Chris T. Evelo
A5075750072- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Computational Drug Discovery Methods
- Microbial Metabolic Engineering and Bioproduction
- Gene expression and cancer classification
- Research Data Management Practices
- Metabolomics and Mass Spectrometry Studies
- Scientific Computing and Data Management
- Glutathione Transferases and Polymorphisms
- Genetics, Bioinformatics, and Biomedical Research
- Adipose Tissue and Metabolism
- Semantic Web and Ontologies
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Diet and metabolism studies
- Epigenetics and DNA Methylation
- Genetics and Neurodevelopmental Disorders
- Adipokines, Inflammation, and Metabolic Diseases
- Nutrition, Genetics, and Disease
- Sulfur Compounds in Biology
- Cancer-related molecular mechanisms research
- Gene Regulatory Network Analysis
- Genomics and Rare Diseases
- Genomics, phytochemicals, and oxidative stress
- Molecular Biology Techniques and Applications
Maastricht University
2016-2025
Radboud University Nijmegen
1984-2024
Leiden University Medical Center
2012-2024
Harry Perkins Institute of Medical Research
2024
Weatherford College
2024
Maastricht University Medical Centre
1996-2021
Center for Systems Biology
2018
University Medical Center
2018
Vrije Universiteit Amsterdam
2018
Harvard University
2014
There is an urgent need to improve the infrastructure supporting reuse of scholarly data. A diverse set stakeholders-representing academia, industry, funding agencies, and publishers-have come together design jointly endorse a concise measureable principles that we refer as FAIR Data Principles. The intent these may act guideline for those wishing enhance reusability their data holdings. Distinct from peer initiatives focus on human scholar, Principles put specific emphasis enhancing ability...
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...
The exponential growth of diverse types biological data presents the research community with an unprecedented challenge and opportunity. is to stay afloat in flood data, keeping it as accessible, up-to-date, integrated possible. opportunity cultivate new models curation exchange that take advantage direct participation by a greater portion community. This combination especially relevant task collecting pathway information. Pathways are critical understanding functions individual genes...
Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well developments community contributors. include zoomable viewer, support ontology annotations, ability to mark pathways private limited time and availability stable hyperlinks elements therein. content is freely available variety formats such BioPAX standard, increasingly adopted by external databases...
The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods manipulate such and perform computations on them. library implements wide variety of algorithms ranging from structure canonicalization molecular descriptor calculations pharmacophore perception. It in drug discovery, metabolomics, toxicology. Over the last 10 years, code base has grown significantly, however, resulting many...
To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability promote growth an open 'data commoning' culture. Here we describe prerequisites for data commoning present established growing ecosystem solutions using shared 'Investigation-Study-Assay' framework vision.
PathVisio is a commonly used pathway editor, visualization and analysis software. Biological pathways have been by biologists for many years to describe the detailed steps in biological processes. Those powerful, visual representations help researchers better understand, share discuss knowledge. Since first publication of 2008, original paper was cited more than 170 times different studies. As an online editor also integrated community curated database WikiPathways. Here we present third...
WikiPathways (http://www.wikipathways.org) is an open, collaborative platform for capturing and disseminating models of biological pathways data visualization analysis. Since our last NAR update, 4 years ago, has experienced massive growth in content, which continues to be contributed by hundreds individuals each year. New aspects the diversity depth collected are described from perspective researchers interested using pathway information their studies. We provide updates on extensions...
Biological pathways are a useful abstraction of biological concepts, and software tools to deal with pathway diagrams can help research. PathVisio is new visualization tool for that mimics the popular GenMAPP completely Java implementation allows better integration other open source projects. The MAPP file format replaced by GPML, XML provides seamless exchange graphical information among multiple programs. be combined bioinformatics up three possible uses: visual compilation knowledge,...
Abstract The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number possible combinations vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca’s large combination dataset, consisting 11,576 experiments from 910 across 85 molecularly characterized cell lines, and results a DREAM Challenge evaluate computational strategies for...
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...
We introduce GO-Elite, a flexible and powerful pathway analysis tool for wide array of species, identifiers (IDs), pathways, ontologies gene sets. In addition to the Gene Ontology (GO), GO-Elite allows user perform over-representation on any structured ontology annotations, database or biological IDs (e.g. gene, protein metabolite). exploits nature report minimal set non-overlapping terms. The results can be visualized WikiPathways as networks. Built-in support is provided over 60 species 50...
Researchers around the world join forces to reconstruct molecular processes of virus-host interactions aiming combat cause ongoing pandemic.
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 The notion that data should be Findable, Accessible, Interoperable and Reusable, according to the FAIR Principles, has become a global norm for good stewardship prerequisite reproducibility. Nowadays, guides policy actions professional practices in public private sectors. Despite such endorsements, however, Principles are aspirational, remaining elusive at best, intimidating worst. To address lack of practical guidance, help with capability gaps, we developed Cookbook, an open,...
Many complementary solutions are available for the identifier mapping problem. This creates an opportunity bioinformatics tool developers. Tools can be made to flexibly support multiple services or could combined get broader coverage. approach requires interface layer between tools and services. Here we present BridgeDb, a software framework gene, protein metabolite mapping. provides standardized through which connected different makes it easier developers Mapping merged multi-omics...
Cardiac hypertrophy can lead to heart failure (HF), but it is unpredictable which hypertrophied myocardium will progress HF. We surmised that apart from hypertrophy-related genes, failure-related genes are expressed before the onset of failure, permitting molecular prediction Hearts hypertensive homozygous renin-overexpressing (Ren-2) rats had progressed early HF were compared by microarray analysis Ren-2 remained compensated. To identify HF-related preceded cardiac biopsy specimens taken...
Background The sequence of events leading to the development insulin resistance (IR) as well underlying pathophysiological mechanisms are incompletely understood. As reductionist approaches have been largely unsuccessful in providing an understanding pathogenesis IR, there is a need for integrative, time-resolved approach elucidate disease. Methodology/Principal Findings Male ApoE3Leiden transgenic mice exhibiting humanized lipid metabolism were fed high-fat diet (HFD) 0, 1, 6, 9, or 12...