Quantitative Biology
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…
Soft X-ray tomography provides detailed structural insight into whole cells but is hindered by experimental artifacts such as the missing wedge and by limited availability of annotated datasets. We present SimAQ, a simulation pipeline that…
Recent voxel-wise multimodal brain encoding studies have shown that multimodal large language models (MLLMs) exhibit a higher degree of brain alignment compared to unimodal models. More recently, instruction-tuned multimodal (IT) models…
Alcohol Use Disorder (AUD) is a prevalent addictive disorder affecting an estimated 29.5 million Americans. It is characterized by impaired control over alcohol consumption despite negative consequences. The number of diagnostic criteria…
We analyse a model that describes the propagation of many pathogens within and between many species. A branching process approximation is used to compute the probability of disease outbreaks. Special cases of aquatic environments with two…
Artificial vision models are often evaluated against the human visual cortex by measuring how accurately their internal representations predict brain responses. However, prediction accuracy alone does not indicate which dimensions of the…
Background: Face morphometry has been shown to work as a diagnosis tool in a set of syndromes. Face similarities are usually indications of more complete genetic similarities. Purpose: To show preliminary results on the face morphometry…
Phylogenetic networks generalize phylogenetic trees by allowing reticulate evolutionary events such as horizontal gene transfer and hybridization. Among the many subclasses of phylogenetic networks, orchard networks have attracted…
Purpose: To investigate psychophysically the ability of low vision individuals with central visual field loss (CFL) to perform a visually-guided pointing task in a virtual reality environment. Methods: Patients with CFL (n=25, ages = 67-90…
Embryology has long played a foundational role in shaping our scientific understanding of animal evolution. In recent decades, growing evidence has also highlighted its role in cancer. Despite the indisputable similarities between embryonic…
Advancements in clinical Brain-Computer Interfaces (BCIs) depend on precise and reliable signal interpretation. However, the high-dimensional and noisy nature of data captured from both implanted and non-implanted BCIs poses significant…
Proteolysis-targeting chimeras (PROTACs) represent a promising therapeutic modality that induces targeted protein degradation by hijacking the ubiquitin-proteasome system. However, rational PROTAC design remains challenging due to the…