個人介紹:

陸劍，beat365官方网站教授、博士生導師，目前擔任Science Bulletin和Molecular Biology and Evolution（MBE）的編委（Associate Editor）。

長期緻力于分子進化和基因組學研究，探索基因組序列及基因調控網絡的進化規律，建立進化和功能的關聯，在MBE、PLOS Biology、Nature Communications、National Science Review等主流學術期刊發表論文50多篇，被引用5000多次（H-index為24，Google Scholar數據），部分成果被Faculty of 1000 推薦或被Trends in Biochemical Sciences雜志作為亮點評論。

近5年來，緊密結合進化與功能基因組學方法，在“蛋白質翻譯調控的機制與進化驅動”這一前沿領域取得重要突破，闡明了上遊開放讀碼框（uORF）、非編碼小RNA和RNA編輯這三類元件/因子在蛋白質翻譯調控中的功能和序列進化規律，建立了翻譯調控與疾病的關聯，推動了進化理論的進一步發展與完善。在此次抗擊新冠病毒疫情工作中，發揮進化基因組學專長，通過分析世界各地不斷積累的病毒基因組變異信息，與合作者率先發現新冠病毒存在“L”和“S”兩個主要譜系，建立了完善的亞譜系命名規則并揭示了新冠病毒基因組變異的演進規律，闡明了早期變異對緻病性的影響，為科學抗疫政策的制定提供了重要參考。

教育經曆:

2002 - 2008，理學博士，進化生物學，芝加哥大學
1999 - 2002，理學碩士，遺傳學，北京大學
1995 - 1999，理學學士，細胞生物學和遺傳學，北京大學

工作經曆:

2022 - 至今，教育部長江學者特聘教授
2022 - 至今，教授,beat365官方网站
2020 - 2021，研究員/長聘副教授，beat365官方网站
2013 - 2020，研究員/助理教授，beat365官方网站
2008 - 2013，博士後，康奈爾大學分子生物學和遺傳學系

榮譽獎勵:

2022年， 長江學者特聘教授
2021年， 全國科技系統抗擊新冠肺炎疫情先進個人
2020年， 北京大學“抗擊新冠肺炎疫情标兵”
2012年， 國家級人才計劃青年項目
2006年， 國家優秀自費留學生獎學金（獎勵金額：5000美元）

學術任職:

2021.12-2024.11　　國家重點研發計劃病原學與防疫技術體系研究重點專項“病原變異及其跨物種傳播的回溯和演進方法體系構建”首席科學家

雜志任職:

Associate Editor, Molecular Biology and Evolution
Associate Editor, hLife
Associate Editor, GPB
Associate Editor, Journal of Systematics and Evolution

評審任職:

Ad hoc grant reviewer for the National Natural Science Foundation of China (Major Program, Key Program, and Excellent Young Scholar Program), Ministry of Science and Technology of China (Budget evaluation), China Postdoctoral Science Foundation, and U.S.-Israel Binational Science Foundation


Ad hoc reviewer for the journals Molecular Biology and Evolution (>20 times), Nature Ecology & Evolution, Genome Research, PLOS Biology, PNAS, Nature Communications, Nature Protocols, Nucleic Acids Research, National Science Review, PLOS Genetics, Genome Biology and Evolution, Journal of Molecular Evolution, PLOS Computational Biology, Genetics, Molecular Genetics and Genomics, Gene, Communications Biology, Current Genomics, and Genomics, Proteomics & Bioinformatics

會議發言與組織:

November 2021 Session Chair, The 6th National Drosophila Conference, Guangzhou, China

July 2021 Session Chair, SMBE2021 Virtual Meeting


December 2020 Session Chair, GPB Frontier Symposium 2020, Beijing, China


August 2019 Session Chair, The 5th National Drosophila Conference of China, Dalian, China


August 2019 Organization Committee & Session Chair, The 14th International Bioinformatics Workshop (IBW), Beijing, China


April 2018 Session Chair, The 1st AsiaEvo Conference, Shenzhen, China


December 2017 Organizer, 2017 Beijing Area Fly Meeting, Beijing, China


June 2017 Session Chair, Beijing Normal University Symposium of Ecology and Evolutionary Biology, Beijing, China


April 2017 Organizer, Symposium of Ecology and Evolution at Peking-Taiwan University Day, Beijing, China

雜志編輯:

Associate Editor, Molecular Biology and Evolution
Associate Editor, hLife
Associate Editor, GPB
Associate Editor, Journal of Systematics and Evolution

執教課程:

