Related papers: MigraR: an open-source, R-based application for an…
For researchers in electromyography (EMG), and similar biosginals, signal processing is naturally an essential topic. There are a number of excellent tools available. To these one may add the freely available open source statistical…
Motivation: The scratch assay is a standard experimental protocol used to characterize cell migration. It can be used to identify genes that regulate migration and evaluate the efficacy of potential drugs that inhibit cancer invasion. In…
Advances in climate science have rendered obsolete gridded observation data sets commonly used in macroecological analyses. Novel climate reanalysis products outperform legacy data products in accuracy, temporal resolution, and provision of…
In this paper, we have discussed initial findings and results of our experiment to predict sexual and reproductive health vulnerabilities of migrants in a data-constrained environment. Notwithstanding the limited research and data about…
Here we report on a set of programs developed at the ZMBH Bio-Imaging Facility for tracking real-life images of cellular processes. These programs perform 1) automated tracking; 2) quantitative and comparative track analyses of different…
The fitting or parameter estimation of complex ecological models is a challenging optimisation task, with a notable lack of tools for fitting complex, long runtime or stochastic models. calibrar is an R package that is dedicated to the…
The ability of a cell to communicate with its environment is essential for key cellular functions like replication, metabolism, or cell fate decisions. The involved molecular mechanisms are highly dynamic and difficult to capture…
Cell migration plays essential roles in development, wound healing, diseases, and in the maintenance of a complex body. Experiments in collective cell migration generally measure quantities such as cell displacement and velocity. The…
Cell shape has long been used to discern cell phenotypes and states, but the underlying premise has not been quantitatively tested. Here, we show that a single cell image can be used to discriminate its migration behavior by analyzing a…
Software is increasingly produced in the form of ecosystems, collections of interdependent components maintained by a distributed community. These ecosystems act as network organizations, not markets, and thus often lack actionable…
Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks and theoretical methods, we can begin to probe the complex lives of microscopic motile…
Experiments of cell migration and chemotaxis assays have been classically performed in the so-called Boyden Chambers. A recent technology, xCELLigence Real Time Cell Analysis, is now allowing to monitor the cell migration in real time. This…
Mathematical modelling has a long history in the context of collective cell migration, with applications throughout development, disease and regenerative medicine. The aim of modelling in this context is to provide a framework in which to…
Background: Determining sample sizes for metabolomic experiments is important but due to the complexity of these experiments, there are currently no standard methods for sample size estimation in metabolomics. Since pilot studies are rarely…
In this and the associated article 'BioBlender: A Software for Intuitive Representation of Surface Properties of Biomolecules', (Andrei et al) we present BioBlender as a complete instrument for the elaboration of motion (here) and the…
The study of complex many-body systems via analysis of the trajectories of the units that dynamically move and interact within them is a non-trivial task. The workflow for extracting meaningful information from the raw trajectory data is…
It is shown how to set up, conduct, and analyze large simulation studies with the new R package simsalapar = simulations simplified and launched parallel. A simulation study typically starts with determining a collection of input variables…
This paper develops a generative statistical model for representing, modeling, and comparing the morphological evolution of biological cells undergoing motility. It uses the elastic shape analysis to separate cell kinematics (overall…
Cell migration is an indispensable physiological and pathological process for normal tissue development and cancer metastasis, which is greatly regulated by intracellular signal pathways and extracellular microenvironment (ECM). However,…
Single-cell trajectory analysis aims to reconstruct the biological developmental processes of cells as they evolve over time, leveraging temporal correlations in gene expression. During cellular development, gene expression patterns…