A5046933371- Computational Drug Discovery Methods
- Biomedical Text Mining and Ontologies
- Bioinformatics and Genomic Networks
- Metabolomics and Mass Spectrometry Studies
- Chemistry and Chemical Engineering
- Molecular Biology Techniques and Applications
- Research Data Management Practices
- Animal testing and alternatives
- Biotechnology and Related Fields
- Gene expression and cancer classification
- Cancer Immunotherapy and Biomarkers
- Genomics and Phylogenetic Studies
- Immune cells in cancer
- Wikis in Education and Collaboration
- Scientific Computing and Data Management
- Statistical and Computational Modeling
- Scientific Research and Philosophical Inquiry
- Radiomics and Machine Learning in Medical Imaging
- Economic and Technological Systems Analysis
- Kruppel-like factors research
- Health, Environment, Cognitive Aging
- Nanomaterials for catalytic reactions
- Machine Learning in Bioinformatics
- Congenital heart defects research
- Peer-to-Peer Network Technologies
Maastricht University
2017-2025
Diabetes Australia
2024
Inserm
2017-2018
Sorbonne Université
2017-2018
Centre National de la Recherche Scientifique
2017-2018
Akademie für Gesundheitsberufe
1995
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 WikiPathways (https://www.wikipathways.org) is a biological pathway database known for its collaborative nature and open science approaches. With the core idea of scientific community developing curating knowledge in models, lowers all barriers accessing using content. Increasingly more content creators, initiatives, projects tools have started WikiPathways. Central this growth increased use are various communities that focus on particular subsets molecular pathways such as rare...
WikiPathways (wikipathways.org) is an open-source biological pathway database. Collaboration and open science are pivotal to the success of WikiPathways. Here we highlight continuing efforts supporting WikiPathways, content growth collaboration among researchers. As evolving database, there a growing need for address overcome technical challenges. In this direction, has undergone major restructuring, enabling renewed approach sharing curating knowledge, thus providing stability future...
Abstract Motivation The AOP-Wiki, a knowledge database for Adverse Outcome Pathways (AOPs), requires an efficient way to present overview of its content the reconstruction networks by experts in given domain. We have developed AOP-networkFinder, user-friendly tool that retrieves AOPs interest, allows network generation and cleaning, finally visualizes built around retrieved AOPs. Our constructs AOP connecting use same Key Events (KEs) versatile but controlled manner. Genes related these KEs...
We need to effectively combine the knowledge from surging literature with complex datasets propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets intervention. Here, we describe a large-scale community effort build an open access, interoperable computable repository COVID-19 molecular mechanisms. The Disease Map (C19DMap) is graphical, interactive representation disease-relevant mechanisms linking many sources. Notably, it computational...
Background Tumor-associated macrophages (TAMs) play a key immunosuppressive role that limits the ability of immune system to fight cancer and hinder antitumoral efficacy most treatments currently applied in clinic. Previous studies have evaluated response triggered by (TLR) agonists, such as poly(I:C), imiquimod (R837) or resiquimod (R848) monotherapies; however, their combination for treatment has not been explored. This study investigates macrophage reprogramming poly(I:C) combined with...
Fluorine has many beneficial features and applications but can cause toxicity at high doses. Herein, we describe its chemical properties benefits to agrochemical design as well potential metabolic liabilities exposure assessment in vivo.
Connective tissues support organs and play crucial roles in development, homeostasis fibrosis, yet our understanding of their formation is still limited. To gain insight into the molecular mechanisms connective tissue specification, we selected five zinc-finger transcription factors - OSR1, OSR2, EGR1, KLF2 KLF4 based on expression patterns and/or known involvement subtype differentiation. RNA-seq ChIP-seq profiling chick limb micromass cultures revealed a set common genes regulated by all...
A paradigm shift is taking place in risk assessment to replace animal models, reduce the number of economic resources, and refine methodologies test growing chemicals nanomaterials. Therefore, approaches such as transcriptomics, proteomics, metabolomics have become valuable tools toxicological research, are finding their way into regulatory toxicity. One promising framework bridge gap between molecular-level measurements concept Adverse Outcome Pathways (AOPs). These pathways comprise...
