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AI systems represented by AlphaFold are rapidly expanding the scale of protein structure modelling data, and the MineProt project provides an effective solution for custom curation of these novel high-throughput data. It enables researchers…

Matrix Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS) is a cornerstone in biomolecular analysis, offering precise identification of pathogens through unique mass spectral signatures. Yet, its reliance on labor-intensive…

Motivation: Flow Injection Analysis coupled to High-Resolution Mass Spectrometry (FIA-HRMS) is a promising approach for high-throughput metabolomics. FIA-HRMS data, however, cannot be preprocessed with current software tools which rely on…

LiDRoSIS is an automated MATLAB-Python software suite for the segmentation and quantification of lipid droplets (LDs) and reactive oxygen species (ROS) in fluorescence microscopy images of irradiated A549 and MCF7 cells exposed to…

Protein identification and profiling is critical for the advancement of cell and molecular biology as well as medical diagnostics. Although mass spectrometry and protein microarrays are commonly used for protein identification, both methods…

Electron cryotomography (CryoET) is currently the only method capable of visualizing cells in 3D at nanometer resolutions. While modern instruments produce massive amounts of tomography data containing extremely rich structural information,…

Different types of spectroscopies, such as X-ray absorption near edge structure (XANES) and Raman spectroscopy, play a very important role in analyzing the characteristics of different materials. In scientific literature, XANES/Raman data…

Large web-sourced multimodal datasets have powered a slew of new methods for learning general-purpose visual representations, advancing the state of the art in computer vision and revolutionizing zero- and few-shot recognition. One crucial…

The surge in high-throughput omics data has reshaped the landscape of biological research, underlining the need for powerful, user-friendly data analysis and interpretation tools. This paper presents GenoCraft, a web-based comprehensive…

X-ray resonant magnetic reflectivity (XRMR) is a powerful method to determine the optical, structural and magnetic depth profiles of a variety of thin films. Here, we investigate samples of different complexity all measured at the Pt L$_3$…

In Proteomics, only the de novo peptide sequencing approach allows a partial amino acid sequence of a peptide to be found from a MS/MS spectrum. In this article a preliminary work is presented to discover a complete protein sequence from…

Foundation models have begun to transform image analysis by acting as pretrained generalist backbones that can be adapted to many tasks even when post-training data are limited, yet their impact on spatial proteomics, imaging that maps…

ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…

With the development of artificial intelligence, its contribution to science is evolving from simulating a complex problem to automating entire research processes and producing novel discoveries. Achieving this advancement requires both…

The R package panelPomp supports analysis of panel data via a general class of partially observed Markov process models (PanelPOMP). This package tutorial describes how the mathematical concept of a PanelPOMP is represented in the software…

The unsupervised and principled diagnosis of multi-scale data is a fundamental obstacle in modern scientific problems from, for instance, weather and climate prediction, neurology, epidemiology, and turbulence. Multi-scale data is…

Synthesis procedures play a critical role in materials research, as they directly affect material properties. With data-driven approaches increasingly accelerating materials discovery, there is growing interest in extracting synthesis…

Biological functions stem from coordinated interactions among proteins, nucleic acids and small molecules. Mass spectrometry technologies for reliable, high throughput single-cell proteomics will add a new modality to genomics and enable…

Survival data is encountered in a range of disciplines, most notably health and medical research. Although Bayesian approaches to the analysis of survival data can provide a number of benefits, they are less widely used than classical (e.g.…

Crosslinking Mass Spectrometry (MS) can uncover protein-protein interactions and provide structural information on proteins in their native cellular environments. Despite its promise, the field remains hampered by inconsistent data formats,…