A5079406761- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Greenhouse Technology and Climate Control
- Bacteriophages and microbial interactions
- Plant and animal studies
- Computational Drug Discovery Methods
- Domain Adaptation and Few-Shot Learning
- Bioinformatics and Genomic Networks
- Machine Learning in Bioinformatics
- Gene Regulatory Network Analysis
- Bayesian Modeling and Causal Inference
- Insect and Arachnid Ecology and Behavior
- Machine Learning and ELM
- Rough Sets and Fuzzy Logic
- Plant Water Relations and Carbon Dynamics
- Machine Learning and Data Classification
- Evolutionary Algorithms and Applications
- Data Management and Algorithms
- Leaf Properties and Growth Measurement
- Electrochemical Analysis and Applications
- Face and Expression Recognition
- Genetics, Bioinformatics, and Biomedical Research
- Gut microbiota and health
- Ecology and Vegetation Dynamics Studies
- Machine Learning and Algorithms
Ghent University
2016-2025
Ghent University Hospital
2023-2024
Abstract Nowadays, bacteriophages are increasingly considered as an alternative treatment for a variety of bacterial infections in cases where classical antibiotics have become ineffective. However, characterizing the host specificity phages remains labor- and time-intensive process. In order to alleviate this burden, we developed new machine-learning-based pipeline predict bacteriophage hosts based on annotated receptor-binding protein (RBP) sequence data. We focus predicting from ESKAPE...
Abstract Despite decades of intensive search for compounds that modulate the activity particular protein targets, a large proportion human kinome remains as yet undrugged. Effective approaches are therefore required to map massive space unexplored compound–kinase interactions novel and potent activities. Here, we carry out crowdsourced benchmarking predictive algorithms kinase inhibitor potencies across multiple families tested on unpublished bioactivity data. We find top-performing...
When studying electrochemical systems, EIS practitioners face the challenge of choosing a relevant equivalent electrical circuit to analyze their measurement data and interpreting role its components. In this review, we take closer look at use circuits (EEC) across various application domains.We aim aid in determining evaluating EEC-based analysis methodology light recent progress from all domains. We review EEC usage interpretation while additionally providing software automatically search...
Abstract Phages are increasingly considered promising alternatives to target drug-resistant bacterial pathogens. However, their often-narrow host range can make it challenging find matching phages against bacteria of interest. Current computational tools do not accurately predict interactions at the strain level in a way that is relevant and properly evaluated for practical use. We present PhageHostLearn, machine learning system predicts strain-level between receptor-binding proteins...
Abstract Careful consideration of how we approach design is crucial to all areas biotechnology. However, choosing or developing an effective methodology not always easy as biology, unlike most engineering, able adapt and evolve. Here, put forward that evolution follow a similar cyclic process therefore methods, including traditional design, directed evolution, even random trial error, exist within evolutionary spectrum. This contrasts with conventional views often place these methods at odds...
Bacteriophages (phages) are viruses that infect bacteria. Many of them produce specific enzymes called depolymerases to break down external polysaccharide structures. Accurate annotation and domain identification these challenging due their inherent sequence diversity. Hence, we present DepoScope, a machine learning tool combines fine-tuned ESM-2 model with convolutional neural network identify depolymerase sequences enzymatic domains precisely. To accomplish this, curated dataset from the...
Abstract To engineer synthetic gene circuits, molecular building blocks are developed which can modulate expression without interference, mutually or with the host’s cell machinery. As complexity of circuits increases, automated design tools and tailored to ensure perfect tuning all components in network required. Despite efforts develop prediction that allow forward engineering promoter transcription initiation frequency (TIF), such a tool is still lacking. Here, we use libraries E. coli...
Phage lytic proteins are a clinically advanced class of novel enzyme-based antibiotics, so-called enzybiotics. A growing community researchers develops phage with the perspective their use as successful translation enzybiotics to market requires well-considered selections in early research stages. Here, we introduce PhaLP, database proteins, which serves an open portal facilitate development proteins. PhaLP is comprehensive, easily accessible and automatically updated (currently 16,095...
Abstract Water potential explains water transport in the soil–plant–atmosphere continuum (SPAC), and is gaining interest as connecting variable between ‘pedo-, bio- atmosphere’. It primarily used to simulate hydraulics SPAC, thus essential for studying drought effects. Recent implementations of large-scale terrestrial biosphere models (TBMs) improved their performance under water-limited conditions, while hydraulic features recent detailed functional–structural plant (FSPMs) open new...
Receptor-binding proteins (RBPs) of bacteriophages initiate the infection their corresponding bacterial host and act as primary determinant for specificity. The ever-increasing amount sequence data enables development predictive models automated identification RBP sequences. However, such is challenged by inconsistent or missing annotation many phage proteins. Recently developed tools have started to bridge this gap but are not specifically focused on sequences, which different annotations...
Historically, plant and crop sciences have been quantitative fields that intensively use measurements modeling. Traditionally, researchers choose between two dominant modeling approaches: mechanistic growth models or data-driven, statistical methodologies. At the intersection of both paradigms, a novel approach referred to as “ simulation intelligence ”, has emerged powerful tool for comprehending controlling complex systems, including plants crops. This work explores transformative...
Recent trends towards lower washing temperatures and a reduction in the use of bleaching agents laundry undoubtedly benefit our environment. However, these conditions impair microbial removal on clothes, leading to malodour generation negative impacts consumer well-being. Clothing undergoes cycles wearing, drying, with variable exposure microorganisms volatilomes originating from skin, machine, water products. Laundry is therefore complex problem that reflects its dynamic ecosystem. To date,...
Quantifying forest microclimate dynamics is vital for improving our understanding of ecosystem processes, biodiversity patterns, and carbon sequestration. While existing mechanistic models effectively simulate conditions within cores, they often fail to capture the complexities inherent edges. This limitation increasingly critical as fragmentation creates more edge environments, profoundly influencing gradients.To address this gap, we developed a high-resolution model capable simulating...
Abstract Balanced energy-protein (BEP) supplementation during pregnancy and lactation can improve birth outcomes infant growth, with the gut microbiome as a potential mediator. The MISAME-III randomized controlled trial (ClinicalTrial.gov: NCT03533712) assessed effect of BEP supplementation, provided first six months lactation, on small-for-gestational age prevalence length-for-age Z-scores at in rural Burkina Faso. Nested within MISAME-III, this sub-study examines impact maternal...
A growing number of proteogenomics and metaproteomics studies indicate potential limitations the application "decoy" database paradigm used to separate correct peptide identifications from incorrect ones in traditional shotgun proteomics. We therefore propose a binary classifier called Nokoi that allows fast yet reliable decoy-free separation peptide-to-spectrum matches (PSMs). was trained on very large collection heterogeneous data using ranks supplied by Mascot search engine label PSMs....
Abstract Bacteriophages (phages) are viruses that infect bacteria. Many of them produce specific enzymes called depolymerases to break down external polysaccharide structures. Accurate annotation and domain identification these challenging due their inherent sequence diversity. Hence, we present DepoScope, a machine learning tool combines fine-tuned ESM-2 model with convolutional neural network precisely identify depolymerase sequences enzymatic domains. To accomplish this, curated dataset...
This study investigated the role of causative infectious agents in ulceration non-glandular part porcine stomach (pars oesophagea). In total, 150 stomachs from slaughter pigs were included, 75 that received a meal feed, an equivalent pelleted feed with smaller particle size. The pars oesophagea was macroscopically examined after slaughter. (q)PCR assays for H. suis, F. gastrosuis and pylori-like organisms performed, as well 16S rRNA sequencing microbiome analyses. All pig showed lesions....