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Publikace
Šmarda P., Šmerda J., Knoll A., Bureš P., & Danihelka J. 2007: Revision of Central European taxa of Festuca ser. Psammophilae Pawlus: morphometrical, karyological and AFLP analysis. 266, 197 - 232.
Danihelka J., Saukel J. & Ehrendorfer F. 2006: Typification of the names Achillea millefolium var. collina and A. pannonica (Asteraceae, Anthemideae). Systematic Botany 55, 507 - 510.
Eckstein R. L., Hölzel N. & Danihelka J. 2006: Biological flora of Central Europe: Viola elatior, V. pumila and V. stagnina. Perspectives in Plant Ecology Evolution and Systematics 8, 45 - 66.
Eckstein R. L., O\'Neil R. A., Danihelka J., Otte A. & Köhler W. 2006: Genetic structure among and within peripheral and central populations of three endangered floodplain violets. Molecular Ecology 15, 2367 - 2379.
Chytrý M., Pyšek P., Tichý L., Knollová I. & Danihelka J. 2005: Invasions by alien plants in the Czech Republic: a quantitative assessment across habitats. Preslia 77, 339 - 354.
Řepka R. & Danihelka J. 2005: Typification of the name Carex muricata var. lamprocarpa Wallr. and its nomenclatural consequences. Preslia 77, 129 - 136.
Danihelka J. & Šumberová K. 2004: O rozšíření některých cévnatých rostlin na nejjižnější Moravě II. Příroda 21, 117 - 192.
Eckstein R. L., Danihelka J., Hölzel N. & Otte A. 2004: The effects of management and environmental variation on population stage structure in three river-corridor violets. Acta Oecologica 25, 83 - 91.
Danihelka J., Petřík P. & Wild J.: Databanka flóry České republiky. 2011.