A5068366960- MicroRNA in disease regulation
- Carcinogens and Genotoxicity Assessment
- Biomedical Text Mining and Ontologies
- Bioinformatics and Genomic Networks
- Computational Drug Discovery Methods
- Epigenetics and DNA Methylation
- Molecular Biology Techniques and Applications
- Ethics and Social Impacts of AI
- Effects and risks of endocrine disrupting chemicals
- Genomics, phytochemicals, and oxidative stress
- Big Data and Business Intelligence
- Air Quality and Health Impacts
- RNA modifications and cancer
- Semantic Web and Ontologies
- Toxic Organic Pollutants Impact
- Health, Environment, Cognitive Aging
- Nanomaterials for catalytic reactions
- Scientific Computing and Data Management
- Fungal and yeast genetics research
- Metabolomics and Mass Spectrometry Studies
- Vitamin C and Antioxidants Research
- Gene expression and cancer classification
- Chemical Reactions and Isotopes
- Electron and X-Ray Spectroscopy Techniques
- Phytoestrogen effects and research
Maastricht University
2013-2024
University of California, Berkeley
2017-2021
Queen Mary Hospital
2019
University of Hong Kong
2019
Seoul National University
2019
National Health Research Institutes
2019
Kyungpook National University Medical Center
2019
Chiayi Chang Gung Memorial Hospital
2019
Human Computer Interaction (Switzerland)
2016
Netherlands Metabolomics Centre
2016
WikiPathways (wikipathways.org) captures the collective knowledge represented in biological pathways. By providing a database curated, machine readable way, omics data analysis and visualization is enabled. other pathway databases are used to analyze experimental by research groups many fields. Due open collaborative nature of platform, our content keeps growing getting more accurate, making reliable rich database. Previously, however, focus was primarily on genes proteins, leaving...
Abstract The key characteristics (KC) of human carcinogens provide a uniform approach to evaluating mechanistic evidence in cancer hazard identification. Refinements the were requested by organizations and individuals applying KCs. We assembled an expert committee with knowledge carcinogenesis experience KCs leveraged this expertise examined literature more clearly describe each KC, identify current emerging assays vivo biomarkers that can be used measure them, make recommendations for...
Background: Identification of female reproductive toxicants is currently based largely on integrated epidemiological and in vivo toxicology data and, to a lesser degree, mechanistic data. A uniform approach systematically search, organize, integrate, evaluate evidence toxicity from various types lacking. Objective: We sought apply key characteristics similar that pioneered for carcinogen hazard identification toxicant identification. Methods: working group international experts was convened...
Increasing amounts of systems toxicology data, including omics results, are becoming publically available and accessible in databases. Data-driven informatics-tool supported pipeline schemas for fitting such data into Adverse Outcome Pathway (AOP) descriptions could potentially aid the development nonanimal-based hazard risk assessment methods. We devised a 6-step workflow that integrated diverse types novel AOP scheme pulmonary fibrosis. Mining literature references sources covering...
Evaluating carcinogenic mechanisms is a challenging part of hazard identification, as mechanistic data are both voluminous and diverse. An evaluation approach based on 10 key characteristics human carcinogens provides holistic unbiased way to tackle this challenge.
Human exposure to trichloroethylene (TCE) is linked kidney cancer, autoimmune diseases, and probably non-Hodgkin lymphoma. Additionally, TCE exposed mice cell cultures show altered DNA methylation. To evaluate associations between methylation in humans, we conducted an epigenome-wide association study (EWAS) workers using the HumanMethylation450 BeadChip. Across individual CpG probes, genomic regions, globally (i.e., 450K methylome), investigated differences mean variability of 73 control (<...
Chemical carcinogenesis can be induced by genotoxic (GTX) or non-genotoxic (NGTX) carcinogens. GTX carcinogens have a well-described mode of action. However, the complex mechanisms which NGTX act are less clear and may result in conflicting results between species [e.g. Wy-14,643 (Wy)]. We hypothesise that common microRNA response pathways exist for each class carcinogenic agents. Therefore, this study compares integrates mRNA expression profiles following short term acute exposure (24 48h)...
The toxic mechanisms of cisplatin have been frequently studied in many species and vitro cell models. Netherlands Toxicogenomics Centre focuses on developing alternatives using genomics technologies for animal-based assays on, e.g. genotoxic hazards. Models such as human hepatocellular carcinoma line (HepG2) cells, mouse primary hepatocytes (PMH) embryonic stem cells (mESC) are used. Our aim was to identify possibly robust conserved between these models model agent. Transcriptomic data newly...
The well-defined battery of in vitro systems applied within chemical cancer risk assessment is often characterised by a high false-positive rate, thus repeatedly failing to correctly predict the vivo genotoxic and carcinogenic properties test compounds. Toxicogenomics, i.e. mRNA-profiling, has been proven successful improving prediction genotoxicity understanding underlying mechanisms. Recently, microRNAs have discovered as post-transcriptional regulators mRNAs. It hypothesised that using...
Data-science is an interdisciplinary research working on data from different fields. When analyzing these data, scientists implicitly agree to follow the rules governing However, responsibilities of involved actors are not necessarily explicit. While novel frameworks supporting open-science being proposed, there currently no that focus within a data-science project. In this paper, we describe Transparency, Accountability, Privacy, and Societal Responsibility Matrix (TAPS-RM) as framework...
Data science is an interdisciplinary research area where scientists are typically working with data coming from different fields. When using and analyzing data, the implicitly agree to follow standards, procedures, rules set in these However, guidance on responsibilities of other involved actors a project missing. While literature shows that novel frameworks tools being proposed support open-science, reuse, management, there currently no can fully express project. In this paper, we describe...
Within the next twenty years, number of cancer patients is expected to rise by 70%. Current treatments still face several limitations, such as severe side effects and a high incidence disease recurrence. Drug combination therapies are promising strategy achieve higher therapeutic while reducing effects. This new direction in drug research has led data-driven medicine. To predict whether certain drugs would have synergistic effect when combined, DREAM Challenge coordinators released data for...
Abstract Accurate and precise information about the therapeutic uses (indications) of a drug is essential for applications in repurposing precision medicine. Leading online resources such as DrugCentral DrugBank provide rich various properties drugs, including their indications. However, because indications databases are often partly automatically mined, some may prove to be inaccurate or imprecise. Particularly challenging text mining methods task distinguishing between general disease...