Quantitative Biology
To maintain coherence in language, the brain must satisfy key competing temporal demands: the gradual accumulation of meaning across extended context (drift) and the rapid reconfiguration of representations at event boundaries (shift). How…
Ecological interactions can dramatically alter evolutionary outcomes in complex communities. Yet, the framework of population genetics largely neglects interactions from a species-rich community. Here, we bridge this gap by using dynamical…
Simulating glucose dynamics in individuals with type 1 diabetes (T1D) is critical for developing personalized treatments and supporting data-driven clinical decisions. Existing models often miss key physiological aspects and are difficult…
We propose a hierarchically modular, dynamical neural network model whose architecture minimizes a specifically designed energy function and defines its temporal characteristics. The model has an internal and an external space that are…
Cancer cell populations often exhibit remarkably similar growth laws despite their heterogeneity. Explanations of universal cell population growth remain partly unresolved to this day. Here, we present a growth-law unification by…
Nitrous oxide (N2O) is a potent greenhouse gas emitted during biological wastewater treatment. A pseudo-mechanistic model describing three biological pathways for nitric oxide (NO) and N2O production was calibrated for mixed culture biomass…
We investigate the role of migration patterns on the spread of epidemics in complex networks. We enhance the SIS-diffusion model on metapopulations to a nonlinear diffusion. Specifically, individuals move randomly over the network but at a…
In studying primate vision, a large body of work focuses on the first feedforward sweep. During this initial time window, information is thought to pass through ventral stream regions in a stage-like fashion in an effort to extract…
Cooperation is central to the organization of complex biological and social systems. Most theoretical models assume homogeneous environments; in reality, populations inhabit spatially varying landscapes in which the payoffs of cooperation…
Command-line bioinformatics tools remain essential for genomic analysis, yet their diversity in syntax and parameterization presents a persistent barrier to productive research. We present oxo-call, a Rust-based command-line assistant that…
Multi-site autism neuroimaging studies routinely control for the confound between full-scale IQ and head motion by regressing framewise displacement against IQ scores and removing shared variance. This procedure assumes that ordinary least…
In this study, we investigate the application of Semidefinite Programming (SDP) to phylogenetics. SDP is a powerful optimization framework that seeks to optimize a linear objective function over the cone of positive semidefinite matrices.…
Fixation probabilities are essential for characterizing stochastic evolutionary dynamics, but analytical results remain limited mainly to systems with two competing types. We develop a perturbative framework to compute fixation…
Understanding epidemic dynamics in urban environments requires models that capture interactions across space and time while incorporating biological constraints. In this work, we propose a probabilistic spatiotemporal framework based on…
Background: Single-cell RNA sequencing (scRNA-seq) enables gene expression profiling at cellular resolution but is inherently affected by sparsity caused by dropout events, where expressed genes are recorded as zeros due to technical…
When mutations are rampant, quasispecies theory or Eigen's model predicts that the fittest type in a population may not dominate. Beyond a critical mutation rate, the population may even be delocalized completely from the peak of the…
Understanding how gene regulatory networks (GRNs) give rise to stable and dynamic cellular states remains a central challenge in theoretical biology, particularly when slow epigenetic feedback reshapes the underlying regulatory landscape.…
The ancestral recombination graph (ARG) is the model of choice in statistical genetics to model population ancestries. Software capable of simulating ARGs on a genome scale within a reasonable amount of time are now widely available for…
This paper describes GeoPl@ntNet, an interactive web application designed to make Essential Biodiversity Variables accessible and understandable to everyone through dynamic maps and fact sheets. Its core purpose is to allow users to explore…
Despite the diversity and volume of brain data acquired and advanced AI-based algorithms to analyze them, brain features are rarely used in clinics for diagnosis and prognosis. Here we argue that the field continues to rely on cohort…