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  1958年,中國科學院新疆分院生物研究室、土壤研究室、地理研究室成立;1961年,在上述三室和中國科學院新疆綜合考察隊等三支考察隊的基礎上,

  成立了中國科學院新疆水土生物資源綜合研究所,結束了新疆無資源、環境類科研機構的歷史。

  1965年,新疆綜合所分建為新疆生物土壤研究所(1974年更名為新疆生物土壤沙漠研究所)和新疆地質地理研究所(1970年改制為新疆地震大隊,1978年恢復新疆地理研究所)。

  1998年7月7日,根據中國科學院黨組關于結構性調整的戰略部署和建設國家創新體系的戰略決策,新疆生物土壤沙漠研究所和新疆地理研究所實現聯合重組,成立中國科學院新疆生態與地理研究所。新疆生地所走上了創新跨越的新歷程。

  1999年1月,新疆生地所進入中國科學院第二批基地型研究所試點單位。

  2001年7月2日,新疆生地所正式納入中國科學院知識創新工程二期試點單位。

  2005年6月,新疆生地所完成二期創新評估,全面完成二期創新考核目標。

  2006年6月,院評估研究中心充分肯定新疆生地所二期創新工作,指出“學科特色與區域優勢明顯,科技競爭力明顯增強,發展態勢強勁”。同時,肯定新疆生地所“創新三期方案合理,目標明確,擬采取的措施切實可行。”研究所正式進入三期創新。

  2008年,新疆生地所對創新三期前期工作進行了全面自評估,結果表明,中國科學院對新疆生地所三期創新的3項建議已初步實現。

  

 
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