定量方法
Deep phenotyping study has become an emerging field to understand the gene function and the structure of biological networks. For the living animal C. elegans, recent advances in genome-editing tools, microfluidic devices and phenotypic…
Beerenwinkel et al.(2007) suggested studying fitness landscapes via regular subdivisions of convex polytopes. Building on their approach we propose cluster partitions and cluster filtrations of fitness landscapes as a new mathematical tool.…
The use of artificial intelligence in clinical care to improve decision support systems is increasing. This is not surprising since, by its very nature, the practice of medicine consists of making decisions based on observations from…
Background. Non-specific Lipid Transfer Proteins (nsLTPs) are widely distributed in the plant kingdom and constitute a superfamily of related proteins. More than 800 different sequences have been characterized so far, but their biological…
The opioid epidemic in the United States claims over 40,000 lives per year, and it is estimated that well over two million Americans have an opioid use disorder. Over-prescription and misuse of prescription opioids play an important role in…
Consider the standard stochastic reaction network model where the dynamics is given by a continuous-time Markov chain over a discrete lattice. For such models, estimation of parameter sensitivities is an important problem, but the existing…
This paper investigates the dynamics of immune response and autoimmunity with particular emphasis on the role of regulatory T cells (Tregs), T cells with different activation thresholds, and cytokines in mediating T cell activity. Analysis…
A new algorithm has been developed for delineation of significant points of various electrocardiographic signal (ECG) waves, taking into account information from all available leads and providing similar or higher accuracy in comparison…
Identifying groups of similar objects using clustering approaches is one of the most frequently employed first steps in exploratory biomedical data analysis. Many clustering methods have been developed that pursue different strategies to…
Cryo-electron tomography enables 3D visualization of cells in a near native state at molecular resolution. The produced cellular tomograms contain detailed information about all macromolecular complexes, their structures, their abundances…
We present the Network-based Biased Tree Ensembles (NetBiTE) method for drug sensitivity prediction and drug sensitivity biomarker identification in cancer using a combination of prior knowledge and gene expression data. Our devised method…
Studies have identified various risk factors associated with the onset of stroke in an individual. Data mining techniques have been used to predict the occurrence of stroke based on these factors by using patients' medical records. However,…
Several studies have used structural correlation networks, derived from anatomical covariance of brain regions, to analyze neurologic changes associated with multiple sclerosis, schizophrenia and breast cancer [1][2]. Graph-theoretical…
Single cell segmentation is critical and challenging in live cell imaging data analysis. Traditional image processing methods and tools require time-consuming and labor-intensive efforts of manually fine-tuning parameters. Slight variations…
Microbial clades modeling is a challenging problem in biology based on microarray genome sequences, especially in new species gene isolates discovery and category. Marker family genome sequences play important roles in describing specific…
Although mechanical cues are crucial to tissue morphogenesis and development, the tissue mechanical stress field remains poorly characterized. Given traction force timelapse movies, as obtained by traction force microscopy of in vitro…
We have advanced a point-process based framework for the regulation of heart beats by the autonomous nervous system and analyzed the model with and without feedback. The model without feedback was found amenable to several analytical…
Cellular signaling is essential in information processing and decision making. Therefore, a variety of experimental approaches have been developed to study signaling on bulk and single-cell level. Single-cell measurements of signaling…
This work considers the method of uniformisation for continuous-time Markov chains in the context of chemical reaction networks. Previous work in the literature has shown that uniformisation can be beneficial in the context of…
The concentration of biochemical oxygen demand, BOD5, was studied in order to evaluate the water quality of the Igap\'o I Lake, in Londrina, Paran\'a State, Brazil. The simulation was conducted by means of the discretization in curvilinear…