perturbation response prediction

The paper uses single-cell genomic data from human cerebral organoids to infer gene regulatory networks and assess transcription factor roles in brain development.

Alpha-XIC improves peptide identification in DIA mass spectrometry by learning robust coelution scores from peak group data, enhancing identification accuracy and recovery of misidentified peptides.

The paper identifies transcription factors that maintain cell identity by analyzing their responsiveness to perturbations in human iPSC-derived cardiac myocytes and fibroblasts.

The paper introduces a genetic controller, WTC846, for precise, adjustable, and variation-free gene expression in yeast, enabling controlled phenotypic studies.

This paper introduces a Cas12a-based CRISPRi system for mycobacteria that enables efficient multigene regulation and studies genetic interactions in Mtb.

This study shows that Cas9 expression levels significantly affect the efficiency and speed of large-scale pooled CRISPR screens, with higher Cas9 expression improving performance.

The paper evaluates the efficacy of CRISPR-Cas nucleases on microsatellites linked to human disorders, identifying variations in cleavage efficiency and off-target mutations.

This study shows that feature-based attention during visual perceptual learning enables long-lasting location transfer and maintains orientation specificity, lasting over a year.

This study compares methods for knocking-in large DNA fragments using CRISPR, finding that HDR with CRISPR is the most reliable and effective approach.

This paper introduces a microfluidic imaging method for long-term, stable, and parallel live-imaging of C. elegans larval development, enabling observation of previously inaccessible processes.

The paper develops a Cre-dependent CRISPR-dCas9 system for gene regulation in neurons, showing improved specificity over traditional methods.

The paper predicts the UEFA EURO 2020 knockout tournament outcomes using phylogenetic methods, finding France vs England as the most probable final with England having a slight edge.

This study shows that individual differences in visuomotor performance and learning can be predicted by resting-state aperiodic neural dynamics parameters, specifically 1/f intercept and slope.

This paper describes a CRISPR-Cas9 method to engineer arm-level chromosomal deletions in neuroblastoma cell lines to study their oncogenic role.

This study uses CRISPR screening to identify 35 genes that modify ACE2 surface abundance in HuH7 cells, revealing regulators of ACE2 expression and their impact on SARS-CoV-2 susceptibility.

This paper introduces PTA, a new WGA method that improves variant calling accuracy in single cells, enabling studies of genetic diversity and CRISPR off-target effects.

The paper shows that sustained neural activity latency reflects rapid perceptual learning of auditory patterns, while magnitude may reflect learning outcomes like better prediction.

CRISPRpas regulates alternative polyadenylation by dCas9, altering PAS usage and demonstrating its impact on gene expression and APA-related SNPs.

This paper engineers improved Cas13 effectors for targeted post-transcriptional regulation, showing efficient translational repression in bacteria and exon skipping in human cells.

The paper introduces Spear-ATAC, a high-throughput scATAC-seq protocol that identifies regulatory networks in cancer by analyzing chromatin accessibility and sgRNA spacer sequences from thousands of cells.

The paper identifies chemically modified crRNAs that enhance CRISPR-Cas13 knockdown efficiency and half-life in human cells.

This paper models transient drug resistance in tumors and finds continuous therapy is optimal under estimated parameters, but alternating schedules can be optimal under different conditions.

TISON is a web-based platform for multi-scale cancer modeling that integrates biomolecular data and patient-specific information to support drug target discovery and personalized therapeutics.

This paper introduces CRISPR-sciATAC, a method linking genetic perturbations to chromatin accessibility in single cells, showing its effectiveness in human and mouse experiments.

The paper uses synthetic CRISPR gRNAs and in vivo pre-screening to identify pro-regenerative genes in spinal cord injury, finding that tgfb1a promotes regeneration by controlling inflammation.

This study evaluates multiscale virtual screening pipelines for drug repurposing using the CANDO platform, showing improved performance with hybrid decision tree pipelines over docking-based methods.

The paper introduces a paired-guide RNA CRISPR-Cas9 system to identify protein-coding and lncRNA genes involved in human B-cell to macrophage transdifferentiation, identifying 26 potential novel genes.

This paper develops a population-scale electroporation method for delivering nucleic acids to C. elegans, enabling efficient RNAi and CRISPR-based genetic targeting.

The paper introduces a method to profile off-target specificity of CRISPR enzymes using ssDNA mapping, applicable to both catalytically dead and active Cas9 variants.