Manuel Luypaert
A5065506125- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Biomedical Text Mining and Ontologies
- Molecular Biology Techniques and Applications
- Genetics, Aging, and Longevity in Model Organisms
- RNA Research and Splicing
- Evolution and Genetic Dynamics
- Sarcoma Diagnosis and Treatment
- Single-cell and spatial transcriptomics
- Genetics, Bioinformatics, and Biomedical Research
- CRISPR and Genetic Engineering
- Cancer-related molecular mechanisms research
- Genomics and Rare Diseases
- Gene expression and cancer classification
- Microbial Community Ecology and Physiology
Wellcome Trust
2022-2024
European Bioinformatics Institute
2021-2024
Ghent University Hospital
2017
RNA-sequencing has become the gold standard for whole-transcriptome gene expression quantification. Multiple algorithms have been developed to derive counts from sequencing reads. While a number of benchmarking studies conducted, question remains how individual methods perform at accurately quantifying levels We performed an independent study using data well established MAQCA and MAQCB reference samples. reads were processed five workflows (Tophat-HTSeq, Tophat-Cufflinks, STAR-HTSeq,...
Abstract Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the project (https://www.ensembl.org). The two collectively present genome annotation through a consistent set of interfaces spanning tree life presenting sequence, annotation, variation, transcriptomic data comparative analysis. Here, we our largest increase in plant, metazoan fungal since project's inception creating one world's...
Abstract WormBase (www.wormbase.org) is the central repository for genetics and genomics of nematode Caenorhabditis elegans. We provide research community with data tools to facilitate use C. elegans related nematodes as model organisms studying human health, development, many aspects fundamental biology. Throughout our 22-year history, we have continued evolve reflect progress innovation in science technologies involved study strive incorporate new types richer sets, integrated displays...
The Alliance of Genome Resources (the Alliance) is a combined effort 7 knowledgebase projects: Saccharomyces Database, WormBase, FlyBase, Mouse the Zebrafish Information Network, Rat and Gene Ontology Resource. seeks to provide several benefits: better service various communities served by these projects; harmonized view data for all biomedical researchers, bioinformaticians, clinicians, students; more sustainable infrastructure. has cross-organism useful comparative views gene function,...
Abstract WormBase has been the major repository and knowledgebase of information about genome genetics Caenorhabditis elegans other nematodes experimental interest for over 2 decades. We have 3 goals: to keep current with fast-paced C. research, provide better integration resources, be sustainable. Here, we discuss state as well progress plans moving core infrastructure Alliance Genome Resources (the Alliance). As an member, will continue interact community, develop new features needed,...
Abstract The Alliance of Genome Resources (Alliance) is an extensible coalition knowledgebases focused on the genetics and genomics intensively studied model organisms. organized as individual knowledge centers with strong connections to their research communities a centralized software infrastructure, discussed here. Model organisms currently represented in are budding yeast, Caenorhabditis elegans, Drosophila, zebrafish, frog, laboratory mouse, rat, Gene Ontology Consortium. project rapid...
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We assess the performance of mRNA capture sequencing to identify fusion transcripts in FFPE tissue different sarcoma types, followed by RT-qPCR confirmation. To validate our workflow, six positive control tumors with a specific chromosomal rearrangement were analyzed using TruSight RNA Pan-Cancer Panel. Fusion transcript calling FusionCatcher confirmed these aberrations and enabled identification both gene partners breakpoints. Next, whole-transcriptome TruSeq Exome was applied 17...
Abstract The Alliance of Genome Resources (Alliance) is an extensible coalition knowledgebases focused on the genetics and genomics intensively-studied model organisms. organized as individual knowledge centers with strong connections to their research communities a centralized software infrastructure, discussed here. Model organisms currently represented in are budding yeast, C. elegans , Drosophila zebrafish, frog, laboratory mouse, rat, Gene Ontology Consortium. project rapid development...