Quantitative Biology
Transmission dynamics of infectious diseases are often studied using compartmental mathematical models, which are commonly represented as systems of autonomous ordinary differential equations. A key step in the analysis of such models is to…
Representations pervade our daily experience, from letters representing sounds to bit strings encoding digital files. While such representations require externally defined decoders to convey meaning, conscious experience appears…
Cancer patients may undergo lengthy and painful chemotherapy treatments, comprising several successive regimens or plans. Treatment inefficacy and other adverse events can lead to discontinuation (or failure) of these plans, or prematurely…
In the process of evolution, the brain has achieved such perfection that artificial intelligence systems do not have and which needs its own mathematics. The concept of cognitome, introduced by the academician K.V. Anokhin, as the cognitive…
The existence of 'what' and 'where' pathways of information processing in the brain was proposed almost 30 years ago, but there is still a lack of a clear mathematical model that could show how these pathways work together. We propose a…
Brain dynamics dominate every level of neural organization -- from single-neuron spiking to the macroscopic waves captured by fMRI, MEG, and EEG -- yet the mathematical tools used to interrogate those dynamics remain scattered across a…
Alzheimer's disease (AD) persists as a paramount challenge in neurological research, characterized by the pathological hallmarks of amyloid-beta (Abeta) plaques and neurofibrillary tangles composed of hyperphosphorylated tau. This review…
Large language models (LLMs) have achieved state-of-the-art performance in a variety of tasks, but remain largely opaque in terms of their internal mechanisms. Understanding these mechanisms is crucial to improve their reasoning abilities.…
Quantifying the neural signatures of consciousness remains a major challenge in neuroscience and AI. Although many theories link consciousness to rich, multiscale, and flexible neural organisation, robust quantitative measures are still…
We present a computational framework that integrates functional-structural plant modeling (FSPM) with an evolutionary algorithm to optimize three-dimensional maize canopy architecture for enhanced light interception under high-density…
Our adaptive immune system relies on the persistence over long times of a diverse set of antigen-experienced B cells to encode our memories of past infections and to protect us against future ones. While longitudinal repertoire sequencing…
Single-cell transcriptomics and proteomics have become a great source for data-driven insights into biology, enabling the use of advanced deep learning methods to understand cellular heterogeneity and gene expression at the single-cell…
The delimitation of biological species, i.e., deciding which individuals belong to the same species and whether and how many different species are represented in a data set, is key to the conservation of biodiversity. Much existing work…
We develop here a stochastic framework for modeling and segmenting transient spindle-like oscillatory bursts in electroencephalogram (EEG) signals. At the modeling level, individual spindles are represented as path realizations of a…
A chloroplast is a subcellular organelle of photosynthesis in plant and algal cells. A chloroplast genome encodes proteins of the photosynthetic electron transport chain and ribosomal proteins required to express them. Chloroplast-encoded…
For two resource-sharing species we explore the interplay of harvesting and dispersal strategies, as well as their influence on competition outcomes. Although the extinction of either species can be achieved by excessive culling, choosing a…
Atom tracing is essential for understanding the fate of labeled atoms in biochemical reaction networks, yet existing computational methods either simplify label correlations or suffer from combinatorial explosion. We introduce a…
The full connectome of an adult Drosophila enables a search for novel neural structures in the insect brain. I describe a new neural structure, called a Parallel Neuron Group (PNG). Two neurons are called parallel if they share a…
Proposing beneficial amino acid substitutions, whether for mutational effect prediction or protein engineering, remains a central challenge in structural biology. Recent inverse folding models, trained to reconstruct sequences from…
Aims: To develop an in-silico model of the aorta and its spinal cord-supplying branches, and to characterise haemodynamic changes following aortic aneurysm (AA) repair with such a model. The work is motivated by the risk of spinal cord…