perturbation response prediction

The paper develops optogenetic circuits with negative feedback to reduce gene expression noise and control gene activity in mammalian cells.

beditor designs guide RNA libraries for CRISPR-mediated base editing across species and editors, using scores to select optimal guides for minimizing off-target effects and maximizing editing efficiency.

The paper identifies genetic modifiers of cell growth in response to a PCSK9 translational inhibitor and reveals their roles in ribosome quality control.

This paper develops CRISPR-Cas9 gene editing systems for multiple Candida species using plasmids, enabling markerless editing and molecular barcode introduction.

drugZ identifies chemogenetic interactions from CRISPR screens, finding more homologous recombination repair pathway genes and confirming KEAP1 loss as a resistance factor for ERK inhibitors.

The paper develops a quantitative stability landscape model to analyze microbiome recovery after antibiotics and finds support for long-term state transitions in gut and salivary microbiomes after ciprofloxacin and clindamycin.

The paper introduces a computational tool to measure muscle activation equilibrium constants and analyze perturbations, applying it to study a mutation causing hypertrophic cardiomyopathy.

This paper introduces zGrad, a nanobody-based degron system for inducible and reversible protein inactivation in zebrafish, demonstrating its utility in studying protein function across different spatial and temporal contexts.

This paper introduces multi-level barcoding to address clonal heterogeneity in pooled genetic screens and demonstrates its ability to resolve cellular heterogeneity issues.

The paper shows that targeting tandem amplified regions in CRISPR-Cas9 screens reduces cellular fitness, while chromosomal duplications have minimal effects.

This study uses an artificial gene drive system in budding yeast to show that appending nuclear localization signals to Cas9 can modulate nuclease activity and act as a molecular safeguard.

This paper demonstrates a method to achieve site-specific RNA cleavage and polyadenylation using CRISPR-Cas13 fused to NUDT21, named Postscriptr, for non-genomic gene expression manipulation.

The paper introduces CRISPRi-FlowFISH to perturb enhancers and an Activity-by-Contact model to predict enhancer-gene regulatory connections.

This paper develops a neuron-optimized CRISPRa system for efficient and specific gene regulation in neurons and the adult brain.

Perturb-ATAC combines CRISPR perturbations with single-cell ATAC-seq to identify gene regulatory networks in human cells.

The paper evaluates and introduces optimized CRISPR libraries for knockout, interference, and activation screens, showing improved performance in gene function interrogation.

scGen models single-cell perturbation responses across cell types, studies, and species using variational autoencoders and latent space arithmetics, showing accurate out-of-sample predictions.

The paper develops strategies to improve CRISPR-Cas9 editing efficiency in C. elegans by optimizing guide RNA design, repair templates, and co-conversion markers, revealing differences in maternal and paternal DSB repair.

The paper introduces a transposon-based system for genetic manipulation of the vertebrate CNS, enabling long-term conditional experiments across cell types and species.

The paper introduces genetic tools in Drosophila to enable spatiotemporally controlled perturbations for studying non-autonomous cell interactions and their effects on phenotypes.

This paper introduces a cloning-free CRISPR/Cas9 method to induce gene expression, showing efficient activation of neural development genes in human cells.

This study evaluates Maritoclax and its combination with ABT-263 in NPC cell lines, showing single-agent and synergistic effects on cell proliferation and resistance in 3D spheroids.

The paper introduces ECCITE-seq, a method that simultaneously captures transcriptomes, immune clonotypes, surface markers, sample identity, and CRISPR perturbations from single cells.

This paper introduces OrthoRep, a system for high-throughput directed evolution of genes in yeast, demonstrating its ability to evolve drug-resistant malarial DHFRs and reveal complex fitness landscapes.

This study uses machine learning to predict motor improvement in chronic stroke patients after therapy, finding that pre-intervention assessments and motor thresholds are key predictors.

The paper introduces a framework to correct inconsistencies in pharmacogenomics datasets by improving drug-wise correlations while preserving cell-wise consistency.

The paper introduces a haploid genetic screening method to identify proteins influencing NMD activity in mammalian cells.

The paper introduces a regression model called Siren to improve peptide detection in DIA mass spectra by accounting for isotope peak interference.

The paper introduces cal-Seq, a pooled knockdown screen using CaMPARI to identify calcium handling genes, finding GPR99 as a regulator of histamine-induced calcium signaling.