定量方法
In particle-based stochastic reaction-diffusion models, reaction rate and placement kernels are used to decide the probability per time a reaction can occur between reactant particles, and to decide where product particles should be placed.…
Compartmentalization of biochemical processes underlies all biological systems, from the organelle to the tissue scale. Theoretical models to study the interplay between noisy reaction dynamics and compartmentalization are sparse, and…
Self-organized pattern behavior is ubiquitous throughout nature, from fish schooling to collective cell dynamics during organism development. Qualitatively these patterns display impressive consistency, yet variability inevitably exists…
Recently, Eklund et al. (2016) analyzed clustering methods in standard FMRI packages: AFNI (which we maintain), FSL, and SPM [1]. They claimed: 1) false positive rates (FPRs) in traditional approaches are greatly inflated, questioning the…
A hallmark of bacterial populations cultured in vitro is their homogeneity of growth, where the majority of cells display identical growth rate, cell size and content. Recent insights, however, have revealed that even cells growing in…
The study of aerosols and droplets emitted from the oral cavity has become increasingly important throughout the COVID-19 pandemic. Studies show particulates emitted while speaking were generally much smaller compared to coughing or…
Motivation: While the analysis of a single RNA sequencing (RNAseq) dataset has been well described in the literature, modern research workflows often have additional complexity in that related RNAseq experiments are performed sequentially…
Detection of extremely rare variant alleles, such as tumour DNA, within a complex mixture of DNA molecules is experimentally challenging due to sequencing errors. Barcoding of target DNA molecules in library construction for next-generation…
Baker's yeast (Saccharomyces cerevisiae) is a model organism for studying the morphology that emerges at the scale of multi-cell colonies. To look at how morphology develops, we collect a dataset of time-lapse photographs of the growth of…
Complex socio-environmental interdependencies drive biological invasions, causing damages across large spatial scales. For widespread invasions, targeting of management activities based on optimization approaches may fail due to…
The zymase activity of the yeast Saccharomyces Cerevisiae is sensitive to environmental parameters and is therefore used as a microbiological sensor for water quality assessment, ecotoxicological characterization or environmental…
RNA 3D architectures are stabilized by sophisticated networks of (non-canonical) base pair interactions, which can be conveniently encoded as multi-relational graphs and efficiently exploited by graph theoretical approaches and recent…
Systems Biology is a fundamental field and paradigm that introduces a new era in Biology. The crux of its functionality and usefulness relies on metabolic networks that model the reactions occurring inside an organism and provide the means…
Deep-learning models based on whole-slide digital pathology images (WSIs) become increasingly popular for predicting molecular biomarkers. Instance-based models has been the mainstream strategy for predicting genetic alterations using WSIs…
Purpose: Develop a deep learning-based automated method to segment meibomian glands (MG) and eyelids, quantitatively analyze the MG area and MG ratio, estimate the meiboscore, and remove specular reflections from infrared images. Methods: A…
Subcortical structures play a critical role in brain function. However, options for assessing electrophysiological activity in these structures are limited. Electromagnetic fields generated by neuronal activity in subcortical structures can…
Cancer detection is one of the key research topics in the medical field. Accurate detection of different cancer types is valuable in providing better treatment facilities and risk minimization for patients. This paper deals with the…
Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…
The prevailing theory for metabolic scaling is based on area-preserved, space-filling fractal vascular networks. However, it's known both theoretically and experimentally that animals' vascular systems obey Murray's cubic branching law.…
DNA has many valuable characteristics that make it suitable for a long-term storage medium, in particular its durability and high information density. DNA can be stored safely for hundreds of years with virtually no degradation, in contrast…