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The ÐÇ¿Õ´«Ã½ has a special relationship with four institutions: the , (Swiss TPH), the (FMI), the research institute, and the , which collaborate intensively and to mutual benefit with various faculties and research groups at the university as associated institutes.

The (Swiss TPH) is a world-leading research institution for global health with the core areas of parasitology, infection biology, health systems and public health. Research at Swiss TPH is interdisciplinary and covers a very broad spectrum. An important topic is research on poverty-related diseases such as malaria, sleeping sickness or tuberculosis. Current research projects are investigating the effects of pesticides in South Africa on children's health, the level of air pollution in Tehran, or the impact of the smoking ban on the health of employees working in the Swiss hospitality industry. Topics such as cell phone radiation and its effects on children, or the heatwave summer of 2018 and its consequences are also being researched.

The (FMI) is a world-class biomedical research institute conducting basic research in molecular biology. Core topics of FMI are neurobiology, quantitative biology and epigenetics. FMI is affiliated with the ÐÇ¿Õ´«Ã½ and the (NIBR).

is a practice-oriented peace research institute that analyzes armed conflicts and develops strategies to improve the prevention of conflicts and their peaceful transformation. Swisspeace conducts innovative research, shapes discourses on international peace policy, and develops new methods of peacebuilding. It provides platforms for dialogue between peacebuilders, researchers, and practitioners in the fields of peacebuilding, humanitarian aid, development cooperation, and security, as well as between parties to conflicts. Swisspeace has organized the annual since 2017.

The (SCAHT) provides expert advice and services in the field of regulatory toxicology to the Swiss authorities, the media, the public and third parties. The Centre promotes research in applied human toxicology and supports the exchange of information and data between the different toxicological disciplines. The SCAHT is funded by the Swiss Confederation and supported by the Universities of Basel, Geneva, Lausanne and the FHNW School of Life Sciences.

The is an independent, non-profit center of excellence working globally to prevent and combat corruption and provide assistance in building strong governance structures. It conducts anti-corruption research to develop and implement future strategies. Project topics include asset recovery assistance, anti-corruption through the International Centre for Collective Action (ICCA), compliance and corporate governance advisory and crisis management, public finance management (PFM) technical assistance, and multidisciplinary intelligence to combat financial crime in the illegal wildlife trade.

The ÐÇ¿Õ´«Ã½ is closely networked with numerous institutions in the city of Basel and the surrounding cantons. It maintains research cooperations and is also a co-founder of various institutions. The spectrum of scientific exchange and cooperation ranges from archaeological, natural science, linguistic and medical topics to the pharmaceutical industry and various departments of the Northwest University of Applied Sciences.

In the (D-BSSE), research is conducted into the design and programming of complex biological systems from the nanoscale to whole organisms. The goals are the translation of research results into biomedical and industrial applications as well as the development of new processes and products in the biotech, chemical and pharmaceutical industries. Basel's location as a center of life sciences in Europe enables collaboration with hospitals, industry and other academic partners in the fields of Personalized Medicine, Molecular System Engineering and Data Science.

The canton of Aargau has been supporting the (SNI) at the ÐÇ¿Õ´«Ã½ with annual grants since 2009 through the . This innovative form of public-public partnership supports excellent basic research and gives industry direct access to cutting-edge technology. The aim is to translate world-class research results at the SNI into marketable products.

The was founded by the ÐÇ¿Õ´«Ã½ together with the Canton of Aargau and is part of the Department of Classical Studies at the ÐÇ¿Õ´«Ã½. The professorship also collaborates with the natural science areas of the (IPAS) of the Department of Environmental Sciences. The main focus is on the Roman sites in the canton of Aargau with the settlements of Vindonissa and Augusta Raurica (Kaiseraugst).

The (PSI) is the largest research institute for natural and engineering sciences in Switzerland and conducts cutting-edge research in the fields of matter and materials, man and health, and energy and the environment. It develops sustainable solutions for central questions from society, economy and science through basic and applied research.

The is the point of contact for SMEs interested in the latest technology and seeking advice on projects, digitization or professional exchange. The center focuses on innovation consulting, nanotechnology and energy technology.

The (FHNW) consists of nine universities located at the main campuses in Basel, Muttenz, Brugg-Windisch and Olten. Its researchers conduct application-oriented research and development and promote the transfer of research results into practice. There are numerous interactions between the FHNW and the ÐÇ¿Õ´«Ã½; for example, the joint was founded, there are numerous joint research projects in the life sciences, and a cooperation agreement has been reached regarding doctoral studies.

The (IOB) was founded in 2018 by the ÐÇ¿Õ´«Ã½, the University Hospital Basel and Novartis. The IOB was established as a foundation to ensure academic freedom for researchers. Basic researchers and clinicians work hand in hand to advance the understanding of vision and its diseases and to develop new therapies for vision loss. The focus is on retinal diseases such as macular degeneration, glaucoma and myopia, which is on the rise worldwide.

The (BRCCH) was founded by the ÐÇ¿Õ´«Ã½ and ETH Zurich and has been in operation since 2019. BRCCH's vision is to establish itself as a leading institution for application-oriented cutting-edge research and to improve the health and well-being of children and adolescents around the world through its projects. The focus is on digital solutions with a focus on artificial intelligence and innovation in pediatrics.

, headquartered in Basel, is one of the world's largest pharmaceutical companies and, with 13,600 employees from over 100 nations, is one of the most important private employers in Switzerland. The biotech company offers new cancer therapies, develops targeted therapies in combination with appropriate diagnostics and promotes active health management. The focus in research and development is on the specialties of oncology, virology, neurology and transplantation medicine.

was formed in 1996 by the merger of Ciba-Geigy AG and Sandoz AG and is one of the largest pharmaceutical companies in the world. The company's core competence is research and development of novel medicines. Basel is home to the corporate headquarters as well as the headquarters of the global Innovative Medicines Division. Novartis promotes its scientific expertise and innovative capacity through collaborations with hospitals, companies and academic institutions and has, for example, founded the (IOB) together with the ÐÇ¿Õ´«Ã½ and the University Hospital Basel. At the (NIBR), interdisciplinary teams are working on powerful new technologies to develop novel treatments. Within NIBR, researchers at the (NITD) are working on compounds to combat tropical infectious diseases.

Das Pharmaunternehmen , ein Spin-off von Actelion, hat seinen Hauptsitz in Allschwil und betreibt Wirkstoffforschung, Entwicklung und Herstellung von pharmazeutischen, biologischen und diagnostischen Produkten. Idorsia entwickelt Medikamente für die Therapiebereiche Zentralnervensystem, Herz-Kreislauf- und Immunkrankheiten sowie seltene Krankheiten.