A5021426410- Genomics and Phylogenetic Studies
- Microbial Metabolic Engineering and Bioproduction
- Biofuel production and bioconversion
- Bioinformatics and Genomic Networks
- CRISPR and Genetic Engineering
- Insect symbiosis and bacterial influences
- RNA and protein synthesis mechanisms
- Chromosomal and Genetic Variations
- Genetics, Bioinformatics, and Biomedical Research
- Gene expression and cancer classification
- Enzyme Catalysis and Immobilization
- Algal biology and biofuel production
- Insect and Arachnid Ecology and Behavior
- Invertebrate Immune Response Mechanisms
- Bioeconomy and Sustainability Development
- Machine Learning in Bioinformatics
- Gene Regulatory Network Analysis
- Medical Imaging and Analysis
- Genomics and Chromatin Dynamics
- Cellular transport and secretion
- Spinal Fractures and Fixation Techniques
- Biomedical Text Mining and Ontologies
- Plant and animal studies
- Shoulder and Clavicle Injuries
- Spine and Intervertebral Disc Pathology
University Medical Center Utrecht
2022-2024
University of Lausanne
2018-2022
SIB Swiss Institute of Bioinformatics
2018-2022
Wageningen University & Research
2014-2021
Erasmus MC
2019-2021
St. Antonius Ziekenhuis
2019
Institut de Biologie systémique et synthétique
2018
The Gene Ontology (GO) is a cornerstone of functional genomics research that drives discoveries through knowledge-informed computational analysis biological data from large-scale assays. Key to this success how the GO can be used support hypotheses or conclusions about biology evolution study system by identifying annotated functions are overrepresented in subsets genes interest. Graphical visualizations such term enrichment results critical aid interpretation and avoid biases presenting...
Chromosomes are hierarchically folded within cell nuclei into territories, domains and subdomains, but the functional importance evolutionary dynamics of these hierarchies poorly defined. Here, we comprehensively profile genome organizations five Anopheles mosquito species show how different levels chromatin architecture influence each other. Patterns observed on Hi-C maps associated with known cytological structures, epigenetic profiles, gene expression levels. Evolutionary analysis reveals...
Abstract Background New sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from ‘finished’. Updating multi-scaffold drafts chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) predict scaffold neighbours (adjacencies) offers a potentially useful...
Background: Lumbar interbody fusion (IF) is a common procedure to fuse the anterior spine. However, lack of consensus on image-based assessment limits validity and comparison IF studies. This systematic review aims (1) report strategies definitions (2) summarize available literature diagnostic reliability accuracy these assessments. Methods: Two searches were performed according Preferred Reporting Items for Systematic Reviews Meta-analyses guidelines. Search 1 identified studies adult...
Cutaneotrichosporon oleaginosus ATCC 20509 is a fast-growing oleaginous basidiomycete yeast that able to grow in wide range of low-cost carbon sources including crude glycerol, byproduct biodiesel production. When glycerol used as source, this can accumulate more than 50% lipids (w/w) with high concentrations mono-unsaturated fatty acids.To increase our understanding and provide knowledge base for further industrial use, FAIR re-annotated genome was build genome-scale, constraint-based...
Significance On more than 100 occasions, animals have independently evolved the ability to produce and deliver potent secretions subdue prey or predators—venom. This prompts following question: Have repeatedly adopted same genetic toolkit for venom production? In this study, we found, surprisingly, that glands of different animal lineages had similar global gene expression patterns. Notably, groups genes involved in protein secretion, especially stress response pathways, levels, revealing...
The wheat stem sawfly, Cephus cinctus, is a major pest of and key ecological player in the grasslands western North America. It also represents distinctive Cephoidea superfamily sawflies (Symphyta) that appeared early during hymenopteran radiation, but after three early-branching eusymphytan superfamilies form base order Hymenoptera. We present high-quality draft genome assembly 162 Mb 1,976 scaffolds with scaffold N50 622 kb. Automated gene annotation identified 11,210 protein-coding models...
In contrast to mammals and vascular plants, microalgae show a high diversity in the N-glycan structures of complex N-glycoproteins. Although homologues for β1,2-N-acetylglucosaminyltransferase I (GnTI), key enzyme formation N-glycans, have been identified several algal species, GnTI-dependent N-glycans not detected so far. We performed an N-glycoproteomic analysis hydrocarbon oils accumulating green Botryococcus braunii. Thereby, intact N-glycopeptides allowed determination compositions....
