Quantitative Biology
Diversity-Generating Retroelements (DGRs) create rapid, targeted variation within specific genomic regions in phages and bacteria. They operate through stochastic retro-transcription of a template region (TR) into a variable region (VR),…
Natural birth and death are fundamental mechanisms of population dynamics in ecosystems and have played pivotal roles in shaping population dynamics. Nevertheless, in studies of cyclic competition systems governed by the rock-paper-scissors…
The loss of biodiversity due to the likely widespread extinction of species in the near future is a focus of current concern in conservation biology. One approach to measure the impact of this extinction is based on the predicted loss of…
Understanding the dynamic nature of brain connectivity is critical for elucidating neural processing, behavior, and brain disorders. Traditional approaches such as sliding-window correlation (SWC) characterize time-varying undirected…
Complex change is often described as "evolutionary" in economics, policy, and technology, yet most system dynamics models remain constrained to fixed state spaces and equilibrium-seeking behavior. This paper argues that evolutionary…
Following limb amputation and targeted muscle reinnervation (TMR), nerves that originally innervated agonist and antagonist muscles are rerouted into one or more residual target muscles. This rerouting profoundly alters the natural…
Neuronal systems often preserve their characteristic functions and signalling patterns, also referred to as regimes, despite parametric uncertainties and variations. For neural models having uncertain parameters with a known probability…
Background: Cognitive impairment in multiple sclerosis (MS) is driven by both focal inflammation and compartmentalized neurodegeneration, yet the relative effect of lesion-independent thalamic atrophy on information processing speed (IPS)…
A central challenge in cognitive neuroscience is to explain how semantic and episodic memory, two major forms of declarative memory, typically associated with cortical and hippocampal processing, interact to support learning, recall, and…
Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-art methods exploit probabilistic models of sequence evolution…
Aquaporins (AQPs) and aquaglyceroporins (AQGPs) play a crucial role in regulating water transport and solute selectivity across biological membranes. Besides their biological relevance, AQPs have at-tracted growing interest as models for…
Synaptic transmission must balance the need for reliable signalling against the metabolic cost of achieving that reliability. How energetic constraints shape synaptic precision and its regulation during plasticity remains unclear. Here we…
Connecting the dynamics of biomolecular networks to experimentally measurable cell phenotypes remains a central challenge in systems biology. Here we introduce a model-based definition of phenotype as a partial steady state that is…
Household size impacts the spread of respiratory infectious diseases: Larger households tend to boost transmission by acquiring external infections more frequently and subsequently transmitting them back into the community. Furthermore,…
We investigate the spatial organization of dengue cases in the city of Recife, Brazil, from 2015 to 2024, using tools from statistical physics and topological data analysis. Reported cases are modeled as point clouds in a metric space, and…
Evaluating large language models (LLMs) on their ability to generate high-quality, accurate, situationally aware answers to clinical questions requires going beyond conventional benchmarks to assess how these systems behave in complex,…
A central challenge in modeling neurodegenerative diseases is connecting cellular-level mechanisms to tissue-level pathology, in particular to determine whether pathology is driven primarily by cell-autonomous triggers or by propagation…
The scarcity of high-quality multimodal biomedical data limits the ability to effectively fine-tune pretrained Large Language Models (LLMs) for specialized biomedical tasks. To address this challenge, we introduce MINT (Multimodal…
In both neuroscience and artificial intelligence, popular functional frameworks and neural network formulations operate by making use of extrinsic error measurements and global learning algorithms. Through a set of conjectures based on…
Social entities only exist in virtue of collective acceptance or recognition, or acknowledgement by two or more individuals in the context of joint activities. Joint activities are made possible by the coordination of plans for action, and…