Quantitative Biology
The "binding problem" of how distributed neural activity unifies into conscious experience has remained an open challenge since its articulation in 1890. We present evidence that conscious integration relies on self-organized criticality…
Stride-to-stride fluctuations in human walking carry a fractal correlation structure that reverses sign under external cueing: self-paced gait is persistent, whereas metronomic or visually cued gait is anti-persistent. Three decades of…
While experiments and computer simulations to study biological phenomena are usually performed in diluted in vitro conditions, such phenomena happen inside the cell, an environment densely packed with diverse macromolecules. Here, we revise…
Constraint-based metabolic modeling is the predominant framework for simulating cellular metabolism. The central assumption of these models is that metabolism operates at a steady state, meaning that the production and consumption rates of…
Attractor dynamics are a hallmark of many complex systems, including the brain. Understanding how such self-organizing dynamics emerge from first principles is crucial for advancing our understanding of neuronal computations and the design…
Brain stroke remains one of the principal causes of death and disability worldwide, yet most tabular-data prediction models still hover below the 95% accuracy threshold, limiting real-world utility. Addressing this gap, the present work…
We show that each member of a broad class of Markovian population models induces a unique stochastic process on the space of genealogies. We construct this genealogy process and derive exact expressions for the likelihood of an observed…
To a given gene tree topology $G$ and species tree topology $S$ with leaves labeled bijectively from a fixed set $X$, one can associate a set of ancestral configurations, each of which encodes a set of gene lineages that can be found at a…
Grid cells in the medial entorhinal cortex and place cells in the hippocampus together support spatial navigation. The two regions are reciprocally connected, and there is a chicken-and-egg problem for how both arise and reinforce each…
What can representational similarity matrices (RSMs) tell us about a neural code? As the popularity of these summary statistics grows, so too does the need for a more complete characterization of their properties. Here, we show that…
The Strong Platonic Representation Hypothesis suggests that representational convergence in artificial neural networks can be harnessed constructively: embeddings can be translated across models through a universal latent space without…
The gut-muscle axis has been proposed to link gut microbiota with skeletal muscle physiology, yet its universality across livestock species remains unclear. Using aged laying hens, a livestock model with a relatively short digestive tract,…
Animal experiments have provided many insights on auditory function, notably in cases of sensorineural hearing loss (SNHL). However, it is not always clear how these findings translate to the human auditory system in clinically relevant…
This work presents the Parallelized Hierarchical Connectome (PHC), a general architectural framework that upgrades temporal-only State-Space Models (SSMs) into spatiotemporal recurrent networks. Conventional SSMs achieve parallel-scan…
Nanopore sequencing can read substantially longer sequences of nucleic acid molecules, called reads, than other sequencing methods, which has led to advances in genomic analysis such as the gapless human genome assembly. By analyzing the…
Large language models (LLMs) have significantly advanced protein representation learning. However, their capacity to interpret and design antibodies through natural language remains limited. To address this challenge, we present…
Cooperation, fairness, trust, and resource coordination are cornerstones of modern civilization, yet their emergence remains inadequately explained by the persistent discrepancies between theoretical predictions and behavioral experiments.…
DNA language models are increasingly used to represent genomic sequence, yet their effectiveness depends critically on how raw nucleotides are converted into model inputs. Unlike natural language, DNA offers no canonical boundaries, making…
Serotonin (5-hydroxytryptamine) is a major neurotransmitter whose release from densely distributed serotonergic varicosities shapes plasticity and network integration throughout the brain, yet its extracellular dynamics remain poorly…
A central goal in ecology is to understand how biodiversity is maintained. Previous theoretical works have employed the rock-paper-scissors (RPS) game as a toy model, demonstrating that population mobility is crucial in determining the…