Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis von Lister, Ryan, O'Malley, Ronan C., Tonti-Filippini, Julian, Gregory, Brian D., Berry, Charles C., Millar, A. Harvey, Ecker, Joseph R.

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Estimating abundances of retroviral insertion sites from DNA fragment length data von BERRY, Charles C, GILLET, Nicolas A, MELAMED, Anat, GORMLEY, Niall, BANGHAM, Charles R. M, BUSHMAN, Frederic D

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HIV integration targeting: a pathway involving Transportin-3 and the nuclear pore protein RanBP2 von Ocwieja, Karen E, Brady, Troy L, Ronen, Keshet, Huegel, Alyssa, Roth, Shoshannah L, Schaller, Torsten, James, Leo C, Towers, Greg J, Young, John A T, Chanda, Sumit K, König, Renate, Malani, Nirav, Berry, Charles C, Bushman, Frederic D

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Efficacy of Gene Therapy for X-Linked Severe Combined Immunodeficiency von Hacein-Bey-Abina, Salima, Hauer, Julia, Lim, Annick, Picard, Capucine, Wang, Gary P, Berry, Charles C, Martinache, Chantal, Rieux-Laucat, Frédéric, Latour, Sylvain, Belohradsky, Bernd H, Leiva, Lily, Sorensen, Ricardo, Debré, Marianne, Casanova, Jean Laurent, Blanche, Stephane, Durandy, Anne, Bushman, Frederic D, Fischer, Alain, Cavazzana-Calvo, Marina

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Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences von Mitchell, Rick S, Beitzel, Brett F, Schroder, Astrid R W, Shinn, Paul, Chen, Huaming, Berry, Charles C, Ecker, Joseph R, Bushman, Frederic D

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Retroviral DNA integration: viral and cellular determinants of target-site selection von Lewinski, Mary K, Yamashita, Masahiro, Emerman, Michael, Ciuffi, Angela, Marshall, Heather, Crawford, Gregory, Collins, Francis, Shinn, Paul, Leipzig, Jeremy, Hannenhalli, Sridhar, Berry, Charles C, Ecker, Joseph R, Bushman, Frederic D

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HIV latency and integration site placement in five cell-based models von Sherrill-Mix, Scott, Lewinski, Mary K, Famiglietti, Marylinda, Bosque, Alberto, Malani, Nirav, Ocwieja, Karen E, Berry, Charles C, Looney, David, Shan, Liang, Agosto, Luis M, Pace, Matthew J, Siliciano, Robert F, O'Doherty, Una, Guatelli, John, Planelles, Vicente, Bushman, Frederic D

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Dynamics of gene-modified progenitor cells analyzed by tracking retroviral integration sites in a human SCID-X1 gene therapy trial von Wang, Gary P., Berry, Charles C., Malani, Nirav, Leboulch, Philippe, Fischer, Alain, Hacein-Bey-Abina, Salima, Cavazzana-Calvo, Marina, Bushman, Frederic D.

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INSPIIRED: A Pipeline for Quantitative Analysis of Sites of New DNA Integration in Cellular Genomes von Sherman, Eric, Nobles, Christopher, Berry, Charles C, Six, Emmanuelle, Wu, Yinghua, Dryga, Anatoly, Malani, Nirav, Male, Frances, Reddy, Shantan, Bailey, Aubrey, Bittinger, Kyle, Everett, John K, Caccavelli, Laure, Drake, Mary J, Bates, Paul, Hacein-Bey-Abina, Salima, Cavazzana, Marina, Bushman, Frederic D

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G-Quadruplex DNA and Other Non-Canonical B-Form DNA Motifs Influence Productive and Latent HIV-1 Integration and Reactivation Potential von Ajoge, Hannah O, Kohio, Hinissan P, Paparisto, Ermela, Coleman, Macon D, Wong, Kemen, Tom, Sean K, Bain, Katie L, Berry, Charles C, Arts, Eric J, Barr, Stephen D

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Integration target site selection by a resurrected human endogenous retrovirus von Brady, Troy, Lee, Young Nam, Ronen, Keshet, Malani, Nirav, Berry, Charles C, Bieniasz, Paul D, Bushman, Frederic D

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A method to sequence and quantify DNA integration for monitoring outcome in gene therapy von Brady, Troy, Roth, Shoshannah L., Malani, Nirav, Wang, Gary P., Berry, Charles C., Leboulch, Philippe, Hacein-Bey-Abina, Salima, Cavazzana-Calvo, Marina, Papapetrou, Eirini P., Sadelain, Michel, Savilahti, Harri, Bushman, Frederic D.

