Bioinformatics Papers of the Week

We sequenced and characterized influenza viruses circulating in Southern Greece (S. Greece) during two consecutive influenza seasons, 2024–2025 and 2025–2026, using Oxford Nanopore Technologies (ONT) sequencing.

By resolving how domain accretion co-evolves with catalytic scaffolds, this work provides a framework for understanding how multi-domain enzymes adapt to complex environments.

In this study, we established high glucose-induced cell models and diabetic rat models to investigate the role and molecular mechanisms of ADSC-exos in mitigating OS in DBD.

We identified a malignant subcluster enriched in non-responsive patients and determined SLC2A1 as the unique overlapping candidate linked to therapeutic failure.

Methods We integrated transcriptomic data from three IDD cohorts (GSE167199, GSE176205, GSE186542) and performed differential expression analysis, WGCNA, consensus clustering, and CIBERSORT to identify oxidative stress-related genes, define molecular subtypes, and evaluate immune infiltration.

Toxicological analysis, target prediction, functional enrichment, Protein-protein interaction (PPI) network, and three machine learning algorithms were applied to prioritize signature genes.

A subcutaneous xenograft model was established in nude mice, and the NRF2 activator TBHQ was used to verify the in vivo role and mechanism of AFF3 in regulating ferroptosis.

Here we ask whether an entire amino acid can be eliminated from a proteome, and develop a computational framework to identify the best target.

All findings in this study are derived from computational virtual screening and molecular docking simulations and require further experimental validation.

Here, we present irAEGIS, a pathway-guided interpretable model for predicting irAE risk from pre-treatment scRNA-seq data.

This study used tandem mass tag (TMT) combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify DEPs in vitreous samples from PDR patients and MH/EMM control patients.

We introduce Pycea, a Python toolkit for lineage analysis and visualization, and TreeData, an extension of AnnData that stores lineage trees alongside cellular measurements.

In this paper, we review the structure of the tropical Grassmannian and present algorithmic methods for its computational study, including procedures for sampling from the tropical Grassmannian. Our aim is to provide a computational perspective on these ideas for readers interested in phylogenetic tree space, and to motivate new research at the interface of tropical geometry and phylogenetic inference.

Because hub labeling and associated methods are defined for directed graphs, we introduce a directed representation of a snarl's bidirected internal "net graph", whose shortest path lengths are the net graph's minimum walk lengths.

Here we present FeatureMAP, an LC-MS feature-centric computational framework that integrates multi-evidence metabolite annotation, network-guided refinement, metabolic module discovery, and structured large language model-based functional interpretation.