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Publications Christian Knüpfer

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@techreport{beckstein2011-computer_supported_research,
  author = {Clemens Beckstein and Christian Knüpfer and Birgitta
    König-Ries},
  title = {Computer-Supported Research -- Konzeptpapier zum
    CoSRe-Projekt},
  institution = {Digitale Bibliothek Thüringen},
  year = 2011,
  url = {http://www.db-thueringen.de/servlets/DocumentServlet?id=21436},
  number = {Dokument 21436},
  type = {techreport},
  language = {german}
}
@inproceedings{beckstein2012-function_bio-models,
  title = {Function of Bio-Models: Linking Structure to
    Behaviour},
  author = {Beckstein, Clemens and Knüpfer, Christian},
  year = 2012,
  booktitle = {Proceedings of the 4th Workshop of the {GI} Group
    "`Ontologies in Biomedicine and Life Sciences"' (OBML)},
  editor = {M. Boeker and H. Herre and R. Hoehndorf and
    F. Loebe},
  url = {http://www.onto-med.de/obml/ws2012/obml2012report.pdf#page=53}
}
@article{courtot11-controlled_vocabularies,
  author = {Courtot, Mélanie and Juty, Nick and Knüpfer,
    Christian and Waltemath, Dagmar and Zhukova, Anna and Dräger,
    Andreas and Dumontier, Michel and Finney, Andrew and Golebiewski,
    Martin and Hastings, Janna and Hoops, Stefan and Keating, Sarah
    and Kell, Douglas B and Kerrien, Samuel and Lawson, James and
    Lister, Allyson and Lu, James and Machne, Rainer and Mendes, Pedro
    and Pocock, Matthew and Rodriguez, Nicolas and Villeger, Alice and
    Wilkinson, Darren J and Wimalaratne, Sarala and Laibe, Camille and
    Hucka, Michael and Le Novère, Nicolas},
  title = {Controlled Vocabularies and Semantics in Systems
    Biology},
  journal = {Molecular Systems Biology},
  year = 2011,
  volume = 7,
  month = oct,
  eid = 543,
  groups = {public},
  keywords = {ontology, systems_biology},
  publisher = {EMBO and Macmillan Publishers Limited},
  doi = {10.1038/msb.2011.77}
}
@inproceedings{juty10-ontologies_systems_biology,
  author = {Juty, Nick and Le Novère, Nicolas and Waltemath,
    Dagmar and Knüpfer, Christian},
  title = {Ontologies for Use in Systems Biology: {SBO},
    {KiSAO} and {TEDDY}},
  booktitle = {COmputational Modeling in BIology NEtwork (COMBINE)
    2010},
  year = 2010,
  publisher = {Nature Precedings},
  doi = {10.1038/npre.2010.5122.1}
}
@inproceedings{juty10-ontologies_systems_biology_2,
  author = {Juty, Nick and Le Novère, Nicolas and Waltemath,
    Dagmar and Knüpfer, Christian},
  title = {Ontologies for Use in Systems Biology: {SBO},
    {KiSAO} and {TEDDY}},
  year = 2010,
  doi = {10.1038/npre.2010.5122.1},
  abstract = {Background: The use of computational modelling in
    the description and analysis of biological systems is at the heart
    of Systems Biology. Besides the information stored in a core
    model, there is increasingly a need to provide additional semantic
    information: to identify model components, to assist in biological
    interpretation of models, to define simulation conditions and to
    describe simulation results. This information deficit can be
    addressed through the use of ontologies.  Objectives:
    Computational modelling can be sub-divided into three areas; model
    construction, concerned with the encoding of a process into a
    defined format; model simulation, concerned with the precise set
    of operations to generate a specified result; model analysis,
    concerned with the categorisation of observed system
    behaviours. We describe here three ontologies created specifically
    to address the needs of the Systems Biology community in each
    sub-division, and illustrate their practical use with the
    'Repressilator' model (Elowitz and Leibler, 2000).  Results: The
