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Publications Christian Knüpfer

knuepfer
[1]
D. Waltemath, J. R. Karr, F. T. Bergmann, V. Chelliah, M. Hucka, M. Krantz, W. Liebermeister, P. Mendes, C. J. Myers, P. Pir, B. Alaybeyoglu, N. K. Aranganathan, K. Baghalian, A. T. Bittig, P. E. P. Burke, M. Cantarelli, Y. H. Chew, R. S. Costa, J. Cursons, T. Czauderna, A. P. Goldberg, H. F. Gómez, J. Hahn, T. Hameri, D. F. H. Gardiol, D. Kazakiewicz, I. Kiselev, V. Knight-Schrijver, C. Knüpfer, M. König, D. Lee, A. Lloret-Villas, N. Mandrik, J. K. Medley, B. Moreau, H. Naderi-Meshkin, S. K. Palaniappan, D. Priego-Espinosa, M. Scharm, M. Sharma, K. Smallbone, N. J. Stanford, J. H. Song, T. Theile, M. Tokic, N. Tomar, V. Touré, J. Uhlendorf, T. M. Varusai, L. H. Watanabe, F. Wendland, M. Wolfien, J. T. Yurkovich, Y. Zhu, A. Zardilis, A. Zhukova, and F. Schreiber. Toward community standards and software for whole-cell modeling. IEEE Transactions on Biomedical Engineering, 63(10):2007--2014, October 2016.
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[2]
Christian Knüpfer. Struktur, Funktion und Verhalten dynamischer Modelle der Systembiologie: Formale Wissensrepräsentation als Grundlage für computergestützte Modellierung und Simulation. Dissertation, Friedrich-Schiller-Universität Jena, 2015.
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[3]
Christian Knüpfer and Clemens Beckstein. Function of dynamic models in systems biology: Linking structure to behaviour. Journal of Biomedical Semantics, 4(1):24, 2013.
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[4]
Christian Knüpfer, Clemens Beckstein, Peter Dittrich, and Nicolas Le Novère. Structure, function, and behaviour of computational models in systems biology. BMC Systems Biology, 7(1):43, 2013.
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[5]
Clemens Beckstein and Christian Knüpfer. Function of bio-models: Linking structure to behaviour. In M. Boeker, H. Herre, R. Hoehndorf, and F. Loebe, editors, Proceedings of the 4th Workshop of the GI Group "`Ontologies in Biomedicine and Life Sciences"' (OBML), 2012.
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[6]
Mélanie Courtot, Nick Juty, Christian Knüpfer, Dagmar Waltemath, Anna Zhukova, Andreas Dräger, Michel Dumontier, Andrew Finney, Martin Golebiewski, Janna Hastings, Stefan Hoops, Sarah Keating, Douglas B Kell, Samuel Kerrien, James Lawson, Allyson Lister, James Lu, Rainer Machne, Pedro Mendes, Matthew Pocock, Nicolas Rodriguez, Alice Villeger, Darren J Wilkinson, Sarala Wimalaratne, Camille Laibe, Michael Hucka, and Nicolas Le Novère. Controlled vocabularies and semantics in systems biology. Molecular Systems Biology, 7, October 2011.
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[7]
Clemens Beckstein, Christian Knüpfer, and Birgitta König-Ries. Computer-Supported Research -- Konzeptpapier zum CoSRe-Projekt. techreport Dokument 21436, Digitale Bibliothek Thüringen, 2011.
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[8]
Dagmar Waltemath, Neil Swainston, Allyson Lister, Frank Bergmann, Ron Henkel, Stefan Hoops, Michael Hucka, Nick Juty, Sarah Keating, Christian Knüpfer, Falko Krause, Camille Laibe, Wolfram Liebermeister, Catherine Lloyd, Goksel Misirli, Marvin Schulz, Morgan Taschuk, and Nicolas Le Novère. SBML level 3 package proposal: Annotation, 2011. Available from Nature Precedings.
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[9]
Nick Juty, Nicolas Le Novère, Dagmar Waltemath, and Christian Knüpfer. Ontologies for use in systems biology: SBO, KiSAO and TEDDY. In COmputational Modeling in BIology NEtwork (COMBINE) 2010. Nature Precedings, 2010.