遺傳學（本）
遺傳學模塊課（研）
分子進化 （暑期課）

      　　　　　　本實驗室以“RNA調控-分子進化-計算設計”三位一體的研究框架為基礎，專注于RNA生物學驅動的翻譯調控機制及其在分子進化中的規律，旨在深入揭示RNA介導的蛋白質翻譯調控如何在生物進化中發揮作用。通過結合分子進化、功能基因組學及生物信息學方法，我們探索RNA調控元件（如uORF、RNA編輯/修飾、非編碼RNA）在基因表達和适應性演化中的作用，力圖為生命科學基礎理論、疾病機制解析及生物技術創新提供理論支撐與方法工具。在方法學上，本實驗室采取跨尺度整合的策略，結合實驗技術和計算分析，在實驗層面使用果蠅模型、體外翻譯系統及RNA生物學多組學技術，在計算層面應用深度學習模型、進化基因組學分析及群體遺傳學統計方法，最終将基礎研究轉化為應用工具，如疫苗設計算法和癌症靶點預測模型。實驗室的當前研究主要包括以下三個方向：
1. RNA生物學驅動的翻譯調控機制與進化規律。本研究結合分子進化基本理論、功能基因組學和生物信息學分析，整合多組學數據，探讨RNA編輯（如A-to-I、C-to-U）、m6A修飾、uORF等調控機制如何動态調控翻譯過程，且如何将這些元件的序列演化與功能适應性相結合。此外，我們還将利用AI技術開發翻譯效率預測模型，實現mRNA穩定性及翻譯效率的精準設計，并進一步探讨RNA編輯及修飾在翻譯延伸中的調控作用，以及其異常如何與癌症、自身免疫病等疾病的發生相關。
2. 結合分子進化與基因組學解析環境适應的RNA調控基礎。通過研究果蠅自然群體的基因組數據和表型關聯分析，本課題旨在揭示RNA表達調控及元件變異在物種适應性演化中的關鍵作用，并拓展“進化修補”理論，提供分子證據，闡明自然選擇如何塑造RNA調控元件的進化軌迹。
3. RNA病毒演化與疫苗智能設計。實驗室結合RNA生物學與分子進化方法，深入揭示新冠病毒等RNA病毒的演化趨勢及驅動力。我們正在利用人工智能等前沿技術，解析新冠病毒基因組演化如何影響其傳播及免疫逃逸機制。同時，探索RNA編輯介導的病毒-宿主翻譯調控互作，揭示免疫應答的新機制，并結合翻譯調控優化疫苗抗原設計，開發AI+分子進化算法優化病毒蛋白表達序列，提升疫苗效力。

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5. Hu B#, Liu R#, Tang X#, Pan Y#, Wang M#, Tong Y#, Ye G#, Shen G#, Ying R#, Fu A, Li D, Zhao W, Peng J, Guo J, Men D, Yao X, Wang Y, Zhang H, Feng Z, Yu J, Chen L, Deng Z, Lu X, Zhang YP*, Li Y*, Liu B*, Yu L*, Li Y*, Lu J*, Liu T* (2021) The concordance between the evolutionary trend and the clinical manifestation of the two SARS-CoV-2 variants. National Science Review. nwab073. DOI: 10.1093/nsr/nwab073

6. Duan Y, Tang X, Lu J* (2021) Evolutionary driving forces of A-to-I editing in metazoans. WIREs RNA. e1666. DOI: 10.1002/wrna.1666

7. Feng Y#, Xu H#, Liu J#, Xie N, Gao L, He Y, Yao Y, Lv F, Zhang Y, Lu J, Zhang W, Li CY, Hu X*, Yang Z*, Xiao RP (2021) Functional and adaptive significance of promoter mutations that affect divergent myocardial expressions of TRIM72 in primates. Molecular Biology and Evolution. msab083. DOI: 10.1093/molbev/msab083

8. Zhang H, Wang Y, Wu X, Tang X, Wu C, Lu J* (2021) Determinants of genome-wide distribution and evolution of uORFs in eukaryotes. Nature Communications. 12: 1076

9. Tang X#, Ying R#, Yao X#, Li G, Wu C, Tang Y, Li Z, Kuang B, Wu F, Chi C, Du X, Qin Y, Gao S, Hu S, Ma J, Liu T, Pang X, Wang J, Zhao G, Tan W*, Zhang Y*, Lu X*, Lu J* (2021) Evolutionary analysis and lineage designation of SARS-CoV-2 genomes. Science Bulletin. DOI: 10.1016/j.scib.2021.02.012

10. Yu T, Huang X, Dou S, Tang X, Luo S, Theurkauf WE*, Lu J*, Weng Z* (2021) A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies. Nucleic Acids Research. gkab010. DOI: 10.1093/nar/gkab010

11. Duan Y, Dou S, Porath HT, Huang J, Eisenberg E*, Lu J* (2021) A-to-I RNA editing in honeybees shows signals of adaptation and convergent evolution. iScience 24(1): 101983. DOI: 10.1016/j.isci.2020.101983

