computational-mathematics

Nature Communications, Published online: 26 May 2026; doi:10.1038/s41467-026-73663-3 The authors compare standard and personalized genome references across multiple assays and find that genome choice has modest effects but can reveal biology missed by standard references, including hidden DNA methylation at non-reference elements.

How we built a model that navigates between genomes and molecules bidirectionally, and why one remarkable database turned out to be the key.

A battle between “slimes” and “zoglins” could be the best way to calculate pi—at least for fans of this megahit game

Nature, Published online: 25 May 2026; doi:10.1038/d41586-026-01621-6 Billie Goolsby’s experience with hearing loss helped her to develop a robotic tadpole for deciphering the secret lives of amphibians.

Scientific Reports, Published online: 25 May 2026; doi:10.1038/s41598-026-54526-9 Benchmarking the prediction of responding cells to perturbations affecting both gene expression and cellular abundance using scRNA sequencing

resLens uses genomic language models to detect antibiotic resistance genes from DNA sequences, performing especially well on long-read data and on some ARGs poorly represented in reference databases.

Osteoarthritis (OA) remains a highly prevalent degenerative joint disorder for which truly disease-modifying therapies are still lacking. Accumulating evidence positions mitochondrial dysfunction and impaired mitochondrial quality control as central drivers of chondrocyte failure, extracellular matrix breakdown, and inflammation amplification. Mitophagy—particularly the phosphatase and tensin hom…

The HugZ/HutZ family has been shown to degrade heme in the presence of ascorbic acid. However, its inability to utilize canonical cytochrome P450 reductase has raised questions regarding its physiological role as a true heme oxygenase. PM0042 from Pasteurella multocida, a member of the HugZ/HutZ family, belongs to the pyridoxamine 5'-phosphate oxidase (PNPOx) family, which utilizes FMN as a cofac…

In this letter, we comment on the study by Jiang et al published in the recent issue of the World Journal of Stem Cells , which explores a combined therapeutic approach of exercise with induced pluripotent stem cells (iPSCs) for Parkinson’s disease (PD) using a mouse model. Currently, PD is primarily treated symptomatically as there are no treatment options available to prevent or cure it. While …

Knee osteoarthritis is recognised as a whole-joint disorder involving cartilage, synovium, subchondral bone and nociceptive pathways. Conventional therapies provide symptomatic relief but rarely alter structural progression. Mesenchymal stromal cell (MSC) injections improve pain and function, yet structural benefits remain modest and variable. Increasing evidence indicates that much of the MSC ef…

Abstract Human papillomavirus (HPV)-negative head and neck squamous cell carcinoma (HNSCC) is associated with a poorer prognosis compared to its HPV-positive counterpart; however, the underlying regulatory molecular mechanisms driving its progression remain poorly understood. In this study, we identify BTB Domain and CNC Homolog 1 (BACH1) as a critical oncogenic regulator that is upregulated in H…

BACKGROUND Stem cell-derived exosomes represent a promising cell-free strategy for bone regeneration, yet the mechanisms underlying their osteogenic effects remain incompletely defined. Hypoxic preconditioning has been reported to enhance exosome bioactivity, but its potential interaction with mechanosensitive signaling pathways during osteogenesis is poorly understood. AIM To evaluate the osteog…

Heart failure (HF) is a complex syndrome driven by structural remodeling, fibrosis, metabolic imbalance, and oxidative stress. Circular RNAs (circRNAs) have emerged as pivotal regulators in HF, distinguished by their covalently closed structure, stability, and tissue specificity. While they modulate myocardial hypertrophy, fibrosis, and metabolic pathways through mechanisms including microRNA (mi…

Advanced therapy medicinal products (ATMPs), encompassing therapies derived from mesenchymal stem cells, induced pluripotent stem cells, and their extracellular vesicles, hold substantial transformative potential for clinical applications. However, their translation from bench to bedside and eventual commercialization is hindered by considerable scientific, manufacturing, and regulatory challenge…

Abstract Vascular restenosis, a pathological recurrence of lumen narrowing following interventions, remains a major limitation to the long-term success of vascular procedures. Its development is centrally driven by neointimal hyperplasia, a process orchestrated by endothelial injury, phenotypic switching of vascular smooth muscle cells (VSMCs) from a contractile to a synthetic state, and a coordi…

BACKGROUND Accumulating studies suggest that mesenchymal stem cell (MSC)-derived extracellular vesicles mitigate myocardial injury by modulating intercellular communication pathways. Notably, exosomes from hypoxia-preconditioned MSCs (HPC-Exo) demonstrate superior therapeutic efficacy in ischemic heart disease compared with those from normoxic MSCs although the underlying molecular mechanisms rem…