Search Results - "van Iersel, Martijn"

PathVisio 3: an extendable pathway analysis toolbox by Kutmon, Martina, van Iersel, Martijn P, Bohler, Anwesha, Kelder, Thomas, Nunes, Nuno, Pico, Alexander R, Evelo, Chris T

“…PathVisio is a commonly used pathway editor, visualization and analysis software. Biological pathways have been used by biologists for many years to describe…”
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Presenting and exploring biological pathways with PathVisio by van Iersel, Martijn P, Kelder, Thomas, Pico, Alexander R, Hanspers, Kristina, Coort, Susan, Conklin, Bruce R, Evelo, Chris

“…Biological pathways are a useful abstraction of biological concepts, and software tools to deal with pathway diagrams can help biological research. PathVisio…”
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The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services by van Iersel, Martijn P, Pico, Alexander R, Kelder, Thomas, Gao, Jianjiong, Ho, Isaac, Hanspers, Kristina, Conklin, Bruce R, Evelo, Chris T

“…Many complementary solutions are available for the identifier mapping problem. This creates an opportunity for bioinformatics tool developers. Tools can be…”
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Mining biological pathways using WikiPathways web services by Kelder, Thomas, Pico, Alexander R, Hanspers, Kristina, van Iersel, Martijn P, Evelo, Chris, Conklin, Bruce R

“…WikiPathways is a platform for creating, updating, and sharing biological pathways [1]. Pathways can be edited and downloaded using the wiki-style website…”
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CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms by Terfve, Camille, Cokelaer, Thomas, Henriques, David, MacNamara, Aidan, Goncalves, Emanuel, Morris, Melody K, van Iersel, Martijn, Lauffenburger, Douglas A, Saez-Rodriguez, Julio

“…Cells process signals using complex and dynamic networks. Studying how this is performed in a context and cell type specific way is essential to understand…”
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WikiPathways: pathway editing for the people by Pico, Alexander R, Kelder, Thomas, van Iersel, Martijn P, Hanspers, Kristina, Conklin, Bruce R, Evelo, Chris

“…Funding: This work was supported by grants from the National Institutes of Health (GM080223, HG003053), the Agilent Technologies Foundation, the BioRange 1.2.4…”
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SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools by Chaouiya, Claudine, Bérenguier, Duncan, Keating, Sarah M, Naldi, Aurélien, van Iersel, Martijn P, Rodriguez, Nicolas, Dräger, Andreas, Büchel, Finja, Cokelaer, Thomas, Kowal, Bryan, Wicks, Benjamin, Gonçalves, Emanuel, Dorier, Julien, Page, Michel, Monteiro, Pedro T, von Kamp, Axel, Xenarios, Ioannis, de Jong, Hidde, Hucka, Michael, Klamt, Steffen, Thieffry, Denis, Le Novère, Nicolas, Saez-Rodriguez, Julio, Helikar, Tomáš

“…Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major…”
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Increasing Soy Isoflavonoid Content and Diversity by Simultaneous Malting and Challenging by a Fungus to Modulate Estrogenicity by Simons, Rudy, Vincken, Jean-Paul, Roidos, Nikolaos, Bovee, Toine F. H, van Iersel, Martijn, Verbruggen, Marian A, Gruppen, Harry

“…Soybeans were germinated on a kilogram-scale, by the application of malting technology used in the brewing industry, and concomitantly challenged with Rhizopus…”
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Software support for SBGN maps: SBGN-ML and LibSBGN by van Iersel, Martijn P, Villéger, Alice C, Czauderna, Tobias, Boyd, Sarah E, Bergmann, Frank T, Luna, Augustin, Demir, Emek, Sorokin, Anatoly, Dogrusoz, Ugur, Matsuoka, Yukiko, Funahashi, Akira, Aladjem, Mirit I, Mi, Huaiyu, Moodie, Stuart L, Kitano, Hiroaki, Le Novère, Nicolas, Schreiber, Falk

“…LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML…”
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WikiPathways: building research communities on biological pathways by Kelder, Thomas, van Iersel, Martijn P., Hanspers, Kristina, Kutmon, Martina, Conklin, Bruce R., Evelo, Chris T., Pico, Alexander R.

“…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…”
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PathVisio-Validator: a rule-based validation plugin for graphical pathway notations by CHANDAN, Kumar, LERSEL, Martijn P. Van, ALADJEM, Mirit I, KOHN, Kurt W, LUNA, Augustin

“…The PathVisio-Validator plugin aims to simplify the task of producing biological pathway diagrams that follow graphical standardized notations, such as…”
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Integrated visualization of a multi-omics study of starvation in mouse intestine by Iersel, Martijn P. van, Sokolović, Milka, Lenaerts, Kaatje, Kutmon, Martina, Bouwman, Freek G., Lamers, Wouter H., Mariman, Edwin C.M., Evelo, Chris T.

