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The University of Hradec Králové develops scientific disciplines that primarily correspond to the focus of individual faculties and their workplaces but also university-wide scientific and research areas that have a multidisciplinary and transdisciplinary character. The Faculty of Education focuses on modern approaches to education, teaching, and the teaching process, and the Faculty of Science on research in selected areas of physics, biology, but also mathematics, chemistry, and informatics. The Faculty of Informatics and Management deals with research in the field of informatics, economics, and management, and the Philosophical Faculty focuses on research in the field of history, sociology, archaeology, philosophy, and political science.

The University responds readily to current social needs and the needs of the region and its administrative and business spheres. Examples of this include cooperation within the Hradecký IT klastr or cooperation with the Council for Development and Innovation of the Hradec Králové Region, etc. Regarding sources of funding, the largest part of the grant activity is covered by national providers, i.e., GACR, TA CR, departmental ministries, as well as the European Union within its grant schemes and regional institutions as part of joint activities. In recent years, the business sphere within the framework of contract research has also shown a growing interest in cooperation with the UHK.

The organization and coordination of affairs related to research, science, and creative activities falls under the Science and Knowledge Transfer Office.