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Dai H-Q*, Hu H, Lou J, Ye AY, Ba Z, Zhang X, Zhang Y, Zhao L, Yoon HS, Chapdelaine-Williams AM, Kyritsis N, Chen H, Johnson K, Lin S, Conte A, Casellas R, Lee C-S*, Alt FW.* (2021) Loop extrusion mediates physiological IgH locus contraction for RAG scanning. Nature https://doi.org/10.1038/s41586-020-03121-7

Ba, Z., Lou, J., Dring, E.W., Ye, A.Y., Lin, S.G., Jain, S., Kieffer-Kwon, K-R., Casellas, R.* and Alt, F.W.* (2020) CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning. Nature 586, 305-310. PMC7554077.

Chen, H., Zhang, Y., Ye, A.Y., Du, Z., Xu, M., Lee, C-S., Hwang, J.K., Kyritsis, N., Ba, Z., Littman, D.R. and Alt, F.W. (2020) BCR Selection and Affinity Maturation in Peyer’s Patches Germinal Centers. Nature 582, 421-425. PMC7478071.

Tian, M.*, McGovern, K., Cheng, H-L., Waddicor, P., Rieble, L., Kimble, M.T., Dao, M., Chen, Y., Cantor, E., Manfredonia, N., Judson, R., Chapendale-Williams, A., Cain, D.W., Haynes, B.F. and Alt F.W.* (2020) Conditional Antibody Expression to Avoid Central B Cell Deletion in Humanized HIV-1 Vaccine Mouse Models. Proc. Natl. Acad. Sci. USA 117, 7929-7940. PMC7149231.

Tena, A., Zhang, Y., Kyritsis, N., Devorak, A., Zurita, J., Wei, P-C.* and Alt, F.W.* (2020) Induction of Recurrent Break Cluster Genes in Neural Progenitor Cells Differentiated from Embryonic Stem Cells In Culture. Proc. Natl. Acad. Sci. USA 117, 10541-10546. PMC7229678.

Wang, M., Wei, P.-C., Lim, C.K., Gallina, I.S., Marshall, S., Marchetto, M.C., Alt, F.W. and Gage, F.H. (2020) Altered proliferation in autism neural progenitor cells induces DNA replication stress-associated genomic instability. Cell Stem Cell 26, 221-233. PMC7175642.

Saunders, K.O.*, Wiehe, K., Tian, M., Acharya, P., Bradley, T., Alam, S.M., Go, E.P., Scearce, R., Sutherland, L., Henderson, R., Hsu, A.L., Borgnia, M.J., Chen, H., Lu, X., Wu, N.R., Watts, B., Jiang, C., Easterhoff, D., Cheng, H-L., McGovern, K., Waddicor, P., Chapdelaine-Williams, A., Eaton, A., Zhang, J., Rountree, W., Verkoczy, L., Tomai, M., Lewis, M.G., Desaire, H.R., Edwards, R.J. Cain, D.W., Bonsignori, M., Montefiori, D., Alt, F.W.* and Haynes, B.F.* (2019) Targeted selection of HIV-specific antibody mutations by engineering B cell maturation. Science 366, eaay7199. PMC7168753.

Zhang, X., Zhang, Y., Ba, Z., Kyritsis, N., Casellas, R. and Alt, F.W. (2019) Fundamental roles of chromatin loop extrusion in antibody class switching.  Nature 575, 385-389. PMC6856444.

Zhang, Y., Zhang, X., Ba, Z., Liang, Z., Dring, E.W., Hu, H., Lou, J., Kyritsis, N., Zurita, J., Shamim, M.S., Presser Aiden, A., Lieberman Aiden E. and Alt, F.W. (2019) The fundamental role of chromatin loop extrusion in physiological V(D)J recombination.  Nature 573, 600-604. PMC6867615.

Chang, A.N., Liang, Z., Dai, H-Q., Chapdelaine-Williams, A.M., Andrews, N., Bronson, R.T., Schwer, B.* and Alt, F.W.* (2018) Neural blastocyst complementation enables mouse forebrain organogenesis. Nature 563, 126-130.

Jain, S., Ba, Z., Zhang, Y., Dai, H-Q and Alt, F.W. (2018) CTCF-binding elements mediate accessibility of RAG substrates during chromatin scanning. Cell 174, 102-116. PMC6026039.

Hwang, J.K., Wang, C., Du, Z., Meyers, R.M., Kepler, T.B., Neuberg, D., Kwong, P.D., Mascola, J.R., Joyce, M.G., Bonsignori, M., Haynes, B.F., Yeap, L-S. and Alt, F.W. (2017) Sequence intrinsic somatic mutation mechanisms contribute to affinity maturation of VRC01-class HIV-1 broadly neutralizing antibodies. Proc. Natl. Acad. Sci. USA 114, 8614-8619. PMC5559054.

Tian, M., Cheng, C., Chen, X., Duan, H., Cheng, H-L., Dao, M., Sheng, Z., Kimble, M., Wang, L., Lin, S., Schmidt, S.D., Du, Z., Joyce, M.G., Chen, Y., DeKosky, B.J., Chen, Y., Normandin, E., Cantor, E., Chen, R.E., Doria-Rose, N.A., Zhang, Y., Shi, W., Kong, W-P., Choe, M., Henry, A.R., Laboune, F., Georgiev, I.S., Huang, P-Y., Jain, S., McGuire, A.T., Georgeson, E., Menis, S., Douek, D.C., Schief, W.R., Stamatatos, L., Kwong, P.D., Shapiro, L., Haynes, B.F., Mascola, J.R.* and Alt, F.W.* (2016) Induction of HIV neutralizing antibody lineages in mice with diverse precursor repertories.  Cell 166, 1471–1484. PMC5103708.

Wei, P-C., Chang, A.N., Kao, J., Du, Z., Meyers, R.M., Alt, F.W.* and Schwer, B.* (2016) Long neural genes harbor recurrent DNA break clusters in neural stem/progenitor cells. Cell 164, 644-655. PMC475272.

Yeap, L.S., Hwang, J.K., Du, Z., Meyers, R.M., Meng, F-L., Jakubauskaite, A., Liu, M., Mani, V., Neuberg, D., Kepler, T.B., Wang, J.H. and Alt, F.W. (2015) Sequence-intrinsic mechanisms that target AID mutational outcomes on antibody genes, Cell 163, 1124-1137. PMC4751889.

Hu, J., Zhang, Y., Zhao, L., Frock, R.L., Du, Z., Meyers, R.M., Meng, F-L., Schatz, D.G. and Alt, F.W. (2015) Chromosomal loop domains direct the recombination of antigen receptor genes. Cell 163, 947-959. PMC4660266.

Dong, J., Panchakshari, R.A., Zhang, T., Zhang, Y., Hu, J., Volpi, S.A., Meyers, R.M., Ho, Y-J., Du, Z., Robbiani, D.F., Meng F., Gostissa, M., Nussenzweig, M.C., Manis, J.P.* and Alt, F.W.* (2015) Orientation-specific joining of AID-initiated DNA breaks promotes antibody class switching. Nature 525, 134-139. PMC4592165.

Frock, R.L., Hu, J., Meyers, R.M., Ho, Y-J., Kii, E. and Alt, F.W. (2015) Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Nature Biotechnology 33, 179-186. PMC4320661

*Co-corresponding author

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