Related papers: FRAP analysis Measuring biophysical kinetic parame…
My analysis uses methods developed for data mining microarray experiments, adapted for ageing research. Methods bridge knowledge of statistical mechanics with data mining methods developed in statistical mathematics. Analyses can reveal how…
Understanding the ultrafast carrier dynamics of graphene on a substrate is a fundamental step in the development of graphene based opto-electronic devices. Here, we present ultrafast pump-probe measurements of supported graphene on quartz…
In most cases the ultrafast dynamics of resonantly excited molecules are considered, and almost always computed in the molecular frame, while experiments are carried out in the laboratory frame. Here we provide a formalism in terms of a lab…
High speed camera imaging is a powerful tool to probe the spatiotemporal features of unsteady processes in plasmas, usually assuming light fluctuations to be a proxy for the plasma density fluctuations. In this article, we systematically…
Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static folded structures, modeling protein motions on microsecond to…
Flux balance analysis has proven an effective tool for analyzing metabolic networks. In flux balance analysis, reaction rates and optimal pathways are ascertained by solving a linear program, in which the growth rate is maximized subject to…
We present a graph theory-based method to characterise flow defects and structural shifts in condensed matter. We explore the connection between dynamical properties, particularly the recently introduced concept of ''softness'', and…
Transcription Factors (TFs) are proteins that regulate gene expression. The regulation mechanism is via the binding of a TF to a specific part of the gene associated with it, the TF's target. The target of a specific TF corresponds to a…
Ultrafast spectroscopy is an important tool for studying photoinduced dynamical processes in atoms, molecules, and nanostructures. Typically, the time to perform these experiments ranges from several minutes to hours depending on the choice…
Phenotypic heterogeneity is a most fascinating property of a population of cells, which shows the differences among individuals even with the same genetic background and extracellular environmental conditions. However, the lack of…
Cells regulate themselves via dizzyingly complex biochemical processes called signaling pathways. These are usually depicted as a network, where nodes represent proteins and edges indicate their influence on each other. In order to…
With the arrival of a number of wide-field snapshot image-plane radio transient surveys, there will be a huge influx of images in the coming years making it impossible to manually analyse the datasets. Automated pipelines to process the…
An important task for many if not all the scientific domains is efficient knowledge integration, testing and codification. It is often solved with model construction in a controllable computational environment. In spite of that, the…
Small-molecule drug discovery requires simultaneous optimization of numerous properties of candidate molecules. These properties can be investigated through the analysis of high-dimensional biological signatures, such as cell morphology and…
Dynamic factor models are often estimated by point-estimation methods, disregarding parameter uncertainty. We propose a method accounting for parameter uncertainty by means of posterior approximation, using variational inference. Our…
The movement of intracellular cargo transported by molecular motors is commonly marked by switches between directed motion and stationary pauses. The predominant measure for assessing movement is effective diffusivity, which predicts the…
A blood cell lineage consists of several consecutive developmental stages from the pluri- or multipotent stem cell to a state of terminal differentiation. Despite their importance for human biology, the regulatory pathways and gene networks…
Optical spectroscopy is an important and widely used technique, for instance, to characterize new materials and to identify unknown compounds. Spectra are typically reported as a function of the wavelength of light, yet the information…
Understanding how transcription factors (TFs) regulate mammalian gene expression in space and time is a central topic in biology. To activate a gene, a TF has first to diffuse in the available space of the nucleus until it reaches a target…
Transcription factors (TFs) play a vital role in the regulation of gene expression thereby making them critical to many cellular processes. In this study, we used graph machine learning methods to create a compendium of TF cascades using…