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| Rasanpreet Kaur; Anwesha Dutta; Martina Kutmon; Martijn Iersel; Chris Evelo. |
| Biological molecules such as proteins and metabolites interact to accomplish a biological function and to respond to environmental stimuli. Pathways capture this information derived through scientific experimentation and data analysis. They contain information about genes that appear in complexes, the interacting genes, the directionality of the interactions (e.g. inhibitors versus activators), the cellular locations where the reactions occur, and the metabolites that are affected by the processes. Using our open-source pathway analysis platform, PathVisio, we will connect pathway analysis to different quantitative approaches already in development for metabolic network modeling, such as flux balance analysis and dynamic simulation. In order to use... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/6970/version/1 |
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| Chris Evelo. |
| Biologists typically use knowledge represented as pathways to better understand the results of genomics experiments. Through integration of data from different omics techniques with what we already know, statistical evaluation and subsequent data visualization the results often start to make sense. An important problem is that we often do not have the relevant pathways, or they may be incomplete or not suitable for usage by analytical tools. Wikipathways is meant to be an answer to the problems described above. It uses mediawiki technology and dedicated open source java code to allow biologists to edit pathway content on the web. We assist this process through the development of helpful software like a Diff tool, Go and KEGG converters, portal mechanism,... |
| Tipo: Presentation |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3115/version/1 |
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| Andra Waagmeester; Chris Evelo. |
| CitedIn is a webservice that can be found at www.citedin.org. It tracks online citations in databases, blogs, wikis, and community sites to the literature covered in Pubmed. For biomedical scientific literature Pubmed is by far the most interesting resource. Pubmed is the interface to the Medline repository which covers over 1 century of publications and contains almost all relevant publications in the field. Pubmed uses very simple unique numeric identifiers. This makes it easy to cite publications using these Pubmed Identifiers (PMIDs) or to link to Pubmed itself based on those. This ease of use results in PMIDs often being used for online citations, this is often the standard in biomedical databases and for instance in Wikipedia. CitedIn uses a federate... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6037/version/1 |
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| Pieter Giesbertz; Jonas Hummel; Stan Gaj; Danyel Jennen; Thomas Kelder; Chris Evelo; Joost van Delft; Jos Kleinjans. |
| Current high-throughput technology in genomics creates a large amount of biological data. Bioinformatics approaches are directed towards understanding such data on a systems biology level. Advanced mathematical methods like principal component analysis, clustering, neural networks, support vector machine (SVM) approaches and neural networks can help to find patterns in the data. However, to really understand the data the patterns must be combined with existing knowledge. One of the approaches to do so is to associate these data to functional classifications such as can be found in the Gene Ontology. Other methods focus on using biological pathways coming from both public and private pathway databases like KEGG, WikiPathways, Reactome, and MetaCore. Some of... |
| Tipo: Poster |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4575/version/1 |
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