根據自然出版集團統計的在過去12個月內在自然雜志《Nature》及其子刊系列上的發文數量，中國科學院一共發表140篇論文，超過日本東京大學排名亞洲機構第一位，這也是Nature Index統計以來中國科研機構首次排名第一。目前2012年全球Nature Index尚未公布，參考2011的數據，中科院可排在全球第7位，也將很有可能成為中國第一個晉級全球前十科研機構的中國單位。（Catalog采購助手）
中國的科研機構及高校2012年的Nature Index普遍有快速的提升，除中科院外，前50名中還有中國科技大學（第8），清華大學（第9），北京大學（第12）等學校入榜。
據筆者觀察，由于在署名方面的不明確，新成立的中國科學院大學（中科院研究生院）自然發表指數僅為1.63（17篇），按照這一數值將排到亞洲70位左右，與中國科學院大學的研究實力嚴重不符。為此筆者建議中科院相關領導負責人出臺政策管理中科院大學的論文署名規范，在中科院系統內指導研究生的所有碩士、博士生導師在發表論文時也建議署名中國科學院大學。（Everlab云端實驗室）
| Institution | CC2 | Articles3 | |
|---|---|---|---|
| 1. | Chinese Academy of Sciences (CAS), China | 40.87 | 140 |
| 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 |
| 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 |