Quantitative Biology
FcsIT is a platform-independent, open-source tool for calculating the correlation and fitting fluorescence correlation spectroscopy data. The software is written in Python and uses a powerful Dear PyGUI engine for its interface. It provides…
Reservoirs, typically implemented as recurrent neural networks with fixed random connection weights, can be combined with a simple trained readout layer to perform a wide range of computational tasks. However, increasing the magnitude of…
Flux sampling is an analysis that, based on a distribution, picks randomly an efficient number of points from the solution space of a metabolic model. Unlike most constraint-based analyses, flux sampling does not require an objective…
The spread of infectious disease and the evolution of antigenically distinct strains are often modeled separately, despite strong feedbacks mediated by host immune memory and heterogeneous contacts. To tackle this challenging problem, we…
Parkinson's disease (PD) affects over ten million people worldwide. Although temporal interference (TI) and deep brain stimulation (DBS) are promising therapies, inter-individual variability limits empirical treatment selection, increasing…
Anthropogenic activity threatens biodiversity through climate change, habitat fragmentation, and increasing frequency and scale of disturbance. Various theoretical studies have sought to shed light on how these factors could promote or…
Evolutionary graph theory (EGT) studies the effect of population structure on evolutionary dynamics. The vertices of the graph represent the $N$ individuals. The edges denote interactions for competitive replacement. Two standard update…
1. Climate change is altering plant phenology globally with potential deleterious impacts on animal species and entire ecosystems, yet the long-term effects of climate change on tropical leaf production remain poorly understood. 2. We…
Arabidopsis root hair patterning is controlled by a complex transcription factor network containing positive and negative feedback loops, epidermal cell-cell signalling, and positional signalling from underlying tissue. Recently, several…
We consider a population constituted by two types of individuals; each of them can produce offspring in two different islands (as a particular case the islands can be interpreted as active or dormant individuals). We model the evolution of…
The dynamics of simple two-alternative forced-choice (2AFC) decisions are well-modeled by a class of random walk models (e.g. Laming, 1968; Ratcliff, 1978; Usher & McClelland, 2001; Bogacz et al., 2006). However, in real-life, even simple…
This report presents three proofs showing that idealized architectures capable of navigation guided by allocentric maps with landmark structure can be computationally universal. The navigation may occur either online (in the environment) or…
Cardiovascular-Kidney-Metabolic (CKM) syndrome represents a growing public health crisis, yet the subclinical heterogeneity of its component systems remains underexplored. Early detection of physiological deviation is critical for…
Understanding how the human brain instantiates distinct emotional states is a key challenge in affective neuroscience. While network-based approaches have advanced emotion processing research,they remain largely descriptive,leaving the…
Quantitatively mapping three-dimensional (3D) flow, diffusion, and particle density in crowded living cells remains challenging because most dynamic optical microscopy measurements are effectively planar and existing analysis methods…
Genomic foundation models trained on DNA sequences have demonstrated remarkable capabilities across diverse biological tasks, from variant effect prediction to genome design. These models are typically trained on massive, publicly sourced…
People infer rich social information from others' actions. These inferences are often constrained by the physical world: what agents can do, what obstacles permit, and how the physical actions of agents causally change an environment and…
Quantitative estimation of information flow in early vision with psychophysically realistic networks is still an open issue. This is because, up to date, the necessary elements (general and plausible network, accurate noise, and reliable…
Although many phenotypic traits are determined by a large number of genetic variants, the behavior of allele frequencies in a polygenic trait is not completely understood. The problem is especially challenging when the quantitative trait of…
As immunotherapies become standard cancer treatments, it is increasingly important to identify a patient's immune profile, which encompasses the activity of immune cells within the tumor microenvironment and the presence of specific…