of the non-homologous DNA end joining pathway in the early steps of retroviral infection.
L. Li, J. M. Olvera, K. E. Yoder, R. S. Mitchell, S. L. Butler, M. Lieber, S. L. Martin, and F. D. Bushman. Role of the Non-Homologous DNA End Joining Pathway in Retroviral Infection. (2001) EMBO J. 20, 3272-3281. PMID 11406603.
EMBO J. 2001
Reports of Original Research Retroviral cDNA integration: stimulation by HMG I family proteins.
L. Li, K. Yoder, M.S. Hansen, J. Olvera, M.D. Miller and F.D. Bushman (2000) Retroviral cDNA Integration: Stimulation by HMG I Family Proteins. J. Virol. 74,10965-10974. PMID 11069991.
J Virol. 2000
Reports of Original Research Low-frequency nevirapine resistance at multiple sites may predict treatment failure in infants on nevirapine-based treatment.
Lehman DA, Wanalwa DC, McCoy CO, Matsen FA, Langat A, Chohan BH, Benki-Nugent S, Custers-Allen R, Bushman FD, John-Stewart GC, Overbaugh J. (2012) Low-frequency nevirapine resistance at multiple sites may predict treatment failure in infants on nevirapine-based treatment. J Acquir Immune Defic Syndr. 2012 Mar 6. [Epub ahead of print] PMID 22395670.
J Acquir Immune Defic Syndr. 2012
Reports of Original Research In vivo genome editing restores haemostasis in a mouse model of haemophilia.
Li H, Haurigot V, Doyon Y, Li T, Wong SY, Bhagwat AS, Malani N, Anguela XM, Sharma R, Ivanciu L, Murphy SL, Finn JD, Khazi FR, Zhou S, Paschon DE, Rebar EJ, Bushman FD, Gregory PD, Holmes MC, High KA. (2011) In vivo genome editing restores haemostasis in a mouse model of haemophilia. Nature. 2011 Jun 26;475(7355):217-21. doi: 10.1038/nature10177. PMID 21706032.
Nature. 2011
Reports of Original Research Assessing the potential for AAV vector genotoxicity in a murine model.
Li H, Malani N, Hamilton SR, Schlachterman A, Bussadori G, Edmonson SE, Shah R, Arruda VR, Mingozzi F, Wright JF, Bushman FD, High KA. Assessing the potential for AAV vector genotoxicity in a murine model.Blood 2010 Nov 24. PMID: 21106988
Blood. 2011
Reports of Original Research Short pyrosequencing reads suffice for accurate microbial community analysis.
Liu Z, Lozupone C, Hamady M, Bushman FD, Knight R. (2007) Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res. 35 (18): e120. PMID 17881377.
Nucleic Acids Res. 2007
Reports of Original Research Human immunodeficiency virus type 2 preintegration complexes: activities in vitro and response to inhibitors.
M. Hansen and F.D. Bushman. (1997) HIV-2 Preintegration Complexes: Activities in vitro and response to inhibitors. J. Virol. 71, 3351-3356. PMID 9060709.
J Virol. 1997
Reports of Original Research DNA cleavage by the A22R resolvase of vaccinia virus.
M. J. Culyba, J. E. Harrison, Y . Hwang, F. D. Bushman. (2006) DNA cleavage by the A22R resolvase of vaccinia virus. Virology. Epub. PMID 16781759.
Virology. 2006
Review Articles Genome-wide analysis of chromosomal features repressing human immunodeficiency virus transcription.
M. K. Lewinski and F. D. Bushman. (2005) Retroviral DNA integration--mechanism and consequences. Advances in Genetics 55, 147-181. PMID 16291214.
J Virol. 2005
Reports of Original Research Retroviral DNA integration--mechanism and consequences.
M. K. Lewinski, D. Bisgrove, P. Shinn, H. Chen, S. Hannenhalli, E. Verdin, C. C Berry, J. R. Eccker, and F. D. Bushman. (2005) Genome-wide analysis of chromosomal features repressing HIV transcription. J. Virol. 79, 6610-6619. PMID 15890899.
Adv Genet. 2005
Reports of Original Research Retroviral DNA integration: viral and cellular determinants of target-site selection.
M. K. Lewinski, M. Yamashita, M. Emerman, A. Ciuffi, H. Marshall, G. Crawford, F. Collins, P. Shinn, J. Leipzig, S. Hannenhalli, C. C. Berry, J. R. Ecker, F. D. Bushman. (2006) Retroviral DNA integration: viral and cellular determinants of target site selection. PLoS Pathog. 2, Epub. PMID 16789841.
PLoS Pathog. 2006
Reports of Original Research Human immunodeficiency virus type 1 preintegration complexes: studies of organization and composition.
M. Miller, C. M. Farnet and F.D. Bushman. (1997) HIV-1 Preintegration Complexes: Studies of Organization and Composition. J. Virol. 71, 5382-5390. PMID 9188609.
J Virol. 1997
Reports of Original Research Integration complexes derived from HIV vectors for rapid assays in vitro.
M. S. T. Hansen, G. J. Smith III, T. Kafri, V. Moltini, J. Siegel, F. D. Bushman. (1999) Integration Complexes Derived from HIV-Vectors for Rapid Assays In Vitro. Nature Biotechnology 17, 578-582. PMID 10385323.
Nat Biotechnol. 1999
Book Chapters Retroviral cDNA integration: mechanism, applications and inhibition.
M. S. T. Hansen, S. Carteau, C. Hoffman, L. Li, F. D. Bushman. (1998) Retroviral cDNA integration: mechanism, applications, and inhibition. In "Genetic Engineering", Vol 20. Plenum Press. p. 41-63.
Genet Eng (N Y). 1998
Reports of Original Research Lamellarin alpha 20-sulfate, an inhibitor of HIV-1 integrase active against HIV-1 virus in cell culture.
