Quantitative Biology
Computer modeling of the cardiovascular system has potential to revolutionize personalized medical care. This is especially promising for congenital heart defects, such as ventricular septal defect (VSD), a hole between the two ventricles…
G-protein-coupled receptors (GPCRs), primary targets for over one-third of approved therapeutics, rely on intricate conformational transitions to transduce signals. While Molecular Dynamics (MD) is essential for elucidating this…
Antimicrobial resistance threatens healthcare sustainability and motivates low-cost computational discovery of antimicrobial peptides (AMPs). De novo peptide generation must optimize antimicrobial activity and safety through low predicted…
Biological memory solves a problem that eludes current AI: storing specific episodic facts without corrupting general semantic knowledge. Complementary Learning Systems theory explains this through two subsystems - a fast hippocampal system…
AI agents are increasingly used in long, multi-turn workflows in both research and enterprise settings. As interactions grow, agent behavior often degrades due to loss of constraint focus, error accumulation, and memory-induced drift. This…
The function of biomolecules such as proteins depends on their ability to interconvert between a wide range of structures or "conformations." Researchers have endeavored for decades to develop computational methods to predict the…
Designing metal-organic frameworks (MOFs) with novel chemistries is a longstanding challenge due to their large combinatorial space and complex 3D arrangements of the building blocks. While recent deep generative models have enabled…
How do different brains create unique visual experiences from identical sensory input? While neural representations vary across individuals, the fundamental architecture underlying these differences remains poorly understood. Here, we…
This study introduces a framework for constructing enviromics matrices in mixed models to integrate genetic and environmental data to enhance phenotypic predictions in plant breeding. Enviromics utilizes diverse data sources, such as…
For a biological system to grow and expand, mass must be transferred from the environment to the system and be assimilated into its reaction network. Here, I characterize the biomass transfer process for growing autocatalytic systems. By…
Sparked by innovations in generative artificial intelligence (AI), the field of protein design has undergone a paradigm shift with an explosion of new models for optimizing existing enzymes or creating them from scratch. After more than one…
Automated analysis of electroencephalography (EEG) has recently undergone a paradigm shift. The introduction of transformer architectures and self-supervised pretraining (SSL) has led to the development of EEG foundation models. These…
Cognition is increasingly framed in terms of information processing, yet most fMRI analyses focus on activation or functional connectivity rather than quantifying how information is stored and transferred. To remedy this problem, we propose…
Zero-shot mutation prediction is vital for low-resource protein engineering, yet existing protein language models (PLMs) often yield statistically confident results that ignore fundamental biophysical constraints. Currently, selecting…
Control of transcription presides over a vast array of biological processes, including those mediated by gene regulatory circuits that exhibit multistability. Within these circuits, two- and three-gene network motifs are particularly…
Drawing parallels between Deep Artificial Neural Networks (DNNs) and biological systems can aid in understanding complex biological mechanisms that are difficult to disentangle. Temporal processing, an extensively researched topic, is one…
We consider a Moran-type model of cultural evolution, which describes how traits emerge, are transmitted, and get lost in populations. Our analysis focuses on the underlying cultural genealogies; they were first described by Aguilar and…
Extensive behavioral experiments reveal that conditional cooperation is a prevalent phenomenon. Previous game-theoretical studies have predominantly relied on hard-manner models, where cooperation is triggered only upon reaching a specific…
The inherent complexity of human beings manifests in a remarkable diversity of responses to intricate environments, enabling us to approach problems from varied perspectives. However, in the study of cooperation, existing research within…
The study of brain differences across Eastern and Western populations provides vital insights for understanding potential cultural and genetic influences on cognition and mental health. Diffusion MRI (dMRI) tractography is an important tool…