perturbation response prediction

This paper develops a CRISPR/retron system for high-throughput generation and tracking of substitution mutations in E. coli, enabling genome-scale screening of chemical responses and fitness changes.

This paper describes a CRISPR/Cas9 method to select recessive lethal mutations in a gene of interest by overexpressing wild-type and loss-of-function alleles in Drosophila.

This paper identifies methodological challenges in translational drug response modeling in cancer and highlights the need for more robust and transferable modeling approaches.

This study uses base editing to systematically mutate over 17,000 sites across 1,500 genes in yeast, identifying 1,100 sites affecting fitness and providing guidelines for effective gRNA design.

The paper compares CBE and ABE base editors for splice-site disruption in T-cells, finding CBEs more reliable and splice-donor targeting most effective.

This paper evolves adenine base editors (ABE8s) to improve editing efficiency and demonstrates their therapeutic application in human cells.

This study shows that adding 13 introns to the Cas9 gene significantly improves gene knockout efficiency in plants.

This study identifies strict target site requirements for effective CRISPRa in bacteria and demonstrates a dCas9 variant with expanded PAM specificity to overcome these limitations.

This paper introduces a method to directly capture CRISPR guides in single-cell RNA-sequencing libraries, enhancing Perturb-seq scalability and enabling multi-omic measurements.

The paper develops tools and barcodes for high-throughput CRISPR bar-seq mutant screens in kinetoplastids, enabling pooled screens across the community.

This study develops an estrogen-inducible CRISPR/Cas9 system in Nicotiana tabacum and demonstrates its efficacy in inducing targeted mutagenesis of the NtPDS gene.

This paper introduces dTAGV-1, a VHL-recruiting dTAG molecule that rapidly degrades FKBP12F36V-tagged proteins, overcoming limitations of CRBN-recruiting dTAGs and enabling combination degrader studies in cells and mice.

The paper identifies that modulating transit-amplifying cell proliferation alters intestinal epithelial cell-type composition through lineage-based mechanisms.

This paper introduces a method to control CRISPR/Cas9 activity using light-activated guide RNAs, enabling precise spatiotemporal gene editing in cells and zebrafish embryos.

The paper develops a statistical test to improve hit detection in CRISPR screens by accounting for asymmetric gRNA abundance changes, allowing smaller experiment sizes.

FreiPose is a deep learning framework for precise 3D motion capture of animals, showing high accuracy and reliability in tracking rats during electrophysiological and optogenetic experiments.

Gene regulatory networks inferred from single-cell transcriptome and epigenome data are perturbed in silico to predict transcription-factor perturbation outcomes and to nominate factors that raise reprogramming yield.

The paper presents a method to generate isogenic cell pairs and screen them with CRISPR-Cas9 libraries to identify genetic interactions, demonstrating applications for BCL2L1, MCL1, and PARP1.

The paper develops CRISPR-based biocontainment circuits using transposable elements to induce cell death and create kill-switches for controlling cell lines.

This paper develops a high-throughput radial migration device for measuring cell migration, enabling therapeutic screening and phenotypic response analysis.

The paper compares PAM-flexible Cas9 variants (xCas9 and Cas9-NG) and wild-type Cas9 across gene knock-out, activation, and suppression using a high-throughput screen, finding that PAM flexibility reduces targeting efficiency and that Cas9-NG outperforms xCas9.

The paper reports Late Holocene fossil remains from a Cuban cave, providing last appearance dates and paleoecological insights into extinct and threatened species.

This paper develops a method to control gene expression using CRISPR interference and deep learning, revealing gene-specific expression-phenotype relationships.

This study shows that sgRNA expression level is a major determinant of CRISPRi knockdown efficiency in K562 cells, more impactful than KRAB-dCas9 expression level.

This study evaluates second-generation proteasome inhibitors and ubiquitination regulators for their efficacy against imatinib-resistant GIST cells, finding that 20S proteasome inhibitors are effective while others show limited activity.

The paper introduces RECAS9, a transgene-free method using CRISPR/Cas9 RNP to induce mitotic recombination in barley, enabling precise breeding and fine mapping of beneficial alleles from wild relatives.

This paper develops CRISPR systems to target and deplete an oncogenic KRAS mutant allele, leading to tumor regression in vitro and in vivo.

This paper develops a population systems biology algorithm to enhance non-nitrogenous metabolite production in E. coli by considering transcriptome diversity and introducing nitrogen-swap strategies.

The paper introduces a remote, automated, and MRI-compatible system for delivering inspiratory resistive loads to study interoception in neuroimaging studies.