定量生物学
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…
There has been renewed interest in understanding the mathematical structure of ecological population models that lead to overcompensation, the process by which a population recovers to a higher level after suffering a permanent increase in…
Under certain cellular conditions, transcription and mRNA translation in prokaryotes appear to be "coupled," in which the formation of mRNA transcript and production of its associated protein are temporally correlated. Such…
Substances of abuse are known to activate and disrupt neuronal circuits in the brain reward system. We propose a simple and easily interpretable dynamical systems model to describe the neurobiology of drug addiction that incorporates the…
Diverse T and B cell repertoires play an important role in mounting effective immune responses against a wide range of pathogens and malignant cells. The number of unique T and B cell clones is characterized by T and B cell receptors (TCRs…
Efficient testing and vaccination protocols are critical aspects of epidemic management. To study the optimal allocation of limited testing and vaccination resources in a heterogeneous contact network of interacting susceptible, recovered,…
We derive the full kinetic equations describing the evolution of the probability density distribution for a structured population such as cells distributed according to their ages and sizes. The kinetic equations for such a "sizer-timer"…
We consider age-structured models with an imposed refractory period between births. These models can be used to formulate alternative population control strategies to China's one-child policy. By allowing any number of births, but with an…
Thanks to advancements in diagnosis and treatment, prostate cancer patients have high long-term survival rates. Currently, an important goal is to preserve quality-of-life during and after treatment. The relationship between the radiation a…
Stochastic models that incorporate birth, death and immigration (also called birth-death and innovation models) are ubiquitous and applicable to many research topics such as quantifying species sizes in ecological populations, describing…
Chemotaxis is typically modeled in the context of cellular motion towards a static, exogenous source of chemoattractant. Here, we propose a time-dependent mechanism of chemotaxis in which a self-propelled particle ({\it e.g.}, a cell)…
Oscillatory activity in auditory cortex is thought to play a central role in auditory and speech processing by synchronizing neural rhythms to external acoustic features of the speech stream. To support this function, cortical oscillators…