M. V. R. Reddy, M. R. Rao, D. Rhodes, M. S. T. Hansen, K. Rubins, F. D. Bushman, Y. Venkateswarlu, D. J. Faulkner. (1999) Lamellarin Alpha 20-Sulfate, An Inhibitor of HIV-1 Integrase Active Against HIV-1 Virus In Vivo. J. Med. Chem. 42, 1901-1907. PMID 10354398.
J Med Chem. 1999
Review Articles HIV integration. Ini1 for integration?
M.D. Miller and F.D. Bushman. (1995) HIV integration: Ini 1 for integration? Current Biology. 5; 368-370. PMID 8883604.
Curr Biol. 1995
Reports of Original Research Human immunodeficiency virus type 1 preintegration complexes containing discontinuous plus strands are competent to integrate in vitro.
M.D. Miller, B. Wang, and F.D. Bushman. (1995) Human immunodeficiency virus type 1 preintegration complexes containing discontinuous plus strands are competent to integrate in vitro. J. Virol. 69: 3938-3944. PMID 7745750.
J Virol. 1995
Reports of Original Research Target DNA capture by HIV-1 integration complexes.
M.D. Miller, Y.-C. Bor and F.D. Bushman. (1995) Target DNA capture by HIV-1 integration complexes. Current Biology 5: 1047-1056. PMID 8542281.
Curr Biol. 1995
Reports of Original Research DNA branch nuclease activity of vaccinia A22 resolvase.
M.J. Culyba, O.-M. J. Benhamou, and F.D. Bushman. Vaccinia virus A22 resolvase: active site mapping and inhibition by diketo acids. J Biol Chem. 2007 Nov 30; 282(48): 34644-52. PMID 17890227.
J Biol Chem. 2007
Reports of Original Research HTLV-1 integration into transcriptionally active genomic regions is associated with proviral expression and with HAM/TSP.
Meekings KN, Leipzig J, Bushman FD, Taylor GP, Bangham CR. HTLV-1 integration into transcriptionally active genomic regions is associated with proviral expression and with HAM/TSP. PLoS Pathog. 2008 Mar 21;4(3):e1000027. PMID: 18369476.
PLoS Pathog. 2008
Reports of Original Research Cxcr2 and Cxcl5 regulate the IL-17/G-CSF axis and neutrophil homeostasis in mice.
Mei J, Liu Y, Dai N, Hoffmann C, Hudock KM, Zhang P, Guttentag SH, Kolls JK, Oliver PM, Bushman FD, Worthen GS. (2012) Cxcr2 and Cxcl5 regulate the IL-17/G-CSF axis and neutrophil homeostasis in mice. J Clin Invest. 2012 Mar 1;122(3):974-86. doi: 10.1172/JCI60588. Epub 2012 Feb 13. PMID 22326959.
J Clin Invest. 2012
Reports of Original Research A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing.
Meylan S, Groner AC, Ambrosini G, Malani N, Quenneville S, Zangger N, Kapopoulou A, Kauzlaric A, Rougemont J, Ciuffi A, Bushman FD, Bucher P, Trono D. (2011) A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing. BMC Genomics. 2011 Jul 26;12:378. PMID 21791101.
BMC Genomics. 2011
Reports of Original Research Hypervariable loci in the human gut virome.
Minot S, Grunberg S, Wu GD, Lewis JD, Bushman FD. (2012) Hypervariable loci in the human gut virome. Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3962-6. Epub 2012 Feb 21. PMID 22355105.
Proc Natl Acad Sci U S A. 2012
Reports of Original Research The human gut virome: inter-individual variation and dynamic response to diet.
Minot S, Sinha R, Chen J, Li H, Keilbaugh SA, Wu GD, Lewis JD, Bushman FD. The human gut virome: Inter-individual variation and dynamic response to diet. Genome Res. 2011 Aug 31. PMID: 21880779
Genome Res. 2011
Reports of Original Research Switching between raltegravir resistance pathways analyzed by deep sequencing.
Mukherjee R, Jensen ST, Male F, Bittinger K, Hodinka RL, Miller MD, Bushman FD. (2011) Switching between raltegravir resistance pathways analyzed by deep sequencing. AIDS. 2011 Oct 23;25(16):1951-9. PMID 21832937.
AIDS. 2011
Reports of Original Research HIV sequence variation associated with env antisense adoptive T-cell therapy in the hNSG mouse model.
Mukherjee R, Plesa G, Sherrill-Mix S, Richardson MW, Riley JL, Bushman FD. HIV sequence variation associated with env antisense adoptive T-cell therapy in the hNSG mouse model. Mol Ther. 2010 Apr;18(4):803-11. PMID: 20104212
Mol Ther. 2010
Reports of Original Research Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes.
N. Minkah, Y. Hwang, K. Perry, G.D. Van Duyne, R.C. Hendrick, E.J. Lefkowitz, S. Hannenhalli, and F.D. Bushman. Variola Virus Topoisomerase: DNA Cleavage Specificity and Distribution of Sites in Poxvirus Genomes. Virology. 2007 Apr 24. PMID 17462694.
Virology. 2007
Reports of Original Research Correction of murine β-thalassemia after minimal lentiviral gene transfer and homeostatic in vivo erythroid expansion.
Negre O, Fusil F, Colomb C, Roth S, Gillet-Legrand B, Henri A, Beuzard Y, Bushman F, Leboulch P, Payen E. (2011) Correction of murine β-thalassemia after minimal lentiviral gene transfer and homeostatic in vivo erythroid expansion. Blood. 2011 May 19;117(20):5321-31. Epub 2011 Mar 24. PMID 21436071.
Blood. 2011
Reports of Original Research HIV integration targeting: a pathway involving Transportin-3 and the nuclear pore protein RanBP2.
