A5039610435- Monoclonal and Polyclonal Antibodies Research
- Advanced Proteomics Techniques and Applications
- vaccines and immunoinformatics approaches
- Protein purification and stability
- Machine Learning in Bioinformatics
- MicroRNA in disease regulation
- Cell Adhesion Molecules Research
- Protein Structure and Dynamics
- Glycosylation and Glycoproteins Research
- Bioinformatics and Genomic Networks
- Prion Diseases and Protein Misfolding
- Alzheimer's disease research and treatments
- RNA and protein synthesis mechanisms
- Extracellular vesicles in disease
- Genetics, Bioinformatics, and Biomedical Research
- Advanced Biosensing Techniques and Applications
- Cancer Genomics and Diagnostics
- Genetics, Aging, and Longevity in Model Organisms
- Gene expression and cancer classification
- Amyotrophic Lateral Sclerosis Research
- Single-cell and spatial transcriptomics
- Biochemical and Structural Characterization
- T-cell and B-cell Immunology
- Computational Drug Discovery Methods
- Genomics and Phylogenetic Studies
Vrije Universiteit Amsterdam
2020-2025
Utrecht University
2024-2025
Neurodegenerative dementias are progressive diseases that cause neuronal network breakdown in different brain regions often because of accumulation misfolded proteins the extracellular matrix, such as amyloids or inside neurons other cell types brain. Several diagnostic protein biomarkers body fluids being used and implemented, for Alzheimer's disease. However, there is still a lack co-pathologies causes dementia. Such biofluid-based enable precision medicine approaches diagnosis treatment,...
Abstract Extracellular vesicles (EVs) are membranous structures released by cells into the extracellular space and thought to be involved in cell‐to‐cell communication. While EVs their cargo promising biomarker candidates, sorting mechanisms of proteins remain unclear. In this study, we ask if it is possible determine EV association based on protein sequence. Additionally, what most important determinants for association. We answer these questions with explainable AI models, using human...
Antibodies play an important role in clinical research and biotechnology, with their specificity determined by the interaction antigen's epitope region, as a special type of protein-protein (PPI) interface. The ubiquitous availability sequence data, allows us to predict epitopes from order focus time-consuming wet-lab experiments toward most promising regions. Here, we extend our previously developed sequence-based predictors for homodimer heterodimer PPI interfaces residues that have...
Antibodies are indispensable in laboratory and clinical applications due to their high specificity affinity for protein antigens. However, selecting the right fragments as immunogens antibody production remains challenging. Leveraging Human Protein Atlas, this study systematically evaluates immunogen properties aiming identify key factors that influence suitability. were classified successful or unsuccessful based on standardized validation experiments, structural functional of analyzed....
The ubiquitous availability of genome sequencing data explains the popularity machine learning-based methods for prediction protein properties from their amino acid sequences. Over years, while revising our own work, reading submitted manuscripts as well published papers, we have noticed several recurring issues, which make some reported findings hard to understand and replicate. We suspect this may be due biologists being unfamiliar with learning methodology, or conversely, experts miss...
Repertoire sequencing allows us to investigate the antibody-mediated immune response. The clustering of sequences is a crucial step in data analysis pipeline, aiding identification functionally related antibodies. conventional approach clonotyping relies on sequence information, particularly CDRH3 identity and V/J gene usage, group into clonotypes. It has been suggested that limitations sequence-based approaches identify sequence-dissimilar but converged antibodies can be overcome by using...
Proteomics studies have shown differential expression of numerous proteins in dementias but rarely led to novel biomarker tests for clinical use. The Marie Curie MIRIADE project is designed experimentally evaluate development strategies accelerate the validation and ultimate implementation biomarkers practice, using proteomics-based main as experimental case studies. We address several knowledge gaps that been identified field. First, there technology-translation gap different technologies...
Cerebrospinal fluid (CSF) is an essential matrix for the discovery of neurological disease biomarkers. However, high dynamic range protein concentrations in CSF hinders detection least abundant biomarkers by untargeted mass spectrometry. It thus beneficial to gain a deeper understanding secretion processes within brain. Here, we aim explore if and how brain proteins can be predicted. By combining curated proteome elevated Human Protein Atlas, were classified as or non-CSF secreted. A machine...
Abstract Background Quantification of tumor heterogeneity is essential to better understand cancer progression and adapt therapeutic treatments patient specificities. Bioinformatic tools assess the different cell populations from single-omic datasets as bulk transcriptome or methylome samples have been recently developed, including reference-based reference-free methods. Improved methods using multi-omic are yet be developed in future community would need systematic perform a comparative...
Abstract Extracellular vesicles (EVs) are membranous structures released by cells into the extracellular space and thought to be involved in cell-to-cell communication. While EVs their cargo promising biomarker candidates, protein sorting mechanisms of proteins remain unclear. In this study, we ask if it is possible determine EV association based on sequence. Additionally, what most important determinants for association. We answer these questions with explainable AI models, using human...
Abstract Motivation Antibodies play an important role in clinical research and biotechnology, with their specificity determined by the interaction antigen’s epitope region, as a special type of protein-protein (PPI) interface. The ubiquitous availability sequence data, allows us to predicting epitopes from order focus time-consuming wet-lab experiments onto most promising regions. Here, we extend our previously developed sequence-based predictors for homodimer heterodimer PPI interfaces...
Repertoire sequencing allows us to investigate the antibody-mediated immune response. The clustering of sequences is a crucial step in data analysis pipeline, aiding identification functionally related antibodies. conventional approach clonotyping relies on sequence information, particularly CDRH3 identity and V/J gene usage, group into clonotypes. It has been suggested that limitations sequence-based approaches identify sequence-dissimilar but converged antibodies can be overcome by using...
ABSTRACT Antibodies are indispensable in laboratory and clinical applications due to their high specificity affinity for protein antigens. However, selecting the right fragments as immunogens antibody production remains challenging. Leveraging Human Protein Atlas, this study systematically evaluates immunogen properties aiming identify key factors that influence suitability. were classified successful or unsuccessful based on standardized validation experiments, structural functional of...
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no introductory level book for the field of Structural Bioinformatics. This aims to give an introduction into Bioinformatics, which where previous topics meet explore three dimensional protein structures through computational analysis. We provide overview existing techniques, validate, simulate, predict analyse structures. More importantly, it...
Discovery of novel protein biomarkers for clinical applications is an active research field across a manifold diseases. Despite some successes and progress, the biomarker development pipeline still frequently ends in failure as candidates cannot be validated or translated to immunoassays. Selection strong disease that further constitute suitable targets antibody binding immunoassays thus important. This essential selection step can supported rationalized using bioinformatics tools such...
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no introductory level book for the field of Structural Bioinformatics. This aims to give an introduction into Bioinformatics, which where previous topics meet explore three dimensional protein structures through computational analysis. We provide overview existing techniques, validate, simulate, predict analyse structures. More importantly, it...