Study programmes
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| Faculty | Study type | Name of the study program | Language of instruction | Study form | ||
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| Faculty of Science | doctoral | Philosophy and History of Science | English | full-time |
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| Faculty of Science | doctoral | Anthropology and Human Genetics | English | full-time |
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| Faculty of Science | doctoral | Developmental and Cell Biology | English | full-time |
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| Faculty of Science | doctoral | Theoretical and Evolutionary Biology | English | full-time |
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| Faculty of Science | doctoral | Organic Chemistry | English | full-time |
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| Faculty of Science | doctoral | Ecology | English | full-time |
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| Faculty of Science | doctoral | Macromolecular Chemistry | English | full-time |
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| Faculty of Science | doctoral | Modelling of Chemical Properties on Nano- and Biostructures | English | full-time |
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| Faculty of Science | doctoral | Demography | English | full-time |
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| Faculty of Science | doctoral | Zoology | English | full-time |
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| Faculty of Science | doctoral | Physical Chemistry | English | full-time |
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| Faculty of Science | doctoral | Inorganic Chemistry | English | full-time |
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| Faculty of Science | doctoral | Analytical Chemistry | English | full-time |
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| Faculty of Science | doctoral | Didactics of Chemistry | English | full-time |
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| Faculty of Science | doctoral | Geoinformatics, Cartography and Remote Sensing | English | full-time |
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| Faculty of Science | doctoral | Social Geography and Regional Development | English | full-time |
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| Faculty of Science | doctoral | Microbiology | English | full-time |
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| Faculty of Science | doctoral | Biochemistry | English | full-time |
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| Faculty of Science | doctoral | Botany | English | full-time |
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| Faculty of Science | doctoral | Regional and Political Geography | English | full-time |
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| Faculty of Science | doctoral | Environmental Science | English | full-time |
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| Faculty of Science | doctoral | Molecular and Cellular Biology, Genetics and Virology | English | full-time |
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| Faculty of Science | doctoral | Geology | English | full-time |
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| Faculty of Science | doctoral | Animal Physiology | English | full-time |
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| Faculty of Science | doctoral | Applied Geology | English | full-time |
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| Faculty of Science | doctoral | Parasitology | English | full-time |
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| Faculty of Science | doctoral | Bioinformatics and computational biology | English | full-time |
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| Faculty of Science | doctoral | Didactics of Geography | English | full-time |
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| Faculty of Science | doctoral | Physical Geography and Geoecology | English | full-time |
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| Faculty of Science | doctoral | General Geography | English | full-time |
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| Faculty of Science | doctoral | Experimental Plant Biology | English | full-time |
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| Faculty of Science | Master's (post-Bachelor) | Social Geography and Regional Development | Czech | combined |
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| Faculty of Science | Master's (post-Bachelor) | Demography | Czech | combined |
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| Faculty of Science | Master's (post-Bachelor) | Demography | English | combined |
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| Faculty of Science | Master's (post-Bachelor) | Inorganic Chemistry | Czech | full-time |
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| Faculty of Science | Master's (post-Bachelor) | Geoinformatics, Cartography and Remote Sensing | Czech | full-time |
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| Faculty of Science | Master's (post-Bachelor) | Theoretical and Evolutionary Biology | Czech | full-time |
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| Faculty of Science | Master's (post-Bachelor) | Experimental Plant Biology | Czech | full-time |
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| Faculty of Science | Master's (post-Bachelor) | Immunology | Czech | full-time |
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| Faculty of Science | Master's (post-Bachelor) | Macromolecular Chemistry | Czech | full-time |
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| Faculty of Science | Master's (post-Bachelor) | Chemistry and Physics of Materials | Czech | full-time |
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| Faculty of Science | Master's (post-Bachelor) | Clinical and Toxicological Analysis | Czech | full-time |
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| Faculty of Science | Master's (post-Bachelor) | Political and Regional Geography | Czech | full-time |
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| Faculty of Science | Master's (post-Bachelor) | Organic Chemistry | Czech | full-time |
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| Faculty of Science | Master's (post-Bachelor) | Zoology | Czech | full-time |
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| Faculty of Science | Master's (post-Bachelor) | Botany | Czech | full-time |
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| Faculty of Science | Master's (post-Bachelor) | Biochemistry | Czech | full-time |
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| Faculty of Science | Master's (post-Bachelor) | Medicinal Chemistry | Czech | full-time |
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| Faculty of Science | Master's (post-Bachelor) | Sustainability Management | Czech | full-time |
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| Faculty of Science | Master's (post-Bachelor) | Protistology | Czech | full-time |
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