教師基本信息：
姓名：石樂明 Leming Shi
職稱：教授 Professor
電子郵箱：lemingshi@fudan.edu.cn
辦公地點：D610
辦公電話：021-31246746
個人網頁/課題組主頁：https://chinese-quartet.org/
研究方向：
Dr. Shi’s research aims to improve the success rate of drug development and the clinical efficacy rate of therapeutics with high-quality biomedical big data. Dr. Shi’s research interests include chemogenomics, pharmacogenomics, precision medicine, biomedical big data, bioinformatics, and chemoinformatics. By ensuring the reproducibility and reliability of multi-omics data generation, analysis, integration, and interpretation, we aim to discover biomarkers and drug targets for disease prevention, diagnosis, and treatment.
石樂明，男，1964年出生於湖南益陽。2011年加入複旦大學，現任生命科學學院和附屬腫瘤醫院特聘教授。國家特聘專家、國家重點研發計劃重點專項項目負責人(2019和2023)、獲10項美國和國際發明專利授權、中國專利金獎(2017，第4完成人)、上海市科技進步獎一等獎(2020，第7完成人)；深圳微芯生物共同創始人，抗癌新藥西達本胺和抗糖尿病新藥西格列他鈉共同發明人；獲批全基因組和全轉錄組國家一級標準物質10項；發表SCI論文200餘篇(含20篇Nature Biotechnology)，SCI他引20,000多次，h-index 70，編著有《大數據與精準醫學》一書(2018)；共同創立國際MAQC組學大數據質量控製學會，擔任其首任主席(2017-2018)、首席科學官和董事；主導或參與製定多項國際ISO、CLSI及IUPAC組學標準及FDA指南。其工作被同行認為“從根本上改變了組學數據分析的實踐，促使基因組醫學成為現實”。
畢業於湖南大學(1985，學士，分析化學)、中國科學技術大學(1988，碩士，計算化學)和中國科學院過程工程研究所(1991，博士，計算化學)，後留所任助理研究員(1991)和副研究員(1993)；曾於美國凱斯西儲大學和美國國家健康研究院腫瘤研究所(NIH/NCI)從事博士後研究(1994-1997)，並任職於美國食品藥品監督管理局(FDA)、Wyeth和BASF (1997-2001)。
2001年參與創辦深圳微芯生物，創建基於化學基因組學的藥物研發平台，開發的多個創新化合物在中國、日本和美國進入臨床試驗，其中1.1類原創新藥HDAC (1/2/3/10) 亞型選擇性抑製劑西達本胺被中國NMPA批準上市，用於治療外周T細胞淋巴瘤(2014)和乳腺癌(2019)，西達本胺治療成人T細胞白血病(ATL)的上市申請獲日本PMDA批準(2021年)；新型胰島素增敏劑PPAR (α/γ/δ)全激動劑西格列他鈉被中國NMPA批準上市 (2021)，用於治療2型糖尿病；微芯生物於2019年在上海科創板上市(688321.SH)。
2003年重新加入美國FDA，發起成立關於基因芯片和新一代測序的國際組學大數據質量控製聯盟MAQC/SEQC，先後就基因表達譜數據、生物標誌物和預測模型、轉錄組測序數據以及基因組DNA測序數據的質量控製和標準化分析進行了係統的探索。其研究成果由Nature Biotechnology雜誌分別於2006年、2010年、2014年和2021年以4個專輯發表，促進了美國FDA基因組學指南和有關國際標準的製定。其工作直接促成了國際MAQC組學大數據質量控製學會(www.maqcsociety.org)的成立，旨在提高多組學高通量技術的可靠性和可重複性，為精準醫學保駕護航(Shi L et al.,Nature Biotechnology 2017)。
Dr. Leming Shi is a professor at the School of Life Sciences and Shanghai Cancer Center of Fudan University since 2011. He is a National Distinguished Expert (2010), Principal Investigator of the National Key R&D Project of China (2019 and 2023), and the recipient of ten issued US and PCT patents and the WIPO-SIPO Award for Chinese Outstanding Patented Invention (2017). Dr. Shi is a co-founder of Chipscreen Biosciences and a co-inventor of the marketed anticancer drug Chidamide (2014) and antidiabetic drug Chiglitazar (2021). He has published over 200 peer-reviewed papers (20 in Nature Biotechnology) with >20,000 citations by SCI journals and an h-index of 70, and is the chief editor of the book “Big Data and Precision Medicine” (2018). As a co-founder of the International MAQC Society, Dr. Shi served as its founding president (2017-2018), and is its Chief Science Officer and a member of board of directors. Dr. Shi (co-)led the development of several ISO and CLSI standards and FDA guidance on genomics.
Dr. Shi received his PhD in computational chemistry from the Chinese Academy of Sciences in Beijing (1991); MSc in computational chemistry and chemometrics from the University of Science and Technology of China in Hefei (1988); and BSc in analytical chemistry from Hunan University in Changsha (1985). He conducted postdoctoral training at Case Western Reserve University (with Dr. Gilles Klopman, 1994-1995) and the NIH/NCI (with Dr. John Weinstein, 1995-1997), and was a research scientist at US FDA, Wyeth (now Pfizer), and BASF before co-founding Chipscreen Biosciences in 2001.
