Quantitative Biology
We investigate the use of additional 3D and phylogenetic non-3D tree balance indices for analyzing and monitoring forests using an exemplary "virtual forest" dataset from the Wytham Woods, Oxford, UK. This study assesses 3D model quality,…
Bacterial cancer therapy exploits anaerobic bacteria's ability to target hypoxia tumor regions, yet the interactions among tumor growth, bacterial colonization, oxygen levels, immunosuppressive cytokines, and bacterial communication remain…
Neural circuits must balance local connectivity constraints against the need for global integration. Here we introduce a minimal wiring rule motivated by synaptic crowding: as a neuron accumulates incoming connections, each additional…
Cerebellar-like networks, in which input activity patterns are separated by projection to a much higher-dimensional space before classification, are a recurring neurobiological motif, present in the cerebellum, dentate gyrus, insect…
This study introduces a pioneering machine learning (ML)-based approach for predicting the impact of nanoparticle (NP) carriers on the functionality of attached small biomolecules. It was hypothesised that NP interactions induce measurable…
Genomic language models (gLMs) have shown mostly modest success in identifying evolutionarily constrained elements in mammalian genomes. To address this issue, we introduce a novel framework for training gLMs that explicitly models…
The article proposes a conceptual approach for evaluating the impact of engineered nanoparticles (NPs) on the functionality of small biomolecules. The developed machine learning (ML) model is based on in-silico 13C NMR spectroscopy chemical…
We present BSTModelKit.jl, an open-source Julia package for constructing, solving, and analyzing Biochemical Systems Theory (BST) models of biochemical networks. The package implements S-system representations, a canonical power-law…
The SIR model is the cornerstone model for mathematical epidemiology, explaining key epidemic features such as the second-order transition between disease-free and epidemic states, the initial exponential growth of outbreaks or the…
Inferring the connectivity of neural circuits from incomplete observations is a fundamental challenge in neuroscience. We present a covariance-based method for estimating the weight matrix of a recurrent neural network from sparse, partial…
Spatial transcriptomics (ST) profiles gene expression across a tissue section while preserving the spatial coordinates. Because current ST technologies typically profile two-dimensional tissue slices, integrating and aligning slices from…
Background Genetic parameters of feeding behaviours traits from electronic feeding stations in relation to feed efficiency have been widely explored. However, genetic determinism of the circadian rhythm of feed intake throughout the…
Replica exchange (REX) is one of the most widely used enhanced sampling methodologies, yet its efficiency is limited by the requirement for a large number of intermediate temperature replicas. Here we present Generative Replica Exchange…
The evolution of natural languages poses a riddle to any theoretical perspective based on efficiency considerations. If languages are already optimally effective means of organization and communication of thought, why do they change? And if…
We explore a functionalist approach to emotion by employing an ansatz -- an initial set of assumptions -- that a hypothetical concept generation model incorporates unproven but biologically plausible traits. From these traits, we…
Human cognition is supported by brain structural connectivity wherein weak connectivity with weights several orders of magnitude smaller than those of strong connectivity, has been treated as noise and ignored from analysis over a long…
In this article, I put forward the idea that the neoplastic process (NP) has deep evolutionary roots and make specific predictions about the connection between cancer and the formation of the first embryo, which allowed for the evolutionary…
The decisive role of Embryology in understanding the evolution of animal forms is founded and deeply rooted in the history of science. It is recognized that the emergence of multicellularity would not have been possible without the…
To make nature mathematically tractable, the scientific model of the world omits qualia--colors, sounds, tastes, sensations--leaving only what admits of numerical characterization. The "hard problem" of consciousness--the enigma of why and…
Normalization is a critical operation in neural circuits. In the brain, there is evidence that normalization is implemented via inhibitory interneurons and allows neural populations to adjust to changes in the distribution of their inputs.…