Related papers: TraianProt: a user-friendly R shiny application fo…
BioStatFlow is a free web application, useful to facilitate the performance of statistical analyses of "omics", including metabolomics, data using R packages. It is a fast and easy on-line tool for biologists who are not experts in…
Metaproteomics has become a crucial omics technology for studying microbiomes. In this area, the Unipept ecosystem, accessible at https://unipept.ugent.be, has emerged as an invaluable resource for analyzing metaproteomic data. It offers…
Deep learning models for skin disease classification require large, diverse, and well-annotated datasets. However, such resources are often limited due to privacy concerns, high annotation costs, and insufficient demographic representation.…
For scientific knowledge to be findable, accessible, interoperable, and reusable, it needs to be machine-readable. Moving forward from post-publication extraction of knowledge, we adopted a pre-publication approach to write research…
This paper presents an approach to the evaluation and validation of mass spectrometry data for construction of an `early warning' diagnostic procedure. We describe implementation of a designed experiment and place emphasis on the consistent…
Persistent homology has been devised as a promising tool for the topological simplification of complex data. However, it is computationally intractable for large data sets. In this work, we introduce multiresolution persistent homology for…
Enhancing cryogenic electron microscopy (cryo-EM) 3D density maps at intermediate resolution (4-8 {\AA}) is crucial in protein structure determination. Recent advances in deep learning have led to the development of automated approaches for…
Radiology reports capture crucial longitudinal information on tumor burden, treatment response, and disease progression, yet their unstructured narrative format complicates automated analysis. While large language models (LLMs) have…
Dynamo is a full-stack software solution for scientific data management. Dynamo's architecture is modular, extensible, and customizable, making the software suitable for managing data in a wide range of installation scales, from a few…
Purpose: The XCAT phantom allows for highly sophisticated multimodality imaging research. It includes a complete set of organs, muscle, bone, soft tissue, while also accounting for age, sex, and body mass index (BMI), which allows phantom…
Medical document analysis plays a crucial role in extracting essential clinical insights from unstructured healthcare records, supporting critical tasks such as differential diagnosis. Determining the most probable condition among…
This paper introduces the \proglang{R} package \pkg{meta4diag} for implementing Bayesian bivariate meta-analyses of diagnostic test studies. Our package \pkg{meta4diag} is a purpose-built front end of the \proglang{R} package \pkg{INLA}.…
When studying multi-body protein complexes, biochemists use computational tools that can suggest hundreds or thousands of their possible spatial configurations. However, it is not feasible to experimentally verify more than only a very…
We propose an image synthesis mechanism for multi-sequence prostate MR images conditioned on text, to control lesion presence and sequence, as well as to generate paired bi-parametric images conditioned on images e.g. for generating…
We present TA-DA, a new software aimed at greatly simplify and improve the analysis of stellar photometric data in comparison with theoretical models, and allow the derivation of stellar parameters from multi-band photometry. Its…
Motivation: We introduce TRONCO (TRanslational ONCOlogy), an open-source R package that implements the state-of-the-art algorithms for the inference of cancer progression models from (epi)genomic mutational profiles. TRONCO can be used to…
Mass spectrometry-based metabolomic analysis depends upon the identification of spectral peaks by their mass and retention time. Statistical analysis that follows the identification currently relies on one main peak of each compound.…
Hyperspectral remote sensing is a promising tool for a variety of applications including ecology, geology, analytical chemistry and medical research. This article presents the new \hsdar package for R statistical software, which performs a…
Recent advancements in deep learning for automated image processing and classification have accelerated many new applications for medical image analysis. However, most deep learning applications have been developed using reconstructed,…
With the advent of GPU-assisted hardware and maturing high-efficiency software platforms such as TensorFlow and PyTorch, Bayesian posterior sampling for neural networks becomes plausible. In this article we discuss Bayesian parametrization…