Quantitative Biology
Background: Autism spectrum disorder (ASD) is characterized by significant clinical and biological heterogeneity. Conventional group-mean analyses of eye movements often mask individual atypicalities, potentially overlooking critical…
The present study evaluated the effectiveness of transcranial alternating current stimulation (tACS) treating patients with post-stroke anomia using a picture-naming task and a Single-Case Experimental Design (SCED). A right-handed…
A central challenge in developing Multimodal Large Language Models (MLLMs) is effectively integrating heterogeneous inputs into a cohesive reasoning engine. Current paradigms predominantly rely on modular architectures that introduce…
Biological intelligence emerges from substrates that are slow, noisy, and energetically constrained, yet it performs rapid and coherent inference in open-ended environments. Classical computational theories, built around vector-space…
Cellular image segmentation is essential for quantitative biology yet remains difficult due to heterogeneous modalities, morphological variability, and limited annotations. We present GenCellAgent, a training-free multi-agent framework that…
In this paper, we introduce gonosomic algebras to algebraically translate the phenomenon of genetic sterility. Gonosomic algebras extend the concept of gonosomal algebras used as algebraic model of genetic phenomena related to…
Peripheral blood smears remain a cornerstone in the diagnosis of hematological neoplasms, offering rapid and valuable insights that inform subsequent diagnostic steps. However, since neoplastic transformations typically arise in the bone…
Microbial adaptation to extreme stress, such as starvation, antimicrobial exposure, or freezing often reveals fundamental trade-offs between survival and proliferation. Understanding how populations navigate these trade-offs in fluctuating…
Automated molecular structure elucidation remains challenging, as existing approaches often depend on pre-compiled databases or restrict themselves to single spectroscopic modalities. Here we introduce SpectraLLM, a large language model…
Proper regulation of cell signaling and gene expression is crucial for maintaining cellular function, development, and adaptation to environmental changes. Reaction dynamics in cell populations is often noisy because of (i) inherent…
Formulating quantitative and predictive models for tissue development requires consideration of the complex, stochastic gene expression dynamics, its regulation via cell-to-cell interactions, and cell proliferation. Including all of these…
The dataset collected at the Cape Rodney-Okakari Point Marine (CR-OPM) reserve on the North Island of New Zealand is rather unique. It describes the cyclic time evolution of a rocky intertidal community, with the relative abundances of the…
Reaction networks have been widely used as generic models in diverse areas of applied sciences, such as biology, chemistry, ecology, epidemiology, and computer science. A reaction network incorporating noisy effects is modeled as a…
Over recent decades, neuroimaging tools, particularly electroencephalography (EEG), have revolutionized our understanding of the brain and its functions. EEG is extensively used in traditional brain-computer interface (BCI) systems due to…
More than 60% of individuals recovering from substance use disorder relapse within one year. Some will resume drug consumption even after decades of abstinence. The cognitive and psychological mechanisms that lead to relapse are not…
We formulate a general, high-dimensional kinetic theory describing the internal state (such as gene expression or protein levels) of cells in a stochastically evolving population. The resolution of our kinetic theory also allows one to…
Cellular signaling, crucial for biological processes like immune response and homeostasis, relies on specificity and fidelity in signal transduction to accurately respond to stimuli amidst biological noise. Kinetic proofreading (KPR) is a…
We construct and analyze monomeric and multimeric models of the stochastic disassembly of a single nucleosome. Our monomeric model predicts the time needed for a number of histone-DNA contacts to spontaneously break, leading to dissociation…
We develop a modeling framework for cancer progression that distinguishes the order of two possible mutations. Recent observations and information on myeloproliferative neoplasms are analyzed within our framework. In some patients with…
Recent studies show that newly sampled monkeypox virus (MPXV) genomes exhibit mutations consistent with Apolipoprotein B mRNA Editing Catalytic Polypeptide-like3 (APOBEC3)-mediated editing, compared to MPXV genomes collected earlier. It is…