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The paper presents a model showing that gut microbiome differences can arise from varied behavioral pathways, challenging the assumption that microbiome states uniquely reflect biological differences.

The paper shows that genetic interactions in yeast change with protein availability and nutrient uptake, revealing new insights into how metabolic constraints affect epistasis.

DiffDose uses automatic differentiation to optimize drug dosing regimens by turning mechanistic PK/PD and QSP models into gradient-based tools for personalized treatment design.

This paper explores how activator-inhibitor cellular automata can function as reservoirs for computation by tuning nonlinear dynamics to enable memory and separability.

The paper describes a panel of genetically diverse embryonic stem cells from Diversity Outbred mice to study natural genetic variation's impact on pluripotency and differentiation.

The paper identifies a senescence-like transitional state in aging human monocytes driven by AP-1, leading to inflammatory monocyte expansion and systemic inflammation.

The paper analyzes single-cell data from human tissues to show that aging involves both cell loss and architectural remodeling, with structural decline independent of cell composition.

The paper refines a genome-wide poxvirus-host interaction screen using a protein language model to improve hit prioritisation and provides the results as a community resource.

LiverDCP models disease biology by integrating single-cell data and protein interactions to identify disease-risk genes and therapeutic targets.

This paper develops a multiscale model of IAV and OP7 coinfection, revealing MOI-dependent antiviral mechanisms and predicting therapeutic efficacy.

This study investigates how Eimeria and Clostridium perfringens contribute to intestinal dysbiosis in necrotic enteritis, showing Eimeria drives dysbiosis and facilitates C. perfringens colonization.

The paper introduces PCLT to map sex-specific physiological changes across the lifespan using NHANES data, identifying five phases and linking them to health outcomes.

The paper benchmarks nDIA and related proteomics methods, showing nDIA with DIA-NN and Tesorai Search provides high coverage and reliable results in proteomic analysis.

This study shows that H6PD deficiency in mice leads to increased hepatic triglycerides and lipid accumulation, linking NADPH availability to fatty acid homeostasis.

This study identifies reversible and persistent molecular changes in diet-induced obesity using multi-omic analysis, showing that microbial functional profiles drive persistent alterations.

The paper shows that single-cell gene expression responses in mammalian systems are all-or-none due to stable epigenetic variability, not bursty transcription or bistability.

This paper develops a network framework to prioritize drug candidates for rare diseases by integrating Orphadata and DisGeNET through gene-bridge harmonization and using a Graph Attention Network for node representation learning.

The paper identifies a signaling network motif where dimerization-linked nucleocytoplasmic shuttling couples protein expression levels with intracellular localization, modulating signaling cascade activity.

This paper introduces a computational framework to calculate net conversions in metabolic networks using elementary flux modes and thermodynamic parameters, with applications in microbial ecology and metabolic engineering.

The paper uses simulations to show that passive prostheses increase walking effort for both propulsion and stabilization, while active prostheses reduce effort but require full sensory feedback to fully restore metabolic cost.