Quantitative Biology
This piece serves two purposes. Firstly, it aims at elucidating the role of epistasis in shaping, at a molecular level, the evolutionary paths of proteins, as well as the extent to which these epistatic effects are the outcome of an…
Objective: Although computational phenotyping is a central informatics activity with resulting cohorts supporting a wide variety of applications, it is time-intensive because of manual data review. We previously assessed the ability of LLMs…
Lipid-protein interactions play essential roles in cellular signaling and membrane dynamics, yet their systematic characterization has long been hindered by the inherent biochemical properties of lipids. Recent advances in functionalized…
The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…
CARTEpigenoQC is an R-based toolkit designed to streamline quality control (QC) for single-cell epigenomic datasets involving Chimeric Antigen Receptor (CAR)-engineered T cells. With the growing application of scATAC-seq, scCUT&Tag, and…
Chronic infection with hepatitis B virus (HBV) can lead to formation of abnormal nodular structures within the liver. To address how changes in liver anatomy affect overall virus-host dynamics, we developed within-host ordinary differential…
Power-law scaling in coarse-grained data suggests critical dynamics, but the true source of this scaling often remains unclear. Here, we analyze neural activity recorded during spatial navigation, reproducing power-law scaling under a…
Achieving complete reproducibility in science, particularly in research fields such as biodiversity, is challenging due to analytical choices, bias and interpretation. Here, we examine examples of reproducibility in biological systematics,…
Biological systems commonly exhibit complex spatiotemporal patterns whose underlying generative mechanisms pose a significant analytical challenge. Traditional approaches to spatiodynamic inference rely on dimensionality reduction through…
We introduce a probabilistic model of early visual processing, beginning with the interaction between a light wavefront and the retina. We argue that perception originates not with deterministic transduction, but with probabilistic…
Spatial transcriptomics (ST) technologies not only offer an unprecedented opportunity to interrogate intact biological samples in a spatially informed manner, but also set the stage for integration with other imaging-based modalities.…
Data in biology is redundant, noisy, and sparse. How does the type and scale of available data impact model performance? In this work, we specifically investigate how protein language models (pLMs) scale with increasing pretraining data. We…
Computational pathology (CPath) has shown great potential in mining actionable insights from Whole Slide Images (WSIs). Deep Learning (DL) has been at the center of modern CPath, and while it delivers unprecedented performance, it is also…
Background: Symptom rating scales in psychiatry are limited by reliance on self-report, and lack of predictive power. Actigraphy, a passive wearable-based method for measuring sleep and physical activity, offers objective, high-resolution…
This work presents BioPykrete, a new sustainable bio-composite material created from ice, nano-crystalline cellulose (CNC), and a tailor-made chimera protein designed to bind the two together. We developed and produced the chimera protein…
Human memory exhibits significant vulnerability in cognitive tasks and daily life. Comparisons between visual working memory and new perceptual input (e.g., during cognitive tasks) can lead to unintended memory distortions. Previous studies…
Measures of tree balance play an important role in many different research areas such as mathematical phylogenetics or theoretical computer science. Typically, tree balance is quantified by a single number which is assigned to the tree by a…
A new age-structured diffusive model for the mathematical modelling of epidemics is suggested. The model can be considered as a generalization of two models suggested earlier for the same purposes. The Lie symmetry classification of the…
Multi-scale systems often exhibit a combination of stochastic and deterministic dynamics. In compartmental models, low occupancy compartments tend to exhibit stochastic dynamics while high occupancy compartments tend to follow deterministic…
This study investigates how the human brain differentiates between intentional human agents and artificial intelligence (AI) agents during real-time social interaction. Using functional near-infrared spectroscopy (fNIRS) hyperscanning, we…