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Single-cell RNA-sequencing technologies may provide valuable insights to the understanding of the composition of different cell types and their functions within a tissue. Recent technologies such as spatial transcriptomics, enable the…
Human and animal tissues consist of heterogeneous cell types that organize and interact in highly structured manners. Bulk and single-cell sequencing technologies remove cells from their original microenvironments, resulting in a loss of…
We present a novel method for automated identification of putative cell types from single-cell RNA-seq (scRNA-seq) data. By iteratively applying a machine learning approach to an initial clustering of gene expression profiles of a given set…
The increasing availability of high-quality optical and near-infrared spectroscopic data, as well as advances in modelling techniques, have greatly expanded the scientific potential of spectroscopic studies. However, the software tools…
Statistical Model Checking (SMC) is a trade-off between testing and formal verification. The core idea of the approach is to conduct some simulations of the system and verify if they satisfy some given property. In this paper we show that…
Computer-based scientific experiments are becoming increasingly data-intensive, necessitating the use of High-Performance Computing (HPC) clusters to handle large scientific workflows. These workflows result in complex data and control…
Identifying cell clusters is a critical step for single-cell transcriptomics study. Despite the numerous clustering tools developed recently, the rapid growth of scRNA-seq volumes prompts for a more (computationally) efficient clustering…
The genome-scale metabolic model with protein constraint (PC-model) has been increasingly popular for microbial metabolic simulations. We present PROSO Toolbox, a unified and simple-to-use PC-model toolbox that takes any high-quality…
In this article an SPC case study is presented. It consists of monitoring a manufacturing process used for different products of similar kind. So far, each of these products is monitored individually. However, if there is e.g. a quality…
We develop an iterative subsampling approach to improve the computational efficiency of our previous work on solution path clustering (SPC). The SPC method achieves clustering by concave regularization on the pairwise distances between…
The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of…
Time series segmentation aims to identify potential change-points in a sequence of temporally dependent data, so that the original sequence can be partitioned into several homogeneous subsequences. It is useful for modeling and predicting…
Recently, many software tools have been developed to perform quantification in LC-MS analyses. However, most of them are specific to either a quantification strategy (e.g. label-free or isotopic labelling) or a mass-spectrometry system…
Modern parallel computing devices, such as the graphics processing unit (GPU), have gained significant traction in scientific and statistical computing. They are particularly well-suited to data-parallel algorithms such as the particle…
Motivation: Recent advances in single-cell analysis have introduced new computational challenges. Researchers often need to use multiple analysis tools written in different programming languages while managing version conflicts between…
Traditional regression models assume stationary relationships between predictors and responses, failing to capture the spatial heterogeneity present in many environmental, epidemiological, and ecological processes. To address this…
Tomographic imaging has benefited from advances in X-ray sources, detectors and optics to enable novel observations in science, engineering and medicine. These advances have come with a dramatic increase of input data in the form of faster…
The customers and users need for new products and services according to high-quality standards have increased in the last time. In that sense, the production processes must be aligned with the organization and development process in order…
We present Full SMS, a multipurpose graphical user interface (GUI)-based software package for analysing single-molecule spectroscopy (SMS) data. SMS typically delivers multiparameter data -- such as fluorescence brightness, lifetime, and…
Single-cell RNA sequencing technologies have revolutionized our understanding of cellular heterogeneity, yet computational methods often struggle to balance performance with biological interpretability. Embedded topic models have been…