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Foundations of Theory of Science. Academia, Prague, 1988 (co-author)
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Innovation policy issues in six candidate countries: the challenges. Directorate Central for Enterprise , EUR 17036 European Communities, 2001 (co-author)
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Gorzelak, G. Ehrlich, É., Falta L., Illner, M. (eds.), Central Europe in Transition: towards EU membership, Regional Studies association, Warsaw, 2001 (co-author)
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Müller, K., From Plan to Market: implications for S and T Systems in Transition Economies, the case of the Czech Republic. In: Brundenius at al., Reconstruction or Destruction. Science and technology at Stake in Transition economies. Universities Press, Haydarabad, 1999.
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Müller, K., Innovation policy in the Czech Republic: from laissez faire to state activism. Journal of International Relations and Development, Vol. 5, No.4 (2002), pp. 403-426
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Müller, K., Innovative Europe – Constrains and Challenges. In: Kuklinski, A. et al (eds.) Towards a New Creative and Innovative Europe, WSB-NLU, Nowy Sacz. Poland), 2007
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Müller, K., The Institutional dimensions of restructuring innovation systems in the accessing countries. In: Jasinski, A. (ed.) Transition Economies in the European Research and Innovations Area. WWZ, Warsaw, 2004, pp.26-46.
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Müller K., 2002, Industrial resources, Economic Growth and Social Change. Sociological Publishing House (SLON), Prague, (in Czech)
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Yearbook of Competitiveness of the Czech Republic, Centre of Economic studies at economic College, annually since 2006 (co-author)
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Special issues on knowledge governance of Central European Journal for Public Policy, Vol. 4, No. 2, 2010 (co-editor)
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Special issue of International Journal of Innovation and Regional Development. Vol. 3, No. 1, 2011 (co-editor)
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Müller, K., Roth, S., Žák (eds.), 2010, Social Dimension of Innovation. Centrum of Economic Studies, Prague
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Müller Karel, 2014, Wissenschaft zwischen Staat un Zivilgesellschaft. In Luft, Havelka, Zwicker (Hg.) Zviligesellschaft und Menschenrechte in oestlichen Mitteleuropa. Vandenhoeck und Ruprecht, München