A5054615637- Research Data Management Practices
- Scientific Computing and Data Management
- Biomedical Text Mining and Ontologies
- Genomics and Rare Diseases
- Bioinformatics and Genomic Networks
- Cancer Genomics and Diagnostics
- Genetics and Neurodevelopmental Disorders
- Semantic Web and Ontologies
- Genetics, Bioinformatics, and Biomedical Research
- Gene Regulatory Network Analysis
- Data Quality and Management
- Genomics and Phylogenetic Studies
- Big Data and Business Intelligence
- Microbial Metabolic Engineering and Bioproduction
- Chronic Disease Management Strategies
- Nutrition and Health Studies
- Global Health Care Issues
- Fibroblast Growth Factor Research
- Renal cell carcinoma treatment
- Fungal and yeast genetics research
- Distributed and Parallel Computing Systems
- Genetics, Aging, and Longevity in Model Organisms
- Cancer-related gene regulation
- Team Dynamics and Performance
- Artificial Intelligence in Healthcare
Leiden University Medical Center
2018-2025
University of Twente
2023
Royal Netherlands Meteorological Institute
2023
Weatherford College
2023
Leiden University
2017-2021
Vrije Universiteit Amsterdam
2016-2019
Merck Institute for Science Education
2019
John Wiley & Sons (United States)
2019
Hudson Institute
2019
Institute of Bioinformatics and Applied Biotechnology
2012
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...
Rare diseases (RD) patient registries are powerful instruments that help develop clinical research, facilitate the planning of appropriate trials, improve care, and support healthcare management. They constitute a key information system supports activities European Reference Networks (ERNs) on rare diseases. A rapid proliferation RD has occurred during last years there is need to guidance for minimum requirements, recommendations standards necessary maintain high-quality registry. In...
The FAIR guiding principles aim to enhance the Findability, Accessibility, Interoperability and Reusability of digital resources such as data, for both humans machines. process making data (“FAIRification”) can be described in multiple steps. In this paper, we describe a generic step-by-step FAIRification workflow performed multidisciplinary team guided by stewards. should applicable any type has been developed used “Bring Your Own Data” (BYOD) workshops, well e.g., rare diseases resources....
The COVID-19 pandemic has challenged healthcare systems and research worldwide. Data is collected all over the world needs to be integrated made available other researchers quickly. However, various heterogeneous information that are used in hospitals can result fragmentation of health data multiple 'silos' not interoperable for analysis. Consequently, clinical observations hospitalised patients prepared reused efficiently timely. There a need adapt management make observational patient...
The European Platform on Rare Disease Registration (EU RD Platform) aims to address the fragmentation of rare disease (RD) patient data, scattered among hundreds independent and non-coordinating registries, by establishing standards for integration interoperability. first practical output this effort was a set 16 Common Data Elements (CDEs) that should be implemented all registries. Interoperability, however, requires decisions beyond data elements - including models, formats, semantics....
Rare diseases may affect the quality of life patients and be life-threatening. Therapeutic opportunities are often limited, in part because lack understanding molecular mechanisms underlying these diseases. This can ascribed to low prevalence rare therefore lower sample sizes available for research. A way overcome this is integrate experimental disease data with prior knowledge using network-based methods. Taking one step further, we hypothesized that combining analyzing results from...
The FAIR principles provide guidance on improving the Findability, Accessibility, Interoperability, and Reusability of digital resources. Since publication principles, several workflows have been proposed to support process making data (FAIRification). However, respect uniqueness different communities, both available deliberately designed remain agnostic in terms standards, tools, implementation choices. Consequently, FAIRification needs be properly planned, details must discussed with...
Abstract Hyperactivation of Wnt and Ras-MAPK signalling are common events in development colorectal adenomas. Further progression from adenoma-to-carcinoma is frequently associated with 20q gain overexpression Aurora kinase A (AURKA). Interestingly, AURKA has been shown to further enhance signalling. However, the molecular details these interactions driving carcinogenesis remain poorly understood. Here we first performed differential expression analysis (DEA) knockdown two cancer (CRC) cell...
Abstract Introduction Rare disease patient data are typically sensitive, present in multiple registries controlled by different custodians, and non-interoperable. Making these Findable, Accessible, Interoperable, Reusable (FAIR) for humans machines at source enables federated discovery analysis across custodians. This facilitates accurate diagnosis, optimal clinical management, personalised treatments. In Europe, twenty-four European Reference Networks (ERNs) work on rare domains. The...
<title>Abstract</title> This paper investigates the impact of restructuring knowl- edge graphs (KGs) with well-founded conceptual models to improve ma- chine learning (ML) predictions, particularly in drug repurposing appli- cations. These were developed using OntoUML, which is grounded Unified Foundational Ontology, and constructed following an established workflow for data FAIRification–a process aimed at making more Findable, Accessible, Interoperable, Reusable. We compared performance a...
