Frederic D Bushman

Summary

Affiliation: The Salk Institute
Country: USA

Publications

  1. doi request reprint Massively parallel pyrosequencing in HIV research
    Frederic D Bushman
    Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104 6076, USA
    AIDS 22:1411-5. 2008
  2. ncbi request reprint A new cellular system opposing HIV infection: implications for gene transfer?
    Frederic Bushman
    Infectious Disease Laboratory, Salk Institute, 10010 North Torrey Pines Road, La Jolla, California, 92037, USA
    Mol Ther 6:441-2. 2002
  3. ncbi request reprint Targeting retroviral integration?
    Frederic Bushman
    Infectious Disease Laboratory, Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
    Mol Ther 6:570-1. 2002
  4. ncbi request reprint RNA interference: applications in vertebrates
    Frederic Bushman
    Infectious Disease Laboratory, Salk Institute, 10010 North Torreny Pines Road, La Jolla, CA 92037, USA
    Mol Ther 7:9-10. 2003
  5. ncbi request reprint Targeting survival: integration site selection by retroviruses and LTR-retrotransposons
    Frederic D Bushman
    Infectious Disease Laboratory, The Salk Institute, 10010 North Torrey Pines Rd, La Jolla, CA 92037, USA
    Cell 115:135-8. 2003
  6. pmc Selection of target sites for mobile DNA integration in the human genome
    Charles Berry
    Department of Family and Preventive Medicine, School of Medicine, University of California San Diego, La Jolla, California, United States of America
    PLoS Comput Biol 2:e157. 2006
  7. ncbi request reprint RNA interference against retroviruses
    Wen Yuan Hu
    Infectious Disease Laboratory, The Salk Institute, 10010 North Torrey Pines Rd, La Jolla, CA 92037, USA
    Virus Res 102:59-64. 2004
  8. pmc Retroviral DNA integration: viral and cellular determinants of target-site selection
    Mary K Lewinski
    Infectious Disease Laboratory, The Salk Institute, La Jolla, California, USA
    PLoS Pathog 2:e60. 2006
  9. pmc Single-particle image reconstruction of a tetramer of HIV integrase bound to DNA
    Gang Ren
    The Scripps Research Institute, Department of Cell Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Mol Biol 366:286-94. 2007
  10. ncbi request reprint Roles of host cell factors in circularization of retroviral dna
    Jennifer M Kilzer
    Infectious Disease Laboratory, The Salk Institute, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
    Virology 314:460-7. 2003

