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根据自然出版集团统计的在过去12个月内在自然杂志《Nature》及其子刊系列上的发文数量，中国科学院一共发表140篇论文，超过日本东京大学排名亚洲机构第一位，这也是Nature Index统计以来中国科研机构首次排名第一。目前2012年全球Nature Index尚未公布，参考2011的数据，中科院可排在全球第7位，也将很有可能成为中国第一个晋级全球前十科研机构的中国单位。
中国的科研机构及高校2012年的Nature Index普遍有快速的提升，除中科院外，前50名中还有中国科技大学（第8），清华大学（第9），北京大学（第12）等学校入榜。完整排名请见http://www.natureasia.com/en/publishing-index/asia-pacific/by-institution
据笔者观察，由于在署名方面的不明确，新成立的中国科学院大学（中科院研究生院）自然发表指数仅为1.63（17篇），按照这一数值将拍到亚洲70位左右，与中国科学院大学的研究实力严重不符。为此笔者建议中科院相关领导负责人出台政策管理中科院大学的论文署名规范，在中科院系统内指导研究生的所有硕士、博士生导师在发表论文时也建议署名中国科学院大学。
Research ArticlesReviewsAllInstitution CC2 Articles3
1. Chinese Academy of Sciences (CAS), China 40.87 140
Shanghai Institutes for Biological Sciences (SIBS), CAS 5.73 14
Institute of Biophysics (IBP), CAS 4.5 14
Institute of Physics (IOP), CAS 4.04 11
Institute of Zoology (IOZ), CAS 2.59 6
Institute of Vertebrate Paleontology and Paleoanthropology (IVPP), CAS 2.46 4
Guangzhou Institutes of Biomedicine and Health (GIBH), CAS 1.73 2
Graduate University of Chinese Academy of Sciences (GUCAS), CAS, Beijing 1.63 17
Institute of Genetics and Developmental Biology (IGDB), CAS 1.63 6
Shanghai Institute of Applied Physics (SINAP), CAS 1.39 4
Dalian Institute of Chemical Physics (DICP), CAS 1.31 3
Institute of Chemistry (ICCAS), CAS 1.3 2
Institute of Tibetan Plateau Research (ITP), CAS 1 2
Changchun Institute of Applied Chemistry (CIAC), CAS 0.98 2
Institute of Botany (IOB), CAS 0.95 4
Institute of Geology and Geophysics, CAS 0.8 3
Institute of Mechanics, CAS 0.67 1
Shanghai Institute of Materia Medica (SIMM), CAS 0.61 3
Nanjing Institute of Geology and Palaeontology, CAS 0.6 1
Institute of Semiconductors, CAS 0.57 2
Shanghai Institute of Ceramics, CAS 0.55 1
Institute of Microbiology (IM), CAS 0.53 1
Institute of Geodesy and Geophysics, CAS 0.48 1
Institute of Oceanology, CAS 0.44 2
Institute of Computing Technology (ICT), CAS 0.42 1
Institute of Metal Research (IMR), CAS 0.42 1
Hefei Institutes of Physical Science, CAS 0.38 1
Institute of Applied Ecology, CAS 0.37 1
Nanjing Institute of Geography & Limnology (NIGLAS), CAS 0.36 1
Institute of Atmospheric Physics (IAP), CAS 0.32 2
Graduate University of Chinese Academy of Sciences (GUCAS), CAS, Shanghai 0.25 1
Yunnan Astronomical Observatory, CAS 0.21 1
Beijing Institute of Genomics (BIG), CAS 0.18 3
Cold and Arid Regions Environmental and Engineering Institute, CAS 0.17 1
Institute of Process Engineering (IPE), CAS 0.17 1
National Centre for Nanoscience and Technology (NCNST), CAS 0.17 1
Kunming Institute of Zoology (KIZ), CAS 0.14 3
Shanghai Advanced Research Institute (SARI), CAS 0.1 1
Shanghai Institute of Technical Physics, CAS 0.1 1
Suzhou Institute of Nano-Tech and Nano-Bionics (SINANO), CAS 0.09 1
Beijing Center for Crystal R&D, CAS 0.08 1
Xinjiang Technical Institute of Physics and Chemistry (XTIPC), CAS 0.08 1
Shanghai Institute of Organic Chemistry (SIOC), CAS 0.07 1
Institut Pasteur of Shanghai (IPS), CAS 0.05 1
Wuhan Botanical Garden, CAS 0.05 2
Center for Space Science and Applied Research (CSSAR), CAS 0.05 1
Institute of Optics and Electronics (IOE), CAS 0.05 1
High Magnetic Field Laboratory (HMFL), CAS 0.04 1
