A single-cell RNA sequencing data classification method called scGMB is proposed. The method captures the topological relationships between cells.

Abstract. Transformers have demonstrated remarkable success in the field of deep learning, attracting significant attention from researchers and driving in

Abstract. Nanopore direct RNA sequencing holds promise for advancing our understanding of the epitranscriptome. Recently, Oxford Nanopore Technologies rele

Abstract. Muscle-invasive bladder cancer (MIBC) is clinically heterogeneous, and current molecular subtyping does not capture the spatial organization of tumor states and microenvironmental context. H...

RNAs adopt complex structures that regulate key biological processes, making accurate structure prediction essential. Chemical probing coupled with Nanopore direct RNA sequencing (DRS) offers a route ...

Multiple lineages and functional states of tumor-associated dendritic cells (TADCs), as essential inducers of anti-tumor immunity, have been reported. Here, the authors have generated single-cell RNA ...

Abstract. Alternative polyadenylation (APA) is a key post-transcriptional regulatory mechanism implicated in various diseases. Existing APA analysis tools

IBDverse is a single-cell RNA atlas of terminal ileal biopsies comprising 1.1 million cells from 111 patients with Crohn’s disease and 232 healthy participants. Analysis of the data identifies genes, ...

In vivo CRISPR genetic perturbations are spatially mapped at scale.

When multiple large language models debate and refine each other’s predictions through iterative deliberation, their consensus cell type annotations improve accuracy by 16 percentage points over singl...

Abstract. Integrative analysis of RNA-seq datasets faces critical challenges in disentangling biologically meaningful signals from implicit confounders, su

Abstract. Single-cell RNA-sequencing (scRNA-seq) can excavate cellular heterogeneity and distinguish different types of cells. Clustering cells into subpop

TrASPr+BOS enables accurate prediction and design of tissue-specific RNA splicing, even for tissues not trained on, uncovering unseen regulatory elements and guiding sequence edits that reshape splici...

Lonza and Oxford Nanopore Technologies Launch Direct RNA Sequencing Solution for GMP mRNA Quality Control

This Perspective discusses the methodologies, application and evaluation of interpretable machine learning (IML) approaches in computational biology, with particular focus on common pitfalls when usin...