User profiles for James Nunez

James K. Nuñez - Verified email at berkeley.edu - Cited by 5303
James Nunez - Verified email at intel.com - Cited by 635

[HTML][HTML] Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing

JK Nuñez, J Chen, GC Pommier, JZ Cogan… - Cell, 2021 - cell.com
A general approach for heritably altering gene expression has the potential to enable many
discovery and therapeutic efforts. Here, we present CRISPRoff—a programmable epigenetic …

Integrase-mediated spacer acquisition during CRISPR–Cas adaptive immunity

JK Nuñez, ASY Lee, A Engelman, JA Doudna - Nature, 2015 - nature.com
Bacteria and archaea insert spacer sequences acquired from foreign DNAs into CRISPR
loci to generate immunological memory. The Escherichia coli Cas1–Cas2 complex mediates …

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

JK Nuñez, PJ Kranzusch, J Noeske, AV Wright… - Nature structural & …, 2014 - nature.com
The initial stage of CRISPR–Cas immunity involves the integration of foreign DNA spacer
segments into the host genomic CRISPR locus. The nucleases Cas1 and Cas2 are the only …

Foreign DNA capture during CRISPR–Cas adaptive immunity

JK Nuñez, LB Harrington, PJ Kranzusch, AN Engelman… - Nature, 2015 - nature.com
Bacteria and archaea generate adaptive immunity against phages and plasmids by integrating
foreign DNA of specific 30–40-base-pair lengths into clustered regularly interspaced …

[HTML][HTML] Biology and applications of CRISPR systems: harnessing nature's toolbox for genome engineering

AV Wright, JK Nuñez, JA Doudna - Cell, 2016 - cell.com
Bacteria and archaea possess a range of defense mechanisms to combat plasmids and viral
infections. Unique among these are the CRISPR-Cas (clustered regularly interspaced short …

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

B Adamson, TM Norman, M Jost, MY Cho, JK Nuñez… - Cell, 2016 - cell.com
Functional genomics efforts face tradeoffs between number of perturbations examined and
complexity of phenotypes measured. We bridge this gap with Perturb-seq, which combines …

Pervasive functional translation of noncanonical human open reading frames

J Chen, AD Brunner, JZ Cogan, JK Nuñez, AP Fields… - Science, 2020 - science.org
Ribosome profiling has revealed pervasive but largely uncharacterized translation outside
of canonical coding sequences (CDSs). In this work, we exploit a systematic CRISPR-based …

PLFS: A checkpoint filesystem for parallel applications

…, B McClelland, P Nowoczynski, J Nunez… - Proceedings of the …, 2009 - dl.acm.org
Parallel applications running across thousands of processors must protect themselves from
inevitable system failures. Many applications insulate themselves from failures by …

[HTML][HTML] CRISPR immunological memory requires a host factor for specificity

JK Nuñez, L Bai, LB Harrington, TL Hinder, JA Doudna - Molecular cell, 2016 - cell.com
Bacteria and archaea employ adaptive immunity against foreign genetic elements using
CRISPR-Cas systems. To generate immunological memory, the Cas1-Cas2 protein complex …

Molecular basis for H3K36me3 recognition by the Tudor domain of PHF1

…, Z Hong, C Allen, S Roy, JK Nuñez… - Nature structural & …, 2012 - nature.com
The PHD finger protein 1 (PHF1) is essential in epigenetic regulation and genome maintenance.
Here we show that the Tudor domain of human PHF1 binds to histone H3 trimethylated …