Quantitative Biology
The striking alignment between large language models (LLMs) and human brain activity positions them as powerful models of healthy cognition. This parallel raises a fundamental question: if LLMs can model the intact brain, can we lesion them…
Understanding the molecular-level mechanisms underpinning Alzheimer's disease (AD) by studying crucial genes associated with the disease remains a challenge. Alzheimer's, being a multifactorial disease, requires understanding the gene-gene…
Modern disease classification often overlooks molecular commonalities hidden beneath divergent clinical presentations. This study introduces a transcriptomics-driven framework for discovering disease relationships by analyzing over 1300…
Genomic language models (gLMs) face a fundamental efficiency challenge: either maintain separate specialized models for each biological modality (DNA and RNA) or develop large multi-modal architectures. Both approaches impose significant…
While multiplex immunofluorescence (mIF) imaging provides deep, spatially-resolved molecular data, integrating this information with the morphological standard of Hematoxylin & Eosin (H&E) can be very important for obtaining complementary…
Understanding the properties of biological systems is an exciting avenue for applying advanced approaches to solving corresponding computational tasks. A specific class of problems that arises in the resolution of biological challenges is…
Numerous living systems are hierarchically organised, whereby replicating components are grouped into reproducing collectives -- e.g., organelles are grouped into cells, and cells are grouped into multicellular organisms. In such systems,…
Although the descriptive epidemiology of primary breast cancer is well characterized in the US, breast cancer recurrence rates have not been measured in an unselected population. The number of breast cancer survivors at risk for recurrence…
The Central Dogma of molecular biology, as originally proposed by Crick, asserts that information passed into protein cannot flow back out. This principle has been interpreted as underpinning modern understandings of heredity and evolution,…
Summary: Ancestral recombination graphs (ARGs) are a complete representation of the genetic relationships between recombining lineages and are of central importance in population genetics. Recent breakthroughs in simulation and inference…
The depiction of populations - of humans or animals - as "population pyramids" is a useful tool for the assessment of various characteristics of populations at a glance. Although these visualisations are well-known objects in various…
Molecular dynamics (MD) is a powerful approach for modelling molecular systems, but it remains computationally intensive on spatial and time scales of many macromolecular systems of biological interest. To explore the opportunities offered…
Comprehending the nature of action potentials is fundamental to our understanding of the functioning of nervous systems in general. The ionic mechanisms underlying action potentials in the squid giant axon were first described by Hodgkin…
Motor cortex (M1) is a crucial brain area for controlling voluntary movements, such as reaching and grasping for a cup of coffee. M1 is organized in a somatotopic manner, such that M1 output driving movement to different parts of the body…
The question of "what is life?" has challenged scientists and philosophers for centuries, producing an array of definitions that reflect both the mystery of its emergence and the diversity of disciplinary perspectives brought to bear on the…
Ecosystems frequently display the coexistence of diverse species under resource competition, typically resulting in skewed distributions of rarity and abundance. A potential driver of such coexistence is environmental fluctuations that…
We develop a systems approach based on an energy-landscape concept to differentiate interactions involving redox activities and conformational changes of proteins and nucleic acids interactions in multi-layered protein-DNA regulatory…
A fundamental idea in neuroscience is that cognitive functions -- such as perception, learning, memory, and locomotion -- are shaped and constrained by the brain's structural organization. Despite significant progress in mapping and…
We present a mathematical model to study the transmission dynamics of soil-transmitted helminth (STH) infections and to assess the impact of community-based water, sanitation, and hygiene (WASH) program interventions. STH infections are a…
Polyphenols and proteins are essential biomolecules that influence food functionality and, by extension, human health. Their interactions -- hereafter referred to as PhPIs (polyphenol-protein interactions) -- affect key processes such as…