Quantitative Biology
Understanding the dynamic behavior of biomolecules is fundamental to elucidating biological function and facilitating drug discovery. While Molecular Dynamics (MD) simulations provide a rigorous physical basis for studying these dynamics,…
Glycans are structurally diverse and flexible biomolecules that play key roles in many biological processes. Their conformational variability makes the modeling of their interactions with proteins particularly challenging. This chapter…
Scalable manufacturing of human induced pluripotent stem cells (iPSCs) is essential for industrial-scale production of cell therapies and regenerative medicines. However, the 3D aggregate cultures used in manufacturing exhibit substantial…
In this paper we expand the concept of biological speciation by symmetry breaking of Golubitsky and Stewart to the case of three clades in which N populations following the same dynamical laws can separate. The underlying differential…
Many diatoms follow a size diminuation - size restoration cycle in their vegetative phase, leading to daughter cells that differ in size. For the diatom Seminavis robusta, we investigated by cell tracking over several generations whether…
Routine oncologic computed tomography (CT) presents an ideal opportunity for screening spinal instability, yet prophylactic stabilization windows are frequently missed due to the complex geometric reasoning required by the Spinal…
Raman spectroscopy is a promising tool for microbial identification, yet its implementation in microbiology and clinical workflow is still restricted due to the accompanying additional preparation required to focus on microbial signals.…
This study presents a mathematical model that captures the interactions among tumor cells, healthy cells, and immune cells in a tumor-bearing host, with a specific focus on breast cancer. Incorporating the concept of delay, the model…
The unprecedented extension of the human lifespan necessitates a parallel evolution in how we quantify the quality of aging and its socioeconomic impact. Traditional metrics focusing on Healthspan (years free of disease) overlook the…
Understanding infectious disease transmission in institutional settings requires models that capture how contacts arise from structured routines, roles, and spatial constraints. In aged care facilities, interactions are driven by care…
Protein fitness landscapes frequently exhibit epistasis, where the effect of a mutation depends on the genetic context in which it occurs, i.e., the rest of the protein sequence. Epistasis increases landscape complexity, often resulting in…
In the context of clinical research, computational models have received increasing attention over the past decades. In this systematic review, we aimed to provide an overview of the role of so-called in silico clinical trials (ISCTs) in…
Comparing information structures in between deep neural networks (DNNs) and the human brain has become a key method for exploring their similarities and differences. Recent research has shown better alignment of vision-language DNN models,…
We investigate a large ensemble of Quadratic Integrate-and-Fire (QIF) neurons with heterogeneous input currents and adaptation variables. Our analysis reveals that for a specific class of adaptation, termed quadratic spike-frequency…
Animals flexibly change their behavior depending on context. It is reported that the hippocampus is one of the most prominent regions for contextual behaviors, and its sequential activity shows context dependency. However, how such…
OBJECTIVE: To propose a new approach to analyze the age-distribution of reported cases for vector-transmitted infections. METHODS: Using officially reported number of cases of dengue, Zika, chikungunya, malaria and leishmaniasis for…
Force fields for molecular dynamics are usually developed manually, limiting their transferability and making systematic exploration of functional forms challenging. We developed a graph neural network that assigns all force field…
We present HistoAtlas, a pan-cancer computational atlas that extracts 38 interpretable histomic features from 6,745 diagnostic H&E slides across 21 TCGA cancer types and systematically links every feature to survival, gene expression,…
Kangaroo mother care (KMC) is an intervention involving skin-to-skin contact that promotes physiological stability and supports long-term neurodevelopment in preterm infants. However, the underlying neurophysiological mechanisms remain…
Pain is strongly influenced by expectations and learning from previous experience, such as in classical conditioning. Conditioned responses and expectations can generalize to perceptually and conceptually related cues, but how…