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Pathogenic Mannheimia haemolytica Invades Differentiated Bovine Airway Epithelial Cells.

Cozens D, Sutherland E, Lauder M, Taylor G, Berry CC, Davies RL.

Infect Immun. 2019 May 21;87(6). pii: e00078-19. doi: 10.1128/IAI.00078-19. Print 2019 Jun.


Mesenchymal stem cell-derived extracellular vesicles may promote breast cancer cell dormancy.

Casson J, Davies OG, Smith CA, Dalby MJ, Berry CC.

J Tissue Eng. 2018 Dec 25;9:2041731418810093. doi: 10.1177/2041731418810093. eCollection 2018 Jan-Dec.


Temporal differentiation of bovine airway epithelial cells grown at an air-liquid interface.

Cozens D, Sutherland E, Marchesi F, Taylor G, Berry CC, Davies RL.

Sci Rep. 2018 Oct 5;8(1):14893. doi: 10.1038/s41598-018-33180-w.


Optimisation of growth conditions for ovine airway epithelial cell differentiation at an air-liquid interface.

O'Boyle N, Sutherland E, Berry CC, Davies RL.

PLoS One. 2018 Mar 8;13(3):e0193998. doi: 10.1371/journal.pone.0193998. eCollection 2018.


Nanoparticle-antagomiR based targeting of miR-31 to induce osterix and osteocalcin expression in mesenchymal stem cells.

McCully M, Conde J, V Baptista P, Mullin M, Dalby MJ, Berry CC.

PLoS One. 2018 Feb 14;13(2):e0192562. doi: 10.1371/journal.pone.0192562. eCollection 2018.


Development and optimization of a differentiated airway epithelial cell model of the bovine respiratory tract.

Cozens D, Grahame E, Sutherland E, Taylor G, Berry CC, Davies RL.

Sci Rep. 2018 Jan 16;8(1):853. doi: 10.1038/s41598-017-19079-y.


Temporal dynamics of ovine airway epithelial cell differentiation at an air-liquid interface.

O'Boyle N, Sutherland E, Berry CC, Davies RL.

PLoS One. 2017 Jul 26;12(7):e0181583. doi: 10.1371/journal.pone.0181583. eCollection 2017.


Magnetically levitated mesenchymal stem cell spheroids cultured with a collagen gel maintain phenotype and quiescence.

Lewis NS, Lewis EE, Mullin M, Wheadon H, Dalby MJ, Berry CC.

J Tissue Eng. 2017 Apr 24;8:2041731417704428. doi: 10.1177/2041731417704428. eCollection 2017 Jan-Dec.


INSPIIRED: A Pipeline for Quantitative Analysis of Sites of New DNA Integration in Cellular Genomes.

Sherman E, Nobles C, Berry CC, 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.

Mol Ther Methods Clin Dev. 2016 Dec 18;4:39-49. doi: 10.1016/j.omtm.2016.11.002. eCollection 2017 Mar 17.


INSPIIRED: Quantification and Visualization Tools for Analyzing Integration Site Distributions.

Berry CC, 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.

Mol Ther Methods Clin Dev. 2016 Dec 18;4:17-26. doi: 10.1016/j.omtm.2016.11.003. eCollection 2017 Mar 17.


A Quiescent, Regeneration-Responsive Tissue Engineered Mesenchymal Stem Cell Bone Marrow Niche Model via Magnetic Levitation.

Lewis EE, Wheadon H, Lewis N, Yang J, Mullin M, Hursthouse A, Stirling D, Dalby MJ, Berry CC.

ACS Nano. 2016 Sep 27;10(9):8346-54. doi: 10.1021/acsnano.6b02841. Epub 2016 Sep 15.


Gold nanoparticle-siRNA mediated oncogene knockdown at RNA and protein level, with associated gene effects.

Child HW, Hernandez Y, Conde J, Mullin M, Baptista P, de la Fuente JM, Berry CC.

Nanomedicine (Lond). 2015;10(16):2513-25. doi: 10.2217/NNM.15.95. Epub 2015 Aug 24.


The influence of particle size and static magnetic fields on the uptake of magnetic nanoparticles into three dimensional cell-seeded collagen gel cultures.

Lewis EE, Child HW, Hursthouse A, Stirling D, McCully M, Paterson D, Mullin M, Berry CC.

J Biomed Mater Res B Appl Biomater. 2015 Aug;103(6):1294-301. doi: 10.1002/jbm.b.33302. Epub 2014 Oct 31.


A modified γ-retrovirus vector for X-linked severe combined immunodeficiency.

Hacein-Bey-Abina S, Pai SY, Gaspar HB, Armant M, Berry CC, 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.

N Engl J Med. 2014 Oct 9;371(15):1407-17. doi: 10.1056/NEJMoa1404588.


