Related papers: MigraR: an open-source, R-based application for an…
Live migration, a technology enabling seamless transition of operational computational entities between various hosts while preserving continuous functionality and client connectivity, has been the subject of extensive research. However,…
Summary: R and Matlab are two high-level scientific programming languages which are frequently applied in computational biology. To extend the wide variety of available and approved implementations, we present the Rcall interface which runs…
The integration of sequencing data with clinical information is a widely accepted strategy in bioinformatics and health informatics. Despite advanced databases and sophisticated tools for processing omics data, challenges remain in handling…
The advent of miniaturized biologging devices has provided ecologists with unprecedented opportunities to record animal movement across scales, and led to the collection of ever-increasing quantities of tracking data. In parallel,…
It is critical to accurately simulate data when employing Monte Carlo techniques and evaluating statistical methodology. Measurements are often correlated and high dimensional in this era of big data, such as data obtained in…
One of the most important issues in data stream processing systems is to use operator migration to handle highly variable workloads in a cost-efficient manner and adapt to the needs at any given time on demand. Operator migration is a…
Tracking many cells in time-lapse 3D image sequences is an important challenging task of bioimage informatics. Motivated by a study of brain-wide 4D imaging of neural activity in C. elegans, we present a new method of multi-cell tracking.…
Cell tracking is a ubiquitous image analysis task in live-cell microscopy. Unlike multiple object tracking (MOT) for natural images, cell tracking typically involves hundreds of similar-looking objects that can divide in each frame, making…
Molecular dynamics simulation is a proven technique for computing and visualizing the time-resolved motion of macromolecules at atomic resolution. The MDsrv is a tool that streams MD trajectories and displays them interactively in web…
Histograms provide a powerful means of summarizing large data sets by representing their distribution in a compact, binned form. The HistogramTools R package enhances R built-in histogram functionality, offering advanced methods for…
There is increasing interest in the analysis of biological tissue, its organization and its dynamics with the help of mathematical models. In the ideal case emergent properties on the tissue scale can be derived from the cellular scale.…
Cancer cell migration between different body parts is the driving force behind cancer metastasis, which is the main cause of mortality of patients. Migration of cancer cells often proceeds by penetration through narrow cavities in locally…
The development of applications for obtaining interpretable results in a simple and summarized manner in multi-state models is a research field with great potential, namely in terms of using open source tools that can be easily implemented…
Cell migration, which is strictly regulated by intracellular and extracellular cues, is crucial for normal physiological processes and the progression of certain diseases. However, there is a lack of an efficient approach to analyze…
Although Raman spectroscopy is widely used for the investigation of biomedical samples and has a high potential for use in clinical applications, it is not common in clinical routines. One of the factors that obstruct the integration of…
Constructing cell developmental trajectories is a critical task in single-cell RNA sequencing (scRNA-seq) analysis, enabling the inference of potential cellular progression paths. However, current automated methods are limited to…
Methods: We have developed a software suite (DataSet Tracker) for real-time analysis designed to run on computers, smartphones, and smart glasses hardware and suitable for resource-constrained, on-the-fly computing in microscopes without…
Researchers would often like to leverage data from a collection of sources (e.g., primary studies in a meta-analysis) to estimate causal effects in a target population of interest. However, traditional meta-analytic methods do not produce…
Cell segmentation is a fundamental task for computational biology analysis. Identifying the cell instances is often the first step in various downstream biomedical studies. However, many cell segmentation algorithms, including the recently…
Single and collective cell migration are fundamental processes critical for physiological phenomena ranging from embryonic development and immune response to wound healing and cancer metastasis. To understand cell migration from a physical…