定量生物学
Anomaly detection is a well-established field in machine learning, identifying observations that deviate from typical patterns. The principles of anomaly detection could enhance our understanding of how biological systems recognize and…
Natural selection acts on traits at different scales, often with opposing consequences. This article identifies the particular forces that act at each scale and how those forces combine to determine the overall evolutionary outcome. A…
A biological circuit is a neural or biochemical cascade, taking inputs and producing outputs. How have biological circuits learned to solve environmental challenges over the history of life? The answer certainly follows Dobzhansky's famous…
Neurons in the brain continuously process the barrage of sensory inputs they receive from the environment. A wide array of experimental work has shown that the collective activity of neural populations encodes and processes this constant…
Organisms gain by anticipating future changes in the environment. Those environmental changes often follow stochastic trends. The greater the slope of the trend, the more likely the trend's momentum carries the future trend in the same…
The "critical brain hypothesis" posits that neural circuitry may be tuned close to a "critical point" or "phase transition" -- a boundary between different operating regimes of the circuit. The renormalization group and theory of critical…
The classic Rosenzweig-MacArthur predator-prey model has been shown to exhibit, like other coupled nonlinear ordinary differential equations (ODEs) from ecology, worrying sensitivity to model structure. This sensitivity manifests as…
Hydrogen peroxide oxidises cysteine residues to control protein function, yet bulk rate constants predict hours for changes that occur in cells in seconds. Here, this work shows that local electromagnetic fields (EMFs), ubiquitous in…
Evolutionary systems must learn to generalize, often extrapolating from a limited set of selective conditions to anticipate future environmental changes. The mechanisms enabling such generalization remain poorly understood, despite their…
Understanding the relationship between antibody sequence, structure and function is essential for the design of antibody-based therapeutics and research tools. Recently, machine learning (ML) models mostly based on the application of large…
DNA cytosine methylation is a critical epigenetic mark regulating gene expression and thus playing an important role in development and differentiation across eukaryotes. Existing tools for high-throughput methylation analysis often lack…
Non-invasive colorectal cancer (CRC) screening represents a key opportunity to improve colonoscopy participation rates and reduce CRC mortality. This study explores the potential of the gut-liver axis for predicting colorectal neoplasia…
The identification of homologous gene families across multiple genomes is a central task in bacterial pangenomics traditionally requiring computationally demanding all-against-all comparisons. PanDelos addresses this challenge with an…
Biomolecular interactions underpin almost all biological processes, and their rational design is central to programming new biological functions. Generative AI models have emerged as powerful tools for molecular design, yet most remain…
There are two approaches to describing DNA-ions interactions. The physical approach is an analysis of electrostatic interactions between ions and charges on the DNA molecule. The coordination chemistry approach is a search for modes of…
Explaining the emergence of self-organized biodiversity and species abundance distribution patterns remians a fundamental challenge in ecology. While classical frameworks, such as neutral theory and models based on pairwise species…
Phylogenetics is a fundamental component of evolutionary analysis frameworks in biology and linguistics. Recently, the advent of large-scale genomics and the SARS-CoV-2 pandemic has highlighted the necessity for phylogenetic software to…
It has been observed that the growth of the nucleus and the cytoplasm is coordinated during cell growth, resulting in a nearly constant nuclear-to-cell volume ratio (N/C) throughout the cell cycle. Previous studies have shown that the N/C…
Cell size varies between different cell types, and between different growth and osmotic conditions. However, the nuclear-to-cell volume ratio (N/C ratio) remains nearly constant. In this paper, we build on existing deterministic models of…
Recent advances in neuroimaging have enabled studies in functional connectivity (FC) of human brain, alongside investigation of the neuronal basis of cognition. One important FC study is the representation of vision in human brain. The…