Quantitative Biology
Working memory - the ability to remember recent events as they recede continuously into the past - requires the ability to represent any stimulus at any time delay. This property requires neurons coding working memory to show mixed…
During cell division, the receptor triple-negative MDA-MB-231 mitotic spindles are the largest in comparison to other BC cell lines. Many of the MDA-MB-231 spindles exhibit rapid lateral twisting during metaphase, which remains unaffected…
Neural manifolds are an attractive theoretical framework for characterizing the complex behaviors of neural populations. However, many of the tools for identifying these low-dimensional subspaces are correlational and provide limited…
Attention is fundamental to cognition, yet it remains a challenge to understand attention in tasks approaching real-world complexity. Here, we approached this problem by modeling gaze patterns of monkeys playing Pac-Man. We first show a…
We introduce RNA-FrameFlow, the first generative model for 3D RNA backbone design. We build upon SE(3) flow matching for protein backbone generation and establish protocols for data preparation and evaluation to address unique challenges…
This work provides a geometric version of the next-generation matrix method for obtaining the basic reproduction number of an epidemiological model. We exhibit a certain correspondence between any system of ODEs and Petri nets. We observe…
The rich and varied ways that genetic material can be passed between species has motivated extensive research into the theory of phylogenetic networks. Features that align with biological processes, or with desirable mathematical…
How could primordial life, before the evolution of genetic systems, adapt to fluctuating environments and achieve homeostasis? This study proposes a minimal, chemically plausible model where homeostasis emerges from a simple chemical…
Vascular access, such as arteriovenous grafts, is crucial for patients undergoing haemodialysis as part of kidney replacement therapy. One of the primary causes of arteriovenous graft failure and loss of patency is disordered blood flow, as…
Trap cropping is a pest management strategy where a grower plants an attractive "trap crop" alongside the primary crop to divert pests away from it. We propose a simple framework for optimizing the proportion of a grower's field or…
Identifiability of phylogenetic models is a necessary condition to ensure that the model parameters can be uniquely determined from data. Mixture models are phylogenetic models where the probability distributions in the model are convex…
We present a novel computational model employing hierarchical active inference to simulate reading and eye movements. The model characterizes linguistic processing as inference over a hierarchical generative model, facilitating predictions…
RNA folding prediction remains challenging, but can be also studied using a topological mathematical approach. In the present paper, the mathematical method to compute the topological classification of RNA structures and based on matrix…
Wastewater surveillance has proven to be a useful tool to monitor pathogens such as SARS-CoV-2 as it is a nonintrusive way to survey the potential disease burden of the population contributing to a sewershed. With the expansion of this…
PhysiBoSS is an open-source platform that integrates agent-based modeling of cell populations with intracellular stochastic Boolean networks, enabling multiscale simulations of complex biological behaviors. To promote model sharing and…
We propose the first fractal frequency mapping, which in a simple form enables to replicate complex neuronal effects. Unlike the conventional filters, which suppress or amplify the input spectral components according to the filter weights,…
Advances in simultaneous recordings of large numbers of neurons have driven significant interest in the structure of neural population activity such as dimension. A key question is how these dynamic features arise mechanistically and their…
Intellectual disability (ID) is defined by an IQ under 70, in addition to deficits in two or more adaptive behaviors that affect everyday living. Throughout history, individuals with ID have often been margin-alized from society and…
Re-entry of travelling excitation loops is a long-suspected driver of human seizures, yet how such loops arise in patient brain networks -- and how susceptible they are to targeted disruption -- remains unclear. We reconstruct a…
Large pre-trained DNA language models such as DNABERT-2, Nucleotide Transformer, and HyenaDNA have demonstrated strong performance on various genomic benchmarks. However, most applications rely on expensive fine-tuning, which works best…