Beijing Institutes of Life Science (BIOLS), CAS 0.03 1
Xishuangbanna Tropical Botanical Garden (XTBG), CAS 0.02 1
National Center for Gene Research (NCGR), CAS 0.01 1
South China Botanical Garden (SCBG), CAS 0.01 1
2. The University of Tokyo, Japan 39.05 117
3. Kyoto University, Japan 22.69 56
4. RIKEN, Japan 19.88 81
5. Osaka University, Japan 15.52 49
6. The University of Melbourne, Australia 10.82 48
7. Nagoya University, Japan 10.48 29
8. University of Science and Technology of China, China 9.85 20
9. Tsinghua University, China 9.37 32
10. Tohoku University, Japan 9.25 29
11. National University of Singapore (NUS), Singapore 9 50
12. Peking University, China 7.77 28
13. National Institute of Advanced Industrial Science and Technology (AIST), Japan 7.26 22
14. Agency for Science, Technology and Research (A*STAR), Singapore 6.86 42
Institute of Materials Research and Engineering (IMRE), A*STAR 2.06 6
Genome Institute of Singapore (GIS), A*STAR 1.53 20
Institute of Molecular and Cell Biology (IMCB), A*STAR 1.38 5
Institute of Microelectronics (IME), A*STAR 0.61 2
Institute of Medical Biology (IMB), A*STAR 0.51 4
Singapore Immunology Network (SIgN), A*STAR 0.21 1
Institute for Infocomm Research, A*STAR 0.18 1
Institute of High Performance Computing (IHPC), A*STAR 0.17 1
Singapore Institute of Manufacturing Technology (SIMTech), A*STAR 0.13 1
Bioinformatics Institute (BII), A*STAR 0.09 1
15. Shanghai Jiao Tong University (SJTU), China 6.56 37
16. Australian National University (ANU), Australia 6.26 20
17. BGI, China 6.09 21
18. The University of Queensland, Australia 5.93 42
19. Kyushu University, Japan 5.71 18
20. Yonsei University, Korea 5.57 16
21. Hokkaido University, Japan 5.52 18
22. Tokyo Institute of Technology, Japan 4.9 17
23. Zhejiang University, China 4.84 15
24. The University of New South Wales, Australia 4.75 23
25. The University of Sydney, Australia 4.58 27
26. Huazhong University of Science and Technology (HUST), China 4.25 12
27. Fudan University, China 4.18 16
28. Korea Advanced Institute of Science & Technology (KAIST), Korea 4.15 16
29. Keio University, Japan 4.09 18
30. Sungkyunkwan University, Korea 3.98 11
31. Seoul National University, Korea 3.84 24
32. Nanyang Technological University (NTU), Singapore 3.82 16
33. Monash University, Australia 3.78 21
34. Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Japan 3.57 16
35. NTT Group, Japan 3.49 6
36. Academia Sinica, Taiwan 3.36 20
37. The Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australia 3.29 19
38. James Cook University, Australia 3.27 11
39. National Institute for Material Science (NIMS), Japan 3.25 15
40. University of Tsukuba, Japan 3.04 12
41. The University of Hong Kong (HKU), China 3 16
42. Nanjing University, China 2.85 7
43. Hiroshima University, Japan 2.77 11
44. Chinese Academy of Agricultural Sciences (CAAS), China 2.67 13
45. The University of Western Australia, Australia 2.64 29
46. Hanyang University, Korea 2.62 11
47. Korea University, Korea 2.43 6
48. Xiamen University, China 2.38 6
49. Tata Institute of Fundamental Research (TIFR), India 2.33 3
50. Kumamoto University, Japan 2.19 12