Comparing DNA integration site clusters with scan statistics.

Berry CC, Ocwieja KE, Malani N, Bushman FD.

Bioinformatics. 2014 Jun 1;30(11):1493-500. doi: 10.1093/bioinformatics/btu035. Epub 2014 Jan 30.


Elucidating the function of penetratin and a static magnetic field in cellular uptake of magnetic nanoparticles.

Chaudhary S, Smith CA, Del Pino P, de la Fuente JM, Mullin M, Hursthouse A, Stirling D, Berry CC.

Pharmaceuticals (Basel). 2013 Feb 6;6(2):204-22. doi: 10.3390/ph6020204.


Formation of octapod MnO nanoparticles with enhanced magnetic properties through kinetically-controlled thermal decomposition of polynuclear manganese complexes.

Douglas FJ, MacLaren DA, Tuna F, Holmes WM, Berry CC, Murrie M.

Nanoscale. 2014 Jan 7;6(1):172-6. doi: 10.1039/c3nr04832b. Epub 2013 Nov 12.


HIV latency and integration site placement in five cell-based models.

Sherrill-Mix S, Lewinski MK, Famiglietti M, Bosque A, Malani N, Ocwieja KE, Berry CC, Looney D, Shan L, Agosto LM, Pace MJ, Siliciano RF, O'Doherty U, Guatelli J, Planelles V, Bushman FD.

Retrovirology. 2013 Aug 16;10:90. doi: 10.1186/1742-4690-10-90.


Design of multifunctional gold nanoparticles for in vitro and in vivo gene silencing.

Conde J, Ambrosone A, Sanz V, Hernandez Y, Marchesano V, Tian F, Child H, Berry CC, Ibarra MR, Baptista PV, Tortiglione C, de la Fuente JM.

ACS Nano. 2012 Sep 25;6(9):8316-24. Epub 2012 Aug 22.


Estimating abundances of retroviral insertion sites from DNA fragment length data.

Berry CC, Gillet NA, Melamed A, Gormley N, Bangham CR, Bushman FD.

Bioinformatics. 2012 Mar 15;28(6):755-62. doi: 10.1093/bioinformatics/bts004. Epub 2012 Jan 11.


Working together: the combined application of a magnetic field and penetratin for the delivery of magnetic nanoparticles to cells in 3D.

Child HW, Del Pino PA, De La Fuente JM, Hursthouse AS, Stirling D, Mullen M, McPhee GM, Nixon C, Jayawarna V, Berry CC.

ACS Nano. 2011 Oct 25;5(10):7910-9. doi: 10.1021/nn202163v. Epub 2011 Sep 12.


Influence of both a static magnetic field and penetratin on magnetic nanoparticle delivery into fibroblasts.

Dejardin T, de la Fuente J, del Pino P, Furlani EP, Mullin M, Smith CA, Berry CC.

Nanomedicine (Lond). 2011 Dec;6(10):1719-31. doi: 10.2217/nnm.11.65. Epub 2011 Aug 2.


Grooved surface topography alters matrix-metalloproteinase production by human fibroblasts.

Brydone AS, Dalby MJ, Berry CC, Dominic Meek RM, McNamara LE.

Biomed Mater. 2011 Jun;6(3):035005. doi: 10.1088/1748-6041/6/3/035005. Epub 2011 Apr 20.


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.

PLoS Pathog. 2011 Mar;7(3):e1001313. doi: 10.1371/journal.ppat.1001313. Epub 2011 Mar 10.


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.

Nucleic Acids Res. 2011 Jun;39(11):e72. doi: 10.1093/nar/gkr140. Epub 2011 Mar 16.


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.

N Engl J Med. 2010 Jul 22;363(4):355-64. doi: 10.1056/NEJMoa1000164.


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.

Blood. 2010 Jun 3;115(22):4356-66. doi: 10.1182/blood-2009-12-257352. Epub 2010 Mar 12.


The effect of static magnetic fields and tat peptides on cellular and nuclear uptake of magnetic nanoparticles.

Smith CA, de la Fuente J, Pelaz B, Furlani EP, Mullin M, Berry CC.

Biomaterials. 2010 May;31(15):4392-400. doi: 10.1016/j.biomaterials.2010.01.096. Epub 2010 Feb 26.


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.

AIDS. 2009 Jul 31;23(12):1461-71. doi: 10.1097/QAD.0b013e32832caf28.


Integration target site selection by a resurrected human endogenous retrovirus.

Brady T, Lee YN, Ronen K, Malani N, Berry CC, Bieniasz PD, Bushman FD.

Genes Dev. 2009 Mar 1;23(5):633-42. doi: 10.1101/gad.1762309.


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.

