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With the goal of meeting both national strategic and industrial development needs, JITRI has built a number of specialized research institutes and technology innovation centers with core R&D capabilities to support the industrial development of Jiangsu Province and China. As of 2021, JITRI has established 59 specialized research institutes in the fields of advanced materials, energy & environmental protection, information technology, advanced manufacturing, biology & medicine, etc.

The specialized research institutes focus on industrial technology R&D, transformational research as well as incubating start-ups. JITRI has established a mechanism to integrate R&D with incubation and investment. Newly established institutes operate in a model of joint investment and joint ownership of equity, where the core R&D team of the institute is the majority shareholder, while JITRI and a local industrial park (where the institute is located) are the minority shareholders. The R&D income belongs to the core team of the institute, and all shareholders can profit from the returns.

A number of specialized research institutes already set up by prominent universities and the Chinese Academy of Sciences (CAS) have been restructured and brought into the JITRI system in accordance with the new model. In this way, JITRI effectively stimulates innovation and motivates researchers. JITRI implements a "one institute, two systems" model at these research institutes, which allows researchers to carry out basic research under the auspices of colleges and universities, while engaging in application development and technology transfer at the institutes.

JITRI does not fund its specialized institutes in the traditional way, but rather implements a performance evaluation system focusing on their efficiency in providing technologies (including technology transfer, technology investment, and technical services) to enterprises, which determines the amount of future financial support from JITRI. By doing so, the institutes' R&D capacities are closely coupled with market needs.

In order to align with major national strategic priorities, JITRI is leading the effort of establishing the Yangtze Delta National Center of Technology Innovation. It has also built innovation platforms in advanced materials, integrated circuits, and other fields, in addition to its specialized research institutes and enterprise joint innovation centers. The national technology innovation centers, guided by the needs of enterprises and projects, aim to attract domestic and overseas top talents, integrate innovation resources, carry out joint R&D across organizations, make breakthroughs in a number of strategically important fields, and form landmark achievements.