Ocwieja KE, Brady TL, Ronen K, Huegel A, Roth SL, Schaller T, James LC, Towers GJ, Young JA, Chanda SK, König R, Malani N, Berry CC, Bushman FD. HIV Integration Targeting: A Pathway Involving Transportin-3 and the Nuclear Pore Protein RanBP2.PLoS Pathog 2011 Mar;7(3):e1001313. PMID: 21423673
PLoS Pathog. 2011
Reports of Original Research HIV nuclear import is governed by the phosphotyrosine-mediated binding of matrix to the core domain of integrase.
P. Gallay, S. Swingler, J. Song, F. Bushman, and D. Trono. (1995) HIV nuclear import is governed by the phosphotyrosine-mediated binding of matrix to the core domain of integrase. Cell 83: 569-576. PMID 7585960.
Cell. 1995
Reports of Original Research The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis.
P. McKenna, C. Hoffmann, J. Leipzig, P.P. Aye, A. Lackner, Z. Liu, C.A. Lozupone, M. Hamady, R. Knight, and F.D. Bushman. The macaque gut microbiome in health, leniviral infection and inflammatory bowel disease. PLoS Pathog. 2008 Feb 8;4(2):e20. PMID: 18248093
PLoS Pathog. 2008
Reports of Original Research Bacteriophage Mu integration in yeast and mammalian genomes.
Paatero AO, Turakainen H, Happonen LJ, Olsson C, Palomäki T, Pajunen MI, Meng X, Otonkoski T, Tuuri T, Berry C, Malani N, Frilander MJ, Bushman FD, Savilahti H. Bacteriophage Mu integration in yeast and mammalian genomes. Nucleic Acids Res. 2008 Dec;36(22):e148. Epub 2008 Oct 25. PMID: 18953026.
Nucleic Acids Res. 2008
Reports of Original Research Genomic safe harbors permit high β-globin transgene expression in thalassemia induced pluripotent stem cells.
Papapetrou EP, Lee G, Malani N, Setty M, Riviere I, Tirunagari LM, Kadota K, Roth SL, Giardina P, Viale A, Leslie C, Bushman FD, Studer L, Sadelain M. Genomic safe harbors permit high β-globin transgene expression in thalassemia induced pluripotent stem cells.Nat Biotechnol. 2011 Jan;29(1):73-8. PMID: 21151124
Nat Biotechnol. 2011
Reports of Original Research Insights from the structure of a smallpox virus topoisomerase-DNA transition state mimic.
Perry K, Hwang Y, Bushman FD, Van Duyne GD. Insights from the structure of a smallpox virus topoisomerase-DNA transition state mimic. Structure. 2010 Jan 13;18(1):127-37. PMID: 20152159
Structure. 2010
Reports of Original Research A rapid in vitro assay for HIV DNA integration.
R. Craigie, K. Mizuuchi, F.D. Bushman and A. Engelman. (1991) A rapid in vitro assay for HIV DNA integration. Nuc. Acids Res. 19: 2729-2734. PMID 2041748.
Nucleic Acids Res. 1991
Reports of Original Research The IN protein of Moloney murine leukemia virus processes the viral DNA ends and accomplishes their integration in vitro.
R. Craigie, T. Fujiwara and F.D. Bushman. (1990) The in protein in Moloney murine leukemia virus processes the viral DNA ends and accomplishes their integration in vitro. Cell 62: 829-837. PMID 2167180.
Cell. 1990
Reports of Original Research Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences.
R. Mitchell, B. Beitzel, A. R. W. Schroder, P. Shinn, H. Chen, C. Berry, J. R. Ecker, and F. D. Bushman. (2004) Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences. PLoS Biology 2(8):E234. PMID 15314653.
PLoS Biol. 2004
Reports of Original Research Global analysis of cellular transcription following infection with an HIV-based vector.
R. Mitchell, E. Chiang, C. Berry, F. D. Bushman. (2003) Global effects on cellular transcription following infection with and HIV-based vector. Mol. Therapy. 8, 674-687. PMID 14529841. (see also cover).
Mol Ther. 2003
Reports of Original Research Distribution of lentiviral vector integration sites in mice following therapeutic gene transfer to treat β-thalassemia.
Ronen K, Negre O, Roth S, Colomb C, Malani N, Denaro M, Brady T, Fusil F, Gillet-Legrand B, Hehir K, Beuzard Y, Leboulch P, Down JD, Payen E, Bushman FD. Distribution of Lentiviral Vector Integration Sites in Mice Following Therapeutic Gene Transfer to Treat β-thalassemia.Mol Ther. 2011 Mar 8. PMID: 21386821
Mol Ther. 2011
Reports of Original Research Gammaretroviral integration into nucleosomal target DNA in vivo.
Roth SL, Malani N, Bushman FD. Gammaretroviral integration into nucleosomal target DNA in vivo. J. Virol. 2011 Jul;85(14):7393-401. PMID: 21561906
J Virol. 2011
Reports of Original Research Integration targeting by avian sarcoma-leukosis virus and human immunodeficiency virus in the chicken genome.
S. Barr, J. Leipzig, P. Shinn, J. Ecker, and F. Bushman. (2005) Integration targeting by ASLV and HIV in the chicken genome. J. Virol. 79, 12035-12044. PMID 16140779. (see also cover)
J Virol. 2005
Reports of Original Research Chromosome structure and human immunodeficiency virus type 1 cDNA integration: centromeric alphoid repeats are a disfavored target.
S. Carteau, C. Hoffmann, and F. D. Bushman (1998) Chromosome structure and HIV-1 cDNA integration: centromeric alphoid repeats are a disfavored target. J. Virol. 72, 4005-4014. PMID 9557688.
J Virol. 1998
Reports of Original Research Coupled integration of human immunodeficiency virus type 1 cDNA ends by purified integrase in vitro: stimulation by the viral nucleocapsid protein.
S. Carteau, R. Gorelick and F. Bushman. (1999) Coupled Joining of HIV-1 cDNA Ends by Purified Integrase In Vitro: Stimulation by the Viral Nucleocapsid Protein. J. Virol. 73, 6670-6679. PMID 10400764.
J Virol. 1999
Reports of Original Research HIV integration site selection: targeting in macrophages and the effects of different routes of viral entry.
