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- Central Office of Administration
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- Division of Mathematics and Physical Sciences
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- Division of Life Sciences
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- Division of Humanities and Social Sciences
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- Cross-Divisional Research Center
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Research Units
- Institute of Mathematics
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- Institute of Physics
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- Institute of Chemistry
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- Institute of Earth Sciences
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- Institute of Information Science
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- Institute of Statistical Science
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- Institute of Atomic and Molecular Sciences
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- Research Center for Environmental Changes
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- Institute of Astronomy and Astrophysics
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- Research Center for Applied Sciences
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- Research Center for Information Technology Innovation
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- Institute of Plant and Microbial Biology
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- Institute of Cellular and Organismic Biology
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- Institute of Biological Chemistry
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- Institute of Biomedical Sciences
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- Institute of Molecular Biology
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- Biodiversity Research Center
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- Agricultural Biotechnology Research Center
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- Genomics Research Center
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- Institute of History and Philology
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- Institute of Ethnology
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- Institute of Modern History
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- Institute of Economics
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- Institute of European and American Studies
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- Institute of Chinese Literature and Philosophy
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- Institute of Taiwan History
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- Institute of Sociology
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- Institute of Linguistics
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- Institute of Political Science
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- Research Center for Humanities and Social Sciences
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- Institutum Iurisprudentiae
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- Biomedical Translation Research Center
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- Research Center for Critical Issues
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