scPair: Boosting single cell multimodal analysis by leveraging implicit feature selection and single cell atlases.

Multimodal single-cell assays profile multiple sets of features in the same cells and are widely used for identifying and mapping cell states between chromatin and mRNA and linking regulatory elements to target genes. However, the high dimensionality of input features and shallow sequencing depth compared to unimodal assays pose challenges in data analysis. Here we present scPair, a multimodal single-cell data framework that overcomes these challenges by employing an implicit feature selection approach.

Deconvolution reveals cell-type-specific transcriptomic changes in the aging mouse brain.

Mounting evidence highlights the crucial role of aging in the pathogenesis of Alzheimer's disease (AD). We have previously explored human apoE-targeted replacement mice across different ages and identified distinct molecular pathways driven by aging. However, the specific contribution of different brain cell types to the gene modules underlying these pathways remained elusive.

Projecting RNA measurements onto single cell atlases to extract cell type-specific expression profiles using scProjection.

Multi-modal single cell RNA assays capture RNA content as well as other data modalities, such as spatial cell position or the electrophysiological properties of cells. Compared to dedicated scRNA-seq assays however, they may unintentionally capture RNA from multiple adjacent cells, exhibit lower RNA sequencing depth compared to scRNA-seq, or lack genome-wide RNA measurements. We present scProjection, a method for mapping individual multi-modal RNA measurements to deeply sequenced scRNA-seq atlases to extract cell type-specific, single cell gene expression profiles.

Protocol for vision transformer-based evaluation of drug potency using images processed by an optimized Sobel operator.

Conventional approaches for screening anticancer drugs rely on chemical reactions, which are time consuming, labor intensive, and costly. Here, we present a protocol for label-free and high-throughput assessment of drug efficacy using a vision transformer and a Conv2D. We describe the steps for cell culture, drug treatment, data collection, and preprocessing.

SIC50: Determining drug inhibitory concentrations using a vision transformer and an optimized Sobel operator.

As a measure of cytotoxic potency, half-maximal inhibitory concentration (IC50) is the concentration at which a drug exerts half of its maximal inhibitory effect against target cells. It can be determined by various methods that require applying additional reagents or lysing the cells. Here, we describe a label-free Sobel-edge-based method, which we name SIC50, for the evaluation of IC50.

Investigation of neurons that express Dpr/DIP cell adhesion molecules.

reproductive behaviors are directed by neurons. A reanalysis of genomic studies shows that genes encoding and immunoglobulin superfamily (IgSF) members are expressed in neurons. We find that each and ( ∩ ) overlapping expression pattern is similar in both sexes, but there are dimorphisms in neuronal morphology and cell number.