定量生物学

Environmental sharing changes the value of diversification even when the marginal statistics experienced by each lineage remain unchanged. A minimal model of cell division couples this effect to the inheritance of a conserved protective…

The field of bioinformatics struggles with legacy code - old code that is commonly used but may no longer have a maintainer, or may be written in an now-unfamiliar language (e.g. Perl, Fortran). This incurs maintenance cost (technical…

Highly pathogenic avian influenza (HPAI) outbreaks require rapid control during active transmission and evidence-based decisions on the safe restocking of depopulated farms. We developed a stochastic spatial SEIR-based metapopulation model…

Neurodegenerative diseases can be viewed as spreading processes on brain networks, in which pathological proteins propagate between anatomically connected brain regions. Mathematical models have been used to study this process, but they…

Microbial populations generally evolve in fluctuating environments under time-varying conditions. These are often described by binary switching models, sometimes seen as coarse-grained feast-famine cycles, in which resource availability…

The classical problem of Other Minds has dogged philosophers for millennia; asking if we have any way to truly understand the experience of another mind. We know our own intrinsic experience by acquaintance, but can only ever hope to…

Identifying individual learning styles optimizes pedagogical efficacy. While traditional questionnaires are structured, behavioral tracking methods require prolonged interaction log accumulation. To overcome these temporal constraints, this…

Scaling relations linking species size, abundance, and resource availability are among the most robust empirical regularities in ecology. However, a mechanistic explanation for how these community-level laws emerge from ecological processes…

SVPLEX is a Nextflow pipeline for cohort-level structural variant detection from short-read whole-genome sequencing data. The pipeline implements six different structural variant callers with different strengths and weaknesses, integrating…

Representational similarity analysis (RSA) is increasingly used to ask which learning rules give convolutional networks brain-like representations. Because biologically plausible rules such as feedback alignment, predictive coding and STDP…

Congruency effects, observed in conflict tasks such as Stroop and flanker tasks, have been investigated for nearly a century in psychology and neuroscience, but their mechanistic basis is not fully understood. We introduce a verbal-only LLM…

AlphaFold3-class structure predictors pair a representational trunk, which processes sequence and context, with a diffusion module, which generates atomic coordinates. How biological information changes as it crosses this architectural…

Drug response prediction (DRP) models are an active area of research in pharmacogenomics, with growing potential to accelerate the identification of effective anticancer drugs. However, their predictive performance is often constrained by…

To be conscious is to have an experience - not a collection of phenomenal atoms, but a structured whole composed of distinctions and the relations that bind them. Integrated Information Theory (IIT) identifies the essential properties of…

Omics datasets, particularly single-cell RNA sequencing data, are high-dimensional, sparse, noisy, and dominated by zero values, making faithful low-dimensional representation challenging. Existing dimensionality-reduction methods may…

Predicting how molecular changes affect large-scale brain activity is a difficult task because of the lack of appropriate methods to link scales. In this perspective, we review a class of mean-field models that can integrate biophysical…

Reproductive hormones regulate a wide range of physiological processes throughout the human lifespan. Estrogen, in particular, varies substantially across the menstrual cycle and is widely used in contraceptives and hormone replacement…

Neural tracking - the time-locking of neural responses to continuous stimuli such as speech, music, and video - is widely used to study how the brain processes natural input. Tracking strength is typically quantified as the correlation…

A key issue in using AI for pathology diagnosis is what image information should be given to the AI and how limited analysis resources should be used. This study compares two ways of processing different types of images under limited…

Protein backbone generation models are often credited with exploring novel fold space based solely on low full-chain similarity to known proteins, yet this cannot distinguish a genuinely new fold from a novel assembly of known structural…