James Nunez, PhD
Assistant Professor
Cellular Molecular Pharmacology
School of Medicine

Education & Training

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• PhD Molecular and Cell Biology University of California, Berkeley 06/2016

Websites

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• @@jamesknunez on Twitter (twitter.com)

Grants and Projects

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• Programming epigenetic memory with CRISPR-based technologies, Howard Hughes Medical Institute, 2017-2025

Publications (14)

Top publication keywords:
Cellular ReprogrammingCaspasesEndonucleasesIntegrasesAdaptive ImmunityDNA, BacterialGene EditingEndodeoxyribonucleasesIntegration Host FactorsClustered Regularly Interspaced Short Palindromic RepeatsCRISPR-Associated ProteinsCRISPR-Cas SystemsEscherichia coli ProteinsVirus IntegrationEscherichia coli

• Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq.
  Nature communications 2023 Sunshine S, Puschnik AS, Replogle JM, Laurie MT, Liu J, Zha BS, Nuñez JK, Byrum JR, McMorrow AH, Frieman MB, Winkler J, Qiu X, Rosenberg OS, Leonetti MD, Ye CJ, Weissman JS, DeRisi JL, Hein MY
• BRD2 inhibition blocks SARS-CoV-2 infection by reducing transcription of the host cell receptor ACE2.
  Nature cell biology 2022 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…
• CRISPR meets caspase.
  Nature microbiology 2021 Hochstrasser ML, Nuñez JK
• Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing.
  Cell 2021 Nuñez JK, Chen J, Pommier GC, Cogan JZ, Replogle JM, Adriaens C, Ramadoss GN, Shi Q, Hung KL, Samelson AJ, Pogson AN, Kim JYS, Chung A, Leonetti MD, Chang HY, Kampmann M, Bernstein BE, Hovestadt V, …
• Pervasive functional translation of noncanonical human open reading frames.
  Science (New York, N.Y.) 2020 Chen J, Brunner AD, Cogan JZ, Nuñez JK, Fields AP, Adamson B, Itzhak DN, Li JY, Mann M, Leonetti MD, Weissman JS

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• Inducible and multiplex gene regulation using CRISPR-Cpf1-based transcription factors.
  Nature methods 2017 Tak YE, Kleinstiver BP, Nuñez JK, Hsu JY, Horng JE, Gong J, Weissman JS, Joung JK
• A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response.
  Cell 2016 Adamson B, Norman TM, Jost M, Cho MY, Nuñez JK, Chen Y, Villalta JE, Gilbert LA, Horlbeck MA, Hein MY, Pak RA, Gray AN, Gross CA, Dixit A, Parnas O, Regev A, Weissman JS
• CRISPR Immunological Memory Requires a Host Factor for Specificity.
  Molecular cell 2016 Nuñez JK, Bai L, Harrington LB, Hinder TL, Doudna JA
• Chemical and Biophysical Modulation of Cas9 for Tunable Genome Engineering.
  ACS chemical biology 2016 Nuñez JK, Harrington LB, Doudna JA
• Biology and Applications of CRISPR Systems: Harnessing Nature's Toolbox for Genome Engineering.
  Cell 2016 Wright AV, Nuñez JK, Doudna JA
• Foreign DNA capture during CRISPR-Cas adaptive immunity.
  Nature 2015 Nuñez JK, Harrington LB, Kranzusch PJ, Engelman AN, Doudna JA
• Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity.
  Nature 2015 Nuñez JK, Lee AS, Engelman A, Doudna JA
• Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity.
  Nature structural & molecular biology 2014 Nuñez JK, Kranzusch PJ, Noeske J, Wright AV, Davies CW, Doudna JA
• Molecular basis for H3K36me3 recognition by the Tudor domain of PHF1.
  Nature structural & molecular biology 2012 Musselman CA, Avvakumov N, Watanabe R, Abraham CG, Lalonde ME, Hong Z, Allen C, Roy S, Nuñez JK, Nickoloff J, Kulesza CA, Yasui A, Côté J, Kutateladze TG