12. Ruan Y, Luo Z, Tang X, Li G, Wen H, He X, Lu X*, Lu J*, Wu CI* (2021) On the founder effect in COVID-19 outbreaks: how many infected travelers may have started them all?. National Science Review 8(1): nwaa246. DOI: 10.1093/nsr/nwaa246

13. Zhang H#, Wang Y#, Tang X, Dou S, Sun Y, Zhang Q, Lu J* (2021) Combinatorial regulation of gene expression by uORFs and microRNAs in Drosophila. Science Bulletin. 66(3): 225–228. DOI: 10.1016/j.scib.2020.10.012

14. Tang X#, Wu C#, Li X#, Song Y#, Yao X, Wu X, Duan Y, Zhang H, Wang Y, Qian Z, Cui J*, Lu J* (2020) On the origin and continuing evolution of SARS-CoV-2. National Science Review. 7(6): 1012–1023

15. Li T#, Tang X#, Wu C, Yao X, Wang Y, Lu X*, Lu J* (2020) The use of SARS-CoV-2-related coronaviruses from bats and pangolins to polarize mutations in SARS-Cov-2. SCIENCE CHINA Life Sciences. 63(10):1608-1611

16. Luo S#, Zhang H#, Duan Y#, Yao X, Clark AG*, Lu J* (2020) The Evolutionary Arms Race between Transposable Elements and piRNAs in Drosophila melanogaster. BMC Evolutionary Biology. DOI: 10.1186/s12862-020-1580-3

17. Zhang H#, Wang YR#, Lu J* (2019). Function and evolution of upstream ORFs in eukaryotes. Trends in Biochemical Sciences 44(9): 782-794. (Invited Review).

18. Wang YR#, Zhang H#, Lu J* (2019). Recent advances in ribosome profiling for deciphering translational regulation. Methods doi: 10.1016/j.ymeth.2019.05.011. (Invited Review, 被Faculty of 1000推薦).

19. Dou SQ#, Wang YR#, Lu J* (2019). Metazoan tsRNAs: biogenesis, evolution and regulatory functions. Non-Coding RNA 5(1): 18. (Invited Review).

20. Wu CC, Lu J* (2019). Diversification of transposable elements in arthropods and its impact on genome evolution. Genes 10(5).

21. Zhang H#, Wang YR#, Li J, Chen H, He XL, Zhang HW, Liang H*, Lu J* (2018). Biosynthetic energy cost for amino acids decreases in cancer evolution. Nature Communications 9(1):4124.

22. Zhang H#, Dou SQ#, He F, Luo JJ, Wei LP, and Lu J* (2018). Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development. PLOS Biology 16(7): e2003903.

23. Luo SQ#, He F#, Luo JJ#, Dou SQ#, Wang YR#, Guo AN, Lu J* (2018). Drosophila tsRNAs preferentially suppress general translation machinery via antisense pairing and participate in cellular starvation response. Nucleic Acids Research 46(10):5250-5268.

24. Luo JJ#, Wang YR#, Yuan J#, Zhao ZL, Lu J* (2018). MicroRNA duplication accelerates the recruitment of new targets during vertebrate evolution. RNA 24(6):787-802.

25. Duan YG#, Dou SQ#, Zhang H#, Wu CC, Wu MM, Lu J* (2018). Linkage of A-to-I RNA editing in metazoans and the impact on genome evolution. Molecular Biology and Evolution 35(1):132-148.

26. Duan YG#, Dou SQ#, Luo SQ#, Zhang H, Lu J* (2017). Adaptation of A-to-I RNA editing in Drosophila. PLOS Genetics 13(3):e1006648.

27. Luo SQ, Lu J* (2017). Silencing of transposable elements by piRNAs in Drosophila: an evolutionary perspective. Genomics, Proteomics & Bioinformatics 15(3):164-176.

28. Wang YR, Luo JJ, Zhang H, and Lu J* (2016). MicroRNAs in the same clusters evolve to coordinately regulate functionally related genes. Molecular Biology and Evolution 33(9):2232-47; author reply in 10.1093/molbev/msz121.

29. Yin S, Fan Y, Zhang H, Zhao Z, Hao Y, Li J, Sun C, Yang J, Yang Z, Yang X, Lu J, Xi JJ*. (2016). Differential TGFβ pathway targeting by miR-122 in humans and mice affects liver cancer metastasis. Nature Communications 7:11012.

30. Zhang XY, Zhu Y, Liu XD, Hong XY, Xu Y, Zhu P, Shen Y, Ji YS, Wen X, Zhang C, Zhao Q, Wang YC, Lu J, Guo HW*. (2015). Suppression of endogenous gene silencing by degradation of normal cytoplasmic RNA in Arabidopsis. Science 348(6230): 120-123.

