A5029941306- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- Gene Regulatory Network Analysis
- Scientific Computing and Data Management
- Plant nutrient uptake and metabolism
- Plant Molecular Biology Research
- Gene expression and cancer classification
- Genomics and Phylogenetic Studies
- Microbial Metabolic Engineering and Bioproduction
- Research Data Management Practices
- Genetics, Bioinformatics, and Biomedical Research
- CRISPR and Genetic Engineering
- Plant Reproductive Biology
- Natural Language Processing Techniques
- Plant Virus Research Studies
- Microtubule and mitosis dynamics
- Genomics and Chromatin Dynamics
- Speech and dialogue systems
- Chromosomal and Genetic Variations
- Evolution and Genetic Dynamics
- Topic Modeling
- Photosynthetic Processes and Mechanisms
- Plant Gene Expression Analysis
Norwegian University of Science and Technology
2012-2021
Vlaams Instituut voor Biotechnologie
2004-2005
Ghent University
2004-2005
Sorbonne Université
2004
Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization between complementary nucleic acid strands, inciting us to create a collection of gene-specific sequence tags (GSTs) representing at least 21,500 Arabidopsis genes which compatible with both approaches. The GSTs were carefully selected ensure that each them shared no significant similarity any...
Abstract Exit from the mitotic cell cycle and initiation of differentiation frequently coincides with onset endoreduplication, a modified during which DNA continues to be duplicated in absence mitosis. Although endoreduplication share much same machinery, regulatory mechanisms controlling transition between both cycles remain poorly understood. We show that A-type cyclin-dependent kinase CDKA;1 its specific inhibitor, Kip-related protein, KRP2 regulate mitosis-to-endocycle Arabidopsis...
Abstract Organ growth results from the progression of component cells through subsequent phases proliferation and expansion before reaching maturity. We combined kinematic analysis, flowcytometry, microarray analysis to characterize cell cycle regulation during process leaves 1 2 Arabidopsis (Arabidopsis thaliana). Kinematic showed that epidermis proliferates until day 12; thereafter, expand 19 when reach Flowcytometry revealed endoreduplication occurs time division rates decline end...
At the onset of lateral root initiation in Arabidopsis thaliana, phytohormone auxin activates xylem pole pericycle cells for asymmetric cell division. However, molecular events leading from to are poorly understood, part because few responsive process embedded and thus difficult access. A induction system, which most were synchronously activated by transport inhibition followed application, was used microarray transcript profiling. Of 4,600 genes analyzed, 906 significantly differentially...
More than one million terms from biomedical ontologies and controlled vocabularies are available through the Ontology Lookup Service (OLS). Although OLS provides ample possibility for querying browsing terms, visualization of parts ontology graphs is rather limited inflexible. We created OLSVis web application, a visualiser all in database. shows customisable subgraphs ontologies. Subgraphs animated via real-time force-based layout algorithm which fully interactive: each time user makes...
Causal molecular interactions represent key building blocks used in computational modeling, where they facilitate the assembly of regulatory networks. Logical networks can be to predict biological and cellular behaviors by system perturbations silico simulations. Today, broad sets causal are available a variety knowledge resources. However, different visions, based on distinct interests, have led development multiple ways describe annotate interactions. It therefore challenging efficiently...
A large variety of molecular interactions occurs between biomolecular components in cells. When a interaction results regulatory effect, exerted by one component onto downstream component, so-called 'causal interaction' takes place. Causal constitute the building blocks our understanding larger networks These causal and biological processes they enable (e.g. gene regulation) need to be described with careful appreciation underlying reactions. proper description this information enables...
A large gap remains between the amount of knowledge in scientific literature and fraction that gets curated into standardized databases, despite many curation initiatives. Yet availability comprehensive databases is crucial for exploiting existing background knowledge, both designing follow-up experiments interpreting new experimental data. Structured resources also underpin computational integration modeling regulatory pathways, which further aids our understanding dynamics. We argue how...
VSM is a recently introduced method for entering and displaying any type of knowledge, in form that both semantically precise computation intuitive human understanding. the combination new semantic model, design dedicated user interface to support it. Here we present implementation this interface, as sophisticated HTML-element, <vsm-box>, can be embedded web-based curation app. We show how developers use it biocuration projects, customize particular end-user needs, contribute...
