Jennifer A. Doudna

The paper shows that VIPR systems in E. coli mediate competition between phages and their satellite counterparts, with satellites using decoy RNAs to counteract repression.

The paper identifies a bacterial immune pathway where tRNA cleavage generates second messengers that trigger cell death via RNA-guided nuclease activity.

This study demonstrates that in vivo delivery of genome editing enzymes can be amplified through cell-to-cell transfer, significantly increasing editing efficiency in mice.

The paper improves RNA secondary structure prediction by training a deep learning model on a new dataset of RNA sequences and structures, showing better generalization to unseen RNA families.

This paper develops a virus-like particle-based system for CRISPR gene editing and screening in primary human myeloid cells, identifying TNFAIP3 as a key regulator of inflammatory polarization.

This paper develops yeast-selected SpCas9 variants with re-specified PAM recognition to enable allele-specific editing, demonstrating improved specificity and catalytic efficiency compared to PAM-broadened variants.

Ymu1 TnpB unwinds DNA via a long-lived partially unwound intermediate before a rarely stable open state; the WFR triple variant stabilizes both, boosting plant editing.

The paper designs active RNA-guided nucleases using AI and structure-guided methods, validated by cryo-EM and functional testing across species.

The paper identifies VIPR systems, which use noncontiguous RNA codes for DNA recognition, suggesting an ancient origin of adaptive immunity through viral interactions.

This paper demonstrates T cells can deliver genome editing machinery to target cells via programmable intercellular interactions.

This study identifies multiple dispersed packaging signals in the SARS-CoV-2 genome that cooperate to direct RNA packaging into virions, revealing a dynamic mechanism for coronavirus genome assembly.

This paper develops a method to selectively kill cancer cells with TP53 mutations by using RNA-guided Cas12a2 to induce chromatin shredding through targeting cancer-specific transcripts.

The paper reveals the structural mechanism of VIPR RNA-guided DNA recognition through triplex formation, showing how noncontiguous RNA sequences direct DNA targeting.

The paper improves a virus-mediated genome editing method in plants by using multiple gRNAs and an enhanced TnpB variant for efficient multiplexed editing.

This paper introduces spligation, a method using CRISPR-Csm complexes to generate chimeric RNA in living cells by enabling site-specific RNA cleavage and trans-ligation.

This study identifies host factors that influence VchCAST activity and demonstrates that the λ-Red recombineering system significantly enhances its editing efficiency in E. coli and other bacteria.

This study identifies diverse 2H phosphodiesterases in viruses that selectively degrade cyclic dinucleotides to evade host immune signaling.

The paper uses spatiotemporal photocatalytic proximity labeling to track dynamic EGFR interactomes both extracellularly and intracellularly upon EGF activation.

The paper investigates DNA repair in postmitotic neurons and shows that manipulating repair pathways can influence CRISPR editing outcomes.

The paper identifies recurrent acquisition of nuclease-protease pairs in bacterial antiviral immunity and shows their proteolytic activation mechanism across different immune systems.

The paper identifies CRISPR-Cas12a variants with expanded PAM recognition, enabling targeting of ~25% of the human genome.

This study identifies a trade-off between PAM recognition breadth and CRISPR-Cas9 editing efficiency, proposing a two-step target capture mechanism to improve genome editing.

This paper engineers a plant virus to deliver a compact CRISPR-Cas system for transgene-free germline editing in Arabidopsis.

The paper shows that Chimalliviridae form a lipid membrane-bound EPI vesicle during early infection, which hosts transcription of the phage genome, and demonstrates the necessity of a second compartment, the phage nucleus, for genome replication.

The paper shows that the CRISPR-related enzyme mCpol produces cyclic oligonucleotides to prevent cell death and counteract viral immune evasion.

The paper develops a CRISPRi-ART system to knock down protein expression in diverse bacteriophages and identifies essential genes, including many with unknown functions.

This paper introduces smLiveFISH, a method for single-molecule live-cell imaging of endogenous RNA using CRISPR-Csm, and identifies two distinct mRNA localization mechanisms.

This study identifies activating mutations in TnpB enzymes that enhance genome editing activity across multiple species.

This study compares electroporation and packaged RNP delivery for genome editing, finding that packaged delivery is significantly more efficient and faster.

This paper introduces a method for functional protein mining with statistical guarantees, improving reliability in homology detection and functional annotation.