This study aimed to evaluate rib fracture rate as well characteristics after thoracic trauma in patients with normal versus diminished bone mineral density (BMD). A retrospective cohort of persons aged 50 years or older presenting the Emergency Department sustaining blunt between July 1, 2014, and December 31, 2017, was performed. Patient DXA scan results were collected. Rib evaluated on a radiograph and/or CT thorax. In total, 119 included for analysis. Fifty-eight them (49%) had BMD....
Abstract The tremendous diversity of Hymenoptera is commonly attributed to the evolution parasitoidism in last common ancestor parasitoid sawflies (Orussidae) and wasp-waisted (Apocrita). However, Apocrita Orussidae differ dramatically their species richness, indicating that diversification was promoted by additional traits. These traits have remained elusive due a paucity sawfly genome sequences, particular those sawflies. Here, we present comparative analyses draft genomes primarily...
Background Protein function prediction is an important part of bioinformatics and genomics studies. There are many different predictors available, however most these in the form web-servers instead open-source locally installable versions. Such local versions necessary to perform large scale studies due presence limitations imposed by web servers such as queues, speed, updatability databases. Methods This paper describes Wei2GO: a weighted sequence similarity python-based protein software....
Characterising gene function for the ever-increasing number and diversity of species with annotated genomes relies almost entirely on computational prediction methods. These software are also numerous diverse, each different strengths weaknesses as revealed through community benchmarking efforts. Meta-predictors that assess consensus conflict from individual algorithms should deliver enhanced functional annotations. To exploit benefits meta-approaches, we developed CrowdGO, an open-source...
Abstract Chromosomes are hierarchically folded within cell nuclei into territories, domains and subdomains, but the functional importance evolutionary dynamics of these hierarchies poorly defined. Here, we comprehensively profiled genome organizations five Anopheles mosquito species showed how different levels chromatin architecture influence contacts between genomic loci. Patterns observed on Hi-C maps associated with known cytological structures, epigenetic profiles, gene expression...
Background: To fully exploit the potential of microalgae as commercial green hosts, scientific community has to improve their understanding these organisms from a systems biology perspective. Compared other model organisms, our genomic knowledge species Chlamydomonas reinhardtii is very limited. Currently, almost 90% functional annotated proteins C. and microalgal are homologs Arabidopsis thaliana proteins, which suggests that for most part only metabolic core conserved between properly...
Roles of constraints in shaping evolutionary outcomes are often considered the contexts developmental biology and population genetics, terms capacities to generate new variants how selection limits or promotes consequent phenotypic changes. Comparative genomics also recognizes role constraints, evolution gene genome architectures, sequence rates, gains losses, as well on molecular phenotypes. Characterizing patterns genomic change where putative functions interactions system components...
Abstract Background Protein function prediction is an important part of bioinformatics and genomics studies. There are many different predictors available, however most these in the form web-servers instead open-source locally installable versions. Such local versions necessary to perform large scale studies due presence limitations imposed by web servers such as queues, speed, updatability databases. Methods This paper describes Wei2GO: a weighted sequence similarity python-based protein...
Abstract The Gene Ontology (GO) is a cornerstone of functional genomics research that drives discoveries through knowledge-informed computational analysis biological data from large- scale assays. Key to this success how the GO can be used support hypotheses or conclusions about biology evolution study system by identifying annotated functions are overrepresented in subsets genes interest. Graphical visualisations such term enrichment results critical aid interpretation and avoid biases...
Abstract Background Characterising gene function for the ever-increasing number and diversity of species with annotated genomes relies almost entirely on computational prediction methods. These software are also numerous diverse, each different strengths weaknesses as revealed through community benchmarking efforts. Meta-predictors that assess consensus conflict from individual algorithms should deliver enhanced functional annotations. Results To exploit benefits meta-approaches, we...
Abstract Background New sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from ‘finished’. Updating multi-scaffold drafts chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) predict scaffold neighbours (adjacencies) offers a potentially useful...
Abstract The role of constraints in shaping evolutionary outcomes is often investigated the contexts developmental biology and population genetics, terms capacity to generate new variants as well how selection either limits or promotes consequent phenotypic change. Comparative genomics also recognises constraints, evolution gene genome architectures, sequence rates, gains losses, on molecular phenotypes. Characterising patterns genomic change where putative functions interactions system...
Abstract The wheat stem sawfly, Cephus cinctus , is a major pest of and key ecological player in the grasslands western North America. It also represents distinctive lineage sawflies that appeared early during hymenopteran radiation, but after clade Eusymphyta sister all other Hymenoptera. We present high-quality draft genome assembly 162 Mbp 1,976 scaffolds with scaffold N50 622 kbp. Automated gene annotation identified 11,210 protein-coding models 1,307 non-coding RNA models. Thirteen...