Publications

PREPRINTS

LEMONmethyl-seq: Targeted long-read DNA methylation profiling reveals dynamics of CRISPR epigenome editing and endogenous DNA methylation patterns

Anna E Christenson, Nikita S Divekar, Justin P Lubin, Luis G Palma, Peter J Colias, Rithu K Pattali, Da Xu, Akane Hubbard, Katie Lin, Ngan T Phan, Bernardo D Moreno, Sarah E Chasins, S. John Liu, James K Nuñez

bioRxiv preprint (2026): https://www.biorxiv.org/content/10.64898/2026.02.24.707761v1

A toolkit for programmable transcriptional engineering across eukaryotic kingdoms

Izaiah J Ornelas, Lauren A Owens, Simon Alamos, Niklas FC Hummel, Mitzi G Hernandez Zamora, Ngan T Phan, Rithu K Pattali, Patrick M Shih, James K Nuñez

bioRxiv pre-print (2026): https://www.biorxiv.org/content/10.64898/2026.02.10.705154v1

Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells

Jung, Devant et al.

bioRxiv preprint (2025): https://www.biorxiv.org/content/10.64898/2025.12.14.692434v1

Transcriptional regulation of disease-relevant microglial activation programs

McQuade, A. et al.

bioRxiv pre-print (2025): https://www.biorxiv.org/content/10.1101/2025.10.12.681832v2

A Multimodal Adaptive Optical Microscope For In Vivo Imaging from Molecules to Organisms

Fu, Liu, Milkie, Ruan et al.

bioRxiv pre-print (2025): https://www.biorxiv.org/content/10.1101/2025.06.02.657494v1

PUBLICATIONS

Next generation technologies for CRISPR-based epigenome and transcriptional modulation

Pattali, R.K., Divekar, N.S., Nuñez, J.K.
Current Opinion in Biomedical Engineering (2026)

Review Article

Programmable epigenome editing by transient delivery of CRISPR epigenome editor ribonucleoproteins

Xu, D.*, Besselink, S.*, Ramadoss, G.N., Dierks, P.H., Lubin, J.P., Pattali, R.K., Brim, J.I., Christenson, A.E., Colias, P.J., Ornelas, I.J., Nguyen, C.D., Chasins, S.E., Conklin, B.R., Nuñez, J.K. *Equal contribution.

Nature Communications (2025)

CRISPR epigenome editing in human cells using plasmid DNA transfection and mRNA nucleofection delivery

Christenson, A.E., Divekar, N.S., Hernández Zamora, M.G., Nguyen, C.D., Nuñez, J.K.

JoVE (2025)

CRISPRoff epigenome editing for programmable gene silencing in human cell lines and primary T cells

Pattali, R.K., Ornelas, I.J., Nguyen, C.D., Xu, D., Divekar, N.S., Nuñez, J.K.

Methods in Enzymology (2025)

Neural space-time model for dynamic scene recovery in multi-shot computational imaging systems

Cao, R., Divekar, N.S., Nuñez, J.K., Upadhyayula, S., Waller, L.

Nature Methods (2024)

Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq

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.

Nature Communications (2023)

BRD2 inhibition blocks SARS-CoV-2 infection in vitro by reducing transcription of the host receptor ACE2

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.

Nature Cell Biology (2022)

CRISPR meets caspase

Hochstrasser, M.L., Nuñez, J.K.

Nature Microbiology 6 (2021)

Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing

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.

Cell 184 (2021)

Pervasive functional micropeptides in humans encoded by non-canonical open reading frames

Chen, J., Brunner, A., Cogan, J.Z., Nuñez, J.K., Fields, A.P., Adamson, B., Mann, M., Leonetti, M.D., Weissman, J.S.

Science 367 (2020)

Inducible and multiplex gene regulation using CRISPR–Cpf1-based transcription factors

Tak, Y.E., Kleinstiver, B.P., Nuñez, J.K., Hsu, J.Y., Horng, J.E., Gong, J., Weissman, J.S., Joung, J.K.

Nature Methods 14 (2017)

A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response

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.

Cell 167 (2016)

CRISPR immunological memory requires a host factor for specificity

Nuñez, J.K., Bai, L., Harrington, L.B., Hinder, T.L., Doudna, J.A.

Molecular Cell 62 (2016)

CRISPR systems: Nature’s toolbox for genome engineering

Wright, A.V., Nuñez, J.K., Doudna, J.A.

Cell 164 (2016). Review article

Chemical and biophysical modulation of Cas9 for tunable genome engineering

Nuñez, J.K., Harrington, L.B., Doudna, J.A.

ACS Chemical Biology 11 (2016). Review article

Foreign DNA capture during CRISPR–Cas adaptive immunity

Nuñez, J.K.*, Harrington, L.B.*, Kranzusch, P.J., Engelman, A.N., Doudna, J.A.

Nature 527 (2015b). *Equal contribution.

Integrase-mediated spacer acquisition during CRISPR–Cas adaptive immunity

Nuñez, J.K., Lee, A.S.Y., Engelman, A.N., Doudna, J.A.

Nature 519 (2015a)

Cas1–Cas2 complex formation mediates spacer acquisition during CRISPR–Cas adaptive immunity

Nuñez, J.K., Kranzusch, P.J., Noeske, J., Wright, A.V., Davies, C.W., Doudna, J.A.

Nature Structural & Molecular Biology 21 (2014)

Molecular basis for H3K36me3 recognition by the Tudor domain of PHF1

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.

Nature Structural & Molecular Biology 19 (2012)