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Charles Berry

TitleProfessor
InstitutionUniversity of California San Diego
DepartmentFamily Medicine and Public Health
Address9500 Gilman Drive #0901
La Jolla CA 92093
Phone858-534-9360
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    Collapse Biography 
    Collapse Education and Training
    Johns Hopkins UniversityPhD1973Sociology
    Dartmouth CollegeBA1969Sociology

    Collapse Overview 
    Collapse Overview
    Dr. Berry's current research interest is on statistical models, methods, and software for exploring populations of integration sites such as occur in retroviral infections (see Berry et al, 2006, PLoS Comput Biol and Berry et al, Bioinformatics, 2012) or in gene therapies using retrovirus-like constructs (see Berry et al, Bioinformatics, 2014) .

    During his career, Dr. Berry has been the principal statistician on multisite clinical trials, the California Tobacco Survey, and cohort studies. He is the author or co-author of more than 175 scientific publications. He has served as a reviewer for NIH Study Sections and been Statistical Editor of two medical journals. He has taught statistics to medical students, graduate students, and postdoctoral fellows in the biomedical sciences.


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    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Sherman E, Nobles C, Berry C, Six E, Wu Y, Dryga A, Malani N, Male F, Reddy S, Bailey A, Bittinger K, Everett JK, Caccavelli L, Drake MJ, Bates P, Hacein-Bey-Abina S, Cavazzana M, Bushman FD. INSPIIRED: A Pipeline for Quantitative Analysis of Sites of New DNA Integration in Cellular Genomes. Mol Ther Methods Clin Dev. 2017 Mar 17; 4:39-49. PMID: 28344990.
      View in: PubMed
    2. Berry C, Nobles C, Six E, Wu Y, Malani N, Sherman E, Dryga A, Everett JK, Male F, Bailey A, Bittinger K, Drake MJ, Caccavelli L, Bates P, Hacein-Bey-Abina S, Cavazzana M, Bushman FD. INSPIIRED: Quantification and Visualization Tools for Analyzing Integration Site Distributions. Mol Ther Methods Clin Dev. 2017 Mar 17; 4:17-26. PMID: 28344988.
      View in: PubMed
    3. Hacein-Bey Abina S, Gaspar HB, Blondeau J, Caccavelli L, Charrier S, Buckland K, Picard C, Six E, Himoudi N, Gilmour K, McNicol AM, Hara H, Xu-Bayford J, Rivat C, Touzot F, Mavilio F, Lim A, Treluyer JM, Héritier S, Lefrère F, Magalon J, Pengue-Koyi I, Honnet G, Blanche S, Sherman EA, Male F, Berry C, Malani N, Bushman FD, Fischer A, Thrasher AJ, Galy A, Cavazzana M. Outcomes following gene therapy in patients with severe Wiskott-Aldrich syndrome. JAMA. 2015 Apr 21; 313(15):1550-63. PMID: 25898053; PMCID: PMC4942841.
    4. Hacein-Bey-Abina S, Pai SY, Gaspar HB, Armant M, Berry C, Blanche S, Bleesing J, Blondeau J, de Boer H, Buckland KF, Caccavelli L, Cros G, De Oliveira S, Fernández KS, Guo D, Harris CE, Hopkins G, Lehmann LE, Lim A, London WB, van der Loo JC, Malani N, Male F, Malik P, Marinovic MA, McNicol AM, Moshous D, Neven B, Oleastro M, Picard C, Ritz J, Rivat C, Schambach A, Shaw KL, Sherman EA, Silberstein LE, Six E, Touzot F, Tsytsykova A, Xu-Bayford J, Baum C, Bushman FD, Fischer A, Kohn DB, Filipovich AH, Notarangelo LD, Cavazzana M, Williams DA, Thrasher AJ. A modified ?-retrovirus vector for X-linked severe combined immunodeficiency. N Engl J Med. 2014 Oct 09; 371(15):1407-17. PMID: 25295500; PMCID: PMC4274995.
    5. Berry C, Ocwieja KE, Malani N, Bushman FD. Comparing DNA integration site clusters with scan statistics. Bioinformatics. 2014 Jun 01; 30(11):1493-500. PMID: 24489369; PMCID: PMC4029028.
    6. Sherrill-Mix S, Lewinski MK, Famiglietti M, Bosque A, Malani N, Ocwieja KE, Berry C, Looney D, Shan L, Agosto LM, Pace MJ, Siliciano RF, O'Doherty U, Guatelli J, Planelles V, Bushman FD. HIV latency and integration site placement in five cell-based models. Retrovirology. 2013 Aug 16; 10:90. PMID: 23953889; PMCID: PMC3765678.