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[10]
Nick Juty, Nicolas Le Novère, Dagmar Waltemath, and Christian Knüpfer. Ontologies for use in systems biology: SBO, KiSAO and TEDDY. In International Conference on Systems Biology (ICSB) 2010, 2010.
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[11]
Christian Knüpfer, Nicolas Le Novère, and Dagmar Köhn. Beyond structure: KiSAO and TEDDY – two ontologies addressing pragmatical and dynamical aspects of computational models in systems biology. In First workshop of the GI group "`Ontologies in Biomedicine and Life Sciences"', pages 41--42. GI, 2009.
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[12]
Dagmar Köhn, Nicolas Le Novère, and Christian Knüpfer. Beyond structure: KiSAO and TEDDY - two ontologies addressing pragmatical and dynamical aspects of computational models in systems biology. In 3rd International Biocuration Conference, 2009.
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[13]
Dagmar Köhn, Christian Knüpfer, and Nicolas Le Novère. Beyond structure: Ontologies for pragmatical and dynamical aspects of computational models in systems biology. In 12th Annual Bio-Ontologies Meeting, SIG at ISMB 2009, 2009.
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[14]
Dagmar Köhn, Christian Knüpfer, and Nicolas Le Novère. Beyond structure: KiSAO and TEDDY - two ontologies addressing pragmatical and dynamical aspects of computational models in systems biology. In SBML Hackathon 2009, 2009.
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[15]
Christian Knüpfer. Field and Noyes (1974): The Oregonator. Model of the Month September 2007: BIOMD0000000040, September 2007.
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[16]
Christian Knüpfer, Clemens Beckstein, and Peter Dittrich. How to formalise the meaning of a bio-model: A case study. In BioSysBio 2007: Systems Biology, Bioinformatics, Synthetic Biology, Meeting abstracts. 11.-13. January Manchester, UK, volume 1, Suppl 1 of BMC Systems Biology, page 28. BioMed Central, 2007.
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[17]
Nicolas Le Novère and Christian Knüpfer. TEDDY -- a terminology for the description of the dynamics of bio-models. In Foundations of Systems Biology in Engineering (FOSBE), 2007.
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[18]
Nicolas Le Novère, Camille Laibe, Melanie Courtot, Christian Knüpfer, and Michael Hucka. Semantic annotation of kinetic models in systems biology. In The Eighth International Conference on Systems Biology (ICSB), page G28, 2007.
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[19]
Nicolas Le Novère, Camille Laibe, Melanie Courtot, Christian Knüpfer, and Michael Hucka. Semantic annotation of kinetic models in systems biology. In 15th Annual International Conference on Intelligent Systems for Molecular Biology, page C126, 2007.
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[20]
Christian Knüpfer, Clemens Beckstein, and Peter Dittrich. Towards a semantic description of bio-models: Meaning facets -- a case study. In Sophia Ananiadou and Juliane Fluck, editors, Proceedings of the Second International Symposium on Semantic Mining in Biomedicine (SMBM 2006), number 177 in CEUR Workshop Proceedings, pages 97--100. Sun SITE Central Europe, RWTH Aachen, 2006.
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[21]
Christian Knüpfer, Peter Dittrich, and Clemens Beckstein. Artificial gene regulation: A data source for validation of reverse bioengineering. In H. Schaub, F. Detje, and U. Brüggemann, editors, Proceedings of the 6th German Workshop on Artificial Life 2004 (GWAL-6), pages 66--75, Bamberg, 2004. Akademische Verlagsgesellschaft Aka, Berlin.
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[22]
Christian Knüpfer. Testdatengenerierung für die Inferenz von Genregulationsnetzen. Diplomarbeit, Friedrich-Schiller-Universität, Jena, 2003.
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[23]
Christian Knüpfer. Lernalgorithmus für das Hydro-NN. Studienarbeit, Friedrich-Schiller-Universität, Jena, 2001.
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[24]
Christian Knüpfer. Vergleichende Untersuchung zur Abtrennung von Biomasse aus mikrobiellen Kulturlösungen unter Verwendung verschiedener Gerätesysteme. Diplomarbeit, Fachhochschule, Merseburg, 1993.
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[25]
Christian Knüpfer. Erarbeitung und Anwendung eines Programms zur rechnergestützten Meßwerterfassung von Potentialabfallkurven an wasserstoffentwickelnden Elektroden. Ingenieurarbeit, Staatliche Technikerschule, Berlin, 1992.
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