Quantitative Biology
Background. Preeclampsia (PE) complicates 2-8% of pregnancies and involves placental hypoxia and HIF-pathway activation, especially in early-onset PE (eoPE). Chemical mimetics like cobalt (II) chloride (CoCl2) and oxyquinoline derivatives…
A grand challenge in modern neuroscience is to bridge the gap between the detailed mapping of microscale neural circuits and mechanistic understanding of cognitive functions. While extensive knowledge exists about neuronal connectivity and…
Intrinsically disordered regions (IDRs) play central roles in cellular function, yet remain poorly evaluated by existing protein structure prediction benchmarks. Current evaluations largely focus on well-folded domains, overlooking three…
Predicting future neural activity is a core challenge in modeling brain dynamics, with applications ranging from scientific investigation to closed-loop neurotechnology. While recent models of population activity emphasize interpretability…
As large language models (LLMs) continue to revolutionize AI research, there is a growing interest in building large-scale brain foundation models to advance neuroscience. While most existing brain foundation models are pre-trained on…
We propose a predator-prey model with an age-structured predator population that exhibits a functional role reversal. The structure of the predator population in our model embodies the ecological concept of an "ontogenetic niche shift," in…
Diffusion models have achieved promising results for Structure-Based Drug Design (SBDD). Nevertheless, high-quality protein subpocket and ligand data are relatively scarce, which hinders the models' generation capabilities. Recently, Direct…
This article presents an artificial intelligence (AI) architecture intended to simulate the iterative updating of the human working memory system. It features several interconnected neural networks designed to emulate the specialized…
Redox biology underpins signalling, metabolism, immunity, and adaptation, yet lacks a unifying theoretical framework capable of formalising structure, function, and dynamics. Current interpretations rely on descriptive catalogues of…
Redox proteomics generates bounded biochemical measurements that are categorically mismatched to conventional linear algebraic formalisms. This work introduces Oxi-Shapes, a tropical geometric framework for the measurement-native analysis…
The crawling motility of many eukaryotic cells is driven by filamentous actin (F-actin), and regulated by a network of signaling proteins and lipids (including small GTPases). The tangle of positive and negative feedback loops gives rise to…
Human activity has an enormous impact on Earth, changing organisms, environments and landscapes, leading to the decline of original ecosystems and irreversible changes that create new combinations of living beings and materials. As a…
Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous…
The Great Filter hypothesis is an extension of the Fermi Paradox: "If life is so common in the universe, why don't we see it?" The Great Filter theory posits there are multiple obstacles or filters life must pass through which ultimately…
Traditional epidemiological models often fail to characterize the extreme volatility and heavy-tailed "Dragon King" events observed in real-world outbreaks. We propose a unified framework that bridges microscopic agent-based simulations…
In this work, we develop a stochastic multiscale model for glioma growth and invasion in the brain, incorporating the effects of therapeutic interventions. The model accounts for tumor cell migration influenced by brain tissue heterogeneity…
Liquid chromatography tandem mass spectrometry (LC-MS/MS) is a critical analytical technique for molecular identification across metabolomics, environmental chemistry, and chemical forensics. A variety of computational methods have emerged…
Background and Objectives: Proximal catheter obstruction is the leading cause of ventriculoperitoneal shunt failure, yet the biological triggers of peri-catheter inflammation and tissue ingrowth remain poorly defined. Evidence of bacterial…
Recent work has shown that scaling large language models (LLMs) improves their alignment with human brain activity, yet it remains unclear what drives these gains and which representational properties are responsible. Although larger models…
How large language models (LLMs) align with the neural representation and computation of human language is a central question in cognitive science. Using representational geometry as a mechanistic lens, we addressed this by tracking…