S. D. Barr, A. Ciuffi, J. Leipzig, P. Shinn, J. R. Ecker, F. D. Bushman. (2006) HIV integration site selection: targeting in macrophages and the effects of different routes of viral entry. Mol Ther. 14, 218-225. PMID 16647883.
Mol Ther. 2006
Reports of Original Research Human immunodeficiency virus cDNA metabolism: notable stability of two-long terminal repeat circles.
S. L. Butler, E. P. Johnson and F. D. Bushman. (2002) Human Immunodeficiency Virus cDNA Metabolism: Notable Stability of Two-Long Terminal Repeat Circles. J. Virol.76, 3739-3747. PMID 11907213.
J Virol. 2002
Reports of Original Research A quantitative assay for HIV DNA integration in vivo.
S. L. Butler, M. S. T. Hansen, and F. D. Bushman. A Quantitative Assay for HIV cDNA Integration In Vivo. (2001) Nat. Med. 7, 631-634. PMID 11329067.
Nat Med. 2001
Reports of Original Research Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon.
S. L. Martin, and F.D. Bushman. (2001). Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon. Mol. Cell Biol. 2, 467-475. PMID 11134335.
Mol Cell Biol. 2001
Reports of Original Research Thiol-mediated degradation of DNA adsorbed on a colloidal gold surface.
S. Mittal, F. D. Bushman, and L. E. Orgel. (2003) Thiol-mediated degradation of DNA adsorbed on a colloidal gold surface. J. Chem. Tech. & Biotech. 78.471-473.
J. Chem. Tech. & Biotech. 2003
Reports of Original Research Cyclodidemniserinol trisulfate, a sulfated serinolipid from the Palauan ascidian Didemnum guttatum that inhibits HIV-1 integrase.
S. S. Mitchell, D. Rhodes, F.D. Bushman, and D.J. Faulkner. (2000). Cyclodidemniserinol trisulfate, a sulfated serinolipid from the Palauan ascidian Didemnum guttatum that inhibits HIV-1 integrase. Org. Lett. 2, 1605-1607. PMID 10841490.
Org Lett. 2000
Reports of Original Research Dolastatin 3 and two novel cyclic peptides from a palauan collection of Lyngbya majuscula.
S.S. Mitchell, D.J. Faulkner, K. Rubins, and F.D. Bushman. (2000). Dolastatin 3 and two novel cyclic peptides from a palauan collection of Lyngbya majuscula. J. Nat Prod. 63, 279-82. PMID 10691729.
J Nat Prod. 2000
Reports of Original Research Safe harbours for the integration of new DNA in the human genome.
Sadelain M, Papapetrou EP, Bushman FD. (2011) Safe harbours for the integration of new DNA in the human genome. Nat Rev Cancer. 2011 Dec 1;12(1):51-8. doi: 10.1038/nrc3179. PMID 22129804.
Nat Rev Cancer. 2011
Reports of Original Research HIV-1 capsid-cyclophilin interactions determine nuclear import pathway, integration targeting and replication efficiency.
Schaller T, Ocwieja KE, Rasaiyaah J, Price AJ, Brady TL, Roth SL, Hué S, Fletcher AJ, Lee K, KewalRamani VN, Noursadeghi M, Jenner RG, James LC, Bushman FD, Towers GJ. (2011) HIV-1 capsid-cyclophilin interactions determine nuclear import pathway, integration targeting and replication efficiency. PLoS Pathog. 2011 Dec;7(12):e1002439. Epub 2011 Dec 8. PMID 22174692.
PLoS Pathog. 2011
Reports of Original Research Decade-long safety and function of retroviral-modified chimeric antigen receptor T cells.
Scholler J, Brady TL, Binder-Scholl G, Hwang WT, Plesa G, Hege KM, Vogel AN, Kalos M, Riley JL, Deeks SG, Mitsuyasu RT, Bernstein WB, Aronson NE, Levine BL, Bushman FD, June CH. (2012) Decade-long safety and function of retroviral-modified chimeric antigen receptor T cells. Sci Transl Med. 2012 May 2;4(132):132ra53. PMID 22553251.
Sci Transl Med. 2012
Reports of Original Research LEDGF/p75-independent HIV-1 replication demonstrates a role for HRP-2 and remains sensitive to inhibition by LEDGINs.
Schrijvers R, De Rijck J, Demeulemeester J, Adachi N, Vets S, Ronen K, Christ F, Bushman FD, Debyser Z, Gijsbers R. (2012) LEDGF/p75-independent HIV-1 replication demonstrates a role for HRP-2 and remains sensitive to inhibition by LEDGINs. PLoS Pathog. 2012 Mar;8(3):e1002558. Epub 2012 Mar 1. PMID 22396646.
PLoS Pathog. 2012
Reports of Original Research 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, et al. (2012) Innate lymphoid cells promote anatomical containment of lymphoid-resident commensal bacteria. Science. 2012 Jun 8;336(6086):1321-5. Epub 2012 Jun 6. PMID 22674331.
Science. 2012
Reports of Original Research Division of labor within human immunodeficiency virus integrase complexes: determinants of catalysis and target DNA capture.
T. Diamond, and F. Bushman. (2005) Division of labor within HIV-1 integrase complexes: determinants of catalysis and target DNA capture. J. virol. 79, 15376-15387. PMID 16306609.
J Virol. 2005
Reports of Original Research Role of metal ions in catalysis by HIV integrase analyzed using a quantitative PCR disintegration assay.
T. L. Diamond TL, F.D. Bushman. Role of metal ions in catalysis by HIV integrase analyzed using a quantitative PCR disintegration assay. Nucleic Acids Res. 2006;34(21):6116-25. 2006 Nov 3. PMID 17085478.
Nucleic Acids Res. 2006
Reports of Original Research A maraviroc-resistant HIV-1 with narrow cross-resistance to other CCR5 antagonists depends on both N-terminal and extracellular loop domains of drug-bound CCR5.
