The aim of the master's degree study branch Business Administration that is being taught in English is to prepare graduates for economic, managerial, entrepreneurial, administrative and other positions and activities within the bounds of both the national and international labour markets. Students obtain advanced theoretical knowledge of commercial and entrepreneurial processes in the Czech Republic and the EU entrepreneurial context. They learn to understand theories, concepts, and methods employed currently in business.

The master's degree study branch European Agrarian Diplomacy that is being taught in English has been established based on a request by the CR Ministry of Agriculture aimed at the education of specialists for the EU Common Agricultural Policy able to occupy the relevant positions both in the national and European institutions. Taking into account width of the problems and the significance of agriculture within the bounds of the European Union policies, the study branch has not been concentrated upon adaptation of the Czech Republic into the EU structures only, but it has been preparing specialists oriented in the current trends, be it within the boundaries of the agrarian sector development of European Union itself (Europe 2020 Strategy), or in the global questions and Europe's position in global agriculture.

The master’s double degree program Land and Environmental Engineering is result of join cooperation between Czech University of Life Sciences Prague (CZU) and University of Naples Federico II (UNINA, Italy). The programme focuses on a comprehensive understanding of the protection and restoration of environmental quality.

The follow-up master's degree program Animal Welfare and Protection is an academically focused study program, corresponding to the current state and level of science and the needs of practice in Europe. The study contains theoretical knowledge and enables the acquisition of the necessary practical skills needed for the performance of the profession, including employment in educational and creative activities, and prepares students for a doctoral study program.

The master's degree study graduate obtains deeper theoretical knowledge in the area of informatics, economics, and management, that offers him the chance to independently apply methods and procedures aimed at increasing efficiency of the production and administration processes.

The Master of Science in Digital Marketing and Analytics program is offered by UNYP, in collaboration with Dublin Business School (DBS), Ireland. The MSc is delivered face-to-face in Prague, including mandatory on-demand content for students to do in their own time and place. The award is conferred by DBS and it is completed in one year full-time.

The study branch is aimed at students who are interested in the area of economics and management. It is being conceived inter-disciplinarily using the integrated economic and managerial basis, quantitative methods, ICT and the social-science disciplines connected.

The Sectoral Management Master's program prepares highly-skilled professionals for mid-and top-level management positions in industry, industrial policy, innovation policy, commercial policy, and finance while allowing the further pursuit of academic and research careers through Ph.D. programs. In the Innovation Project Management major, students have an opportunity to gain more specific proficiency in Financial Management, Project Management, Process Management, or Logistics & Supply Chain Management.

The Chemical Industry major is aimed at students who seek more technical expertise particularly relevant for positions in the chemical, food-processing, fuels, rubber, or environmental protection industries. This major is particularly suitable for graduates in technical disciplines or life sciences.

The MSc programme offers theoretical and applied knowledge about the sustainable use and management of natural resources (soil, water, and air) and the positive as well as the negative influence of agriculture and forestry on these resources.

The MSc course is intended to provide students with a detailed understanding of the sustainability of agriculture and food production. The students will be able to determine key characteristics and processes in agricultural systems, and critically evaluate the production, environmental, and social aspects.

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Introduction Project Management has become essential in virtually all areas of business and industry, including Engineering, Construction, Oil & Gas, Mining, Communications, Healthcare, Information Technology, Utilities, Education, Military, Government, Transportation, Retail and other sectors.

The focus is on management of global supply chain systems with an emphasis on managerial leadership, information technology and international business practices.

Master's degree course in Bioorganic Chemistry and Toxicology of Pollutants is designed for students who are interested in a broader study of biologically active chemical compounds. This study builds on undergraduate courses in Chemistry and Toxicology and Analysis of Pollutants.