上海市免疫研究所是上海市政府和上海交通大学医学院（原上海第二医学院）于1979年共建的我国第一个免疫学专职研究机构，致力于免疫相关疾病的基础和转化研究。一级教授余㵑先生是上海市免疫学研究所创始人和首任所长。余㵑先生也是国内第一个免疫学专业学术团体—上海市免疫学会的重要创始人和第一届理事长，并创办我国第一个免疫学专科杂志《上海免疫学杂志》，成立国内首个世界卫生组织免疫遗传合作中心，先后由余㵑教授、陈仁彪教授和周光炎教授担任该合作中心主任。免疫所率先在国内完成HLA抗血清的制备和特异性鉴定，是我国免疫遗传学发展的重要里程碑之一，获卫生部甲级科学技术成果奖。2003年，免疫所领衔组建了上海高校E-免疫学研究院，由第六任所长臧敬五教授担任首席主任，被上海市教委评为全市E－研究院的典范。2005年获教委“优势学科”称号，2006年入选“教育部免疫学创新团队”。
2012年上海交通大学医学院从耶鲁大学引进国家高层次人才、上海交通大学“王宽诚”讲席教授苏冰教授担任免疫所第八任所长。近年来，利用国家“双一流”建设项目、上海“高原高峰”计划、和地方高水平大学项目建设契机，免疫所以推动科技创新发展和高水平人才培养为目标，全面实施所长领导下的课题组长负责制，积极推动体制机制改革，实现了免疫所在学科建设、科研水平、人才培养和师资队伍等方面的跨越式发展。2015年，在医学院的有力支持下赋予上海市免疫学研究所“学术特区”新使命，并在2021年继续全面实施“学术特区”2.0版发展规划。近年来免疫所装修了7个楼层近3500平米的实验空间，组建了一流的公共仪器平台，包括流式分析平台、显微成像平台、免疫组化平台、生物标记物研究与开发平台、测序诊断平台、基因工程小鼠实验与分析平台，平台实施的课题组长负责制使公共平台的高效运转得到了学术和体制保障。
2013年，在上海交通大学医学院基础医学院支持下，通过合并免疫和微生物学科成立了免疫学与微生物学系，苏冰教授担任创系系主任。在苏冰教授的领导下，免疫所同免微系近年来进行全面整合。目前系所共有教职工109人，其中博导26人，硕导8人，在站博士后25人，在读研究生140人。现有22个独立课题组，课题组长中包括国家自然科学基金委杰出青年基金项目获得者、国家自然科学基金委优秀青年项目获得者、国家高层次青年人才、上海优秀学科带头人、以及上海高层次人才、浦江学者等。主要聚焦肿瘤免疫、感染免疫、移植免疫、区域免疫、自身免疫、耐药细菌控制、病原基因组学、分子微生态学、微生物与宿主相互作用等研究方向，并下设免疫学科课程组和病原学科课程组，承担医学院本科生与研究生的免疫学、微生物学理论和实验课教学任务。免疫所/免微系在研究生培养中以培养具有国际视野的高水平人才为目标定位，通过实验室轮转、成立研究生论文指导委员会以及研究生科研进展报告等全过程培养体系的建设和实施，并设立“余㵑研究生奖学金”和“中-以博士双学位”项目等举措，逐步建立了与国际接轨的高水平免疫学人才培养的新模式。
国际化建设也是免疫所/免微系持续发展的必由之路。自2012年以来，免疫所与包括美国、法国、英国、澳大利亚以及中国香港、中国台湾、大陆地区在内的近五十所知名院校、研究机构开展了积极深入的合作交流，邀请超过300人次的国内外顶尖专家学者来访交流并作学术报告等；建立上海交通大学医学院-耶鲁大学免疫代谢研究院，法国国立马赛吕米尼免疫中心(CIML)共建免疫调控联合中心，推动国际化发展的实体机构建设。同时，免疫所也是科技部国际科技合作基地“上海转化医学国际联合研究中心”的重要基地，在2021年全国评估中获“优秀”。
最后，免疫所/免微系的研究团队近年来承担多项国家科技部重大/重点研发计划、国家自然科学基金重大/重点项目，在国际顶尖期刊如Nature、Cell、Nature Immunology、Cell Metabolism、Immunity、Molecular Cell、Nature Medicine、Nature Neuroscience、Nature Communications等发表原创性科研成果，为免疫所乃至医学院不断实现零的突破。通过加强与各附属医院的合作，以疾病为导向的基础-临床研究团队成为推动免疫所科研不断突破的新的亮点。
Shanghai Institute of Immunology &
Department of Immunology and Microbiology
Shanghai Institute of Immunology (SII), established in 1979 by the Shanghai Municipal Government and Shanghai Jiao Tong University School of Medicine (formerly Shanghai Second Medical College), is the first immunology research institute in China dedicated to basic and clinical research on immune system and immune-related diseases. The founding Director was Dr. He Yu, a first-class Professor and a pioneer for modern immunology research in China. Dr. Yu was also the key founder and first president of the Shanghai Immunology Society, which is also the first professional academic society for immunology community in China. Under the leadership of Dr. Yu, SII also launched the first specialized immunology journal in China, the Shanghai Journal of Immunology. The first WHO Collaborating Center for Immunogenetics in China was also established here at SII, which was led successively by Drs He Yu, Renbiao Chen, and Guangyen Chou. Immunologists at SII were the first to use antisera to study and identify HLA polymorphism in China, an important milestone in immunogenetics study in China. Its work won top “Science and Technology Achievement Award” from the National Health Commission. In 2003, SII established the E-Immunology Institute, the first Shanghai Institutions of Higher Learning under the leadership of then SII Director, Dr. Jingwu Zang. The E-Immunology Institute was a highly successful model recognized by the Shanghai Municipal Education Commission. In 2005, SII also won the "Key Discipline" title given by Shanghai Municipal Education Commission, and was awarded the "Innovative Team” for immunology research by the Ministry of Education China in 2006.
