Quantitative Biology
Many models of population dynamics are formulated as deterministic iterated maps although real populations are stochastic. This is justifiable in the limit of large population sizes, as the stochastic fluctuations are negligible then.…
The spotted lanternfly is rapidly establishing itself as a major insect pest with global implications. Despite significant management efforts, its spread continues in invaded regions, and refined management strategies are required. A recent…
The U.S. launched the Secure Pork Supply (SPS) Plan for Continuity of Business, a voluntary program providing foreign animal disease (FAD) guidance and setting biosecurity standards to maintain business continuity amid FAD outbreaks. The…
How DNA-binding proteins locate specific genomic targets remains a central challenge in molecular biology. Traditional protein-centric approaches, which rely on wet-lab experiments and visualization techniques, often lack genome-wide…
Neuroscience and artificial intelligence (AI) both face the challenge of interpreting high-dimensional neural data, where the comparative analysis of such data is crucial for revealing shared mechanisms and differences between these complex…
In the study of life's origins, a key challenge is understanding how RNA could have polymerized and subsequently replicated in early Earth. We present a theoretical and computational framework to model the non-enzymatic polymerization of…
The critical brain hypothesis posits that neural systems operate near a phase transition, optimizing the processing of information. While scale invariance and non-Gaussian dynamics--hallmarks of criticality--have been observed in brain…
Decoding the activity of the nervous system is a critical challenge in neuroscience and neural interfacing. In this study, we present a neuromuscular recording system that enables large-scale sampling of muscle activity using microelectrode…
Neural mass models describe the mean-field dynamics of populations of neurons. In this work we illustrate how fundamental ideas of physics, such as energy and conserved quantities, can be explored for such models. We show that…
Electroencephalographic neurofeedback (EEG-NF) has been proposed as a promising technique to modulate brain activity through real-time EEG-based feedback. Alpha neurofeedback in particular is believed to induce rapid self-regulation of…
The cerebellum is implicated in nearly every domain of human cognition, yet our understanding of how this subcortical structure contributes to cognition remains elusive. Efforts on this front have tended to fall into one of two camps. On…
Large-scale single-cell and Perturb-seq investigations routinely involve clustering cells and subsequently annotating each cluster with Gene-Ontology (GO) terms to elucidate the underlying biological programs. However, both stages,…
Aortic shape analysis plays a key role in cardiovascular diagnostics, treatment planning, and understanding disease progression. We present a robust, fully automated pipeline for aortic shape analysis from cardiac MRI, combining deep…
Protein Language Models (PLMs), pre-trained on extensive evolutionary data from natural proteins, have emerged as indispensable tools for protein design. While powerful, PLMs often struggle to produce proteins with precisely specified…
Computational models are critical to advance our understanding of how neural, biomechanical, and physical systems interact to orchestrate animal behaviors. Despite the availability of near-complete reconstructions of the Drosophila…
Shelf seas are important for carbon sequestration and carbon cycle, but shelf sea observations for carbon pools are often sparse, or highly uncertain. Alternative can be provided by reanalyses, but these are often expensive to run. We…
High-level theories rooted in the Bayesian Brain Hypothesis often frame cognitive effort as the cost of resolving the conflict between habits and optimal policies. In parallel, evidence accumulator models (EAMs) provide a mechanistic…
Longitudinal medical images are essential for monitoring disease progression by capturing spatiotemporal changes associated with dynamic biological processes. While current methods have made progress in modeling spatiotemporal patterns,…
Humans typically walk at low speeds and run at higher speeds. Previous studies of transitions between walking and running were mostly on treadmills, but real-world locomotion allows more flexibility. Here, we study overground locomotion…
How do phylogenetic reconstruction algorithms go astray when they return incorrect trees? This simple question has not been answered in detail, even for maximum parsimony (MP), the simplest phylogenetic criterion. Understanding MP has…