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The technological advancements of the modern era have enabled the collection of huge amounts of data in science and beyond. Extracting useful information from such massive datasets is an ongoing challenge as traditional data visualization…
Raman spectroscopy's capability to provide meaningful composition predictions is heavily reliant on a pre-processing step to remove insignificant spectral variation. This is crucial in biofluid analysis. Widespread adoption of diagnostics…
The matrixdist R package provides a comprehensive suite of tools for the statistical analysis of matrix distributions, including phase-type, inhomogeneous phase-type, discrete phase-type, and related multivariate distributions. This paper…
Cryo-electron tomography enables 3D visualization of cells in a near native state at molecular resolution. The produced cellular tomograms contain detailed information about all macromolecular complexes, their structures, their abundances…
Proteomics will celebrate its 20th year in 2014. In this relatively short period of time, it has invaded most areas of biology and its use will probably continue to spread in the future. These two decades have seen a considerable increase…
This is the documentation of Computed Tomography (CT) data of a pen-spring. The open data set is available at https://zenodo.org/record/3266936#.XRyMdCZS9oA and can be freely used for scientific purposes with appropriate references to the…
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…
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…
Among the different types of skin cancer, melanoma is considered to be the deadliest and is difficult to treat at advanced stages. Detection of melanoma at earlier stages can lead to reduced mortality rates. Desktop-based computer-aided…
Metaproteomics are becoming widely used in microbiome research for gaining insights into the functional state of the microbial community. Current metaproteomics studies are generally based on high-throughput tandem mass spectrometry (MS/MS)…
Recent advances in big data and analytics research have provided a wealth of large data sets that are too big to be analyzed in their entirety, due to restrictions on computer memory or storage size. New Bayesian methods have been developed…
Diffusion-weighted magnetic resonance imaging (dMRI) is widely used to assess the brain white matter. One of the most common computations in dMRI involves cross-subject tract-specific analysis, whereby dMRI-derived biomarkers are compared…
Prokaryotic organisms usually possess compact genomes, which are particularly suitable to complete sequencing with existing technologies, which led to an escalating accumulation of available genome data. In response to this ever-expanding…
Structural dynamics of macromolecules is critical to their structural-function relationship. Cryogenic electron microscopy (CryoEM) provides snapshots of vitrified protein at different compositional and conformational states, and the…
Unbiased, label-free proteomics is becoming a powerful technique for measuring protein expression in almost any biological sample. The output of these measurements after preprocessing is a collection of features and their associated…
Our growing ability to tailor healthcare to the needs of individuals has the potential to transform clinical treatment. However, the measurement of multiple biomarkers to inform clinical decisions requires rapid, effective, and affordable…
Understanding a plant's root system architecture (RSA) is crucial for a variety of plant science problem domains including sustainability and climate adaptation. Minirhizotron (MR) technology is a widely-used approach for phenotyping RSA…
The numerical availability of statistical inference methods for a modern and robust analysis of longitudinal- and multivariate data in factorial experiments is an essential element in research and education. While existing approaches that…
Conventional histopathology has long been essential for disease diagnosis, relying on visual inspection of tissue sections. Immunohistochemistry aids in detecting specific biomarkers but is limited by its single-marker approach, restricting…
The R package trajmsm provides functions designed to simplify the estimation of the parameters of a model combining latent class growth analysis (LCGA), a trajectory analysis technique, and marginal structural models (MSMs) called LCGA-MSM.…