perturbation response prediction

This paper introduces PRESCIENT, a generative model for inferring cell differentiation landscapes from single-cell time-series data, showing improved prediction of cell fate and perturbation responses.

This study evaluates the effectiveness of different CRISPR effectors for targeting mitochondria, finding that LbCas12a shows better targeting and tolerance than Cas9 variants.

This paper shows ivermectin converts cold tumors to hot by inducing immunogenic cancer cell death and enhancing T cell infiltration, synergizing with anti-PD1 to improve breast cancer treatment outcomes.

The paper applies rTMS to SH-SY5Y cells to study its effects on neural activity using live calcium imaging, finding opposing effects of iTBS and cTBS on depolarization response.

This paper introduces a CRISPR-Cas9 conjugation platform for multivalent display of molecules, enhancing genome editing precision and enabling β-cell engineering to secrete interleukin-10.

This study demonstrates that CRISPR-Cas13d efficiently knocks down specific mRNAs in zebrafish, medaka, killifish, and mouse embryos, leading to significant transcript level reduction and embryonic phenotypes.

The paper uses high-throughput siRNA screening to identify functional interactions and redundancies among human processive exoribonucleases in RNA metabolism.

The paper identifies a microprotein-independent role for LINC00261 in endocrine cell differentiation during human pancreas development through genetic ablation of lncRNAs.

The paper performs a genome-wide CRISPR/Cas9 screen to identify modulators of DUX4 cytotoxicity in FSHD but finds no key effectors other than DUX4 itself.

This study uses CRISPR-based epigenetic editing to activate pancreatic beta-cell genes in human cells, showing that sequential activation of transcription factors is more effective than simultaneous activation.

This study shows that using Cas9 to induce a double-strand break at CTG trinucleotide repeats leads to chromosomal rearrangements, highlighting risks of using Cas9 near microsatellites.

This paper optimizes AsCas12a for combinatorial genetic screens in human cells by improving on-target and off-target activity and enabling higher-order multiplexing.

The paper uses a CRISPR-based screen in 3T3-L1 cells to identify regulators of adipogenesis, finding that protein translation and stability mechanisms are critical for adipocyte expansion and lipogenesis.

This paper develops a deep learning system to design multitarget antipsychotic drugs, generating novel compounds with activity against multiple receptors and demonstrating efficacy in animal models.

This study uses CRISPR interference to show that TMEM97 knockdown protects ARPE19 cells from oxidative stress-induced death, supporting its role in AMD pathobiology.

This study shows that SALL4 can be induced in cancer cells to make them dependent on it, enabling targeted therapy with drugs like DAC and ENT.

This study decodes and modulates multiregional communication in the primate mood processing network using neuromodulation and causal network analysis.

This study validates CRISPR/Cas9 as a therapeutic strategy for SCA1 by downregulating ATXN1 expression in patient fibroblasts with minimal off-target effects.

The paper develops a method to predict the mechanism of action of cellular perturbations by analyzing pathway network topology and transcriptional signatures.

The paper introduces AI-Photoswitchable Screening (AI-PS) to identify genes affecting subcellular localization, validating factors involved in TFEB relocation.

The paper develops a CRISPR-Cas9-based AAV system to knock out multiple circadian clock genes and demonstrates its effectiveness in disrupting molecular circadian rhythms in vivo.

This paper identifies a novel CRISPR-Cas transcription activator, dCas9-AsiA, that can activate gene expression up to 200-fold in bacteria and is portable across species.

The paper investigates cancer protein-protein interaction networks, finding they are scale-free and vulnerable to hub-directed combination therapy.

This study identifies a dopamine-induced gene expression signature in the nucleus accumbens that drives cocaine-induced physiological and behavioral adaptations in rats.

A fixed-weight, biologically parameterised V1 front-end gives standard image classifiers adversarial and corruption robustness at no extra training cost; its simulated neuronal noise drives most of the adversarial gain.

NICEdrug.ch is a database of 250,000 bio-active molecules that identifies reactive similarities to aid drug discovery, repurposing, and toxicity evaluation.

The paper assesses how p53 status affects CRISPR-Cas9 screen performance by comparing wild-type and TP53 knockout cells, showing that optimal design can still yield reliable results.

This paper describes the development of NTR 2.0, a modified nitroreductase with significantly improved efficacy for targeted cell ablation using metronidazole.

The paper uses a CRISPR-Cas9 screen in Chinese hamster ovary cells to identify glutamine-sensitive genes, revealing a novel lipase involved in TCA cycle regulation.

The paper identifies CDC7 inhibition as a method to enhance HDR efficiency in CRISPR-Cas9 gene editing by inducing an early S-phase cell cycle arrest.