Tilton JC, Wilen CB, Didigu CA, Sinha R, Harrison JE, Agrawal-Gamse C, Henning EA, Bushman FD, Martin JN, Deeks SG, Doms RW. A maraviroc-resistant HIV-1 with narrow cross-resistance to other CCR5 antagonists depends on both N-terminal and extracellular loop domains of drug-bound CCR5.J Virol. 2010 Oct;84(20):10863-76. PMID: 20702642
J Virol. 2010
Reports of Original Research A new class of HIV-1 integrase inhibitors: the 3,3,3', 3'-tetramethyl-1,1'-spirobi(indan)-5,5',6,6'-tetrol family.
V. Molteni, D. Rhodes, K. Rubins, M. Hansen, F. D. Bushman, and J.S. Siegel. (2000). A new class of HIV-1 integrase inhibitors: the 3,3,3', 3'-tetramethyl-1, 1'-spirobi(indan)-5,5',6,6'-tetrol family. J Med Chem. 43, 2031-2039. PMID 10821715.
J Med Chem. 2000
Reports of Original Research Identification of a small-molecule binding site at the dimer interface of the HIV integrase catalytic domain.
V. Molteni, J. Greenwald, D. Rhodes, Y. Hwang, W. Kwiatkowski, F. D. Bushman, J. S. Siegel and S. Choe. A small molecule binding site at the dimer interface of the HIV integrase catalytic domain: X-ray analysis and design of inhibitors. (2001) Acta Cryst. 57, 536-54. PMID 11264582.
Acta Crystallogr D Biol Crystallogr. 2001
Book Chapters Structure and developmental expression of actin genes in the sea urchin.
W. R. Crain, D. S. Durica, A. D. cooper, K. Van Doren and F. D. Bushman. (1982) Structure and developmental expression of actin genes in the sea urchin. In " Muscle Development: Molecular and Cellular Control" (M. Pearson and H. F. Epstein, eds.) Academic Press, London, pp.177-191.
1982
Reports of Original Research Inhibition of retroviral pathogenesis by RNA interference.
W.-Y. Hu, C. Meyer, J. Kilzer, S. Pfaff and F. D. Bushman. (2002) Inhibition of Retroviral Pathogenesis by RNA Interference. Cur. Bio. 12, 1310-1317. PMID 12176358.
Curr Biol. 2002
Review Articles RNA interference against retroviruses.
W.-Y. Hu, F.D. Bushman, and A.C. Siva. (2004) RNA interference against retroviruses. Virus Res. 102: 59-64. PMID 15068881.
Virus Res. 2004
Reports of Original Research Transcripts of paternal and maternal actin gene alleles are present in interspecific sea urchin embryo hybrids.
W.R. Crain and F.D. Bushman. (1983) Transcripts of paternal and maternal actin gene alleles are present in interspecific sea urchin embryo hybrids. Dev. Biol. 100: 190-196. PMID 6617991.
Dev Biol. 1983
Reports of Original Research Dynamics of gene-modified progenitor cells analyzed by tracking retroviral integration sites in a human SCID-X1 gene therapy trial.
Wang GP, Berry CC, Malani N, Leboulch P, Fischer A, Hacein-Bey-Abina S, Cavazzana-Calvo M, Bushman FD. Dynamics of gene-modified progenitor cells analyzed by tracking retroviral integration sites in a human SCID-X1 gene therapy trial. Blood. 2010 Jun 3;115(22):4356-66. PMID: 20228274
Blood. 2010
Reports of Original Research DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer.
Wang GP, Garrigue A, Ciuffi A, Ronen K, Leipzig J, Berry C, Lagresle-Peyrou C, Benjelloun F, Hacein-Bey-Abina S, Fischer A, Cavazzana-Calvo M, Bushman FD. DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer. Nucleic Acids Res. 2008 May;36(9):e49. Epub 2008 Apr 14. PMID: 18411205.
Nucleic Acids Res. 2008
Reports of Original Research Analysis of lentiviral vector integration in HIV+ study subjects receiving autologous infusions of gene modified CD4+ T cells.
Wang GP, Levine BL, Binder GK, Berry CC, Malani N, McGarrity G, Tebas P, June CH, Bushman FD. Analysis of lentiviral vector integration in HIV+ study subjects receiving autologous infusions of gene modified CD4+ T cells. Mol Ther. 2009 May;17(5):844-50. Epub 2009 Mar 3. PMID: 19259065.
Mol Ther. 2009
Reports of Original Research Hepatitis C virus transmission bottlenecks analyzed by deep sequencing.
Wang GP, Sherrill-Mix SA, Chang KM, Quince C, Bushman FD. Hepatitis C virus transmission bottlenecks analyzed by deep sequencing. J Virol. 2010 Jun;84(12):6218-28. PMID: 20375170
J Virol. 2010
Reports of Original Research Engineering HIV-resistant human CD4+ T cells with CXCR4-specific zinc-finger nucleases.
Wilen CB, Wang J, Tilton JC, Miller JC, Kim KA, Rebar EJ, Sherrill-Mix SA, Patro SC, Secreto AJ, Jordan AP, Lee G, Kahn J, Aye PP, Bunnell BA, Lackner AA, Hoxie JA, Danet-Desnoyers GA, Bushman FD, Riley JL, Gregory PD, June CH, Holmes MC, et al. (2011) Engineering HIV-resistant human CD4+ T cells with CXCR4-specific zinc-finger nucleases. PLoS Pathog. 2011 Apr;7(4):e1002020. Epub 2011 Apr 14. PMID 21533216.
PLoS Pathog. 2011
Reports of Original Research Linking long-term dietary patterns with gut microbial enterotypes.
Wu GD, Chen J, Hoffman C, Bittinger K, Chen Y, Keilbaugh SA, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Bushman FD, Lewis JD. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011 Sept 1. PMID: 21885731
Science. 2011
Reports of Original Research 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. Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags.BMC Microbiol. 2010 Jul 30;10:206. PMID: 20673359
BMC Microbiol. 2010
Reports of Original Research DNA contacts stimulate catalysis by a poxvirus topoisomerase.