    7. Berry C, Gillet NA, Melamed A, Gormley N, Bangham CR, Bushman FD. Estimating abundances of retroviral insertion sites from DNA fragment length data. Bioinformatics. 2012 Mar 15; 28(6):755-62. PMID: 22238265; PMCID: PMC3307109.
    8. Brady T, Roth SL, Malani N, Wang GP, Berry C, 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 Jun; 39(11):e72. PMID: 21415009; PMCID: PMC3113588.
    9. 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 C, 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.
      View in: PubMed
    10. 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.
      View in: PubMed
    11. Hacein-Bey-Abina S, Hauer J, Lim A, Picard C, Wang GP, Berry C, 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; PMCID: PMC2957288.
    12. Wang GP, Berry C, 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 03; 115(22):4356-66. PMID: 20228274; PMCID: PMC2881494.
    13. Brady T, Agosto LM, Malani N, Berry C, 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; PMCID: PMC2862484.
    14. Wang GP, Levine BL, Binder GK, Berry C, 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. PMID: 19259065; PMCID: PMC2835137.
    15. Brady T, Lee YN, Ronen K, Malani N, Berry C, Bieniasz PD, Bushman FD. Integration target site selection by a resurrected human endogenous retrovirus. Genes Dev. 2009 Mar 01; 23(5):633-42. PMID: 19270161; PMCID: PMC2658518.
    16. Ciuffi A, Ronen K, Brady T, Malani N, Wang G, Berry C, Bushman FD. Methods for integration site distribution analyses in animal cell genomes. Methods. 2009 Apr; 47(4):261-8. PMID: 19038346; PMCID: PMC4104535.
    17. 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. PMID: 18953026; PMCID: PMC2602771.
    18. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry C, Millar AH, Ecker JR. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 2008 May 02; 133(3):523-36. PMID: 18423832; PMCID: PMC2723732.
    19. 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. PMID: 18411205; PMCID: PMC2396413.
    20. Marshall HM, Ronen K, Berry C, Llano M, Sutherland H, Saenz D, Bickmore W, Poeschla E, Bushman FD. Role of PSIP1/LEDGF/p75 in lentiviral infectivity and integration targeting. PLoS One. 2007 Dec 19; 2(12):e1340. PMID: 18092005; PMCID: PMC2129110.
    21. Wang GP, Ciuffi A, Leipzig J, Berry C, Bushman FD. HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications. Genome Res. 2007 Aug; 17(8):1186-94. PMID: 17545577; PMCID: PMC1933515.
    22. Loredo JS, Berry C, Nelesen RA, Dimsdale JE. Prediction of continuous positive airway pressure in obstructive sleep apnea. Sleep Breath. 2007 Mar; 11(1):45-51. PMID: 17089145.
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    23. Berry C, Moore P, Dimsdale JE. Assessing the trade-offs between crossover and parallel group designs in sleep research. J Sleep Res. 2006 Dec; 15(4):348-57. PMID: 17118091.
      View in: PubMed
    24. Berry C, Hannenhalli S, Leipzig J, Bushman FD. Selection of target sites for mobile DNA integration in the human genome. PLoS Comput Biol. 2006 Nov 24; 2(11):e157. PMID: 17166054; PMCID: PMC1664696.
    25. Lewinski MK, Yamashita M, Emerman M, Ciuffi A, Marshall H, Crawford G, Collins F, Shinn P, Leipzig J, Hannenhalli S, Berry C, Ecker JR, Bushman FD. Retroviral DNA integration: viral and cellular determinants of target-site selection. PLoS Pathog. 2006 Jun; 2(6):e60. PMID: 16789841; PMCID: PMC1480600.
    26. Cheng TC, Manorek G, Samimi G, Lin X, Berry C, Howell SB. Identification of genes whose expression is associated with cisplatin resistance in human ovarian carcinoma cells. Cancer Chemother Pharmacol. 2006 Sep; 58(3):384-95. PMID: 16404635.
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    27. Zangwill LM, Weinreb RN, Beiser JA, Berry C, Cioffi GA, Coleman AL, Trick G, Liebmann JM, Brandt JD, Piltz-Seymour JR, Dirkes KA, Vega S, Kass MA, Gordon MO. Baseline topographic optic disc measurements are associated with the development of primary open-angle glaucoma: the Confocal Scanning Laser Ophthalmoscopy Ancillary Study to the Ocular Hypertension Treatment Study. Arch Ophthalmol. 2005 Sep; 123(9):1188-97. PMID: 16157798.
