A5016959285- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Gut microbiota and health
- Plant Virus Research Studies
- Diatoms and Algae Research
- Machine Learning in Bioinformatics
- Microbial Community Ecology and Physiology
- Glycosylation and Glycoproteins Research
- Chromosomal and Genetic Variations
- Aquatic Invertebrate Ecology and Behavior
- Bacteriophages and microbial interactions
- Enzyme Structure and Function
- Plant Reproductive Biology
- Genetic and Environmental Crop Studies
- Protein Structure and Dynamics
- Plant and animal studies
- Plant Molecular Biology Research
- Environmental DNA in Biodiversity Studies
- Gene expression and cancer classification
- Plant biochemistry and biosynthesis
- Cellular transport and secretion
- Algorithms and Data Compression
- Antibiotic Resistance in Bacteria
- Microbial Metabolic Engineering and Bioproduction
- Genetics, Bioinformatics, and Biomedical Research
Vrije Universiteit Amsterdam
2006-2024
University of Applied Sciences Leiden
2024
Cognitive Research (United States)
2024
Bioclear Earth (Netherlands)
2008-2023
University of Zurich
2022
University of California, Berkeley
2013
Leiden University
2010
Institute of Bioinformatics
2006-2010
Amsterdam UMC Location Vrije Universiteit Amsterdam
2009
De novo assembly tools play a main role in reconstructing genomes from next-generation sequencing (NGS) data and usually yield number of contigs. Using paired-read it is possible to assess the order, distance orientation contigs combine them into so-called scaffolds. Although latter process crucial step finishing genomes, scaffolding algorithms are often built-in functions de cannot be independently controlled. We here present new tool, called SSPACE, which stand-alone scaffolder...
De novo assembly is a commonly used application of next-generation sequencing experiments. The ultimate goal to puzzle millions reads into one complete genome, although draft assemblies usually result in number gapped scaffold sequences. In this paper we propose an automated strategy, called GapFiller, reliably close gaps within scaffolds using paired reads. method shows good results on both bacterial and eukaryotic datasets, allowing only few errors. As consequence, the amount additional...
The recent introduction of the Pacific Biosciences RS single molecule sequencing technology has opened new doors to scaffolding genome assemblies in a cost-effective manner. long read sequence information is promised enhance quality incomplete and inaccurate draft constructed from Next Generation Sequencing (NGS) data. Here we propose novel hybrid assembly methodology that aims scaffold pre-assembled contigs an iterative manner using PacBio as backbone. On test set comprising six bacterial...
Significance Snake venoms are toxic protein cocktails used for prey capture. To investigate the evolution of these complex biological weapon systems, we sequenced genome a venomous snake, king cobra, and assessed composition venom gland expressed genes, small RNAs, secreted proteins. We show that regulatory components secretory system may have evolved from pancreatic origin toxin genes were co-opted by distinct genomic mechanisms. After co-option, important capture massively expanded gene...
Abstract Supergenes are nonrecombining genomic regions ensuring the coinheritance of multiple, coadapted genes. Despite importance supergenes in adaptation, little is known on how they originate. A classic example supergene S locus controlling heterostyly, a floral heteromorphism occurring 28 angiosperm families. In Primula, heterostyly characterized by cooccurrence two complementary, self-incompatible morphs and controlled five genes clustered hemizygous, ca. 300-kb locus. Here, we present...
Abstract Motivation: Membrane-bound proteins are a special class of proteins. The regions that insert into the cell-membrane have profoundly different hydrophobicity pattern compared with soluble Multiple alignment techniques use scoring schemes tailored for sequences and therefore in principle not optimal to align membrane-bound Results: Transmembrane (TM) protein can be reliably recognized using state-of-the-art sequence prediction techniques. Furthermore, membrane-specific matrices...
The Japanese eel is a much appreciated research object and very important for Asian aquaculture; however, its genomic resources are still limited. We have used streamlined bioinformatics pipeline the de novo assembly of genome sequence from raw Illumina reads. total assembled has size 1.15 Gbp, which divided over 323,776 scaffolds with an N50 52,849 bp, minimum scaffold 200 bp maximum 1.14 Mbp. Direct comparison representative set revealed that all Hox genes their intergenic distances almost...
The emergence of carbapenem-resistant Pseudomonas aeruginosa represents a worldwide problem. To understand the carbapenem-resistance mechanisms and their spreading among P. strains, whole genome sequences were determined two extensively drug-resistant strains that are endemic in Dutch hospitals. Strain Carb01 63 is O-antigen serotype O12 sequence type ST111, whilst S04 90 O11 strain ST446. Both carry gene for metallo-β-lactamase VIM-2 flanked by aacA29 genes encoding aminoglycoside...