Y. Hwang, A. Burgin Jr., and F. D. Bushman. (1999) DNA Contacts Stimulate Catalysis by a Poxvirus Topoisomerase. J. Biol. Chem. 274, 9160-9168. PMID 10092587.
J Biol Chem. 1999
Reports of Original Research Molluscum contagiosum virus topoisomerase: purification, activities, and response to inhibitors.
Y. Hwang, B. Wang, and F. Bushman (1998) Molluscum contagiosum virus topoisomerase: purification, activities, and response to inhibitors. J. Virol. 72, 3401-3406. PMID 9525670.
J Virol. 1998
Reports of Original Research Rapid microtiter assays for poxvirus topoisomerase, mammalian type IB topoisomerase and HIV-1 integrase: application to inhibitor isolation.
Y. Hwang, D. Rhodes, and F.D. Bushman. (2000). Rapid Microtiter assays for poxvirus topoisomerase, mammalian type IB topoisomerase and HIV-1 integrase: application to inhibitor isolation. Nucleic Acids Res. 28, 4884-4892. PMID 11121479.
Nucleic Acids Res. 2000
Reports of Original Research Mechanism of inhibition of a poxvirus topoisomerase by the marine natural product sansalvamide A.
Y. Hwang, D. Rowley, D. Rhodes, J. Gertsch, W. Fenical, and F. D. Bushman. (1999) Mechanism of inhibition of a poxvirus topoisomerase by the marine natural product sansalvamide A. Mol. Pharmacol. 55, 1049-1053. PMID 10347247.
Mol Pharmacol. 1999
Reports of Original Research DNA contacts by protein domains of the molluscum contagiosum virus type-1B topoisomerase.
Y. Hwang, M. Park, W. H. Fischer, and F. D. Bushman. (1999) Domain structure of the type 1B topoisomerase encoded by molluscum contagiosum virus. Virology 262, 479-491. PMID 10502526.
Virology. 1999
Reports of Original Research Regulation of catalysis by the smallpox virus topoisomerase.
Y. Hwang, N. Minkah, K. Perry, G. D. Van Duyne, F. D. Bushman. Regulation of catalysis by the smallpox virus topoisomerase. J Biol Chem. 2006 Dec 8;281(49):38052-60. 2006 Oct 10. PMID 17032643.
J Biol Chem. 2006
Reports of Original Research In vitro integration of human immunodeficiency virus type 1 cDNA into targets containing protein-induced bends.
Y.-C. Bor, F.D. Bushman and L.E. Orgel. (1995) In vitro integration of HIV-1 cDNA into targets containing protein-induced bends. Proc. Natl. Acad. Sci. USA 92: 10334-10338. PMID 7479779.
Proc Natl Acad Sci U S A. 1995
Reports of Original Research Target-sequence preferences of HIV-1 integration complexes in vitro.
Y.-C. Bor, M. Miller, F. Bushman, and L. Orgel. (1996) Target sequence preferences of HIV-1 integration complexes in vitro. Virology 222: 238-242. PMID 8806511.
Virology. 1996
Reports of Original Research Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.
Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, et al. (2011) Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol. 2011 May;29(5):415-20. PMID 21552244.
Nat Biotechnol. 2011
Reports of Original Research Crystal structure of an active two-domain derivative of Rous sarcoma virus integrase.
Z-N Yang, T.C. Mueser, F.D. Bushman, and C.C. Hyde. (2000) Crystal structure of an active two-domain derivative of Rous Sarcoma Virus integrase. JMB 296, 535-548. PMID 10669607.
J Mol Biol. 2000
Reports of Original Research Directly Infected Resting CD4+T Cells Can Produce HIV Gag without Spreading Infection in a Model of HIV Latency
Pace MJ, Graf EH, Agosto LM, Mexas AM, Male F, et al. (2012) Directly Infected Resting CD4+T Cells Can Produce HIV Gag without Spreading Infection in a Model of HIV Latency. PLoS Pathog 8(7): e1002818. doi:10.1371/journal.ppat.1002818
PLoS Pathog 2012
Reports of Original Research A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples
Serena Dollive, Gregory L Peterfreund, Scott Sherrill-Mix, Kyle Bittinger, Rohini Sinha, Christian Hoffmann, Christopher S Nabel, David A Hill, David Artis, Michael A Bachman, Rebecca Custers-Allen, Stephanie Grunberg, Gary D Wu, James D Lewis and Frederic D Bushman A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples Genome Biology 2012, 13:R60 doi:10.1186/gb-2012-13-7-r60 Published: 3 July 2012 Serena Dollive, Gregory L Peterfreund, Scott Sherrill-Mix, Kyle Bittinger, Rohini Sinha, Christian Hoffmann, Christopher S Nabel, David A Hill, David Artis, Michael A Bachman, Rebecca Custers-Allen, Stephanie Grunberg, Gary D Wu, James D Lewis and Frederic D Bushman A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples Genome Biology 2012, 13:R60 doi:10.1186/gb-2012-13-7-r60 Published: 3 July 2012
Genome Biology 2012
Reports of Original Research Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing
Karen E. Ocwieja, Scott Sherrill-Mix, Rithun Mukherjee, Rebecca Custers-Allen, Patricia David, Michael Brown, Susana Wang, Darren R. Link, Jeff Olson, Kevin Travers, Eric Schadt, and Frederic D. Bushman Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing Nucl. Acids Res. first published online August 25, 2012 doi:10.1093/nar/gks753
Nucl. Acids Res. 2012
Reports of Original Research Comparative analysis of the recently discovered hAT transposon TcBuster in human cells
L.E. Woodard, X. Li, N. Malani, A. Kaja, R.H. Hice, P.W. Atkinson, F. D. Bushman, N.L. Craig, M.H. Wilson. (2012) Comparative analysis of the recently discovered hAT transposon TcBuster in human cells. PLoS One 7: e42666.