As a co-founder of Chipscreen, Dr. Shi co-developed a chemogenomics-based drug discovery platform, leading to the discovery of several novel small-molecule drug candidates with promising efficacy and safety profiles in anticancer and antidiabetic clinical trials in China, Japan, and the US. One novel subtype-selective HDAC inhibitor (Chidamide) was approved for treating T-cell lymphoma (2014) and advanced breast cancers (2019) in China, and for treating adult T-cell leukemia in Japan (2021). One PPARα/γ/δ pan-agonist (Chiglitazar) was approved for treating type 2 diabetes (2021) in China. Chipscreen went to IPO in August 2019 at Shanghai Stock Exchange (688321.SH).
As a principal investigator at the US FDA, Dr. Shi conceived and led the MicroArray and Sequencing Quality Control (MAQC/SEQC) consortia for quality control and standardization on the generation, analysis, and interpretation of transcriptomic and genomic data, publishing four special issues in Nature Biotechnology. These efforts, fundamentally changed the practice of genomic data analysis and helped make genomic medicine a reality, leading to the launch of the International Massive Analysis and Quality Control (MAQC) Society (www.maqcsociety.org) to enhance the reproducibility of high-throughput technologies for precision medicine (Shi L et al.,Nature Biotechnology 2017).
授課情況：
《大數據與精準醫學》
“Big Data and Precision Medicine”
招生專業：
生物學、生物與醫藥、生物信息學、醫學遺傳學
Biology, biomedicine, bioinformatics, and medical genetics
科研項目：
1、 人體表型解析技術體係及標準體係研發，國家重點研發計劃前沿生物技術重點專項，2023YFC3402500, 1697萬元，2023年12月至2028年11月，項目負責人
2、 人類表型組學數據的質量控製與標準化研究，國家重點研發計劃戰略性國際科技創新合作重點專項，2018YFE0201600，1144萬元，2019年8月至2022年7月，項目負責人
3、 組學大數據的質量控製與臨床應用標準化研究，國家高技術研究發展計劃(863計劃)，2015AA020104，1609萬元，2015年1月至2017年12月，項目負責人
4、 腫瘤高置信基因組突變分析方法學研究和優化，國家自然科學基金重點國際合作研究項目，31720103909，243萬元，2018年1月至2022年12月，項目負責人
5、 高置信全基因組胚係變異標準數據集的構建和應用，國家自然科學基金麵上項目，32170657，58萬元，2022年1月至2025年12月，項目負責人
6、 多組學數據整合的質量控製方法和應用，國家自然科學基金麵上項目，32370701，50萬元，2024年1月至2027年12月，項目負責人
獲獎情況：
1、邵誌敏、江一舟、李大強、吳炅、餘科達、黃薇、石樂明、胡欣、柳光宇、王中華、狄根紅、李俊傑、馬丁、肖毅、沈鎮宙，中國乳腺癌分子分型和精準治療的研究和成果推廣，上海市科技進步獎一等獎，2020年。
2、魯先平、李誌斌、謝愛華、石樂明、李伯玉、寧誌強、山鬆、鄧拓、胡偉明，具有分化和抗增殖活性的苯甲酰胺類組蛋白去乙酰化酶抑製劑及其藥用製劑(ZL03139760.3)，中國專利金獎，國家知識產權局和世界知識產權組織，2017年。
1. Zheng Y#*, Liu Y#, Yang J#, Dong L#, Zhang R#, Tian S#, …, Ding C*, Li J*, Fang X*, Shi L*. Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials. Nature Biotechnology, 42(7), 1133-1149 (2024).
2. Yu Y#, Hou W#, Liu Y#, Wang H#, Dong L#, …, Xu J*, Qian F*, Zhang R*, Shi L*, Zheng Y*. Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling. Nature Biotechnology, 42(7), 1118-1132 (2024).
3. Xiao W#*, Ren L#, …, Wang C*, Shi L*. Towards best practice in cancer mutation detection with whole-genome and whole-exome sequencing. Nature Biotechnology, 39(9), 1141-1150 (2021).
4. Fang LT#, Zhu B#, Zhao Y#, …, Hong H*, Shi L*, Wang C*, Xiao W*. Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing. Nature Biotechnology, 39(9), 1151-1160(2021).
5. Jiang YZ#, Ma D#, Suo C#, Shi J#, Xue M#, Hu X#, …, Wang P*, Shi L*, Huang W*, Shao ZM*. Genomic and transcriptomic landscape of triple-negative breast cancers: subtypes and treatment strategies.Cancer Cell, 35(3), 428-440 (2019).
6. Shi L, …, Tong W. The international MAQC Society launches to enhance reproducibility of high-throughput technologies. Nature Biotechnology, 35(12), 1127-1128 (2017).
7. Su Z#, Łabaj PP#, Li S#, …, Kreil DP*, Mason CE*, Shi L*. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequence Quality Control consortium. Nature Biotechnology, 32(9), 903-914 (2014).
8. Shi L#*, …, Wolfinger RD. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature Biotechnology, 28(8), 827-838 (2010).
9. Guo L#*, …, Shi L*. Rat toxicogenomic study reveals analytical consistency across microarray platforms. Nature Biotechnology,24(9), 1162-1169 (2006).
10.Shi L#*, …, Slikker W, Jr. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nature Biotechnology,24(9), 1151-1161 (2006).