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Protein interaction networks (PIN) are popular means to visualize the proteome. However, PIN datasets are known to be noisy, incomplete and biased by the experimental protocols used to detect protein interactions. This paper aims at…
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…
Mass spectrometry (MS) plays a critical role in molecular identification, significantly advancing scientific discovery. However, structure elucidation from MS data remains challenging due to the scarcity of annotated spectra. While…
The use of synthetic data has emerged as an essential tool in Magnetic Resonance Spectroscopy (MRS) research and applications, providing advantages for optimization of acquisition, software validation, deep learning applications, and…
Machine learning tools have empowered a qualitatively new way to perform differential cross section measurements whereby the data are unbinned, possibly in many dimensions. Unbinned measurements can enable, improve, or at least simplify…
Multiple sequence alignments (MSAs) of proteins encode rich biological information and have been workhorses in bioinformatic methods for tasks like protein design and protein structure prediction for decades. Recent breakthroughs like…
Scientific research relies on well-structured, standardized data; however, much of it is stored in formats such as free-text lab notebooks, non-standardized spreadsheets, or data repositories. This lack of structure challenges…
Microbial identification is a central issue in microbiology, in particular in the fields of infectious diseases diagnosis and industrial quality control. The concept of species is tightly linked to the concept of biological and clinical…
Real-world data such as digital images, MRI scans and electroencephalography signals are naturally represented as matrices with structural information. Most existing classifiers aim to capture these structures by regularizing the regression…
Mass spectrometry has experienced a rapid development since its first application for protein analysis in the 1980s. While the most common use of mass spectrometry for protein analysis is identification and quantification workflows on…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
Record linkage is the process of bringing together the same entity from overlapping data sources while removing duplicates. Huge amounts of data are now being collected by public or private organizations as well as by researchers and…
Machine learning (ML) is poised to drive innovations in clinical microbiomics, such as in disease diagnostics and prognostics. However, the successful implementation of ML in these domains necessitates the development of reproducible,…
The effective utilization of structural information in data while ensuring statistical validity poses a significant challenge in false discovery rate (FDR) analyses. Conformal inference provides rigorous theory for grounding complex machine…
By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to…
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…
To ensure the fairness and trustworthiness of machine learning (ML) systems, recent legislative initiatives and relevant research in the ML community have pointed out the need to document the data used to train ML models. Besides,…
When nanoparticles (NPs) are introduced into a biological solution, layers of biomolecules form on their surface, creating a corona. Understanding how the structure of the protein evolves into the corona is essential for evaluating the…
Magnetic resonance spectroscopic imaging is a widely available imaging modality that can non-invasively provide a metabolic profile of the tissue of interest, yet is challenging to integrate clinically. One major reason is the expensive,…
Accurate identification of protein nucleic-acid-binding residues poses a significant challenge with important implications for various biological processes and drug design. Many typical computational methods for protein analysis rely on a…