31. Yu FL#, Lu J#, Liu XM#, Gazave E, Chang D, Raj S, Hunter-Zinck H, Blekhman R, Arbiza L, Hout C, Morrison A, Johnson AD, Bis J, Cupples LA, Psaty BM, Muzny D, Yu J, Gibbs RA, Keinan A, Clark G, Boerwinkle E* (2015). Population genomics analyses of 962 whole genomes of humans reveal natural selection in non-coding regions. PLOS One 10(3): e0121644.

32. Ye KX, Lu J, Ma F, Keinan A, Gu ZL* (2014). Extensive Pathogenicity of Mitochondrial Heteroplasmy in Healthy Human Individuals. Proceedings of the National Academy of Sciences of the United States of America 111(29): 10654-10659.

33. Ye KX*, Lu J, Raj SM, Gu ZL* (2013). Human expression QTLs are enriched in signals of environmental adaptation. Genome Biology and Evolution 5(9):1689-701.

34. Lu J* & Clark AG* (2012). Impact of microRNA regulation on variation in human gene expression. Genome Research 22(7): 1243–1254.

35. Zhou RC#, Ling SP#, Zhao WM#, Osada N, Chen SF, Zhang M, He ZW, Bao H, Zhong CR, Zhang B, Lu XM, Turissini D, Duke NC, Lu J*, Shi SH*, Wu CI* (2011). Population genetics in non-model organisms: II. Natural selection in marginal habitats revealed by deep sequencing on dual platforms. Molecular Biology and Evolution 28(10):2833-42.

36. Tang T#, Kumar S#, Shen Y, Lu J, Wu ML, Shi S, Li WH, Wu CI* (2010). Adverse interactions between micro-RNAs and target genes from different species. Proceedings of the National Academy of Sciences of the United States of America 107: 12935-12940.

37. Lu J, Clark AG* (2010). Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila. Genome Research 20: 212-227.

38. Lu J, Shen Y,Wu QF, Kumar S, He B, Carthew RW, Wang SM*, Wu CI* (2008). The birth and death of microRNA genes in Drosophila. Nature Genetics 40: 351-355; author reply in 42: 9-10.

39. Lu J, Fu Y, Kumar S, Shen Y, Zeng K, Xu A, Carthew RW, Wu CI* (2008). Adaptive evolution of newly emerged micro-RNA genes in Drosophila. Molecular Biology and Evolution 25: 929-938.

40. Wang HY, Fu Y, McPeek MS, Lu X, Nuzhdin S, Xu A, Lu J, Wu ML, Wu CI* (2008). Complex genetic interactions underlying expression differences between Drosophila races: analysis of chromosome substitutions. Proceedings of the National Academy of Sciences of the United States of America 105: 6362-6367.

41. Wu QF, Kim YC, Lu J, Xuan ZY, Chen J, Zheng YL, Zhou T, Zhang MQ, Wu CI, Wang SM* (2008). Poly A- transcripts expressed in HeLa cells. PLOS ONE 3(7): e2803.

42. Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA et al (2007). Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218 (Lu J is a coauthor of this paper).

43. Shapiro JA, Huang W, Zhang C, Hubisz MJ, Lu J, Turissini DA, Fang S, Wang HY, Hudson RR, Nielsen R, Chen Z, Wu CI* (2007). Adaptive genic evolution in the Drosophila genomes. Proceedings of the National Academy of Sciences of the United States of America 104: 2271-2276.

44. Lu J#, Tang T#, Tang H, Huang JZ, Shi SH*, Wu CI* (2006). The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication. Trends in Genetics 22: 126-131.

45. Tang T#, Lu J#, Huang J, He J, McCouch SR, Purugganan MD, Shi SH*, Wu CI* (2006). Genomic variation in rice - Genesis of highly polymorphic linkage blocks during domestication. PLOS Genetics 2(11):e199.

46. Lu J, Wu CI* (2005). Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee. Proceedings of the National Academy of Sciences of the United States of America 102: 4063-4067.

47. Tang H, Wyckoff GJ, Lu J, Wu CI* (2004) A universal evolutionary index for amino acid changes. Molecular Biology and Evolution 21: 1548-1556.

48. Lu J, Li WH, Wu CI* (2003) Comment on Chromosomal speciation and molecular divergence-accelerated evolution in rearranged chromosomes. Science 302: 988.

49. Lu J, Lü J, Chen HX, Zhang WX, Dai ZH* (2002) Molecular phylogeny of Drosophila auraria species complex (in Chinese). Acta Genetica Sinica 29: 39-49.

50. Zhao Z, Lu J, Dai ZH* (2001). Genetic differentiation within Drosophila auraria species complex revealed by Random Amplified Polymorphic DNA (RAPD) (in Chinese). Acta Zoologica Sinica 47: 625-631.