Related papers: TraianProt: a user-friendly R shiny application fo…
Theranostics, the combination of diagnosis and therapy, has long held promise as a means to achieving personalised precision cancer treatments. However, despite its potential, theranostics has yet to realise significant clinical…
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins…
Imaging mass spectrometry (IMS) has transformed proteomics by providing an avenue for collecting spatially distributed molecular data. Mass spectrometry data acquired with matrix assisted laser desorption ionization (MALDI) IMS consist of…
Liquid Chromatography coupled to Mass Spectrometry (LC-MS) based methods are commonly used for high-throughput, quantitative measurements of the proteome (i.e. the set of all proteins in a sample at a given time). Targeted LC-MS produces…
The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools…
High-throughput technologies to collect field data have made observations possible at scale in several branches of life sciences. The data collected can range from the molecular level (genotypes) to physiological (phenotypic traits) and…
Current histopathological grading of prostate cancer relies primarily on glandular architecture, largely overlooking the tumor microenvironment. Here, we present PROTAS, a deep learning framework that quantifies reactive stroma (RS) in…
Motivation: The visualization and analysis of high-dimensional data are essential in biomedical research. There is a need for secure, scalable, and reproducible tools to facilitate data exploration and interpretation. Results: We introduce…
We describe a computer application designed to analyze hyperspectral data collected by the Compact Infrared Spectrometer for Mars (CRISM). The application links the spectral, imaging and mapping perspectives on the eventual CRISM dataset by…
This paper introduces PROTEUS, a fully automated system that produces data-driven hypotheses from raw data files. We apply PROTEUS to clinical proteogenomics, a field where effective downstream data analysis and hypothesis proposal is…
Summary: Biospectrogam is an open-source software for the spectral analysis of DNA and protein sequences. The software can fetch (from NCBI server), import and manage biological data. One can analyze the data using Digital Signal Processing…
Tabulated content is omnipresent in scientific literature. This work presents the R package *tableParser*, designed to extract and postprocess tables from NISO-JATS-encoded XML, HTML, DOCX, and, with limitations, PDF documents.…
We present ProbMetab, an R package which promotes substantial improvement in automatic probabilistic LC-MS based metabolome annotation. The inference engine core is based on a Bayesian model implemented to: (i) allow diverse source of…
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…
We present AngstromPro, a versatile, modular and open-source software built on Python for managing, visualizing and analyzing large datasets acquired via Scanning Tunneling Microscopes (STM). Its robust architecture features a top-level…
Omic data are characterized by the presence of strong dependence structures that result either from data acquisition or from some underlying biological processes. In metabolomics, for instance, data resulting from Liquid Chromatography-Mass…
MALDIquant and associated R packages provide a versatile and completely free open-source platform for analyzing 2D mass spectrometry data as generated for instance by MALDI and SELDI instruments. We first describe the various methods and…
Liquid chromatography mass spectrometry (LC-MS)-based metabolomics and exposomics aim to measure detectable small molecules in biological samples. The results facilitate hypothesis-generating discovery of metabolic changes and disease…
Atom probe tomography (APT) has matured to a versatile nanoanalytical characterization tool with applications that range from materials science to geology and possibly beyond. Already, well over 100 APT microscopes exist worldwide.…
Analyzing proteins from single cells by tandem mass spectrometry (MS) has become technically feasible. While such analysis has the potential to accurately quantify thousands of proteins across thousands of single cells, the accuracy and…