个人介绍:

陆剑，金沙集团wwW3354CC教授、博士生导师，目前担任Science Bulletin和Molecular Biology and Evolution（MBE）的编委（Associate Editor）。 长期致力于分子进化和基因组学研究，探索基因组序列及基因调控网络的进化规律，建立进化和功能的关联，在MBE、PLOS Biology、Nature Communications、National Science Review等主流学术期刊发表论文50多篇，被引用5000多次（H-index为24，Google Scholar数据），部分成果被Faculty of 1000 推荐或被Trends in Biochemical Sciences杂志作为亮点评论。 近5年来，紧密结合进化与功能基因组学方法，在“蛋白质翻译调控的机制与进化驱动”这一前沿领域取得重要突破，阐明了上游开放读码框（uORF）、非编码小RNA和RNA编辑这三类元件/因子在蛋白质翻译调控中的功能和序列进化规律，建立了翻译调控与疾病的关联，推动了进化理论的进一步发展与完善。在此次抗击新冠病毒疫情工作中，发挥进化基因组学专长，通过分析世界各地不断积累的病毒基因组变异信息，与合作者率先发现新冠病毒存在“L”和“S”两个主要谱系，建立了完善的亚谱系命名规则并揭示了新冠病毒基因组变异的演进规律，阐明了早期变异对致病性的影响，为科学抗疫政策的制定提供了重要参考。

教育经历:

2002 - 2008，理学博士，进化生物学，芝加哥大学
1999 - 2002，理学硕士，遗传学，北京大学
1995 - 1999，理学学士，细胞生物学和遗传学，北京大学

工作经历:

2022 - 至今，教育部长江学者特聘教授
2022 - 至今，教授,金沙集团wwW3354CC
2020 - 2021，研究员/长聘副教授，金沙集团wwW3354CC
2013 - 至今，研究员/助理教授，金沙集团wwW3354CC
2008 - 2013，博士后，康奈尔大学分子生物学和遗传学系

荣誉奖励:

2022年， 长江学者特聘教授
2021年， 全国科技系统抗击新冠肺炎疫情先进个人
2020年， 北京大学“抗击新冠肺炎疫情标兵”
2012年， 国家级人才计划青年项目
2006年， 国家优秀自费留学生奖学金（奖励金额：5000美元）

学术任职:

2021.12-2024.11　　国家重点研发计划病原学与防疫技术体系研究重点专项“病原变异及其跨物种传播的回溯和演进方法体系构建”首席科学家

杂志任职:

2018- Associate Editor, Science Bulletin 2020- Associate Editor, Molecular Biology and Evolution

评审任职:

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

会议发言与组织:

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

杂志编辑:

2018- Associate Editor, Science Bulletin 2020- Associate Editor, Molecular Biology and Evolution

执教课程:

遗传学（本）
遗传学模块课（研）
分子进化 （暑期课）

      　　 生物的表型进化不仅可以通过改变基因功能，还可以通过基因表达模式变化而实现。由于自然选择的不完美性以及生存环境不断变化，生物进化过程常伴随着从基因型到表型多个层次的不断修补。然而当前对进化修补过程的分子基础及自然选择在此过程中的作用机理却缺乏深入了解。本实验室长期致力于群体遗传学、进化基因组学和基因表达调控等领域的研究，近五年以（共同）通讯作者身份在Molecular Biology and Evolution、National Science Review和Nature Communications等期刊发表论文25篇，多维度解析基因表达调控的进化机制和基因组进化规律，建立了功能与进化规律的关联。当前本实验室紧密结合进化与功能基因组学方法，从三个层面探索生物基因组和表型适应性演化的机制和规律：
1）蛋白质合成调控的演化机制和规律。结合分子演化和基因学方法多维度探索上游开放读码框（uORF）、非编码小RNA和RNA编辑这三类元件/因子在蛋白质翻译调控中的功能和序列进化规律，探索翻译调控与疾病的关联。

2）以果蝇为模式解析环境适应的遗传和进化机制。本实验从中国不同地区采集了10000多个果蝇品系，通过基因组测序和表型相关分析，探索果蝇适应复杂自然环境的遗传架构以及蝇环境适应中自然选择作用的靶点及机制。

3）新冠病毒的分子演化和全球动态研究。本实验室通过新冠病毒基因组的分子演化研究，与合作者率先发现新冠病毒存在“L”和“S”两个主要谱系，建立了完善的亚谱系命名规则并揭示了变异的演进规律，探索新冠病毒分子演化动态及驱动因素。相关研究获得科技部等有关部门表彰。

1. Peng MS#, *, Li JB#, Cai ZF#, Liu H#, Tang X#, Ying R, Zhang JN, Tao JJ, Yin TT, Zhang T, Hu JY, Wu RN, Zhou ZY, Zhang ZG, Yu L, Yao YG, Shi ZL, Lu XM, Lu J*, Zhang YP* (2021) The high diversity of SARS-CoV-2-related coronaviruses in pangolins alters potential ecological risks. Zoological Research. 42(6): 833–843. DOI: 10.24272/j.issn.2095-8137.2021.334 .

2. Sun Q, Shu C, Shi W, Luo Y, Fan G, Nie J, Bi Yu, Wang Q, Qi J, Lu J, Zhou Y, Shen Z, Meng Z, Zhang X, Yu Z, Gao S*, Wu L*, Ma J*, Hu S* (2021) VarEPS: an evaluation and prewarning system of known and virtual variations of SARS-CoV-2 genomes. Nucleic Acids Research. DOI: 10.1093/nar/gkab921 .

3. Wu Z, Jin Q, Wu G, Lu J, Li M, Guo D, Lan K, Feng L, Qian Z, Ren L, Tan W, Xu W, Yang W, Wang J*, Wang C (2021) SARS-CoV-2`s origin should be investigated worldwide for pandemic prevention. The Lancet. DOI: 10.1016/S0140-6736(21)02020-1 .

4. Wu CI*, Wen H, Lu J, Su X, Hughes AC, Zhai W, Chen C, Chen H, Li M, Song S, Qian Z, Wang Q, Chen B, Guo Z, Ruan Y, Lu X, Wei F, Jin L, Kang L, Xue Y, Zhao G, Zhang YP (2021) On the origin of SARS-CoV-2—The blind watchmaker argument. Science China Life Sciences. DOI: 10.1007/s11427-021-1972-1

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推荐).

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.