perturbation response prediction

This study uses CRISPR-Cas13 to functionally screen circRNAs, identifying roles in cell growth and development.

The paper identifies low micromolar SARS-CoV-2 Mpro inhibitors from in silico screens through biochemical testing of synthesized compounds.

The paper introduces FLiCRE, a molecular tool for tagging calcium-activated cells, and uses it to identify and manipulate a striatal cell-type involved in aversion behavior.

This paper introduces light-activated tetrazines to enable precise spatiotemporal control of bioorthogonal reactions in live cells.

This paper develops an inducible CRISPRi system in mouse embryonic stem cells and generates a knockin mouse model for gene function studies.

This paper introduces an optogenetic tool to control NmeCas9 activity using a light-switchable anti-CRISPR protein, enabling precise genome editing in mammalian cells.

This study identifies genetic regulators of PARP inhibitor response using CRISPR screens, revealing TIP60 as a key factor that reverses PARPi sensitivity in BRCA2-deficient cells.

The paper quantifies how varying expression of translation termination factors in Bacillus subtilis affects fitness, revealing spurious regulatory connections that reduce fitness when expression deviates from endogenous levels.

The paper develops a dCas12a-based tool for programmable gene activation and repression in prokaryotes, demonstrating its utility in metabolic engineering.

The paper develops a framework to predict the effects of neural perturbations using functional causal flow inferred from resting state activity in monkeys.

This paper demonstrates the effectiveness of Cas13 for RNA manipulation in Drosophila, including targeting endogenous transcripts and editing mRNAs.

The paper uses a computationally designed PRC2 inhibitor, EBdCas9, to identify functional TATA boxes in distal promoter regions and demonstrate their role in gene activation.

This paper reanalyzes an in vivo drug synergy study and finds that most drug pairs do not show statistically significant synergy when using appropriate statistical methods.

The paper introduces a high-throughput instrument called GIZMO to screen fluorescent protein mutants under two-photon excitation, enabling efficient evolution of proteins optimized for this excitation method.

This study identifies Cas10d as a multi-functional nuclease in CRISPR type I-D system, enabling targeted mutagenesis in human cells with specific deletion and insertion capabilities.

CIGAR-seq identifies mRNA modification regulators through CRISPR screening and RNA modification readout, revealing NSUN6 as a novel m5C methyltransferase.

This study develops and optimizes CRISPR-Cas13 tools for RNA knockdown in Drosophila cells, improving efficiency and reducing toxicity.

This paper develops an optogenetic system to control BMP signaling using blue light, enabling precise and dynamic activation in human cells.

This study shows that combining CDK4/6 and HSP90 inhibitors reduces HIF1 expression and cancer cell viability, including in Rb-deficient cells.

The paper develops a CRISPRi system to modulate gene expression in bacteria and shows that essential gene expression-fitness relationships are conserved across species.

The paper shows that paralog buffering limits detection of synthetic lethal interactions in CRISPR screens, revealing many under-detected genetic dependencies.

This study identifies CD14 as a key target to enhance antibacterial activity in mesenchymal stromal cells through systems-level analysis and CRISPR activation.

This study demonstrates that dual drug administration of RapaLink-1 and RapaBlock selectively inhibits mTORC1 in the brain while protecting it in the periphery, reducing side effects and moderating alcohol use in mice.

The paper introduces scene wheels, a method to control visual properties of natural scenes using GANs, and validates their use in assessing perceptual and mnemonic representations through behavioral experiments.

The paper uses a genome-wide CRISPR/Cas9 knockout screen to identify novel transporters involved in nanoparticle uptake, finding SLC18B1 mediates polymeric micellar nanoparticle uptake.

This study predicts adverse drug reactions from two-drug combinations using structural and transcriptomic data in an artificial neural network, achieving 82% average accuracy.

The paper uses CRISPRi screens in yeast to identify genes affecting growth in lignocellulose hydrolysate, revealing known and new targets for improving industrial fermentation.

This paper presents a CRISPR homing gene drive in Drosophila that reduces resistance allele formation by targeting a haplolethal gene, achieving high efficiency in allele spreading.

This paper introduces ASAP-seq, a method to simultaneously profile chromatin accessibility, protein levels, and mtDNA in single cells, demonstrating its application in hematopoietic differentiation and T cell perturbations.

This paper introduces scNT-Seq, a method to measure newly-transcribed and pre-existing RNAs in single cells, revealing gene regulatory networks and RNA dynamics in neurons and embryonic stem cells.