      View in: PubMed
    28. Geng W, Cosman P, Berry C, Feng Z, Schafer WR. Automatic tracking, feature extraction and classification of C elegans phenotypes. IEEE Trans Biomed Eng. 2004 Oct; 51(10):1811-20. PMID: 15490828.
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    29. Samimi G, Manorek G, Castel R, Breaux JK, Cheng TC, Berry C, Los G, Howell SB. cDNA microarray-based identification of genes and pathways associated with oxaliplatin resistance. Cancer Chemother Pharmacol. 2005 Jan; 55(1):1-11. PMID: 15378272.
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    30. Mitchell RS, Beitzel BF, Schroder AR, Shinn P, Chen H, Berry C, Ecker JR, Bushman FD. Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biol. 2004 Aug; 2(8):E234. PMID: 15314653; PMCID: PMC509299.
    31. Stepnowsky CJ, Berry C, Dimsdale JE. The effect of measurement unreliability on sleep and respiratory variables. Sleep. 2004 Aug 01; 27(5):990-5. PMID: 15453560.
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    32. Wolyn DJ, Borevitz JO, Loudet O, Schwartz C, Maloof J, Ecker JR, Berry C, Chory J. Light-response quantitative trait loci identified with composite interval and eXtreme array mapping in Arabidopsis thaliana. Genetics. 2004 Jun; 167(2):907-17. PMID: 15238539; PMCID: PMC1470895.
    33. Prakken BJ, Samodal R, Le TD, Giannoni F, Yung GP, Scavulli J, Amox D, Roord S, de Kleer I, Bonnin D, Lanza P, Berry C, Massa M, Billetta R, Albani S. Epitope-specific immunotherapy induces immune deviation of proinflammatory T cells in rheumatoid arthritis. Proc Natl Acad Sci U S A. 2004 Mar 23; 101(12):4228-33. PMID: 15024101; PMCID: PMC384723.
    34. Zangwill LM, Weinreb RN, Berry C, Smith AR, Dirkes KA, Liebmann JM, Brandt JD, Trick G, Cioffi GA, Coleman AL, Piltz-Seymour JR, Gordon MO, Kass MA. The confocal scanning laser ophthalmoscopy ancillary study to the ocular hypertension treatment study: study design and baseline factors. Am J Ophthalmol. 2004 Feb; 137(2):219-27. PMID: 14962409.
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    35. Stuart RO, Wachsman W, Berry C, Wang-Rodriguez J, Wasserman L, Klacansky I, Masys D, Arden K, Goodison S, McClelland M, Wang Y, Sawyers A, Kalcheva I, Tarin D, Mercola D. In silico dissection of cell-type-associated patterns of gene expression in prostate cancer. Proc Natl Acad Sci U S A. 2004 Jan 13; 101(2):615-20. PMID: 14722351; PMCID: PMC327196.
    36. Zangwill LM, Weinreb RN, Berry C, Smith AR, Dirkes KA, Coleman AL, Piltz-Seymour JR, Liebmann JM, Cioffi GA, Trick G, Brandt JD, Gordon MO, Kass MA. Racial differences in optic disc topography: baseline results from the confocal scanning laser ophthalmoscopy ancillary study to the ocular hypertension treatment study. Arch Ophthalmol. 2004 Jan; 122(1):22-8. PMID: 14718290.
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    37. Geng W, Cosman P, Baek JH, Berry C, Schafer WR. Quantitative classification and natural clustering of Caenorhabditis elegans behavioral phenotypes. Genetics. 2003 Nov; 165(3):1117-26. PMID: 14668369; PMCID: PMC1462821.
    38. Blumenthal EZ, Sample PA, Berry C, Lee AC, Girkin CA, Zangwill L, Caprioli J, Weinreb RN. Evaluating several sources of variability for standard and SWAP visual fields in glaucoma patients, suspects, and normals. Ophthalmology. 2003 Oct; 110(10):1895-902. PMID: 14522760.
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    39. Mitchell R, Chiang CY, Berry C, Bushman F. Global analysis of cellular transcription following infection with an HIV-based vector. Mol Ther. 2003 Oct; 8(4):674-87. PMID: 14529841.
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    40. Natarajan L, Berry C, Gasche C. Estimation of spontaneous mutation rates. Biometrics. 2003 Sep; 59(3):555-61. PMID: 14601756.
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    41. Mills PJ, Farag NH, Hong S, Kennedy BP, Berry C, Ziegler MG. Immune cell CD62L and CD11a expression in response to a psychological stressor in human hypertension. Brain Behav Immun. 2003 Aug; 17(4):260-7. PMID: 12831828.
