A5029869005- Research Data Management Practices
- Scientific Computing and Data Management
- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- Genetic Neurodegenerative Diseases
- Data Quality and Management
- Bioinformatics and Genomic Networks
- Muscle Physiology and Disorders
- Computational Drug Discovery Methods
- Mitochondrial Function and Pathology
- Adipose Tissue and Metabolism
- Big Data and Business Intelligence
- Biomedical and Engineering Education
- Genomics and Rare Diseases
- Genetics, Bioinformatics, and Biomedical Research
- Advanced Text Analysis Techniques
- Gene expression and cancer classification
- Microbial Metabolic Engineering and Bioproduction
- Genetic and Kidney Cyst Diseases
- Advanced MRI Techniques and Applications
- demographic modeling and climate adaptation
- Muscle metabolism and nutrition
- Big Data Technologies and Applications
- Ubiquitin and proteasome pathways
- Distributed and Parallel Computing Systems
Leiden University
2012-2024
Scientific Computing & Modelling (Netherlands)
2024
Leiden University Medical Center
2013-2022
Digital Scholar (United States)
2022
Erasmus MC
2007-2014
Maastricht University
2009-2013
AstraZeneca (Sweden)
2007
AstraZeneca (United Kingdom)
2007
Erasmus University Rotterdam
2007
The FAIR principles have been widely cited, endorsed and adopted by a broad range of stakeholders since their publication in 2016. By intention, the 15 guiding do not dictate specific technological implementations, but provide guidance for improving Findability, Accessibility, Interoperability Reusability digital resources. This has likely contributed to adoption principles, because individual stakeholder communities can implement own solutions. However, it also resulted inconsistent...
From the scientific community, a lot of effort has been spent on correct identification gene and protein names in text, while less chemical names. Dictionary-based term power to recognize diverse representation information literature map chemicals their database identifiers.We developed dictionary for small molecules drugs combining from UMLS, MeSH, ChEBI, DrugBank, KEGG, HMDB ChemIDplus. Rule-based filtering, manual check highly frequent terms disambiguation rules were applied. We tested...
Scientific workflows are a popular mechanism for specifying and automating data-driven in silico experiments. A significant aspect of their value lies potential to be reused. Once shared, become useful building blocks that can combined or modified developing new However, previous studies have shown storing workflow specifications alone is not sufficient ensure they successfully reused, without being able understand what the aim achieve re-enact them. To gain an understanding workflow, how it...
Workflows provide a popular means for preserving scientific methods by explicitly encoding their process. However, some of them are subject to decay in ability be re-executed or reproduce the same results over time, largely due volatility resources required workflow executions. This paper provides an analysis root causes based on empirical study collection Taverna workflows from myExperiment repository. Although our was specific type workflow, outcomes and methodology should applicable other...
Spinocerebellar ataxia type 3 (SCA3) is a progressive neurodegenerative disorder caused by expansion of the polyglutamine repeat in ataxin-3 protein. Expression mutant known to result transcriptional dysregulation, which can contribute cellular toxicity and neurodegeneration. Since exact causative mechanisms underlying this process have not been fully elucidated, gene expression analyses brains transgenic SCA3 mouse models may provide useful insights.Here we characterised MJD84.2 model...
Metabolic changes have been frequently associated with Huntington's disease (HD). At the same time peripheral blood represents a minimally invasive sampling avenue little distress to patients especially when brain or other tissue samples are difficult collect.We investigated levels of 163 metabolites in HD patient and control serum order identify related changes. Additionally, we integrated metabolomics data our previously published next generation sequencing-based gene expression from...
Abstract Background Analysis of muscle biopsies allowed to characterize the pathophysiological changes Duchenne and Becker muscular dystrophies (D/BMD) leading clinical phenotype. Muscle tissue is often investigated during interventional dose finding studies show in situ proof concept pharmacodynamics effect tested drug. Less invasive readouts are needed objectively monitor patients' health status, quality, response treatment. The identification serum biomarkers correlating with function...
Medication for nonalcoholic fatty liver disease (NAFLD) is an unmet need. Glucocorticoid (GC) stress hormones drive fat metabolism in the liver, but both full blockade and stimulation of GC signaling aggravate NAFLD pathology. We investigated efficacy selective glucocorticoid receptor (GR) modulator CORT118335, which recapitulates only a subset actions, reducing lipid accumulation mice. Male C57BL/6J mice received low-fat diet or high-fat mixed with vehicle CORT118335. Livers were analyzed...