PLoS One 2012
Reports of Original Research A resurrected mammalian hAT transposable element and a closely related insect element are highly active in human cell culture
X. Li, H. Ewis, R. H. Hice, N. Malani, N. Parker, L. Zhou, C. Feschotte, F. D. Bushman, P. W. Atkinson, N. L. Craig. A resurrected mammalian hAT transposable element and a closely related insect element are highly active in human cell culture. Proc. Natl. Acad. Sci. USA 110: E478487. PMCID: PMC 3568352.
PNAS 2012
Reports of Original Research Conservation of gene cassettes among diverse viruses of the human gut.
S. Minot J. Lewis, G. Wu and F. D. Bushman. (2012) Conservation of gene cassettes among diverse viruses of the human gut. PLoS One, 7:e42342. PMCID: PMC3416800.
PLoS One 2012
Reports of Original Research Assessing bacterial populations in the lung by comparing replicate samples from the upper and lower respiratory tracts.
E. S. Charlson, K. Bittinger, J. Chen, J. M. Diamond, H. Li, R. G. Collman, and F. D. Bushman. (2012) Assessing bacterial populations in the lung by comparing replicate samples from the upper and lower respiratory tracts. PLoS One 7: e42786. PMCID: PMC343
PLoS One 2012
Reports of Original Research Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota following lung transplant.
E. S. Charlson, J. M. Diamond, K. Bittinger, A. S. Fitzgerald, A. Yadav, A. R. Hass, and F. D. Bushman, and R. G. Collman. (2012) Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota following lung transplant. Am. J. Resp. Crit. Care Med. 186: 536-545.
Am. J. Resp. Crit. Care Med. 2012
Reports of Original Research Associating microbiome composition with environmental covariates using generalized UniFrac distances.
J. Chen, K. Bittinger, E. S. Charlson, C. Hoffmann, J. Lewis, G. Wu, R. G. Collman, F. D. Bushman, H. Li. (2012) Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics 28: 2106-2113. PMCID: PMC3413390.
Bioinformatics 2012
Reports of Original Research Structure-Constrained Sparse Canonical Correlation Analysis with an Application to Microbiome Data Analysis
J. Chen, F. D. Bushman, J. Lewis, G. D. Wu, and H. Li. (2012) Structure-Constrained Sparse Canonical Correlation Analysis with an Application to Microbiome Data Analysis. Biostatistics 14: 244-258. PMCID: PMC3590923.
Biostatistics 2013
Reports of Original Research Succession in the gut microbiome following antibiotic and antibody therapy for Clostridium difficile
G. L. Peterfreund, L. Vandivier, R. Sinha, A. J. Marozsan, W. C. Olson, J. Zhu, and F. D. Bushman. (2012) Succession in the gut microbiome following antibiotic and antibody therapy for Clostridium difficile. PLoS One 7: e46966. PMCID: PMC3468616.
PLoS One 2012
Reports of Original Research Recombinant adeno-associated virus integration sites in murine liver after ornithine transcarbamylase gene correction.
L. Zhong, N. Malani, M. Li, T. Brady, J. Xie, P. Bell, S. Li, H. Jones, J. M. Wilson, T. Flotte, F. D. Bushman, G. Gao. (2013) Recombinant adeno-associated virus integration sites in murine liver after ornithine transcarbamylase gene correction. Hum. Gene Ther. 24: 520-525.
Hum. Gene Ther. 2013
Reports of Original Research HRP-2 determines HIV-1 integration site selection in LEDGF/p75 depleted cells.
R. Schrijvers, S. Vets, J. D. Rijck, N. Malani, F. D. Bushman, Z. Debyser, and R. Gijsbers. (2012) HRP-2 determines HIV-1 integration site selection in LEDGF/p75 depleted cells. Retrovirology 9:84. PMCID: PMC3485173.
Retrovirology 2012
Reports of Original Research Quantification of HIV DNA integration: effects of differential integration site distributions on Alu-PCR assays.
T. Brady, B. J. Kelly, F. Male, S. Roth, A. Bailey, N. Malani, R. Gijbsers, U. O'Doherty, and F. D. Bushman. (2013) Quantification of HIV DNA integration: effects of differential integration site distributions on Alu-PCR assays. J. Virol. Methods 189: 53-57. PMCID: PMC3608829.
J. Virol. Methods 2013
Reports of Original Research Antiviral effects of autologous CD4 cells genetically modified with a conditionally replicating lentiviral vector expressing long anti-sense to HIV.
P. Tebas, D. Stein, G. Binder-Scholl, R. Mukherjee, T. Brady, T. Rebello, L. Humeau, M. Kalos, E. Papsavvas, L. J. Montaner, D. Schullery, F. Shaheen, A. L. Brennan, Z. Zheng, J. Cotte, V. Slepushkin, E. Veloso, A. Mackley, W.-T. Hwang, F. Aberra, J. Zhan, J. Boyer, R. G. Collman, F. D. Bushman, B. L. Levine, C. H. June. (2013) Antiviral effects of autologous CD4 cells genetically modified with a conditionally replicating lentiviral vector expressing long anti-sense to HIV. Blood 121: 1524-1533. PMCID: PMC3587318.
Blood 2013
Reports of Original Research Rapid evolution of the human gut virome.
S. Minot, A. Bryson, C. Chehoud, G. D. Wu, J. D. Lewis and F. D. Bushman. Rapid evolution of the human gut virome. Proc. Natl. Acad. Sci. USA 2013 110(30): 12450-12455.
PNAS 2013
Reports of Original Research Viral DNA tethering domains complement replication-defective mutation sin the p12 protein of MuLV Gag.