Collaborators

Detail Information

Publications37

  1. doi request reprint Massively parallel pyrosequencing in HIV research
    Frederic D Bushman
    Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104 6076, USA
    AIDS 22:1411-5. 2008
  2. ncbi request reprint A new cellular system opposing HIV infection: implications for gene transfer?
    Frederic Bushman
    Infectious Disease Laboratory, Salk Institute, 10010 North Torrey Pines Road, La Jolla, California, 92037, USA
    Mol Ther 6:441-2. 2002
  3. ncbi request reprint Targeting retroviral integration?
    Frederic Bushman
    Infectious Disease Laboratory, Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
    Mol Ther 6:570-1. 2002
  4. ncbi request reprint RNA interference: applications in vertebrates
    Frederic Bushman
    Infectious Disease Laboratory, Salk Institute, 10010 North Torreny Pines Road, La Jolla, CA 92037, USA
    Mol Ther 7:9-10. 2003
  5. ncbi request reprint Targeting survival: integration site selection by retroviruses and LTR-retrotransposons
    Frederic D Bushman
    Infectious Disease Laboratory, The Salk Institute, 10010 North Torrey Pines Rd, La Jolla, CA 92037, USA
    Cell 115:135-8. 2003
    ..Despite these differences, recent data hints at a common targeting mechanism-tethering of integration complexes to proteins bound at favorable sites...
  6. pmc Selection of target sites for mobile DNA integration in the human genome
    Charles Berry
    Department of Family and Preventive Medicine, School of Medicine, University of California San Diego, La Jolla, California, United States of America
    PLoS Comput Biol 2:e157. 2006
    ....
  7. ncbi request reprint RNA interference against retroviruses
    Wen Yuan Hu
    Infectious Disease Laboratory, The Salk Institute, 10010 North Torrey Pines Rd, La Jolla, CA 92037, USA
    Virus Res 102:59-64. 2004
    ..Here we describe the use of RNA interference (RNAi) in live chick embryos to block replication of an avian retrovirus. We also describe inhibition of ASLV and HIV replication in cell culture with RNAi...
  8. pmc Retroviral DNA integration: viral and cellular determinants of target-site selection
    Mary K Lewinski
    Infectious Disease Laboratory, The Salk Institute, La Jolla, California, USA
    PLoS Pathog 2:e60. 2006
    ....
  9. pmc Single-particle image reconstruction of a tetramer of HIV integrase bound to DNA
    Gang Ren
    The Scripps Research Institute, Department of Cell Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Mol Biol 366:286-94. 2007
    ..The asymmetry of the complex is a feature not incorporated in previous structural models and potentially provides the first view of an asymmetric reaction intermediate...
  10. ncbi request reprint Roles of host cell factors in circularization of retroviral dna
    Jennifer M Kilzer
    Infectious Disease Laboratory, The Salk Institute, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
    Virology 314:460-7. 2003
    ..None of the cellular mutations showed a strong effect on normal integration, consistent with the idea that the cellular pathways leading to circularization are not involved in productive integration...
  11. pmc Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication
    Renate König
    Infectious and Inflammatory Disease Center, Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
    Cell 135:49-60. 2008
    ..Taken together, the multiscale approach described here has uncovered multiprotein virus-host interactions that likely act in concert to facilitate the early steps of HIV-1 infection...
  12. ncbi request reprint Modeling HIV-1 integrase complexes based on their hydrodynamic properties
    Alexei A Podtelezhnikov
    Howard Hughes Medical Institute, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093 0365, USA
    Biopolymers 68:110-20. 2003
    ..Our model of the integrase tetramer bound to DNA may help to design anti-integrase inhibitors...
  13. ncbi request reprint Inhibition of retroviral pathogenesis by RNA interference
    Wen Yuan Hu
    Infectious Disease Laboratory, La Jolla, CA 92037, USA
    Curr Biol 12:1301-11. 2002
    ..It has been widely conjectured that RNAi may also serve as an antiviral system in vertebrates...
  14. ncbi request reprint Retroviral DNA integration--mechanism and consequences
    Mary K Lewinski
    Infectious Disease Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92186, USA
    Adv Genet 55:147-81. 2005
    ..Research into the mechanisms of retroviral integration site selection has shed light on the phenomena of insertional mutagenesis and viral latency...
  15. pmc Comparing DNA integration site clusters with scan statistics
    Charles C Berry
    Division of Biostatistics and Bioinformatics, Department of Family and Preventive Medicine, University of California at San Diego, La Jolla, CA 92093 0901 and Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 425 Johnson Pavilion, Philadelphia, PA 19104 6076, USA
    Bioinformatics 30:1493-500. 2014
    ..Scan statistics allow the discovery of spatial differences in clustering and calculation of false discovery rates providing statistical methods for comparing retroviral vectors...
  16. pmc Estimating abundances of retroviral insertion sites from DNA fragment length data
    Charles C Berry
    Department of Family and Preventive Medicine, University of California, La Jolla, CA, USA
    Bioinformatics 28:755-62. 2012
    ..The difficulty in calibrating this relation is compounded by sample-specific variations in the relative frequencies of clones of each length...
  17. ncbi request reprint Thalassiolins A-C: new marine-derived inhibitors of HIV cDNA integrase
    David C Rowley
    Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
    Bioorg Med Chem 10:3619-25. 2002
    ..4 microM) and an antiviral IC50 of 30 microM. Molecular modeling studies indicate a favorable binding mode is probable at the catalytic core domain of HIV-1 integrase...
  18. pmc Human immunodeficiency virus cDNA metabolism: notable stability of two-long terminal repeat circles
    Scott L Butler
    Infectious Disease Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
    J Virol 76:3739-47. 2002
    ..We also used the quantitative PCR methods to analyze the effects of MG132, a proteasome inhibitor, which revealed that viral complexes containing mostly completed cDNAs are the primary substrates for proteasome-mediated degradation...
  19. pmc HTLV-1 integration into transcriptionally active genomic regions is associated with proviral expression and with HAM/TSP
    Kiran N Meekings
    Department of Immunology, Wright Fleming Institute, Imperial College London, London, United Kingdom
