A5015802960- Advanced Proteomics Techniques and Applications
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Metabolomics and Mass Spectrometry Studies
- Gut microbiota and health
- Teaching and Learning Programming
- Cystic Fibrosis Research Advances
- Scientific Measurement and Uncertainty Evaluation
- Microbial Community Ecology and Physiology
- Software Engineering Research
- Online Learning and Analytics
- Academic integrity and plagiarism
- Scientific Computing and Data Management
- Machine Learning in Bioinformatics
- Advanced MRI Techniques and Applications
- Theoretical and Computational Physics
- Intelligent Tutoring Systems and Adaptive Learning
- Oral microbiology and periodontitis research
- Electron Spin Resonance Studies
- Gene expression and cancer classification
- Advanced Malware Detection Techniques
- Biomedical Text Mining and Ontologies
- Tracheal and airway disorders
- Probiotics and Fermented Foods
- Software Testing and Debugging Techniques
Ghent University Hospital
2020-2025
Ghent University
2016-2025
VIB-UGent Center for Medical Biotechnology
2017-2025
Hôpital Beaujon
2015
Unipept (https://unipept.ugent.be) is a web application for metaproteome data analysis, with an initial focus on tryptic-peptide-based biodiversity analysis of MS/MS samples. Because the true potential metaproteomics lies in gaining insight into expressed functions complex environmental samples, 4.0 release introduces complementary functional based GO terms and EC numbers. Integration this new existing important asset extended pipeline. As proof concept, human faecal set from 15 healthy...
The Unipept web application (http://unipept.ugent.be) supports biodiversity analysis of large and complex metaproteome samples using tryptic peptide information obtained from shotgun MS/MS experiments. Its underlying index structure is designed to quickly retrieve all occurrences a in UniProtKB records. Taxon-specificity the successively derived these novel lowest common ancestor approach that robust against taxonomic misarrangements, misidentifications, inaccuracies. Not taking into account...
Unipept ( http://unipept.ugent.be ) is a web application that offers user‐friendly way to explore the biodiversity of complex metaproteome samples by providing interactive visualizations. In this article, updates and changes since its initial release are presented. This includes addition sunburst treeview visualizations multipeptide analysis, foundations an programming interface (API) command line interface, updated data sources, open‐sourcing entire under MIT license.
Abstract Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out community-driven, multi-laboratory comparison metaproteomics: critical assessment metaproteome investigation study (CAMPI). Based well-established workflows, evaluate effect sample preparation, mass spectrometry, and bioinformatic analysis using two...
Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As primary catalytic and structural components of provide unique insights into active processes ecological roles communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding ecology, interactions, functional dynamics. This review, developed by Initiative...
Unipept, a pioneering software tool in metaproteomics, has significantly advanced the analysis of complex ecosystems by facilitating both taxonomic and functional insights from environmental samples. From onset, Unipept's capabilities focused on tryptic peptides, utilizing predictability consistency trypsin digestion to efficiently construct protein reference database. However, evolving landscape proteomics emerging fields like immunopeptidomics necessitate more versatile approach that...
Abstract Chitin is a valuable peat substrate amendment by increasing lettuce growth and reducing the survival of zoonotic pathogen Salmonella enterica on leaves. The production chitin-catabolic enzymes (chitinases) play crucial role are mediated through microbial community. A higher abundance plant-growth promoting microorganisms genera involved in N chitin metabolism present chitin-enriched substrate. In this study, we hypothesize that addition to stimulates chitinase production....
Unipept is an open source web application that designed for metaproteomics analysis with a focus on interactive datavisualization. It underpinned by fast index built from UniProtKB and the NCBI taxonomy enables quick retrieval of all UniProt entries in which given tryptic peptide occurs. version 2.4 introduced services provide programmatic access to features. This integration functionality custom applications data processing pipelines.The are freely available at http://api.unipept.ugent.be...
To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional relevance expressed microbial genes or proteins. This can be accomplished through metaproteomics, which characterizes protein expression microbiomes. Several software tools exist for analyzing microbiomes at level by measuring their combined proteome-level response to environmental perturbations. In this survey, we explore performance six available tools, enable make informed decisions regarding...