The adverse outcome pathway (AOP) is a conceptual construct that facilitates organisation and interpretation of mechanistic data representing multiple biological levels deriving from range methodological approaches including
The AOP-Wiki is the main platform for development and storage of adverse outcome pathways (AOPs). These AOPs describe mechanistic information about toxicodynamic processes can be used to develop effective risk assessment strategies. However, it challenging automatically systematically parse, filter, use its contents. We explored solutions better structure content, link with chemical biological resources. Together, this allows more detailed exploration, which automated.We converted complete...
Adverse outcome pathways (AOPs) provide evidence for demonstrating and assessing causality between measurable toxicological mechanisms human or environmental adverse effects. AOPs have gained increasing attention over the past decade are believed to necessary steppingstone more effective risk assessment of chemicals materials moving beyond need animal testing. However, as with all types data knowledge today, be reusable by machines, i.e., machine-actionable, in order reach their full impact...
Abstract Adverse Outcome Pathways (AOPs) have been proposed to facilitate mechanistic understanding of interactions chemicals/materials with biological systems. Each AOP starts a molecular initiating event (MIE) and possibly ends adverse outcome(s) (AOs) via series key events (KEs). So far, the interaction engineered nanomaterials (ENMs) biomolecules, biomembranes, cells, structures, in general, is not yet fully elucidated. There also huge lack information on which AOPs are ENMs-relevant or...
Computational toxicology is central to the current transformation occurring in and chemical risk assessment. There a need for more efficient use of existing data characterize human toxicological response environmental chemicals US Europe. The Adverse Outcome Pathway (AOP) framework helps organize mechanistic information contributes what currently being described as New Approach Methodologies (NAMs). AOP knowledge are submitted directly by users stored AOP-Wiki (https://aopwiki.org/)....
The sequence of the chicken genome, like several other draft genome sequences, is presently not fully covered. Gaps, contigs assigned with low confidence and uncharacterized chromosomes result in gene fragmentation imprecise annotation. Transcript abundance estimation from RNA sequencing (RNA-seq) data relies on read quality, library complexity expression normalization. In addition, quality used to map reads, annotation that defines features, must also be taken into account. A partially...
Abstract We describe a large-scale community effort to build an open-access, interoperable, and computable repository of COVID-19 molecular mechanisms - the Disease Map. discuss tools, platforms, guidelines necessary for distributed development its contents by multi-faceted biocurators, domain experts, bioinformaticians, computational biologists. highlight role relevant databases text mining approaches in enrichment validation curated mechanisms. Map their relevance pathophysiology...
Malignant pleural mesothelioma (MPM) is a highly aggressive malignancy mainly triggered by exposure to asbestos and characterized complex biology. A significant body of knowledge has been generated over the decades research community which improved our understanding disease toward prevention, diagnostic opportunities new treatments. Omics technologies are opening for additional levels information hypotheses. Given growing complexity technological spread biological in MPM, there an increasing...
Abstract Adverse Outcome Pathways (AOPs) are designed to provide mechanistic insights into toxicological processes after exposure a stressor and facilitate the replacement of animal studies with in vitro testing systems. Starting Molecular Initiating Event (MIE) ending an Outcome, sequence Key Events (KEs) spans across biological levels, but majority KEs AOP-Wiki describe molecular cellular processes. That suggests that established transcriptome-wide can be used validate or measure multitude...
<ns4:p>Toxicology has been an active research field for many decades, with academic, industrial and government involvement. Modern omics computational approaches are changing the field, from merely disease-specific observational models into target-specific predictive models. Traditionally, toxicology strong links other fields such as biology, chemistry, pharmacology, medicine. With rise of synthetic new engineered materials, alongside ongoing prioritisation needs in chemical risk assessment...
<ns3:p>Toxicology has been an active research field for many decades, with academic, industrial and government involvement. Modern omics computational approaches are changing the field, from merely disease-specific observational models into target-specific predictive models. Traditionally, toxicology strong links other fields such as biology, chemistry, pharmacology medicine. With rise of synthetic new engineered materials, alongside ongoing prioritisation needs in chemical risk assessment...