Publications

Pattali, R.K., Ornelas, I.J., Nguyen, C.D., Xu, D., Divekar, N.S., Nuñez, J.K. CRISPRoff epigenetic editing for programmable gene silencing in human cells without DNA breaks. bioRxiv pre-print (2024): https://www.biorxiv.org/content/10.1101/2024.09.09.612111v2

 

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Cao, R., Divekar, N., Nuñez, J.K., Upadhyayula, S., Waller, L. Neural space-time model for dynamic scene recovery in multi-shot computational imaging systems. Nature Methods (2024).​​

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Sunshine, S., Puschnik, A.S., Replogle, J.M., Laurie, M.T., Liu, J., Zha, B.S., Nuñez, J.K., Byrum, J.R., McMorrow, A.H., Frieman, M.B., Winkler, J., Qiu, X., Rosenberg, O.S., Leonetti, M.D., Ye, C.J., Weissman, J.S., DeRisi, J.L., Hein, M.Y. Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq. Nature Communications (2023).

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Samelson AJ, Tran QD, Robinot R, Carrau L, Rezelj VV, Kain AM, Chen M, Ramadoss GN, Guo X, Lim SA, Lui I, Nuñez JK, Rockwood SJ, Wang J, Liu N, Carlson-Stevermer J, Oki J, Maures T, Holden K, Weissman JS, Wells JA, Conklin BR, TenOever BR, Chakrabarti LA, Vignuzzi M, Tian R, Kampmann M. BRD2 inhibition blocks SARS-CoV-2 infection in vitro by reducing transcription of the host receptor ACE2. Nature Cell Biology (2022).​

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Hochstrasser, M.L., Nuñez, J.K. CRISPR meets caspase. Nature Microbiology 6 (2021).

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Nuñez, J.K., Chen, J., Pommier, G.C., Cogan, J.Z., Replogle, J.M., Adriaens, C., Ramadoss, G.N., Shi, Q., Hung, K.L., Samelson, A.J., Pogson, A.N., Kim, J.Y.S., Chung, A., Leonetti, M.D., Chang, H.Y., Kampmann, M., Bernstein, B.E., Hovestadt, V., Gilbert, L.A., Weissman, J.S. Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing. Cell 184 (2021).

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Chen, J., Brunner, A., Cogan, J.Z., Nuñez, J.K., Fields, A.P., Adamson, B., Mann, M., Leonetti, M.D., Weissman, J.S. Pervasive functional micropeptides in humans encoded by non-canonical open reading frames. Science 367 (2020).

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Tak, Y.E., Kleinstiver, B.P., Nuñez, J.K., Hsu, J.Y., Horng, J.E., Gong, J., Weissman, J.S., Joung, J.K. Inducible and multiplex gene regulation using CRISPR–Cpf1-based transcription factors. Nature Methods 14 (2017).

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Adamson B., Norman, T.M., Jost, M., Cho, M.Y., Nuñez, J.K., Chen, Y., Villalta, J.E., Gilbert, L.A., Horlbeck, M.A., Hein, M.Y., Pak, R.A., Gray, A.N., Gross, C.A., Dixit, A., Parnas, O., Regev, A., Weissman, J.S. A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response. Cell 167 (2016).

 

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Nuñez, J.K., Bai, L., Harrington, L.B., Hinder, T.L., Doudna, J.A. CRISPR immunological memory requires a host factor for specificity. Molecular Cell 62 (2016).

 

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Wright, A.V., Nuñez, J.K., Doudna, J.A. CRISPR systems: Nature’s toolbox for genome engineering. Cell 164 (2016). Review article.

 

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Nuñez, J.K., Harrington, L.B., Doudna, J.A. Chemical and biophysical modulation of Cas9 for tunable genome engineering. ACS Chemical Biology 11 (2016). Review article.

 

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Nuñez, J.K.*, Harrington, L.B.*, Kranzusch, P.J., Engelman, A.N., Doudna, J.A. Foreign DNA capture during CRISPR–Cas adaptive immunity. Nature 527 (2015b). *Equal contribution.

 

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Nuñez, J.K., Lee, A.S.Y., Engelman, A.N., Doudna, J.A. Integrase-mediated spacer acquisition during CRISPR–Cas adaptive immunity. Nature 519 (2015a).

 

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Nuñez, J.K., Kranzusch, P.J., Noeske, J., Wright, A.V., Davies, C.W., Doudna, J.A. Cas1–Cas2 complex formation mediates spacer acquisition during CRISPR–Cas adaptive immunity. Nature Structural & Molecular Biology 21 (2014).

 

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Musselman, C.A., Avvakumov, N., Watanabe, R., Abraham, C.G., Lalonde, M.E., Hong, Z., Allen, C., Roy, S., Nuñez, J.K., Nickoloff, J., Kulesza, C.A., Yasui, A., Côté, J., Kutateladze, T.G. Molecular basis for H3K36me3 recognition by the Tudor domain of PHF1. Nature Structural & Molecular Biology 19 (2012).