Quantitative Biology
Athletic training is characterized by physiological systems responding to repeated exercise-induced stress, resulting in gradual alterations in the functional properties of these systems. The adaptive response leading to improved…
Organ segmentation in Positron Emission Tomography (PET) plays a vital role in cancer quantification. Low-dose PET (LDPET) provides a safer alternative by reducing radiation exposure. However, the inherent noise and blurred boundaries make…
At the microscopic scale, open chemical reaction networks are described by stochastic reactions that follow mass-action kinetics and are coupled to chemostats. We show that closed chemical reaction networks -- with specific stoichiometries…
Integrated population models (IPMs) are a promising approach to test ecological theories and assess wildlife populations in dynamic and uncertain conditions. By combining multiple data sources into a unified model, they enable the…
We present an asymptotic analysis of a stochastic two-compartmental cell division system with regulatory mechanisms inspired by Getto et al. (2013). The hematopoietic system is modeled as a two-compartment system, where the first…
The science of consciousness has been successful over the last decades. Yet, it seems that some of the key questions remain unanswered. Perhaps, as a science of consciousness, we cannot move forward using the same theoretical commitments…
Virtual brain twins are personalized digital models of individual human subject or patient's brains, allowing for mechanistic interpretation of neuroimaging data features. Training and inference with these models however presents a pair of…
Molecular docking plays a crucial role in predicting the binding mode of ligands to target proteins, and covalent interactions, which involve the formation of a covalent bond between the ligand and the target, are particularly valuable due…
The human niche represents the intersection of biological, ecological, cultural, and technological processes that have co-evolved to shape human adaptation and societal complexity. This paper explores the human niche through the lens of…
The objective of this paper is to investigate the structural stability, dynamic properties, and potential interactions among Amyloid Precursor Protein (APP), Tau, and Alpha-synuclein through a series of molecular dynamics simulations that…
Background. Chronic pain afflicts 20 % of the global population. A strictly biomedical mind-set leaves many sufferers chasing somatic cures and has fuelled the opioid crisis. The biopsychosocial model recognises pain subjective,…
The accurate development, assessment, interpretation, and benchmarking of bioinformatics frameworks for analyzing transcriptional regulatory grammars rely on controlled simulations to validate the underlying methods. However, existing…
The advent of single-cell multi-omics technologies has enabled the simultaneous profiling of diverse omics layers within individual cells. Integrating such multimodal data provides unprecedented insights into cellular identity, regulatory…
Biological systems are non-linear, include unobserved variables and the physical principles that govern their dynamics are partly unknown. This makes the characterization of their behavior very challenging. Notably, their activity occurs on…
Protein structure prediction models such as AlphaFold3 (AF3) push the frontier of biomolecular modeling by incorporating science-informed architectural changes to the transformer architecture. However, these advances come at a steep system…
We develop and apply a learning framework for parameter estimation in initial value problems that are assessed only indirectly via aggregate data such as sample means and/or standard deviations. Our comprehensive framework follows Bayesian…
The evolution of cognition is frequently discussed as the evolution of cognitive abilities or the evolution of some neuronal structures in the brain. However, since such traits or abilities are often highly complex, understanding their…
Mathematical modeling has played a central role in understanding how infectious disease transmission manifests in populations. These models have demonstrated the importance of key community-level factors in structuring epidemic risk, and…
We derive the main properties of adaptive Hagen-Poiseuille flows in elastic microchannel networks similar to biological veins found in organisms. We demonstrate that adaptive Hagen-Poiseuille flows effectively simulate key features of…
Human languages differ widely in their forms, each having distinct sounds, scripts, and syntax. Yet, they can all convey similar meaning. Do different languages converge on a shared neural substrate for conceptual meaning? We used language…