A5038356859- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- Bioinformatics and Genomic Networks
- RNA and protein synthesis mechanisms
- Biomedical Text Mining and Ontologies
- Genetics, Bioinformatics, and Biomedical Research
- Scientific Computing and Data Management
- Gene expression and cancer classification
- Advanced Biosensing Techniques and Applications
- vaccines and immunoinformatics approaches
- Cancer-related molecular mechanisms research
- Identification and Quantification in Food
- Computational Drug Discovery Methods
- Cell Image Analysis Techniques
- Advanced biosensing and bioanalysis techniques
- RNA modifications and cancer
- Analytical Chemistry and Chromatography
- Biosensors and Analytical Detection
- Enzyme Structure and Function
- Peptidase Inhibition and Analysis
- Single-cell and spatial transcriptomics
- Cellular Mechanics and Interactions
VIB-UGent Center for Medical Biotechnology
2016-2025
Ghent University
2016-2025
Ghent University Hospital
2013-2025
Université de Strasbourg
2025
Centre National de la Recherche Scientifique
2025
Vlaams Instituut voor Biotechnologie
2002-2023
European Bioinformatics Institute
2006-2023
KU Leuven
2023
Medical Genetics Center
2021
University of Manchester
2020
Mass spectrometry is a fundamental tool for discovery and analysis in the life sciences. With rapid advances mass technology methods, it has become imperative to provide standard output format data that will facilitate sharing analysis. Initially, efforts develop resulted multiple formats, each designed with different underlying philosophy. To resolve issues associated having vendors, researchers, software developers convened under banner of HUPO PSI single standard. The new incorporated...
Abstract The advent of high‐throughput proteomics has enabled the identification ever increasing numbers proteins. Correspondingly, number publications centered on these protein identifications increased dramatically. With first results HUPO Plasma Proteome Project being analyzed and many other large‐scale projects about to disseminate their data, this trend is not likely flatten out any time soon. However, publication mechanism identified proteins lagged behind in technical terms. Often...
While long non-coding RNA (lncRNA) research in the past has primarily focused on discovery of novel genes, today it shifted towards functional annotation this large class genes. With thousands lncRNA studies published every year, current challenge lies keeping track which lncRNAs are functionally described. This is further complicated by fact that nomenclature not straightforward and scattered across different resources with their own quality metrics definition a lncRNA. To overcome issue,...
Here, we present LNCipedia (http://www.lncipedia.org), a novel database for human long non-coding RNA (lncRNA) transcripts and genes. LncRNAs constitute large diverse class of Although several lncRNAs have been functionally annotated, the majority remains to be characterized. Different high-throughput methods identify new (including sequencing annotation chromatin-state maps) applied in various studies resulting multiple unrelated lncRNA data sets. offers 21 488 annotated obtained from...
High-throughput sequencing of full-length transcripts using long reads has paved the way for discovery thousands novel transcripts, even in well-annotated mammalian species. The advances technology have created a need studies and tools that can characterize these variants. Here, we present SQANTI, an automated pipeline classification long-read assess quality data preprocessing 47 unique descriptors. We apply SQANTI to neuronal mouse transcriptome Pacific Biosciences (PacBio) illustrate how...
Abstract The identification of proteins by mass spectrometry is a standard technique in the field proteomics, relying on search engines to perform identifications acquired spectra. Here, we present user‐friendly, lightweight and open‐source graphical user interface called SearchGUI ( http://searchgui.googlecode.com ), for configuring running freely available OMSSA (open algorithm) X!Tandem simultaneously. Freely under permissible Apache2 license, supported Windows, Linux OSX.
The human genome is pervasively transcribed, producing thousands of non-coding RNA transcripts. majority these transcripts are long RNAs (lncRNAs) and novel lncRNA genes being identified at rapid pace. To streamline efforts, we created LNCipedia, an online repository annotation. Here, present LNCipedia 3.0 (http://www.lncipedia.org), the latest version publicly available database. Compared to previous database grew over five times in size, gaining 90 000 new Assessment protein-coding...
The Proteomics Identifications database (PRIDE, http://www.ebi.ac.uk/pride) at the European Bioinformatics Institute has become one of main repositories mass spectrometry-derived proteomics data. For last 2 years, PRIDE data holdings have grown substantially, comprising 60 different species, more than 2.5 million protein identifications, 11.5 peptides and over 50 spectra by September 2009. We here describe several new improved features in PRIDE, including revised submission process, which...
The field of computational proteomics is approaching the big data age, driven both by a continuous growth in number samples analyzed per experiment as well growing amount obtained each analytical run. In order to process these large amounts data, it increasingly necessary use elastic compute resources such Linux-based cluster environments and cloud infrastructures. Unfortunately, vast majority cross-platform tools are not able operate directly on proprietary formats generated diverse mass...
The enormous challenges of mass spectrometry-based metaproteomics are primarily related to the analysis and interpretation acquired data. This includes reliable identification spectra meaningful integration taxonomic functional meta-information from samples containing hundreds unknown species. To ease these difficulties, we developed a dedicated software suite, MetaProteomeAnalyzer, an intuitive open-source tool for data interpretation, which multiple search engines feature decrease...
The placenta is the interface between mother and fetus inadequate function contributes to short long-term ill-health. absent from most large-scale RNA-Seq datasets. We therefore analyze long small RNAs (~101 20 million reads per sample respectively) 302 human placentas, including 94 cases of preeclampsia (PE) 56 fetal growth restriction (FGR). placental transcriptome has seventh lowest complexity 50 tissues: 271 genes account for 50% all reads. identify multiple circular validate 6 these by...
Immunopeptidomics aims to identify major histocompatibility complex (MHC)-presented peptides on almost all cells that can be used in anti-cancer vaccine development. However, existing immunopeptidomics data analysis pipelines suffer from the nontryptic nature of immunopeptides, complicating their identification. Previously, peak intensity predictions by MS2PIP and retention time DeepLC have been shown improve tryptic peptide identifications when rescoring peptide-spectrum matches with...
Abstract Human leukocyte antigen (HLA) class I peptide ligands (HLAIps) are key targets for developing vaccines and immunotherapies against infectious pathogens or cancer cells. Identifying HLAIps is challenging due to their high diversity, low abundance, patient individuality. Here, we develop a highly sensitive method identifying using liquid chromatography-ion mobility-tandem mass spectrometry (LC-IMS-MS/MS). In addition, train timsTOF-specific peak intensity MS 2 PIP model tryptic...
Abstract The Proteomics Identifications Database (PRIDE, www.ebi.ac.uk/pride ) is one of the main repositories MS derived proteomics data. Here, we point out functionalities PRIDE both as a submission repository and source for We describe features data retrieval visualization available through web BioMart interfaces. also highlight mechanism by which tailored queries in can join to other resources such Reactome, Ensembl or UniProt execute extremely powerful across‐domain queries. then...
A novel gel-free proteomic technology was used to identify more than 800 proteins from 50 million Escherichia coli K12 cells in a single analysis. peptide mixture is first obtained total unfractionated cell lysate, and only the methionine-containing peptides are isolated identified by mass spectrometry database searching. The sorting procedure based on concept of diagonal chromatography but adapted for highly complex mixtures. Statistical analysis predicts that we have 40% expressed...