According to a survey of Nature covering 2012, the ranking of Chinese institutions is Chinese Academy of Sciences (CAS), the University of Science and Technology of China (USTC), Tsinghua University, Peking University, Shanghai Jiao Tong University (SJTU), BGI, Zhejiang University, Huazhong University of Science and Technology (HUST), Fudan University, and the University of Hong Kong (HKU). CAS takes an overwheming lead, publishing 140 articles in Nature-branded primary research journals during the last 12 months. Among the universities, USTC is No. 1 ahead of Tsinghua University and Peking University.
CAS press release, Jan. 18, 2013