“…Our understanding of complex biological processes can be enhanced by combining different kinds of high-throughput experimental data, but the use of…”
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BridgeDb app: unifying identifier mapping services for Cytoscape by Gao, Jianjiong, Zhang, Chao, van Iersel, Martijn, Zhang, Li, Xu, Dong, Schultz, Nikolaus, R Pico, Alexander

“…The BridgeDb app for Cytoscape allows users to map and annotate identifiers of genes, proteins and metabolites in the context of biological networks. The app…”
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Path2Models: large-scale generation of computational models from biochemical pathway maps by Büchel, Finja, Rodriguez, Nicolas, Swainston, Neil, Wrzodek, Clemens, Czauderna, Tobias, Keller, Roland, Mittag, Florian, Schubert, Michael, Glont, Mihai, Golebiewski, Martin, van Iersel, Martijn, Keating, Sarah, Rall, Matthias, Wybrow, Michael, Hermjakob, Henning, Hucka, Michael, Kell, Douglas B, Müller, Wolfgang, Mendes, Pedro, Zell, Andreas, Chaouiya, Claudine, Saez-Rodriguez, Julio, Schreiber, Falk, Laibe, Camille, Dräger, Andreas, Le Novère, Nicolas

“…Systems biology projects and omics technologies have led to a growing number of biochemical pathway models and reconstructions. However, the majority of these…”
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The systems biology format converter by Rodriguez, Nicolas, Pettit, Jean-Baptiste, Dalle Pezze, Piero, Li, Lu, Henry, Arnaud, van Iersel, Martijn P, Jalowicki, Gael, Kutmon, Martina, Natarajan, Kedar N, Tolnay, David, Stefan, Melanie I, Evelo, Chris T, Le Novère, Nicolas

“…Interoperability between formats is a recurring problem in systems biology research. Many tools have been developed to convert computational models from one…”
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The NuGO proof of principle study package: a collaborative research effort of the European Nutrigenomics Organisation by Baccini, Michela, Bachmaier, Eva-Maria, Biggeri, Annibale, Boekschoten, Mark V, Bouwman, Freek G, Brennan, Lorraine, Caesar, Robert, Cinti, Saverio, Coort, Susan L, Crosley, Katie, Daniel, Hannelore, Drevon, Christian A, Duthie, Susan, Eijssen, Lars, Elliott, Ruan M, van Erk, Marjan, Evelo, Chris, Gibney, Mike, Heim, Carolin, Horgan, Graham W, Johnson, Ian T, Kelder, Thomas, Kleemann, Robert, Kooistra, Teake, van Iersel, Martijn P, Mariman, Edwin C, Mayer, Claus, McLoughlin, Gerard, Müller, Michael, Mulholland, Francis, van Ommen, Ben, Polley, Abigael C, Pujos-Guillot, Estelle, Rubio-Aliaga, Isabel, Roche, Helen M, de Roos, Baukje, Sailer, Manuela, Tonini, Giulia, Williams, Lynda M, de Wit, Nicole

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CySBGN: a Cytoscape plug-in to integrate SBGN maps by Gonçalves, Emanuel, van Iersel, Martijn, Saez-Rodriguez, Julio

“…A standard graphical notation is essential to facilitate exchange of network representations of biological processes. Towards this end, the Systems Biology…”
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Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment by Bohler, Anwesha, Eijssen, Lars M T, van Iersel, Martijn P, Leemans, Christ, Willighagen, Egon L, Kutmon, Martina, Jaillard, Magali, Evelo, Chris T

“…Biological pathways are descriptive diagrams of biological processes widely used for functional analysis of differentially expressed genes or proteins. Primary…”
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PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways by Fried, Jake Y, van Iersel, Martijn P, Aladjem, Mirit I, Kohn, Kurt W, Luna, Augustin

“…The PathVisio-Faceted Search plugin helps users explore and understand complex pathways by overlaying experimental data and data from webservices, such as…”
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PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs) by Luna, Augustin, Sunshine, Margot L., van Iersel, Martijn P., Aladjem, Mirit I., Kohn, Kurt W.

“…Motivation: A plugin for the Java-based PathVisio pathway editor has been developed to help users draw diagrams of bioregulatory networks according to the…”
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