定量方法
Many cytoskeletal systems are now sufficiently well known to permit their precise quantitative modelling. Microtubule and actin filaments are well characterized, and the associated proteins are often known, as well as their abundance and…
We propose a machine learning framework for the data-driven discovery of macroscopic chemotactic Partial Differential Equations (PDEs) -- and the closures that lead to them -- from high-fidelity, individual-based stochastic simulations of…
Infections from parasitic nematodes (or roundworms) contribute to a significant disease burden and productivity losses for humans and livestock. The limited number of anthelmintics (or antinematode drugs) available today to treat these…
In a recent opinion article, Muff et al. recapitulate well-known objections to the Neyman-Pearson Null-Hypothesis Significance Testing (NHST) framework and call for reforming our practices in statistical reporting. We agree with them on…
What is the influence of chronic maternal prenatal stress (PS) on fetal iron homeostasis? In a prospective case-control study in 164 pregnant women, we show that cord blood transferrin saturation is lower in male stressed neonates. The…
The soybean cyst nematode (SCN), Heterodera glycines, is the most damaging pathogen of soybeans in the United States. To assess the severity of nematode infestations in the field, SCN egg population densities are determined. Cysts (dead…
We consider how mathematical models enable predictions for conditions that are qualitatively different from the training data. We propose techniques based on information topology to find models that can apply their learning in regimes for…
Developing accurate and reliable methods to estimate vaccine protection is a key goal in immunology and public health. While several statistical methods have been proposed, their potential inaccuracy in capturing fast intra-seasonal waning…
Living cells need a constant availability of certain resources to have a sustained gene expression process. Limited availability of cellular resources for gene expression, like ribosomes, along with a variation of resource affinity,…
Protein function is inherently linked to its localization within the cell, and fluorescent microscopy data is an indispensable resource for learning representations of proteins. Despite major developments in molecular representation…
Biofilms are spatially organized microorganism colonies embedded in a self-produced matrix, conferring to the microbial community resistance to environmental stresses. Motile bacteria have been observed swimming in the matrix of pathogenic…
In this Ansatz we consider theoretical constructions of RNA polymers into automata, a form of computational structure. The basis for transitions in our automata are plausible RNA enzymes that may perform ligation or cleavage. Limited to…
Movements in imagery captivate the human eye and imagination. They are also of interest in variety of scientific disciplines that study spatiotemporal dynamics. Popular methods for quantifying movement in imagery include particle image…
Many systems on our planet are known to shift abruptly and irreversibly from one state to another when they are forced across a "tipping point," such as mass extinctions in ecological networks, cascading failures in infrastructure systems,…
In many situations, the gene expression signature is a unique marker of the biological state. We study the modification of the gene expression distribution function when the biological state of a system experiences a change. This change may…
Background and Purpose: Radiomics features are used to identify disease types and predict therapy outcomes. However, how the radiomics features are different among different anatomical structures has never been investigated. Hence, we…
Drug resistance is a major threat to the global health and a significant concern throughout the clinical treatment of diseases and drug development. The mutation in proteins that is related to drug binding is a common cause for adaptive…
Genome-wide epistasis analysis is a powerful tool to infer gene interactions, which can guide drug and vaccine development and lead to a deeper understanding of microbial pathogenesis. We have considered all complete SARS-CoV-2 genomes…
Encoding models that predict brain response patterns to stimuli are one way to capture this relationship between variability in bottom-up neural systems and individual's behavior or pathological state. However, they generally need a large…
Molecular dynamics (MD) simulations have been widely applied to study macromolecules including proteins. However, high-dimensionality of the datasets produced by simulations makes it difficult for thorough analysis, and further hinders a…