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http://dx.doi.org/10.1016/j.molp.2023.12.007 | DOI Listing |
Bioinformatics
September 2025
Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
Motivation: RNA velocity has become a powerful tool for uncovering transcriptional dynamics in snapshot single-cell data. However, current RNA velocity approaches often assume constant transcriptional rates and treat genes independently with gene-specific times, which may introduce biases and deviate from biological realities. Here, we present InterVelo, a novel deep learning framework that simultaneously learns cellular pseudotime and RNA velocity.
View Article and Find Full Text PDFFront Pharmacol
August 2025
AbbVie Bay Area, South San Francisco, CA, United States.
In clinical practice, a variety of techniques are employed to generate diverse data types for each cancer patient. These data types, spanning clinical, genomics, imaging, and other modalities, exhibit significant differences and possess distinct data structures. Therefore, most current analyses focus on a single data modality, limiting the potential of fully utilizing all available data and providing comprehensive insights.
View Article and Find Full Text PDFDiagn Cytopathol
September 2025
Department of General Surgery, Qianwei Hospital of Jilin Province, Changchun, China.
Colorectal cancer (CRC) is a major global health burden, ranking among the leading causes of cancer-related deaths. Despite improvements in screening and treatment, challenges such as late-stage diagnosis, high recurrence rates, and therapy resistance continue to impede optimal outcomes. Liquid biopsy, a minimally invasive technique that analyzes tumor-derived components in bodily fluids-including circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and extracellular vesicles (EVs)-is emerging as a powerful tool to transform CRC management across the disease continuum.
View Article and Find Full Text PDFJ Cell Mol Med
September 2025
Institute of Cellular Biology and Pathology "Nicolae Simionescu", Bucharest, Romania.
Calcific aortic valve disease (CAVD) is a growing global health burden, with no approved pharmacological treatments to date, indicating a substantial therapeutic gap and the need for deeper insight into its underlying mechanisms. Transcriptomic approaches, particularly RNA sequencing (RNAseq) and single-cell sequencing (scRNAseq), are emerging as powerful tools for unravelling the complex biology of the aortic valve (AV) in both normal and diseased states. This review summarises recent advances in our understanding of AV structure and function, with emphasis on valvular cell plasticity, heterogeneity and intercellular interactions-especially between valvular endothelial cells (VECs) and monocytes under physiological and pathological conditions.
View Article and Find Full Text PDFBiotechnol J
September 2025
Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P. R. China.
Nucleotides are indispensable biomolecules, playing vital roles in genetic information transfer, energy metabolism, cofactor biosynthesis, and cellular communication. These compounds (including purine nucleotides, nucleosides, and nucleobases) have become increasingly valuable as foodstuff additives and pharmaceutical intermediates. Although microbial production offers an eco-friendly alternative, its efficiency remains constrained by complex metabolic networks and growth-production tradeoffs.
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