Unipept Desktop 2.0 is the most recent iteration of tool that adds support for analysis metaproteogenomics datasets. now supports automatic construction targeted protein reference databases only contain proteins (originating from UniProtKB resource) associated with a predetermined list taxa. This improves both taxonomic and functional resolution metaproteomic yields several technical advantages. By limiting present in database, it also possible to perform (meta)proteogenomics analyses. Since...
The impact of microbial communities, also known as the microbiome, on human health and environment is receiving increased attention. Studying translated gene products (proteins) comparing metaproteomic profiles may elucidate how microbiomes respond to specific environmental stimuli, interact with host organisms. Characterizing proteins expressed by a complex microbiome interpreting their functional signature requires sophisticated informatics tools workflows tailored metaproteomics....
Metaproteomics has become an important research tool to study microbial systems, which resulted in increased metaproteomics data generation. However, efficient tools for processing the acquired have lagged behind. One widely used interpretation is Unipept, a web-based that provides, among others, interactive and insightful visualizations. Due its implementation, however, Unipept web application limited amount of can be analyzed. In this manuscript we therefore present Desktop, desktop...
Abstract Background Learning to code is increasingly embedded in secondary and higher education curricula, where solving programming exercises plays an important role the learning process formative summative assessment. Unfortunately, students admit that copying from each other a common practice teachers indicate they rarely use plagiarism detection tools. Objectives We want lower barrier for detect by introducing new source tool (Dolos) powered state‐of‐the art similarity algorithms, offers...
Abstract Unipept, a pioneering software tool in metaproteomics, has significantly advanced the analysis of complex ecosystems by facilitating both taxonomic and functional insights from environmental samples. From onset, Unipept’s capabilities focused on tryptic peptides, utilizing predictability consistency trypsin digestion to efficiently construct protein reference database. However, evolving landscape proteomics emerging fields like immunopeptidomics necessitate more versatile approach...
One Health seeks to integrate and balance the health of humans, animals, environmental systems. These three spheres are intricately interconnected through microbiomes, which universally present exchange microbes genes, influencing not only human animal but also key environmental, agricultural, biotechnological processes. Preventing emergence pathogens as well monitoring controlling composition microbiomes microbial effectors including virulence factors, toxins, antibiotics, non-ribosomal...
Background: Metaproteomics, the study of collective proteome within microbial ecosystems, has gained increasing interest over past decade. However, peptide identification rates in metaproteomics remain low compared to single-species proteomics. A key challenge is limited sequence resolution current algorithms, which were primarily designed for analyses. To address this, we applied machine learning-driven MS 2 Rescore tool multiple datasets from diverse environments and benchmark studies....
Pattern matching is a fundamental challenge in bioinformatics, especially the fields of genomics, transcriptomics and proteomics. Efficient indexing structures, such as suffix arrays, are critical for searching large datasets. While sparse arrays offer significant memory savings compared to full they typically still require construction array prior sampling step, resulting substantial overhead during phase. We present an alternative method directly construct using simple, yet powerful text...
Liquid chromatography–mass spectrometry (LC-MS/MS) extends the matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) Zooarcheology by Mass Spectrometry (ZooMS) "mass fingerprinting" approach to species identification providing fragmentation spectra for each peptide. However, ancient bone samples generate sparse data containing only a few collagen proteins, rendering target–decoy strategies unusable and increasing uncertainty in peptide annotation. To ameliorate this issue,...
Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As primary catalytic and structural components of provide unique insights into active processes ecological roles communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding ecology, interactions, functional dynamics. This review, developed by Initiative...
Microbiome research offers promising insights into the impact of microorganisms on biological systems. Metaproteomics, study microbial proteins at community level, integrates genomic, transcriptomic, and proteomic data to determine taxonomic functional state a microbiome. However, standard metaproteomics software is subject several limitations, commonly supporting only spectral counts, emphasizing exploratory analysis rather than hypothesis testing rarely offering ability analyze interaction...