    practical use of three ontologies is demonstrated: Systems Biology
    Ontology (SBO, www.biomodels.net/sbo/ ), Kinetic Simulation
    Algorithm Ontology (KiSAO, www.biomodels.net/kisao/ ) and
    Terminology for the Description of Dynamics (TEDDY,
    www.biomodels.net/teddy/ ). SBO provides semantic information
    including that of participant roles (e.g. inhibitor, SBO:0000020)
    and quantitative parameter types (e.g. Hill coefficient,
    SBO:0000190). KiASO supplies information about existing algorithms
    available for the simulation of Systems Biology models, their
    characterisation, and inter-relationships (e.g. Gibson and Bruck's
    next reaction method, KiSAO:0000027). TEDDY categorises observed
    behaviours (e.g. Stable Limit Cycle, TEDDY\_0000114) and
    diversifications of behaviours (e.g. Supercritical Hopf
    Bifurcation, TEDDY\_0000074).  Conclusion: The provision of
    semantic information extends model longevity and facilitates their
    reuse. It can provide useful insight into the biology of modelled
    processes, or be used to make informed decisions on subsequent
    simulation experiments. The ontologies described are freely
    available to view or download at the websites indicated, or
    through BioPortal ( http://bioportal.bioontology.org/ )},
  booktitle = {International Conference on Systems Biology (ICSB)
    2010},
  type = {Poster}
}
@mastersthesis{knuepfer03-testdaten,
  author = {Christian Knüpfer},
  title = {Testdatengenerierung für die Inferenz von
    Genregulationsnetzen},
  school = {Friedrich-Schiller-Universität},
  year = 2003,
  type = {Diplomarbeit},
  language = {german},
  address = {Jena},
  file = {http://www.informatik.uni-jena.de/~tral/data/diplom.pdf}
}
@inproceedings{knuepfer04-artificial_gene_regulation,
  author = {Christian Knüpfer and Peter Dittrich and Clemens
    Beckstein},
  title = {Artificial Gene Regulation: A Data Source for
    Validation of Reverse Bioengineering},
  booktitle = {Proceedings of the 6th German Workshop on Artificial
    Life 2004 (GWAL-6)},
  year = 2004,
  editor = {H. Schaub and F. Detje and U. Brüggemann},
  pages = {66-75},
  address = {Bamberg},
  publisher = {Akademische Verlagsgesellschaft Aka, Berlin},
  file = {http://www.informatik.uni-jena.de/~tral/data/paper_gwal04.pdf}
}
@inproceedings{knuepfer06-semantic_description,
  author = {Christian Knüpfer and Clemens Beckstein and Peter
    Dittrich},
  title = {Towards a Semantic Description of Bio-Models:
    Meaning Facets -- A Case Study},
  booktitle = {Proceedings of the Second International Symposium on
    Semantic Mining in Biomedicine (SMBM 2006)},
  venue = {Jena, Germany},
  eventdate = {2006-04-09/2006-04-12},
  year = 2006,
  editor = {Sophia Ananiadou and Juliane Fluck},
  series = {CEUR Workshop Proceedings},
  number = 177,
  pages = {97-100},
  publisher = {Sun SITE Central Europe, RWTH Aachen},
  url = {http://ceur-ws.org/Vol-177/poster_knuepfer.pdf}
}
@inproceedings{knuepfer07-formalise_meaning,
  author = {Christian Knüpfer and Clemens Beckstein and Peter
    Dittrich},
  title = {How to Formalise the Meaning of a Bio-Model: A Case
    Study},
  booktitle = {BioSysBio 2007: Systems Biology, Bioinformatics,
    Synthetic Biology, Meeting abstracts. 11.-13. January Manchester,
    UK},
  year = 2007,
  volume = {1, Suppl 1},
  series = {BMC Systems Biology},
  pages = 28,
  journal = {BMC Systems Biology},
  doi = {10.1186/1752-0509-1-S1-P28},
  publisher = {BioMed Central}
}
@inproceedings{knuepfer09-KiSAO_TEDDY,
  author = {Knüpfer, Christian and Le Novère, Nicolas and Köhn,
    Dagmar},
  title = {Beyond Structure: {KiSAO} and {TEDDY} – Two
    Ontologies Addressing Pragmatical and Dynamical Aspects of