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INSPIIRED: Quantification and Visualization Tools for Analyzing Integration Site Distributions von Berry, Charles C, Nobles, Christopher, Six, Emmanuelle, Wu, Yinghua, Malani, Nirav, Sherman, Eric, Dryga, Anatoly, Everett, John K, Male, Frances, Bailey, Aubrey, Bittinger, Kyle, Drake, Mary J, Caccavelli, Laure, Bates, Paul, Hacein-Bey-Abina, Salima, Cavazzana, Marina, Bushman, Frederic D

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Large-scale identification of single-feature polymorphisms in complex genomes von Borevitz, Justin O, Liang, David, Plouffe, David, Chang, Hur-Song, Zhu, Tong, Weigel, Detlef, Berry, Charles C, Winzeler, Elizabeth, Chory, Joanne

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In silico Dissection of Cell-Type-Associated Patterns of Gene Expression in Prostate Cancer von Stuart, Robert O., Wachsman, William, Berry, Charles C., Wang-Rodriguez, Jessica, Wasserman, Linda, Klacansky, Igor, Masys, Dan, Arden, Karen, Goodison, Steven, McClelland, Michael, Wang, Yipeng, Sawyers, Anne, Kalcheva, Iveta, Tarin, David, Mercola, Dan

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HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications von Wang, Gary P, Ciuffi, Angela, Leipzig, Jeremy, Berry, Charles C, Bushman, Frederic D

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Natural variation in light sensitivity of Arabidopsis von Maloof, Julin N., Borevitz, Justin O., Dabi, Tsegaye, Lutes, Jason, Nehring, Ramlah B., Redfern, Joanna L., Trainer, Gabriel T., Wilson, Jeanne M., Asami, Tadao, Berry, Charles C., Weigel, Detlef, Chory, Joanne

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HIV integration site distributions in resting and activated CD4+ T cells infected in culture von BRADY, Troy, AGOSTO, Luis M, MALANI, Nirav, BERRY, Charles C, O'DOHERTY, Una, BUSHMAN, Frederic

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Outcomes of hematopoietic stem cell gene therapy for Wiskott-Aldrich syndrome von Labrosse, Roxane, Chu, Julia I., Armant, Myriam A., Everett, John K., Pellin, Danilo, Kareddy, Niharika, Frelinger, Andrew L., Henderson, Lauren A., O’Connell, Amy E., Biswas, Amlan, Coenen-van der Spek, Jet, Miggelbrink, Alexandra, Fiorini, Claudia, Adhikari, Hriju, Berry, Charles C., Cantu, Vito Adrian, Fong, Johnson, Jaroslavsky, Jason, Karadeniz, Derin F., Li, Quan-Zhen, Reddy, Shantan, Roche, Aoife M., Zhu, Chengsong, Whangbo, Jennifer S., Dansereau, Colleen, Mackinnon, Brenda, Morris, Emily, Koo, Stephanie M., London, Wendy B., Baris, Safa, Ozen, Ahmet, Karakoc-Aydiner, Elif, Despotovic, Jenny M., Forbes Satter, Lisa R., Saitoh, Akihiko, Aizawa, Yuta, King, Alejandra, Nguyen, Mai Anh Thi, Vu, Vy Do Uyen, Snapper, Scott B., Galy, Anne, Notarangelo, Luigi D., Bushman, Frederic D., Williams, David A., Pai, Sung-Yun

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Comparing DNA integration site clusters with scan statistics von Berry, Charles C, Ocwieja, Karen E, Malani, Nirav, Bushman, Frederic D

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