    PLoS Pathog 4:e1000027. 2008
    ....
  20. pmc Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences
    Rick S Mitchell
    Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
    PLoS Biol 2:E234. 2004
    ..Thus, each of the three retroviruses studied showed unique integration site preferences, suggesting that virus-specific binding of integration complexes to chromatin features likely guides site selection...
  21. pmc Gene transfer in humans using a conditionally replicating lentiviral vector
    Bruce L Levine
    Abramson Family Cancer Research Institute, University of Pennsylvania Cancer Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    Proc Natl Acad Sci U S A 103:17372-7. 2006
    ..There is no evidence for insertional mutagenesis after 21-36 months of observation. Immune function improved in four subjects. Lentiviral vectors appear promising for gene transfer to humans...
  22. pmc DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer
    Gary P Wang
    University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104 6076, USA
    Nucleic Acids Res 36:e49. 2008
    ..The methods described here should allow integration site populations from human gene therapy to be deeply characterized with spatial and temporal resolution...
  23. ncbi request reprint Retroviral DNA integration: HIV and the role of LEDGF/p75
    Angela Ciuffi
    University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104 6076, USA
    Trends Genet 22:388-95. 2006
    ..Understanding viral integration will help improve the safety of retrovirus-based vectors used in gene therapy...
  24. pmc Retroviral integration and human gene therapy
    Frederic D Bushman
    Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104 6076, USA
    J Clin Invest 117:2083-6. 2007
    ....
  25. pmc The interferon response inhibits HIV particle production by induction of TRIM22
    Stephen D Barr
    Department of Medical Microbiology and Immunology, University of Alberta, Alberta Institute for Viral Immunology, Edmonton, Alberta, Canada
    PLoS Pathog 4:e1000007. 2008
    ..Mutational analyses of TRIM22 showed that the catalytic amino acids Cys15 and Cys18 of the RING domain are required for TRIM22 antiviral activity. These data disclose a pathway by which Type 1 interferons obstruct HIV replication...
  26. pmc Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1
    Salima Hacein-Bey-Abina
    Department of Biotherapy, Hopital Necker Enfants Malades, Assistance Publique Hopitaux de Paris AP HP, Universite Rene Descartes, Paris, France
    J Clin Invest 118:3132-42. 2008
    ..Successful chemotherapy was associated with restoration of polyclonal transduced T cell populations. As a result, the treated patients continued to benefit from therapeutic gene transfer...
  27. pmc Role of PSIP1/LEDGF/p75 in lentiviral infectivity and integration targeting
    Heather M Marshall
    Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 2:e1340. 2007
    ..A cellular protein, PSIP1/LEDGF/p75, binds tightly to the lentiviral-encoded integrase protein (IN), and has been reported to be important for HIV infectivity and integration targeting...
  28. pmc DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations
    Christian Hoffmann
    Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104 6076, USA
    Nucleic Acids Res 35:e91. 2007
    ....
  29. ncbi request reprint HIV integration site selection: targeting in macrophages and the effects of different routes of viral entry
    Stephen D Barr
    Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, 19104 6076, USA
    Mol Ther 14:218-25. 2006
    ..Analysis of additional published integration site sequences also indicated that the route of entry did not affect integration site selection for other viral envelopes as well...
  30. ncbi request reprint DNA cleavage by the A22R resolvase of vaccinia virus
    Matthew J Culyba
    Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104 6076, USA
    Virology 352:466-76. 2006
    ..Analysis of the reaction products revealed that A22R cleaves to leave a 3' hydroxyl at the cleaved phosphodiester bond...
  31. pmc Division of labor within human immunodeficiency virus integrase complexes: determinants of catalysis and target DNA capture
    Tracy L Diamond
    University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104 6076, USA
    J Virol 79:15376-87. 2005
    ..These data specify the ligands bound at the catalytically relevant IN monomer and allow more-specific modeling of the mechanism of inhibitors that also bind this surface of IN...
  32. ncbi request reprint Modulating target site selection during human immunodeficiency virus DNA integration in vitro with an engineered tethering factor
    Angela Ciuffi
    Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 6076, USA
    Hum Gene Ther 17:960-7. 2006
    ....
  33. ncbi request reprint Regulation of catalysis by the smallpox virus topoisomerase
    Young Hwang
    Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
    J Biol Chem 281:38052-60. 2006
    ..These findings help elucidate the amino acid side chains involved in DNA binding and catalysis and provide guidance for designing topoisomerase poisons for use as smallpox antivirals...
  34. pmc Integration targeting by avian sarcoma-leukosis virus and human immunodeficiency virus in the chicken genome
    Stephen D Barr
    University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104 6076, USA
    J Virol 79:12035-44. 2005
    ..Further analysis indicated that ERVs in humans, mice, and rats showed similar distributions, suggesting purifying selection dictated their distributions as well...
  35. pmc Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes
    Nana Minkah
    Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 6076, USA
    Virology 365:60-9. 2007
    ..These data define the full variola virus topoisomerase recognition site and provide a new window on topoisomerase function in vivo...
  36. pmc HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications
    Gary P Wang
    University of Pennsylvania, School of Medicine, Department of Microbiology, Philadelphia, PA 19104 6076, USA
    Genome Res 17:1186-94. 2007
    ..The pyrosequencing and bioinformatic methods described here should be useful for investigating many aspects of retroviral DNA integration...
  37. ncbi request reprint A statistical method for comparing viral growth curves
    Gary P Wang
    Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104 6076, USA
    J Virol Methods 135:118-23. 2006
    ..A web-based tutorial for implementing this method is available at http://microb230.med.upenn.edu/tutorials/wangTutorial...