139 papers
By integrating multi-omic data from the dorsolateral prefrontal cortex, this study reconstructs a metabolic regulatory network in Alzheimer's disease that reveals a coordinated downregulation of energy-producing pathways driven by reduced enzyme abundance and inhibitory allosteric effects, alongside conflicting regulatory influences on glycolysis.
TwinCell is a large causal cell model that leverages in vitro perturbation data and a multiomics interactome to identify and interpret upstream therapeutic targets driving disease-to-healthy state transitions, outperforming existing methods in both zero-shot and clinical validation scenarios.
This study from the MoTrPAC consortium reveals that acute endurance and resistance exercises trigger distinct, temporally ordered multi-omic responses in human skeletal muscle, characterized by early epigenetic and signaling changes that precede transcriptomic and proteomic shifts to regulate processes such as autophagy, angiogenesis, and protein turnover.
This study identifies nicotinic acid riboside (NaR) as a liver clock-controlled circulating metabolite that engages the prefoldin complex to modulate unfolded protein response signaling and adipogenesis in a time-dependent manner, thereby linking systemic circadian rhythms to tissue-specific physiological outcomes.
This study introduces dAMN, a hybrid neural-mechanistic model that integrates neural networks with genome-scale dynamic flux balance analysis to accurately predict bacterial growth dynamics and substrate consumption across diverse nutrient environments, including realistic lag phase adaptation and acetate overflow phenomena.
The Molecular Transducers of Physical Activity Consortium (MoTrPAC) study successfully established a framework for investigating the distinct acute and chronic physiological and molecular adaptations to endurance and resistance exercise in healthy sedentary adults, demonstrating high sample collection success and significant improvements in fitness parameters following supervised training.
This paper introduces a neural posterior estimation framework for likelihood-free parameter inference in spatiotemporal stochastic biological models, demonstrating its ability to accurately recover biologically interpretable parameters for cell migration from both summary statistics and raw spatial data without relying on surrogate approximations or explicit noise models.
This study integrates multi-omics and multi-trait analyses to identify and prioritize 39 candidate genes for metabolic dysfunction-associated steatotic liver disease (MASLD), revealing their stage-specific expression patterns and experimentally validating the role of MLIP in lipid metabolism.
This study demonstrates that age-related kidney fibrosis is primarily driven by impaired extracellular matrix degradation, characterized by significantly prolonged protein half-lives, altered protease accessibility, and disrupted matrix interactions that collectively hinder basement membrane renewal and tissue remodeling.
This study systematically compares three transcriptomics-based computational frameworks applied to glioblastoma snRNA-seq data, revealing that tumor-associated macrophages are the metabolically dominant microenvironment population with coordinated lipid metabolism and nutrient support functions, thereby highlighting them as a promising therapeutic target.
This paper addresses the inconsistency among Boolean network control tools by proposing a taxonomy of control problems, developing a framework to empirically compare their solutions, and introducing a coverage-consistent metric to prioritize effective genetic interventions for desired phenotypes.
This study reveals that prior stress history induces a transient tolerant state in resuscitating bacterial cells, which significantly enhances their survival against beta-lactam antibiotics and drives rapid population regrowth, thereby offering a new framework for optimizing antibiotic dosing strategies.
Through numerical simulations and single-cell measurements, this study reveals that coreceptors in TGFβ signaling systems predominantly inhibit downstream signaling and modulate ligand competition, thereby enabling cells to dynamically switch active signaling landscapes via the variable expression of a single gene.
This paper proposes the Generalized Morphogenesis Theory (GMT), a domain-independent flow-inertia modeling framework that unifies cross-scale morphogenetic dynamics—from crop growth to molecular transcriptomics—under a single structural principle, revealing consistent multiplicative dynamics, validated inertia constants, and 12 canonical design patterns governing regime transitions in dissipative systems.
This paper unifies the mathematical frameworks of various single-sample network inference methods to reveal a critical trade-off between accuracy and specificity, demonstrating that while some methods prioritize one metric at the expense of the other, LIONESS offers a balanced approach and highlighting the potential for a common framework to advance the field.
AOPGraphExplorer 2.0 is an interactive, graph-based platform that integrates multi-domain mechanistic annotations from AOP-Wiki and external biomedical resources to enable scalable visualization, dynamic filtering, and systems-level analysis of Adverse Outcome Pathways for enhanced toxicological research and risk assessment.
By employing a robotic pipeline to analyze 90 million single-cell images across thousands of yeast strains, this study constructs an age-resolved proteome atlas that reveals widespread spatial remodeling during aging and identifies biophysical structural determinants that dictate why specific proteins are susceptible to age-related breakdown.
By leveraging a single-cell spatial proteomics atlas of aging yeast, this study reveals that hallmark phenotypes arise from compartment-specific protein disorganization, identifies conserved molecular changes in human aging, and establishes a hierarchical sequence of cellular failures driven by early nucleolar, proteostatic, and mitochondrial dysfunction.
This study demonstrates that while vaping induces acute inflammation and coagulation abnormalities in female rats, high-dose vitamin D supplementation significantly mitigates these adverse effects on blood markers and organ pathology while also reducing nicotine and cotinine levels.
This study demonstrates that increasing recipient age at heart transplantation is associated with a reduced risk of acute allograft rejection, driven by age-related shifts in immune cell composition and transcriptomic profiles characterized by immunosenescence and chronic inflammation, suggesting a need for personalized immunosuppression strategies in older patients.