Multiple sequence alignments are often used to reveal functionally important residues within a protein family. They can be particularly useful for the identification of key that determine functional differences between subfamilies. We present new entropy-based method, Sequence Harmony (SH) accurately detects subfamily-specific positions from multiple alignment. The SH algorithm implements novel formula, able score compositional subfamilies, without imposing conservation, in simple manner on...
This study describes how the complete mitogenome of a terrestrial snail, Cylindrus obtusus (Draparnaud, 1805) was sequenced without PCRs from collection specimen that had been in 70% ethanol for 8 years. The obtained with Illumina GAIIx shot gun sequencing. Although used collected relatively recently and kept DNA-friendly preservative (not formalin as frequently old museum specimens), we believe exclusion facilitated by NGS (Next Generation Sequencing) removes great obstacle DNA sequencing...
Over the past years deep sequencing experiments have opened novel doors to reconstruct viral populations in a high-throughput and cost-effective manner. Currently substantial number of studies been performed which employ next generation techniques either analyze known viruses by means reference-guided approach or discover using de novo-based strategy. Taking advantage well-known Cymbidium ringspot virus we carried out comparison different bioinformatics tools genome based on 21-27 nt short...
Marchantia polymorpha has recently become a prime model for cellular, evo-devo, synthetic biological, and evolutionary investigations. We present pseudomolecule-scale assembly of the M. genome, making comparative genome structure analysis classical genetic mapping approaches feasible. anchored 88% draft to high-density linkage map resulting in eight pseudomolecules. found that overall is some respects different from moss Physcomitrella patens. Specifically, collinearity between two bryophyte...
The human gastrointestinal tract consists of different regions, each characterized by a distinct physiology, anatomy, and microbial community. While the colonic microbiota has received lot attention in recent research projects, little is known about small intestinal its interactions with ingested compounds, primarily due to inaccessibility this region vivo . This study therefore aimed develop validate dynamic, long-term simulation ileal using SHIME ® -technology. Essential parameters were...
Multiple sequence alignments are often used for the identification of key specificity-determining residues within protein families. We present a web server implementation Sequence Harmony (SH) method previously introduced. SH accurately detects subfamily specific positions from multiple alignment by scoring compositional differences between subfamilies, without imposing conservation. The allows quick selection subtype sites given grouping. In addition, it predicted to be directly mapped onto...
The plant ARGONAUTE1 protein (AGO1) is a central functional component of the posttranscriptional regulation gene expression and RNA silencing-based antiviral defense. By genomic molecular approaches, we here reveal presence two homeologs AGO1-like in Nicotiana benthamiana, NbAGO1-1H NbAGO1-1L. Both retain capacity to transcribe messenger RNAs (mRNAs), which mainly differ one 18-nucleotide insertion/deletion (indel). indel does not modify frame open reading frame, it located eight nucleotides...
This paper announces the genome sequence and annotation of genetically modified (GM) Bacillus subtilis strain 2014-3557 overproducing riboflavin (vitamin B2). GM-strain is unauthorized in European Union. Nevertheless, it has been isolated from a lot vitamin B2 (riboflavin) 80% feed grade imported to Europe China.
Both academia and dermatological cosmetic industries have acknowledged that healthy skin microbiota contribute to overall integrity well-being. This implies formulations developed for personal care (skin, scalp, hair etc) or (medical cosmetic) treatment need be compatible with conservation possibly even improvement. The various chemical biological components mixtures thereof intended direct application the should not extensively affect qualitative quantitative composition of microbiota. A...
Malassezia restricta, one of the predominant basidiomycetous yeasts present on human skin, is involved in scalp disorders. Here, we report complete genome sequence lipophilic restricta CBS 7877 strain, which will facilitate study mechanisms underlying its commensal and pathogenic roles within skin microbiome.
In contrast to surveys based on a few genes that often provide limited taxonomic resolution, transcriptomes wealth of genomic loci can resolve relationships among taxonomically challenging lineages. Diatoms are diverse group aquatic microalgae includes important bioindicator species and many such One example is Nitzschia palea , widespread complex with several morphologically defined varieties, some which critical pollution indicators. Morphological differences the varieties subtle...
Plant viruses modify gene expression in infected tissues by altering the micro (mi)RNA-mediated regulation of genes. Among conserved miRNA targets there are transcripts coding for transcription factors, RNA silencing core, and disease-resistance proteins. Paralogs these families widely present plant genomes known to respond differently miRNA-mediated during virus infections. Using genome-wide approaches applied Solanum lycopersicum a nuclear-replicating virus, we highlighted cleavage events...