定量生物学
In chemical safety assessment, validation studies rely on reference compound lists to evaluate the applicability of alternative methods prior to regulatory acceptance. These lists are expected to cover multiple aspects, including chemical…
Biochemical and environmental modeling typically relies on reaction networks to represent complex transformations. While the Linkage Class Decomposition (LCD) partitions networks based on visual standard connectivity, it often misaligns…
Understanding how simple local interactions give rise to emergent exploration patterns is a fundamental question in statistical physics. We introduce a minimal model of two coupled agents that avoid retracing their own paths while being…
Optic deconvolution in light microscopy (LM) refers to recovering the object details from images, revealing the ground truth of samples. Traditional explicit methods in LM rely on the point spread function (PSF) during image acquisition.…
For mathematical and experimental ease, models with time varying parameters are often simplified to assume constant parameters. However, this simplification can potentially lead to identifiability issues (lack of uniqueness of parameter…
Light microscopy is a widespread and inexpensive imaging technique facilitating biomedical discovery and diagnostics. However, light diffraction barrier and imperfections in optics limit the level of detail of the acquired images. The…
Planning entails identifying sequences of actions to reach a goal, yet we still have incomplete knowledge of how problem constraints, such as difficulty and available time, influence the visual strategies supporting plan construction, both…
Hippocampal neurons exhibit precise phase locking to network oscillations, but the computational principle governing this temporal precision is still unclear. Neural information is conveyed jointly by firing rates and spike timing, but…
Adeno-associated viral (AAV) vectors are widely used delivery platforms in gene therapy, and the design of improved capsids is key to expanding their therapeutic potential. A central challenge in AAV bioengineering, as in protein design…
We propose a model of the functional architecture of curvature-sensitive cells in the primary visual cortex. The model accounts for the modular and hierarchical organization of the cortex, the horizontal connectivity, and the shape of…
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…