Discover, rate, and discuss biology preprints.

The paper models the eukaryotic cell cycle as a tetra-stable excitable system using ODEs, phase plane analysis, and bifurcation theory, showing that two existing frameworks represent the same underlying architecture.

This paper develops a multi-phenotype model of E. coli's iron and oxidative stress response, achieving 93% accuracy and outperforming single-phenotype models.

PTMOverlay visualizes post-translational modifications across species by aligning PTM sites to protein sequences, revealing conserved modifications in bacterial central carbon metabolism.

The paper shows that opposing range-dependent interactions between microbial exoproducts create complex spatial patterns of antibiotic tolerance in biofilms.

The paper introduces a coherence matrix to analyze directional regulatory coordination in gene regulatory networks, showing how hierarchical structures mitigate scaling penalties in sparse networks.

The paper evaluates transcriptomic integration methods for cyanobacterial metabolic models, finding that method selection depends on model configuration and that certain approaches improve flux predictions.

This study develops a computational model of blood pressure regulation and calcium-magnesium homeostasis in rats, showing how disruptions in these systems affect each other and contribute to hypertension and hyperparathyroidism.

The paper identifies prey-specific toxins in cephalopod venom, including neurotensin-mimicking peptides that target fish, revealing an evolutionary strategy for broad venom activity.

The paper develops selective glucocorticoid receptor modulators (SGRMs) that modulate immune checkpoint function by altering GR activity states through structural design and machine learning.

This study identifies sudden transitions in Notch signaling using early warning signals and analyzes how system parameters influence these transitions in one- and two-cell models.

The paper maps cytokine interaction networks in ulcerative colitis to uncover novel pathogenic mechanisms and therapeutic targets.

This paper introduces NIS, a method to simplify genome-scale metabolic models for comparing metabolic capabilities across organisms, revealing conserved and divergent patterns in metabolism.

The paper uses Molecular Pixelation to analyze surface proteomic signatures of CAR T cells under acute and chronic stimulation, identifying spatial patterns linked to exhaustion.

The paper develops a functional metabolomics framework using synthetic microbial communities and computational analysis to track drug metabolism by gut microbes, identifying metabolites and their correlations with microbial taxa.

This study evaluates the effects of Tamarindus indica pulp extract on hemolytic anemia induced by phenylhydrazine in rats, showing improved hematopoiesis and reduced anemia markers.

The paper proposes a four-process model of ageing that connects DNA damage, metabolic slowdown, and cellular selection to explain age-related diseases and the evolutionary basis of ageing.

The paper develops an age and generation-based model of metastatic cancer that reformulates tumor growth and spread using age and generational ancestry, improving numerical stability and interpretability over traditional size-based models.

Tensor-cell2cell v2 jointly analyzes protein- and metabolite-mediated cell-cell communication over time, revealing coordinated dynamics in brain organoid development.

The paper demonstrates that capillary zone electrophoresis-mass spectrometry (CZE-MS) can reproducibly measure peptides, proteoforms, and complexoforms across multiple biological samples.

This paper introduces eLSHADE+, a metaheuristic for robust model calibration in systems biology, showing improved convergence and accuracy over existing methods.