    Computational Models in Systems Biology},
  year = 2009,
  url = {http://www.onto-med.de/obml/ws2009/s5-4-knuepfer.pdf},
  booktitle = {First workshop of the {GI} group "`Ontologies in
    Biomedicine and Life Sciences"'},
  pages = {41-42},
  organization = {GI}
}
@mastersthesis{knuepfer2001-lernalgorithmus_hydro_nn,
  author = {Christian Knüpfer},
  title = {Lernalgorithmus für das Hydro-NN},
  school = {Friedrich-Schiller-Universität},
  year = 2001,
  type = {Studienarbeit},
  language = {german},
  address = {Jena}
}
@misc{knuepfer2007-biomd0000000040_MoM,
  author = {Christian Knüpfer},
  month = sep,
  year = 2007,
  title = {{Field} and {Noyes} (1974): {The Oregonator}},
  url = {https://www.ebi.ac.uk/biomodels-main/static-pages.do?page=ModelMonth/2007-09},
  organization = {BioModels Database},
  howpublished = {Model of the Month September 2007:
    {BIOMD0000000040}}
}
@article{knuepfer2013-function_bio-models,
  author = {Christian Knüpfer and Clemens Beckstein},
  title = {Function of Dynamic Models in Systems Biology:
    Linking Structure to Behaviour},
  journal = {Journal of Biomedical Semantics},
  year = 2013,
  volume = 4,
  number = 1,
  pages = 24,
  url = {http://www.jbiomedsem.com/content/4/1/24},
  doi = {10.1186/2041-1480-4-24},
  issn = {2041-1480},
  abstract = {Background: Dynamic models in Systems Biology are
    used in computational simulation experiments for addressing
    biological questions. The complexity of the modelled biological
    systems and the growing number and size of the models calls for
    computer support for modelling and simulation in Systems
    Biology. This computer support has to be based on formal
    representations of relevant knowledge fragments. Results: In this
    paper we describe different functional aspects of dynamic
    models. This description is conceptually embedded in our "`meaning
    facets"' framework which systematises the interpretation of
    dynamic models in structural, functional and behavioural
    facets. Here we focus on how function links the structure and the
    behaviour of a model. Models play a specific role (teleological
    function) in the scientific process of finding explanations for
    dynamic phenomena. In order to fulfil this role a model has to be
    used in simulation experiments (pragmatical function). A
    simulation experiment always refers to a specific situation and a
    state of the model and the modelled system (conditional
    function). We claim that the function of dynamic models refers to
    both the simulation experiment executed by software (intrinsic
    function) and the biological experiment which produces the
    phenomena under investigation (extrinsic function). We use the
    presented conceptual framework for the function of dynamic models
    to review formal accounts for functional aspects of models in
    Systems Biology, such as checklists, ontologies, and formal
    languages. Furthermore, we identify missing formal accounts for
    some of the functional aspects. In order to fill one of these gaps
    we propose an ontology for the teleological function of
    models. Conclusion: We have thoroughly analysed the role and use
    of models in Systems Biology. The resulting conceptual framework
    for the function of models is an important first step towards a
    comprehensive formal representation of the functional knowledge
    involved in the modelling and simulation process. Any progress in
    this area will in turn improve computer-supported modelling and
    simulation in Systems Biology.}
}
@article{knuepfer2013-structure_function_behaviour,
  author = {Christian Knüpfer and Clemens Beckstein and Peter
    Dittrich and Le Novère, Nicolas},