A large variety of molecular interactions occurs between biomolecular components in cells. When one or a cascade results regulatory effect, by component onto downstream component, so-called ‘causal interaction’ takes place. Causal constitute the building blocks our understanding larger networks These causal and biological processes they enable (e.g., gene regulation) need to be described with careful appreciation that occur entities. proper description this information...
As computational modeling becomes more essential to analyze and understand biological regulatory mechanisms, governance of the many databases knowledge bases that support this domain is crucial guarantee reliability interoperability resources. To address this, COST Action Gene Regulation Ensemble Effort for Knowledge Commons (GREEKC, CA15205, www.greekc.org) organized nine workshops in a four-year period, starting September 2016. The brought together wide range experts from all over world...
Ideally each Life Science article should get a ‘structured digital abstract’. This is structured summary of the paper’s findings that both human-verified and machine-readable. But articles can contain large variety information types contextual details all need to be reconciled with appropriate names, terms identifiers, which poses challenge any curator. Current approaches mostly use tagging or limited entry-forms for semantic encoding. We implemented ‘controlled language’ as more expressive...
Scientific progress is increasingly dependent on knowledge in computation-ready forms. In the life sciences, among others, many scientists therefore extract and structure from literature. a process called manual curation, they enter into spreadsheets, or databases where it serves their others' research. Valuable as these curation efforts are, range detail of what can practically be captured shared remains limited, because constraints current tools. Many important contextual aspects...
Abstract Summary: We present SIM-plex, a genetic network simulator with very intuitive interface in which user can easily specify interactions as simple ‘if-then’ statements. The is based on the mathematical model of Piecewise Linear Differential Equations (PLDEs). With PLDEs, are approximated acting switch-like manner. Availability: Java program, examples and tutorial available at http://www.psb.ugent.be/cbd/ Contact: {stcru,makui}@psb.ugent.be
Molecular causal interactions are defined as regulatory connections between biological components. They commonly retrieved from experiments, and can be used for connecting molecules into computational models that represent systems. However, including a molecular interaction model requires assessing its relevance to model, based on detailed knowledge about the biomolecules, type, context. In order standardize representation of this in ‘causal statements’, we recently...
We present a set of software packages that provide uniform access to diverse biological vocabulary resources are instrumental for current biocuration efforts and tools. The Unified Biological Dictionaries (UniBioDicts or UBDs) single query-interface accessing the online API services leading data providers. Given search string, UBDs return list matching term, identifier metadata units from databases (e.g. UniProt), controlled vocabularies PSI-MI) ontologies GO, via BioPortal). This...
Molecular causal interactions are defined as regulatory connections between biological components. They commonly retrieved from experiments and can be used for connecting molecules together to enable the building of computational models that represent systems. However, including a molecular interaction in model requires assessing its relevance model, based on detailed knowledge about biomolecules, type context. In order standardize representation this 'causal statements', we recently...
We present a set of software packages that provide uniform access to diverse biological vocabulary resources are instrumental for current biocuration efforts and tools. The Unified Biological Dictionaries (UniBioDicts or UBDs) single query-interface accessing the online API services leading data providers. Given search string, UBDs return list matching term, identifier metadata units from databases (e.g. UniProt), controlled vocabularies PSI-MI), ontologies GO, via BioPortal). This can be...
Causal molecular interactions represent key building blocks used in computational modeling, where they facilitate the assembly of regulatory networks. These networks can then be to predict biological and cellular behavior by system perturbations silico simulations. Today, broad sets these are being made available a variety knowledge resources. Moreover, different visions, based on distinct interests, have led development multiple ways describe annotate causal interactions. Therefore, data...
Scientific progress is increasingly dependent on knowledge in computation-ready forms. In the life sciences, among others, many scientists carefully extract and structure from scientific literature. a process called manual curation, they enter into spreadsheets, or databases where it serves their others' research. Valuable as these curation efforts are, range detail of what can practically be captured shared remains limited, because constraints current tools. Many important contextual...
One of the many challenges that biocurators face, is continuous evolution ontologies and controlled vocabularies their lack coverage biological concepts. To help annotate new information cannot yet be covered with terms from authoritative resources, we produced an update PubDictionaries: a resource publicly editable, simple-structured dictionaries, accessible through dedicated REST API. PubDictionaries was equipped both enhanced API software client connects it to Unified Biological...