perturbation response prediction

This paper develops two new strategies for constructing large variant DMS libraries in mammalian cells using piggyBac-mediated genomic integration and in-vitro ligation.

The paper shows that targeting ATM, ATR, or DNA topoisomerases causes widespread protein aggregation through chaperone system overload, similar to proteotoxic stress and proteinopathies.

The paper uses a CRISPR/Cas9 screen to identify type I interferon-stimulated genes that regulate Toxoplasma gondii infection in macrophages.

This study reports that lentiviral-based CRISPR-Cas9 vectors can integrate into the target genomic location, unexpectedly activating the target gene.

This paper describes a low-cost DIY caging apparatus for chronic stimulation and recording in awake rodents, enabling continuous and flexible experimental paradigms.

The paper evaluates DNA repair protein-Cas9 fusions for improving CRISPR editing efficiency, finding that most require optimization for specific cell types and genomic loci.

This paper introduces a CRISPR-based system called FAST-HDR that simplifies and accelerates the generation of knock-in cell lines for studying endogenous proteins.

This paper demonstrates that targeting a single marker RNA with CRISPR/RfxCas13d causes collateral transcriptome destruction, enabling inhibition of cell proliferation or suppression of cell state transition in human cells.

This paper demonstrates the use of dFnCas12a-VPR for multiplexed gene activation in mammalian cells, showing enhanced activity of 5' crRNAs in arrays.

The paper uses CRISPR-Cas9 screens in vitro and in vivo to identify gene knockouts that enhance neural stem cell activation in aged mice, finding that GLUT4 knockout is a top rejuvenating intervention.

This study investigates the cell-type- and region-specific role of miR-1 in modulating cocaine-seeking behaviors in mice, showing distinct effects in D1- and D2-SPNs of the dorsal striatum.

This study shows that breaking DNA-cell size scaling in E. coli leads to a linear growth regime and resource reallocation to plasmid-borne gene expression.

The paper presents C. elegans strains with constitutively expressed Cas9 from integrated transgenes, significantly improving CRISPR editing efficiency and reducing workload.

This study uses phage-delivered CRISPR-Cas9 to deplete specific E. coli strains and induce genomic deletions in the gut microbiome of mice.

The paper develops an in vitro cell-free system to evaluate quorum sensing inhibitors by reconstituting Pseudomonas aeruginosa pathways in Escherichia coli.

TEMPO enables sequential genetic labeling and manipulation of vertebrate cell lineages to study birth-order-dependent cell fates.

The paper describes a method to improve enzymes for plant applications using continuous directed evolution in yeast, demonstrating its effectiveness with a bacterial thiamin synthesis enzyme.

This study uses CRISPR screening and single-cell transcriptomics to analyze the functional roles of host and viral factors in HCMV infection, revealing distinct impacts on infection trajectories.

The paper presents a CRISPR-mediated method for inducing genetic changes in hematopoietic cells using PCR-generated constructs, showing comparable efficiency to ribonucleoprotein strategies without off-target effects.

This paper introduces a suspension culture technique for cancer organoids that improves expansion efficiency and enables large-scale perturbation screens.

This study shows a low-dose drug combination effectively suppresses NSCLC PDX tumors with high response and complete remission rates.

This study shows that cGAS-STING signaling in cancer cells promotes drug resistance by responding to cytosolic DNA from chemotherapy, suggesting caution in combining STING agonists with chemotherapy.

This paper introduces a triple dgRNP CRISPR system for efficient biallelic gene disruption in zebrafish, enabling rapid cardiovascular phenotyping in F0 embryos.

This paper introduces RESCUE-MM, a one-step method to correct gene-independent effects in CRISPR-Cas9 screens by integrating restricted cubic splines and mixed models, improving accuracy over two-step approaches.

The paper introduces CZON-cutter, a CRISPR-Cas9 system for genome editing and organelle visualization in Cyanidioschyzon merolae, enabling validation of essential gene functions.

This study identifies Ptgs2 as a stress-induced gene in specific prefrontal cortical neurons that mediates anxiety-like behaviors in mice.

This paper develops a genetic toolbox for tissue-derived human organoids, enabling efficient gene manipulation through CRISPR-based methods and flow cytometry.

The paper introduces a POAK system using Cas9 and NHEJ for markerless gene knockouts in two bacteria, showing it works in both Gram-negative and Gram-positive organisms.

This study shows that pre-stimulus alpha-band activity in occipital-parietal regions enhances perceptual sensitivity and information content in visual detection tasks.

CRISPRpath enables parallel characterization of cis-regulatory elements for multiple genes in a pathway, identifying functional enhancers and distinguishing their impact on gene expression.