  title = {Structure, Function, and Behaviour of Computational
    Models in Systems Biology},
  journal = {BMC Systems Biology},
  year = 2013,
  volume = 7,
  number = 1,
  pages = 43,
  url = {http://www.biomedcentral.com/1752-0509/7/43},
  doi = {10.1186/1752-0509-7-43},
  pubmedid = 23721297,
  issn = {1752-0509}
}
@phdthesis{knuepfer2015-struktur_funktion_verhalten,
  author = {Christian Knüpfer},
  title = {Struktur, Funktion und Verhalten dynamischer Modelle
    der Systembiologie: Formale Wissensrepräsentation als Grundlage
    für computergestützte Modellierung und Simulation},
  type = {Dissertation},
  school = {Friedrich-Schiller-Universität Jena},
  year = 2015,
  language = {german},
  date = {2015-10-19},
  url = {http://nbn-resolving.de/urn:nbn:de:gbv:27-20151112-130829-2}
}
@mastersthesis{knuepfer92,
  author = {Christian Knüpfer},
  title = {Erarbeitung und Anwendung eines Programms zur
    rechnergestützten Meßwerterfassung von Potentialabfallkurven an
    wasserstoffentwickelnden Elektroden},
  school = {Staatliche Technikerschule},
  year = 1992,
  type = {Ingenieurarbeit},
  language = {german},
  address = {Berlin}
}
@mastersthesis{knuepfer93,
  author = {Christian Knüpfer},
  title = {Vergleichende Untersuchung zur Abtrennung von
    Biomasse aus mikrobiellen Kulturlösungen unter Verwendung
    verschiedener Gerätesysteme},
  school = {Fachhochschule},
  year = 1993,
  type = {Diplomarbeit},
  language = {german},
  address = {Merseburg}
}
@inproceedings{koehn09-KiSAO_TEDDY,
  author = {Köhn, Dagmar and Le Novère, Nicolas and Knüpfer,
    Christian},
  title = {Beyond Structure: {KiSAO} and {TEDDY} - Two
    Ontologies Addressing Pragmatical and Dynamical Aspects of
    Computational Models in Systems Biology},
  year = 2009,
  doi = {10.1038/npre.2009.3137.1},
  abstract = {Computational models are becoming more and more the
    central scientific paradigm for understanding the complexity of
    living systems. With the increasing number and size of these
    models there is a growing need for model reuse and
    exchange. Furthermore, detailed models are not manageable without
    computer support. There are efforts to formalise the mathematical
    structure of models (e.g. SBML) and to standardise the kinetic and
    biological meaning of model components (e.g. SBO, GO,
    UniProt). However, formalising only the structure of computational
    models is not sufficient to easily exchange and reuse models and
    to achieve full computer support for modelling. We also need to
    formalise the pragmatical and dynamical aspects of models. For
    this purpose we propose two ontologies: The Kinetic Simulation
    Algorithm Ontology (KiSAO) and the TErminology for the Description
    of DYnamics (TEDDY). KiSAO covers algorithms used for simulation
    of computational models. The ontology classifies and puts into
    context existing simulation algorithms. For the classification, it
    uses several criteria such as deterministic/stochastic or
    spatial/non-spatial. The aim of TEDDY is to provide terms for
    describing and characterising dynamical behaviours, observable
    dynamical phenomena, and control elements of biological models and
    biological systems in Systems Biology and Synthetic Biology.},
  booktitle = {3rd International Biocuration Conference},
  type = {Poster}
}
@inproceedings{koehn09-beyond_structure,
  author = {Köhn, Dagmar and Knüpfer, Christian and Le Novère,
    Nicolas},
  title = {Beyond Structure: Ontologies for Pragmatical and
    Dynamical Aspects of Computational Models in Systems Biology},
  year = 2009,
  booktitle = {12th Annual Bio-Ontologies Meeting, SIG at ISMB
    2009},
  type = {Poster}
}
@inproceedings{koehn09-beyond_structure_2,
