Quantitative Biology
Collective cell migration is a fundamental biological process that drives events such as embryonic development, wound healing, and cancer metastasis. In this study, we develop a biophysically informed phase-field model to investigate the…
Proteins perform nearly all cellular functions and constitute most drug targets, making their analysis fundamental to understanding human biology in health and disease. Tandem mass spectrometry (MS$^2$) is the major analytical technique in…
While linear registration is a critical step in MRI preprocessing pipelines, its numerical uncertainty is understudied. Using Monte-Carlo Arithmetic (MCA) simulations, we assessed the most commonly used linear registration tools within…
The microtubule cytoskeleton is comprised of dynamic, polarized filaments that facilitate transport within the cell. Polarized microtubule arrays are key to facilitating cargo transport in long cells such as neurons. Microtubules also…
Anyone who has tried to memorize a one-hundred-digit number can attest that the human brain acquires abstract information slowly. However, following a three-decade increase of results at memory competitions, the best competitors manage to…
In many species of songbirds, juvenile males learn their songs from adult male tutors. In this paper we formulate a novel Markov model for birdsong transmission developed by analogy with models used in biological sequence analysis. We fit…
I consider motivation and value-alignment in AI systems from the perspective of (constrained) entropy maximization. Though the structures encoding knowledge in any physical system can be understood as energetic constraints, only living…
The mitigation of stress is a key challenge for all biological systems. Conditions of unresolvable stress have been associated with a diverse array of pathologies, from cancer to post-traumatic stress disorder (PTSD). Here, I unify insights…
Vector-borne diseases arise from the coupled dynamics of human mobility and mosquito ecology, producing outbreaks shaped by both spatial distributions and temporal patterns of movement. Here we develop a coarse-grained hub--leaf reduction…
Bacteria often develop distinct phenotypes to adapt to environmental stress. In particular, they can produce biofilms, dense communities of bacteria that live in a complex extracellular matrix. Bacterial biofilms provide a safe haven from…
As the global population continues to age, there is an increasing demand for ways to accurately quantify the biological processes underlying aging. Biological age, unlike chronological age, reflects an individual's physiological state,…
CRISPR-based genome editing has revolutionized biotechnology, yet optimizing guide RNA (gRNA) design for efficiency and safety remains a critical challenge. Recent advances (2020--2025, updated to reflect current year if needed) demonstrate…
A unified theory of language combines a Bayesian cognitive linguistic model of language processing, with the proposal that language evolved by sexual selection for the display of intelligence. The theory accounts for the major facts of…
Tree rings provide long-term records of tree growth and climate changes, which makes them ideal benchmarks for forest modeling. Tree-ring information has greatly improved the reliability of 3-PG, which is one of the most commonly used…
Modeling forest dynamics under novel climatic conditions requires a careful balance between process-based understanding and empirical flexibility. Dynamic Vegetation Models (DVM) represent ecological processes mechanistically, but their…
Telomeres are repetitive sequences of nucleotides at the end of chromosomes, whose evolution over time is intrinsically related to biological ageing. In most cells, with each cell division, telomeres shorten due to the so-called end…
Group synchrony in the animal kingdom is usually associated with mating. Being in sync is likely advantageous, as it may help in luring the opposite sex. Yet there are also disadvantages -- such as the homogenization of the group -- which…
Neuron models built from experimental data have successfully predicted observed voltage oscillations within and beyond training range. A tantalising prospect is the possibility of estimating the unobserved dynamics of ion channels which is…
Foundation models have recently emerged as powerful feature extractors in computational pathology, yet they typically omit mechanisms for leveraging the global spatial structure of tissues and the local contextual relationships among…
We envision the Full-Body AI Agent as a comprehensive AI system designed to simulate, analyze, and optimize the dynamic processes of the human body across multiple biological levels. By integrating computational models, machine learning…