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    42. Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, Shinn P, Stevenson DK, Zimmerman J, Barajas P, Cheuk R, Gadrinab C, Heller C, Jeske A, Koesema E, Meyers CC, Parker H, Prednis L, Ansari Y, Choy N, Deen H, Geralt M, Hazari N, Hom E, Karnes M, Mulholland C, Ndubaku R, Schmidt I, Guzman P, Aguilar-Henonin L, Schmid M, Weigel D, Carter DE, Marchand T, Risseeuw E, Brogden D, Zeko A, Crosby WL, Berry C, Ecker JR. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science. 2003 Aug 01; 301(5633):653-7. PMID: 12893945.
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    43. Mills PJ, Farag NH, Matthews S, Nelesen RA, Berry C, Dimsdale JE. Hormone replacement therapy does not affect 24-h ambulatory blood pressure in healthy non-smoking postmenopausal women. Blood Press Monit. 2003 Apr; 8(2):57-61. PMID: 12819556.
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    44. Borevitz JO, Liang D, Plouffe D, Chang HS, Zhu T, Weigel D, Berry C, Winzeler E, Chory J. Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res. 2003 Mar; 13(3):513-23. PMID: 12618383; PMCID: PMC430246.
    45. Massa M, Costouros N, Mazzoli F, De Benedetti F, La Cava A, Le T, De Kleer I, Ravelli A, Liotta M, Roord S, Berry C, Pachman LM, Martini A, Albani S. Self epitopes shared between human skeletal myosin and Streptococcus pyogenes M5 protein are targets of immune responses in active juvenile dermatomyositis. Arthritis Rheum. 2002 Nov; 46(11):3015-25. PMID: 12428245.
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    46. von Känel R, Bardwell WA, Berry C, Dimsdale JE. Independent contribution of psychological factors to fibrin turnover in subjects with sleep apnoea and/or systemic hypertension. Clin Sci (Lond). 2002 Oct; 103(4):331-7. PMID: 12241529.
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    47. McKenzie TL, Sallis JF, Broyles SL, Zive MM, Nader PR, Berry C, Brennan JJ. Childhood movement skills: predictors of physical activity in Anglo American and Mexican American adolescents? Res Q Exerc Sport. 2002 Sep; 73(3):238-44. PMID: 12230330.
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    48. Schröder AR, Shinn P, Chen H, Berry C, Ecker JR, Bushman F. HIV-1 integration in the human genome favors active genes and local hotspots. Cell. 2002 Aug 23; 110(4):521-9. PMID: 12202041.
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    49. Saelens BE, Sallis JF, Nader PR, Broyles SL, Berry C, Taras HL. Home environmental influences on children's television watching from early to middle childhood. J Dev Behav Pediatr. 2002 Jun; 23(3):127-32. PMID: 12055494.
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    50. Lee AC, Sample PA, Blumenthal EZ, Berry C, Zangwill L, Weinreb RN. Infrequent confirmation of visual field progression. Ophthalmology. 2002 Jun; 109(6):1059-65. PMID: 12045044.
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    51. Zive MM, Berry C, Sallis JF, Frank GC, Nader PR. Tracking dietary intake in white and Mexican-American children from age 4 to 12 years. J Am Diet Assoc. 2002 May; 102(5):683-9. PMID: 12008994.
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    52. Boehm AG, Helmke K, Berry C, Weinreb RN. Comparison of two transducers for color Doppler imaging of the retrobulbar vessels. J Glaucoma. 2002 Apr; 11(2):148-53. PMID: 11912363.
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    53. Masu R, Sallis JF, Berry C, Broyles SL, Elder JP, Nader PR. The relationship between health beliefs and behaviors and dietary intake in early adolescence. J Am Diet Assoc. 2002 Mar; 102(3):421-4. PMID: 11902380.
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    54. Borevitz JO, Maloof JN, Lutes J, Dabi T, Redfern JL, Trainer GT, Werner JD, Asami T, Berry C, Weigel D, Chory J. Quantitative trait loci controlling light and hormone response in two accessions of Arabidopsis thaliana. Genetics. 2002 Feb; 160(2):683-96. PMID: 11861571; PMCID: PMC1461994.
    55. Nordborg M, Borevitz JO, Bergelson J, Berry C, Chory J, Hagenblad J, Kreitman M, Maloof JN, Noyes T, Oefner PJ, Stahl EA, Weigel D. The extent of linkage disequilibrium in Arabidopsis thaliana. Nat Genet. 2002 Feb; 30(2):190-3. PMID: 11780140.
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