Methods

Differential allele-specific expression (ASE) is a powerful tool to study context-specific cis-regulation of gene expression. Such effects can reflect the interaction between genetic or epigenetic factors...

Identifying cancerous samples or cells using transcriptomic data is critical for cancer related basic research, early diagnosis, and targeted therapy. However, the high transcriptional heterogeneity of...

Alzheimer’s disease (AD) is the most common cause of dementia worldwide, but the molecular and cellular mechanisms underlying cognitive impairment remain poorly understood. To address this, MIT...

Cell-cell interactions (CCIs) play critical roles in many biological processes such as cellular differentiation, tissue homeostasis, and immune response. With the rapid development of high throughput single-cell RNA..

Machine learning methods, particularly neural networks trained on large datasets, are transforming how scientists approach scientific discovery and experimental design. However, current state-of-the...

The accurate estimation of cell surface receptor abundance for single cell transcriptomics data is important for the tasks of cell type and phenotype categorization and cell-cell interaction quantification. Dartmouth...

Simple CUT&Tag adaptation gives information about genetic regulatory elements in formalin-fixed tumor samples. Tumor samples usually get soaked in formalin and then embedded in paraffin wax, ready for a pathologist to examine under a microscope...

Alternative polyadenylation is a main driver of transcriptome diversity in mammals, generating transcript isoforms with different 3′ ends via cleavage and polyadenylation at distinct...

Single-cell RNA sequencing (scRNAseq) technologies have been beneficial in revealing and describing cellular heterogeneity within mammalian tissues, including solid tumors. However, many of these...

Wheat is a global staple food and plays a pivotal role in the livelihoods of billions of people. Although long non-coding RNAs (lncRNAs) have been recognized as crucial regulators of numerous biological processes...