Mol Ther. 2009 May;17(5):844-50. doi: 10.1038/mt.2009.16. Epub 2009 Mar 3.


Cell-generated forces influence the viability, metabolism and mechanical properties of fibroblast-seeded collagen gel constructs.

Berry CC, Shelton JC, Lee DA.

J Tissue Eng Regen Med. 2009 Jan;3(1):43-53. doi: 10.1002/term.133.


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. 2009 Apr;47(4):261-8. doi: 10.1016/j.ymeth.2008.10.028. Epub 2008 Nov 25.


Intracellular delivery of nanoparticles via the HIV-1 tat peptide.

Berry CC.

Nanomedicine (Lond). 2008 Jun;3(3):357-65. doi: 10.2217/17435889.3.3.357. Review.


Highly integrated single-base resolution maps of the epigenome in Arabidopsis.

Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR.

Cell. 2008 May 2;133(3):523-36. doi: 10.1016/j.cell.2008.03.029.


Nuclear localization of HIV-1 tat functionalized gold nanoparticles.

Berry CC, de la Fuente JM, Mullin M, Chu SW, Curtis AS.

IEEE Trans Nanobioscience. 2007 Dec;6(4):262-9.


Human fibroblast and human bone marrow cell response to lithographically nanopatterned adhesive domains on protein rejecting substrates.

Berry CC, Curtis AS, Oreffo RO, Agheli H, Sutherland DS.

IEEE Trans Nanobioscience. 2007 Sep;6(3):201-9.


HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications.

Wang GP, Ciuffi A, Leipzig J, Berry CC, Bushman FD.

Genome Res. 2007 Aug;17(8):1186-94. Epub 2007 Jun 1.


Assessing the trade-offs between crossover and parallel group designs in sleep research.

Berry CC, Moore P, Dimsdale JE.

J Sleep Res. 2006 Dec;15(4):348-57.


The interaction of human bone marrow cells with nanotopographical features in three dimensional constructs.

Berry CC, Dalby MJ, Oreffo RO, McCloy D, Affrosman S.

J Biomed Mater Res A. 2006 Nov;79(2):431-9.


Retroviral DNA integration: viral and cellular determinants of target-site selection.

Lewinski MK, Yamashita M, Emerman M, Ciuffi A, Marshall H, Crawford G, Collins F, Shinn P, Leipzig J, Hannenhalli S, Berry CC, Ecker JR, Bushman FD.

PLoS Pathog. 2006 Jun;2(6):e60. Epub 2006 Jun 23.


Fluorescent aromatic platforms for cell patterning.

de la Fuente JM, Andar A, Gadegaard N, Berry CC, Kingshott P, Riehle MO.

Langmuir. 2006 Jun 20;22(13):5528-32.


The influence of elastin-coated 520-nm- and 20-nm-diameter nanoparticles on human fibroblasts in vitro.

Berry CC, Rudershausen S, Teller J, Curtis AS.

IEEE Trans Nanobioscience. 2002 Sep;1(3):105-9.


Nanoparticle targeting at cells.

de la Fuente JM, Berry CC, Riehle MO, Curtis AS.

Langmuir. 2006 Mar 28;22(7):3286-93.


Identification of genes whose expression is associated with cisplatin resistance in human ovarian carcinoma cells.

Cheng TC, Manorek G, Samimi G, Lin X, Berry CC, Howell SB.

Cancer Chemother Pharmacol. 2006 Sep;58(3):384-95. Epub 2006 Jan 11.


Tat peptide as an efficient molecule to translocate gold nanoparticles into the cell nucleus.

de la Fuente JM, Berry CC.

Bioconjug Chem. 2005 Sep-Oct;16(5):1176-80.


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.

Zangwill LM, Weinreb RN, Beiser JA, Berry CC, Cioffi GA, Coleman AL, Trick G, Liebmann JM, Brandt JD, Piltz-Seymour JR, Dirkes KA, Vega S, Kass MA, Gordon MO.

Arch Ophthalmol. 2005 Sep;123(9):1188-97.


Genome-wide analysis of chromosomal features repressing human immunodeficiency virus transcription.

Lewinski MK, Bisgrove D, Shinn P, Chen H, Hoffmann C, Hannenhalli S, Verdin E, Berry CC, Ecker JR, Bushman FD.

J Virol. 2005 Jun;79(11):6610-9.


Quantum dots protected with tiopronin: a new fluorescence system for cell-biology studies.

de la Fuente JM, Fandel M, Berry CC, Riehle M, Cronin L, Aitchison G, Curtis AS.

Chembiochem. 2005 Jun;6(6):989-91. No abstract available.


The fibroblast response to tubes exhibiting internal nanotopography.

Berry CC, Dalby MJ, McCloy D, Affrossman S.

Biomaterials. 2005 Aug;26(24):4985-92.


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