  author = {Köhn, Dagmar and Knüpfer, Christian and Le Novère,
    Nicolas},
  title = {Beyond Structure: {KiSAO} and {TEDDY} - Two
    ontologies Addressing Pragmatical and Dynamical Aspects of
    Computational Models in Systems Biology},
  year = 2009,
  booktitle = {SBML Hackathon 2009},
  type = {Poster}
}
@inproceedings{novere2007-TEDDY,
  author = {Le Novère, Nicolas and Christian Knüpfer},
  title = {{TEDDY} -- A Terminology for the Description of the
    Dynamics of Bio-Models},
  booktitle = {Foundations of Systems Biology in Engineering
    (FOSBE)},
  year = 2007,
  url = {http://www.ebi.ac.uk/~lenov/POSTERS/Poster_TEDDY_FOSBE2007.pdf}
}
@inproceedings{novere2007-semantic_annotation,
  author = {Le Novère, Nicolas and Camille Laibe and Melanie
    Courtot and Christian Knüpfer and Michael Hucka},
  title = {Semantic Annotation of Kinetic Models in Systems
    Biology},
  url = {http://www.icsb07.caltech.edu/proceedings/abstracts/G28.pdf},
  booktitle = {The Eighth International Conference on Systems
    Biology (ICSB)},
  year = 2007,
  pages = {G28}
}
@inproceedings{novere2007-semantic_annotation_2,
  author = {Le Novère, Nicolas and Camille Laibe and Melanie
    Courtot and Christian Knüpfer and Michael Hucka},
  title = {Semantic Annotation of Kinetic Models in Systems
    Biology},
  url = {https://www.ebi.ac.uk/compneur-srv/miriam/elements/Poster_Semantics_ISMB-2007.pdf},
  booktitle = {15th Annual International Conference on Intelligent
    Systems for Molecular Biology},
  year = 2007,
  pages = {C126}
}
@misc{waltemath11-sbml_annotation_package,
  author = {Waltemath, Dagmar and Swainston, Neil and Lister,
    Allyson and Bergmann, Frank and Henkel, Ron and Hoops, Stefan and
    Hucka, Michael and Juty, Nick and Keating, Sarah and Knüpfer,
    Christian and Krause, Falko and Laibe, Camille and Liebermeister,
    Wolfram and Lloyd, Catherine and Misirli, Goksel and Schulz,
    Marvin and Taschuk, Morgan and Le Novère, Nicolas},
  title = {{SBML} Level 3 Package Proposal: Annotation},
  year = 2011,
  doi = {10.1038/npre.2011.5610.1},
  note = {Available from Nature Precedings}
}
@article{waltemath2016-community_standards,
  author = {D. Waltemath and J. R. Karr and F. T. Bergmann and
    V. Chelliah and M. Hucka and M. Krantz and W. Liebermeister and
    P. Mendes and C. J. Myers and P. Pir and B. Alaybeyoglu and
    N. K. Aranganathan and K. Baghalian and A. T. Bittig and
    P. E. P. Burke and M. Cantarelli and Y. H. Chew and R. S. Costa
    and J. Cursons and T. Czauderna and A. P. Goldberg and H. F. Gómez
    and J. Hahn and T. Hameri and D. F. H. Gardiol and D. Kazakiewicz
    and I. Kiselev and V. Knight-Schrijver and C. Knüpfer and M. König
    and D. Lee and A. Lloret-Villas and N. Mandrik and J. K. Medley
    and B. Moreau and H. Naderi-Meshkin and S. K. Palaniappan and
    D. Priego-Espinosa and M. Scharm and M. Sharma and K. Smallbone
    and N. J. Stanford and J. H. Song and T. Theile and M. Tokic and
    N. Tomar and V. Touré and J. Uhlendorf and T. M. Varusai and
    L. H. Watanabe and F. Wendland and M. Wolfien and J. T. Yurkovich
    and Y. Zhu and A. Zardilis and A. Zhukova and F. Schreiber},
  journal = {IEEE Transactions on Biomedical Engineering},
  title = {Toward Community Standards and Software for
    Whole-Cell Modeling},
  year = 2016,
  volume = 63,
  number = 10,
  pages = {2007-2014},
  keywords = {Biological system modeling;Computational
    modeling;Mathematical model;Optical wavelength
    conversion;Standards;Systems biology;Computational
    biology;education;simulation;standards;systems biology;whole-cell
    (WC) modeling},
  doi = {10.1109/TBME.2016.2560762},
  issn = {0018-9294},
  month = oct
}

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