Publications
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DeepRibo : a neural network for precise gene annotation of prokaryotes by combining ribosome profiling signal and binding site patterns Ghent University
Annotation of gene expression in prokaryotes of-ten finds itself corrected due to small variations ofthe annotated gene regions observed between differ-ent (sub)-species. It has become apparent that tradi-tional sequence alignment algorithms, used for thecuration of genomes, are not able to map the fullcomplexity of the genomic landscape. We presentDeepRibo, a novel neural network utilizing featuresextracted from ribosome profiling information ...
Production of dissolved organic matter by phytoplankton and its assimilation by heterotrophic prokaryotes in large tropical lakes KU Leuven
In pelagic ecosystems, phytoplankton extracellular release can extensively subsidize the heterotrophic prokaryotic carbon demand. Time-course experiments were carried out to quantify primary production, phytoplankton excretion, and the microbial uptake of freshly released dissolved organic carbon (DOC) derived from phytoplankton extracellular release (DOCp) in four large tropical lakes distributed along a productivity gradient: Kivu, Edward, ...
SASpector: analysis of missing genomic regions in draft genomes of prokaryotes KU Leuven
SUMMARY: Missing regions in short-read assemblies of prokaryote genomes are often attributed to biases in sequencing technologies and to repetitive elements, the former resulting in low sequencing coverage of certain loci and the latter to unresolved loops in the de novo assembly graph. We developed SASpector, a command-line tool that compares short-read assemblies (draft genomes) to their corresponding closed assemblies and extracts missing ...
QCM-D study of time-resolved cell adhesion and detachment: Effect of surface free energy on eukaryotes and prokaryotes KU Leuven
Cell–material interactions are crucial for many biomedical applications, including medical implants, tissue engineering, and biosensors. For implants, while the adhesion of eukaryotic host cells is desirable, bacterial adhesion often leads to infections. Surface free energy (SFE) is an important parameter that controls short- and long-term eukaryotic and prokaryotic cell adhesion. Understanding its effect at a fundamental level is essential for ...
International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Bifidobacterium, Lactobacillus and related organisms. Minutes of closed and open meetings, 3 September 2018, Berlin, Germany Vrije Universiteit Brussel
The meeting of International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Bifidobacterium,
Lactobacillus and related organisms was held within the frame of the FoodMicro 2018 Congress (FoodMicro 2018, 3–6
September 2018, Berlin, Germany). The meeting comprised an open session with a workshop entitled ‘Modern approaches of
LAB identification and conservation’ and a closed session on issues related ...
Lactobacillus and related organisms was held within the frame of the FoodMicro 2018 Congress (FoodMicro 2018, 3–6
September 2018, Berlin, Germany). The meeting comprised an open session with a workshop entitled ‘Modern approaches of
LAB identification and conservation’ and a closed session on issues related ...