perturbation response prediction

Shuffle-Seq enables large-scale genetic interaction screens by leveraging barcode co-inheritance in dividing cells, applied to study drug resistance mechanisms in melanoma.

This paper introduces a minimized double guide RNA library for CRISPR/Cas9 screens, reducing scale by fivefold while maintaining performance.

The paper introduces a homology-independent CRISPR-based method for efficient genomic knock-ins in Drosophila, demonstrating its use for fluorescent tagging and gene disruption.

The paper uses CRISPRi screening in Synechocystis to identify gene targets that enhance growth, lactate tolerance, and chemical production.

The paper develops a method to efficiently edit LT-HSCs at single-cell resolution and demonstrates distinct functional outcomes of GATA1 editing.

This paper presents a synthetic small RNA-based system for modulating gene expression in P. putida to redesign its metabolism for industrial biocatalysis.

The paper investigates the temporal dynamics of CRISPR/Cas gene editing in lung cancer cells, showing a delay between nuclear entry and NRF2 gene disruption.

The paper applies ESP embeddings to predict drug-drug interactions, showing better performance, faster training, and simplicity compared to graph convolutional neural networks.

This study shows that inhibiting SETD8 reduces multiple myeloma cell survival and overcomes drug resistance regardless of p53 status.

This paper introduces enhanced CRISPR epigenetic editing systems to analyze enhancer function in vivo, showing improved modulation of gene transcription with minimal off-target effects.

This study shows that CRISPR/Cas9-induced INDELs can lead to mRNA misregulation by creating foreign mRNAs or proteins in about half of edited cell lines.

The paper identifies off-target effects in CRISPR-Cas9 screens for non-coding elements and shows that strict filtering with specificity scores improves the identification of essential regulatory regions.

This paper introduces a CRISPRi screening method combining time-lapse imaging and microfluidic devices to study gene knockdown effects on E. coli cell cycle dynamics.

This paper demonstrates efficient CRISPR/Cas9 gene ablation in uncultured naive mouse T cells for in vivo studies, showing gene deletion occurs independently of T cell activation.

This study introduces qCas9, a modified CRISPR/Cas9 system that enhances genome editing efficiency and reduces off-target effects in zebrafish and mammalian cells.

The paper develops a multiplexed CRISPR/Cas9-based screening strategy using AsCpf1 to create a smaller, more efficient genome-wide knockout library.

The paper shows auditory contrast gain control occurs in subcortical and cortical auditory systems and predicts perceptual adaptation in humans.

The paper develops experimental methodologies to control temporal changes in extracellular stimuli for studying dynamic cellular processes in single cells.

The paper transfers the MIMIVIRE defence system from Mimiviruses to E. coli to eliminate a plasmid by targeting tetracycline resistance sequences.

The paper introduces MULTI-seq, a method for scalable sample multiplexing in scRNA-seq, enabling analysis of multiple tissues and perturbation experiments while improving data quality.

The paper improves the auxin-inducible degron system to enable rapid, specific protein depletion while preserving native protein levels and patterns.

This study uses CRISPRa to correct β3 integrin haplo-insufficiency in neurons, rebalancing network activity without causing hyperactivity seen with exogenous gene expression.

This paper introduces conditional guide RNAs (cgRNAs) that control CRISPR/Cas activity via RNA triggers, enabling programmable gene regulation in E. coli with varying dynamic ranges and crosstalk levels.

This study shows that targeting splice donor sites with sgRNAs improves CRISPR/Cas9 knockout efficiency by increasing frameshift mutations and disrupting pre-mRNA splicing.

CellTag Indexing enables genetic barcode-based multiplexing for single-cell genomics, allowing simultaneous sample identification and transcriptional analysis across diverse cell types.

Inserting theophylline aptamers into the sgRNA yields ligand-activated and ligand-deactivated guides that tune CRISPRi in E. coli over 11x to 13x dynamic ranges, enabling two-ligand multiplexing.

This study develops a CRISPR/Cas9 method to reversibly disrupt specific transcription factor-DNA interactions and assess their functional impact on gene expression and cell division.

The paper introduces a new CRISPR/Cas9-based transcriptional activator, dCasEV2.1, which shows strong activation and genome-wide specificity in plants.

The paper uses RNAi screens in isogenic human stem cells to identify SMARCA4 as a differential regulator of stemness and differentiation in hematopoietic and neural stem cells.