Previously, we developed a combined dictionary dubbed Chemlist for the identification of small molecules and drugs in text based on number publicly available databases tested it an annotated corpus. To achieve acceptable recall precision used automatic semi-automatic processing steps together with disambiguation rules. However, remained to be investigated which impact extensive manual curation multi-source chemical would have term text. ChemSpider is database that has undergone aimed at...
Open Science is encouraged by the European Union and many other political scientific institutions. However, practice proving slow to change. We propose, as early career researchers, that it our task change research into open commit principles.
Abstract Compounds that are candidates for drug repurposing can be ranked by leveraging knowledge available in the biomedical literature and databases. This knowledge, spread across a variety of sources, integrated within graph, which thereby comprehensively describes known relationships between concepts, such as drugs, diseases, genes, etc. Our work uses semantic information disease concepts features, extracted from an existing graph integrates 200 different biological sources. RepoDB,...
Huntington's disease (HD) is a devastating brain disorder with no effective treatment or cure available. The scarcity of tissue makes it hard to study changes in the and impossible perform longitudinal studies. However, peripheral pathology HD suggests that possible using as monitoring tool for progression and/or efficacy novel therapies. In this study, we investigated if blood can be used monitor severity brain. Since previous attempts only gene expression proved unsuccessful, compared...
Abstract Background Patient experience surveys often include free-text responses. Analysis of these responses is time-consuming and underutilized. This study examined whether Natural Language Processing (NLP) techniques could provide a data-driven, hospital-independent solution to indicate points for quality improvement. Methods retrospective used routinely collected patient data from two hospitals. A data-driven NLP approach was used. Free-text were categorized into topics, subtopics (i.e....
Identification of terms is essential for biomedical text mining.. We concentrate here on the use vocabularies term identification, specifically Unified Medical Language System (UMLS). To make UMLS more suitable mining we implemented and evaluated nine rewrite eight suppression rules. The rules rely properties that have been identified in previous work by others, together with an additional set new discovered our group during UMLS. Our complements earlier measure impact number different a...
The past decade has seen an upsurge in the number of publications chemistry. ever-swelling volume available documents makes it increasingly hard to extract relevant new information from such unstructured texts. BioCreative CHEMDNER challenge invites development systems for automatic recognition chemicals text (CEM task) and ranking recognized compounds at document level (CDI task). We investigated ensemble approach where dictionary-based named entity is used along with grammar-based...
Abstract Background One of the main challenges for biomedical research lies in computer-assisted integrative study large and increasingly complex combinations data order to understand molecular mechanisms. The preservation materials methods such computational experiments with clear annotations is essential understanding an experiment, this recognized bioinformatics community. Our assumption that offering means digital, structured aggregation annotation objects experiment will provide...
Abstract Muscular dystrophies are characterized by a progressive loss of muscle tissue and/or function. While metabolic alterations have been described in patients’‐derived biopsies, non‐invasive readouts able to describe these needed order objectively monitor condition and response treatment targeting abnormalities. We used metabolomic approach study metabolites concentration serum patients affected multiple forms muscular dystrophy such as Duchenne Becker dystrophies, limb‐girdle type 2A...
High-throughput experimental methods such as medical sequencing and genome-wide association studies (GWAS) identify increasingly large numbers of potential relations between genetic variants diseases. Both biological complexity (millions gene-disease associations) the accelerating rate data production necessitate computational approaches to prioritize rationalize relations. Here, we use concept profile technology expose from biomedical literature both explicitly stated (the explicitome) a...
Scientific workflows are a popular mechanism for specifying and automating data-driven in silico experiments. A significant aspect of their value lies potential to be reused. Once shared, become useful building blocks that can combined or modified developing new However, previous studies have shown storing workflow specifications alone is not sufficient ensure they successfully reused, without being able understand what the aim achieve re-enact them. To gain an understanding workflow, how it...
Abstract Duchenne muscular dystrophy is a severe pediatric neuromuscular disorder caused by the lack of dystrophin. Identification biomarkers needed to support and accelerate drug development. Alterations metabolites levels in muscle plasma have been reported pre-clinical clinical cross-sectional comparisons. We present here 7-month longitudinal study comparing metabolomic data wild-type mdx mice. A mass spectrometry approach was used up five time points per mouse at 6, 12, 18, 24 30 weeks...
We describe the development of a chemical entity recognition system and its application in CHEMDNER-patent track BioCreative 2015. This community challenge includes Chemical Entity Mention Patents (CEMP) task Passage Detection (CPD) classification task. addressed both tasks by an ensemble that combines dictionary-based approach with statistical one. For this purpose performance several lexical resources was assessed using Peregrine, our open-source indexing engine. combined results on patent...