"FAIR enough"?… A question asked on a daily basis in the rapidly evolving field of open science and underpinning data stewardship profession. After publication FAIR principles 2016, they have sparked theoretical debates, but some communities already begun to implement FAIR-guided services. No-one really argues against idea that data, as well accompanying workflows services should be findable, accessible under well-defined conditions, interoperable without munging, thus optimally reusable....
Abstract Rett syndrome (RTT) is a rare neurological disorder mostly caused by genetic variation in MECP2 . Making new variants and the related phenotypes available provides data for better understanding of disease mechanisms faster identification diagnosis. This is, however, currently hampered lack interoperability between genotype-phenotype databases. Here, we demonstrate on example RTT that making more Findable, Accessible, Interoperable, Reusable (FAIR), can facilitate prioritization...
Existing methods to make data Findable, Accessible, Interoperable, and Reusable (FAIR) are usually carried out in a post hoc manner: after the research project is conducted collected. De-novo FAIRification, on other hand, incorporates FAIRification steps process of project. In medical research, often collected stored via electronic Case Report Forms (eCRFs) Electronic Data Capture (EDC) systems. By implementing de novo such system, reusability and, thus, scalability across projects can be...
The Wnt/β-catenin signaling pathway is important for multiple developmental processes and tissue maintenance in adults. Consequently, deregulated involved a range of human diseases including cancer defects. A better understanding the intricate regulatory mechanism effect physiological (active) pathophysiological (hyperactive) WNT predicting treatment response developing novel therapies. constitutively expressed CTNNB1 (commonly hereafter referred to as β-catenin) degraded by destruction...
Biological pathways play a key role in most cellular functions. To better understand these functions, diverse computational and cell biology researchers use biological pathway data for various analysis modeling purposes. For specifying pathways, community of has defined BioPAX provided tools creating, validating visualizing models. However, generic software framework simulating models is missing. Here, we attempt to fill this gap by introducing simulation BioPAX. The explicitly separates the...
Abstract Background Patient data registries that are FAIR—Findable, Accessible, Interoperable, and Reusable for humans computers—facilitate research across multiple resources. This is particularly relevant to rare diseases, where often scarce scattered. Specific questions can be asked FAIR disease other resources without physically combining the data. Further, implies well-defined, transparent access conditions, which supports making sensitive as open possible closed necessary. Results We...
Rett syndrome (RTT) is a monogenic rare disorder that causes severe neurological problems.In most cases, it results from loss-of-function mutation in the gene encoding methyl-CPG-binding protein 2 (MECP2).Currently, about 900 unique MECP2 variations (benign and pathogenic) have been identified suspected different mutations contribute to levels of disease severity.For researchers clinicians, important genotype-phenotype information available identify disease-causing for diagnosis, aid...
The FAIR principles articulate the behaviors expected from digital artifacts that are Findable, Accessible, Interoperable and Reusable by machines people. Although now widely accepted, Principles design do not explicitly consider actual implementation choices enabling behaviors. As different communities have their own, often well-established preferences priorities for data reuse, coordinating a broadly used approach remains global challenge. In an effort to accelerate broad community...
Objective: This paper reports on the development of a dynamic data management planning questionnaire to guide stewards European Reference Network (ERN) rare disease patient registries make their findable, accessible, interoperable, and reusable (FAIR). As part this work, was validated through expert review aligned with existing resources diseases FAIR management. Materials Methods: The developed for Data Stewardship Wizard, tool planning. Knowledge sources data, ERN registries, were used...
Abstract The FAIR Principles provide guidance on how to improve the findability, accessibility, interoperability, and reusability of digital resources. Since publication principles in 2016, several workflows have been proposed support process making data (FAIRification). However, respect uniqueness different communities, both available deliberately designed remain agnostic terms standards, tools, related implementation choices. Consequently, FAIRification needs be properly planned advance,...
This report summarizes the scientific content and activities of annual symposium organized by Student Council International Society for Computational Biology (ISCB), held in conjunction with Intelligent Systems Molecular (ISMB) conference Boston, USA, on July 11th, 2014.
Abstract Background Patient data registries that are FAIR - Findable, Accessible, Interoperable, and Reusable for humans computers facilitate research across multiple resources. This is particularly relevant to rare diseases, where often scarce scattered. Specific questions can be asked disease other resources without physically combining the data. Results We successfully developed implemented a process of making registry vascular anomalies from its conception de novo . Here, we describe...
Introduction Existing methods to make data Findable, Accessible, Interoperable, and Reusable (FAIR) are usually carried out in a post-hoc manner: after the research project is conducted collected. De-novo FAIRification, on other hand, incorporates FAIRification steps process of project. In medical research, often collected stored via electronic Case Report Forms (eCRFs) Electronic Data Capture (EDC) systems. By implementing de-novo such system, reusability and, thus, scalability across...