W. M. Schneider, J. D. Brzezinski, S. Aiyer, N. Malani, M. Gyuricza, F. D. Bushman, M. J. Roth. (2013) Viral DNA tethering domains complement replication-defective mutation sin the p12 protein of MuLV Gag. Proc. Natl. Acad. Sci. USA 110: 9487-9492. PMCID: PMC3677494.
PNAS 2013
Reports of Original Research Widespread colonization of the lung by Tropheryma whipplei in HIV infection.
C. A. Lozupone, A. Cota-Gomez, B. Palmer, E. Charlson, E. Sodergren, M. Mitreva, S. Abubucker, J. Martin, G. Yao, T. Campbell, S. Flores, G. Ackerman, J. Stombaugh L. Ursell, J. Beck, J. Curtis, V. Young, S. V. Lynch, L. Huang, G. M Weinstock, K. Knox, H. L. Twigg III, A. Morris, E. Ghodin, F. D. Bushman, R. Collman, R. Knight, A. P. Fontenot. (2013) Widespread colonization of the lung by Tropheryma whipplei in HIV infection. Am. J. Resp. Crit. Care Med. 187: 1110-1117.
Am. J. Respir. Crit. Care. Med. 2013
Reports of Original Research Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis.
R. A. Koeth, Z. Wang, B. S. Levinson, J. A. Buffa, E. Org, B. T. Sheehy, E. B. Britt, X. Fu, Y. Wu, L. Li, J. D. Smith, J. A. DiDonato, J. Chen, H. Li, G. D. Wu, J. D. Lewis, M. Warrier, J. M. Brown, R. M. Krauss, W. H. W. Tang, F. D. Bushman, A. J. Lusis, S. L. Hazen. (2013) Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat. Med. 19:576-585. PMCID: PMC3650111.
Nat. Med. 2013
Reports of Original Research Plasmodium falciparum-like parasites infecting wild African apes do not represent a recurrent source of human malaria.
S. A. Sundararaman, W. Liu, B. F. Keele, G. H. Learn, K. Bittinger, F. Mouacha, S. Ahuka-Mundeke, S. Sherrill-Mix, Y. Li, J. A. Malenke, E. Delaporte, C. Laurent, E. M. Ngole, D. P. Kwiatkowski, G. M. Shaw, J. C. Rayner, M. Peeters, P. M. Sharp, F. D. Bushman, B. H. Hahn. (2013) Plasmodium falciparum-like parasites infecting wild African apes do not represent a recurrent source of human malaria. Proc. Natl. Acad. Sci. USA 110:7020-7025. PMCID: PMC3637760.
PNAS 2013
Reports of Original Research Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial Residents.
C. Hoffmann, S. Dollive, S. Grunberg, J. Chen, H. Li, G. D. Wu, J. D. Lewis, and F. D. Bushman. (2013) Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial Residents PLoS One 8:e66019. PMCID: PMC36844604.
PLoS One 2013
Reports of Original Research Quantitative Phosphoproteomics Reveals Extensive Cellular Reprogramming During HIV-1 Entry.
J. A. Wojcechowskyj, C. A. Didigu, J. Y. Lee, N. F. Parrish, R. Sinha, B. H. Hahn, F. D. Bushman, S. T. Jensen, S. H. Seeholzer, and R. W. Doms. Quantitative Phosphoproteomics Reveals Extensive Cellular Reprogramming During HIV-1 Entry. Cell Host Microbe 2013 13:613-623.
Cell Host Microbe 2013
Reports of Original Research BET proteins promote efficient murine leukemia virus integration at transcription start sites.
A. Sharma, R. C. Larue, M. R. Plumb, N. Malani, A. Slaughter, J. J. Kessl, N. Shkriabai, S. S Aiyer, P. L. Green, L. Wu, M. J. Roth, F. D. Bushman, and M. Kvaratskhelia. (2013) BET proteins promote efficient murine leukemia virus integration at transcription start sites. Proc Natl Acad Sci U S A. 2013 2013 110(29):12036-41.
PNAS 2013
Reports of Original Research Innate lymphoid cells regulate CD4+ T-cell responses to intestinal commensal bacteria.
M. R. Hepworth, L. A. Monticelli, T. C. Fung, C. G. Ziegler, S. Grunberg, R. Sinha, A. R. Mantegazza, H.-L. Ma, A. Crawford, J. M. Angelosanto, E. J. Wherry, P. A. Koni, F. D. Bushman, C. O. Elson, G. Eberi, D. Artis, and G. F. Sonnenberg. (2013) Innate lymphoid cells regulate CD4+ T-cell responses to intestinal commensal bacteria. Nature 498: 113-117. PMCID: PMC3699860.
Nature 2013
Reports of Original Research piggyBac transposase tools for genome engineering.
X. Li, E. R. Burnight, A. L. Cooney, N. Malani, T. Brady, J. D. Sander, J. Staber, S. J. Wheelan, J. K. Joung, P. B. McCray Jr., F. D. Bushman, P. L. Sinn, and N. L. Craig. (2013) piggyBac transposase tools for genome engineering. Proc. Natl. Acad. Sci. USA 110:E2279-E2287. PMCID: PMC3690869.
PNAS 2013
Review Article Bringing it all together: Big Data and HIV research.
F. D. Bushman, S. Barton, A. Bailey, C. Greig, N. Malani, S. Bandyopadhyay, J. Young, S. Chanda, and N. Krogan. Bringing it all together: Big Data and HIV research. AIDS 27: 835-838. PMCID: PMC3671485.
AIDS 2013
Reports of Original Research HIV latency and integration site placement in five cell-based models
S. Sherrill-Mix, M. K. Lewinski, M. Famiglietti, A. Bosque, N. Malani, K. E. Ocwieja, C. C. Berry, D. Looney, L. Shan, L. M. Agosto, M. J. Pace, R. F. Siliciano, U. O’Doherty, J. Guatelli, V. Planelles and Frederic D. Bushman. (2013) HIV latency and integration site placement in five cell-based models. Retrovirology, 10:90.
Retrovirology 2013
Reports of Original Research Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation
Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation
Science 2014