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This study quantifies how dose-response relationships in signaling systems affect information transmission under various noise distributions and identifies design principles for improved signaling fidelity.

The paper evaluates metabolic representations in synthetic systems, finding that adequacy, compactness, and responsiveness are distinct properties, and adequacy certification does not guarantee predictive accuracy.

The paper presents the first curated genome-scale metabolic model for L. rhamnosus GG, validated using multiple approaches and provides insights into its nutrient requirements and secretions.

This paper develops a framework combining a protein language model and a screening assay to predict kinase-substrate interactions and map the human kinome.

The paper models oxidative stress response in E. coli using a genome-scale metabolic model to show that bimodal killing under H2O2 stress emerges from network topology and stochastic sampling.

The paper uses a deep learning framework to analyze drug-induced transcriptomics and identifies a four-node module involved in TGFβ-IFNα competition in MASH.

The paper identifies synergistic drug pairs in branched metabolic networks by analyzing topological complementarity in the E. coli folate pathway.

The paper introduces taxon-in-context to capture individualized microbial context in the human gut microbiome, showing that microbes occupy different contexts across individuals and over time, improving recurrence prediction.

The paper uses network analysis, MD simulations, and experiments to identify critical residues in human PrP that affect structural stability and misfolding.

This study identifies CAMKK2 as a key driver of kinase signaling in gastric cancer through phosphoproteomic analysis, showing its role in promoting proliferation and malignant traits.

This paper uses serum protein profiling to identify aging trajectories and strain-specific resilience in mice, revealing pathway-level changes and heterogeneity between strains.

FluxSprout identifies metabolic dependencies in zebrafish sprouting angiogenesis by integrating single-cell RNA sequencing with genome-scale metabolic modeling, revealing biosynthetic capacity as a key feature of sprouting vessels.

This paper develops a mathematical model showing that induced muscle wasting (IMW) supports wound healing and that inhibiting IMW can prevent cachexia and restore muscle mass with nutritional support.

This study uses yeast large-scale absolute quantitative proteomics to reveal universal principles of protein resource allocation among cellular organelles and its relationship to physiological parameters and species divergence.

The paper develops scalable cell-free protein synthesis platforms to generate single-cell RNA-sequencing data on immune cell responses to cytokines and other signals, enabling functional discovery and drug target prioritization.

This study identifies a lymphatic vascular network and immune surveillance system in the cochlea following implantation, contributing to inflammatory responses.

The paper compares the SIR model and DyMES framework to study how downward causation affects disease transmission dynamics.

This study identifies that plasma proteins selectively reflect tissue-specific aging processes in muscle and ovary, revealing context-dependent age-related changes.

Signal Associa identifies coupling regimes in NK cell dynamics across tumor microenvironments, showing hot tumors elicit more integrated NK cell networks.