In 2012, Professor Bing Su, the National High-level Talent Distinguished Expert and KC Wong Endowed Chair Professor of Shanghai Jiao Tong University, joined SII as the 8th Director from Yale University. With the strong support from Shanghai Jiao Tong University School of Medicine, SII has become a Special Academic Zone in 2015, which is successfully renewed in in 2021. In 2013, a brand-new Department of Immunology and Microbiology (DIM) was established in the College of Basic Medical Sciences at Shanghai Jiao Tong University School of Medicine with Professor Bing Su as its founding Chair. Since then, the Department and SII has been fully integrated as one unit with the support from both Shanghai Municipal Government and Shanghai Jiao Tong University School of Medicine.
At the moment, SII/DIM has 109 faculty and staff members including twenty-six Ph.D. supervisors and eight MS supervisors in SII/DIM. We also have twenty-five talented postdoctoral fellows and 140 graduate students. SII & DIM now have twenty-two independent research groups lead by twenty-two highly energetic and enthusiastic Principal Investigator (PI), focusing on different aspects of immunology including cancer immunity, infection immunity, transplantation immunity, regional immunity, autoimmunity, drug-resistant bacteria control, pathogen Many of our PI are recipients of prestigious awards such as the National Science Fund for Distinguished Young Scholars, the National Science Fund for Excellent Young Scholars, National High-Level Young Talents, Shanghai Subject Chief Scientists, and Shanghai High-Level Talents, etc. We also have two key course teams for Immunology and Pathogenesis Course, respectively, responsible for teaching theoretical and laboratory courses of immunology and microbiology for undergraduate and graduate students at our medical school. In terms of graduate student training, the supervisory committee of SII has established the management and training system for graduate student rotation, Research in Progress seminar held weekly in English and the "Yu He Graduate Student Scholarship". By cooperating with the Hebrew University of Jerusalem, a Joint Ph.D. Degree Program was launched in 2018 to explore a new model of international training for graduate students. In addition, SII/DIM is currently equipped with cutting-edge core facilities, including Flow Cytometry Core, Imaging Core, Immunohistochemistry Core, Biomarker Research & Development Core, Sequencing Core, and Mouse Common Strain Collection Core. Our Cores are managed and supervised by our Principal Investigator.
SII/DIM actively interact and collaborate nationally and internationally with renowned universities and research institutes from the United States, France, the United Kingdom, Australia, as well as within China including Hong Kong and Taiwan. World and national renowned scientists have been invited to visit the institute and give seminars to our faculty and students. We established the Shanghai Jiao Tong University School of Medicine-Yale University Institute of Immune Metabolism (SYIIM), a joint center for immune regulation with the Centre d'Immunologie de Marseille-Luminy (CIML). In recent years, our teams have won many Major/Key Program grants from the Ministry of Science and Technology and National Natural Science Foundation of China, and have published breakthrough original research papers in top journals including Nature, Cell, Nature Immunology, Cell Metabolism, Immunity, Molecular Cell, Nature Medicine, Nature Neuroscience, Nature Communications, Nature Neuroscience, Nature Communications, etc., and many are considered "0 to 1 breakthrough" for SII and our Medical School. SII is also the home of "Shanghai International Joint Research Center for Translational Medicine", supported by the prestigious “International Science and Technology Cooperation Base of the Ministry of Science and Technology”. We are glad to report that our Center was awarded "Super achievement" in Year 2021 national assessment.
