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- Secretariat
- Department of General Affairs
- Department of Budget, Accounting and Statistics
- Department of Personnel
- Institute of Mathematics
- Institute of Physics
- Institute of Chemistry
- Institute of Earth Sciences
- Institute of Information Science
- Institute of Plant and Microbial Biology
- Institute of Cellular and Organismic Biology
- Institute of Biological Chemistry
- Institute of History and Philology
- Institute of Ethnology
- Institute of Modern History
- Institute of Economics
- Institute of European and American Studies
- Institute of Statistical Science
- Institute of Biomedical Sciences
- Institute of Atomic and Molecular Sciences
- Institute of Molecular Biology
- Department of Information Technology Services
- Research Center for Environmental Changes
- Biodiversity Research Center
- Institute of Chinese Literature and Philosophy
- Institute of Astronomy and Astrophysics
- Institute of Taiwan History
- Institute of Sociology
- Institute of Linguistics
- Agricultural Biotechnology Research Center
- Research Center for Applied Sciences
- Institute of Political Science
- Genomics Research Center
- Research Center for Humanities and Social Sciences
- Institutum Iurisprudentiae
- Research Center for Information Technology Innovation
- Biomedical Translation Research Center
- Department of Ethics
- Department of Intellectual Property and Technology Transfer
- Department of Academic Affairs and Instrument Service
- Department of International Affairs
- Center for Sustainability Science
- Department of Legal Affairs
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