2002 - 2008 Ph.D. Evolutionary Biology, the University of Chicago
1999 - 2002 M.S. Genetics, Peking University
1995 -1999 B.S. Cell Biology and Genetics, Peking University

2022 - current Changjiang Scholar Professor
2022 - current Professor,School of Life Sciences, Peking University
2020 - 2021 Tenured Associate Professor，School of Life Sciences, Peking University
2013 - 2020 Principal Investigator，School of Life Sciences, Peking University
2008 - 2013, Postdoc, Department of Molecular Biology and Genetics, Cornell University

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）

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

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

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

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

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

My laboratory is based on a "RNA regulation - molecular evolution - computational design" integrated research framework, focusing on the translation regulation mechanisms driven by RNA biology and their patterns in molecular evolution. The goal is to explore how RNA-mediated protein translation regulation plays a role in biological evolution. By combining molecular evolution, functional genomics, and bioinformatics approaches, we investigate the role of RNA regulatory elements (such as uORF, RNA editing/modifications, and non-coding RNAs) in gene expression and adaptive evolution, aiming to provide theoretical support and methodological tools for basic life sciences, disease mechanism analysis, and biotechnological innovation.

In terms of methodology, my laboratory adopts an interdisciplinary strategy, integrating experimental techniques and computational analysis. At the experimental level, we use Drosophila models, in vitro translation systems, and RNA biological multi-omics technologies. At the computational level, we apply deep learning models, evolutionary genomics analysis, and population genetics statistical methods. Ultimately, we aim to translate basic research into applied tools, such as vaccine design algorithms and cancer target prediction models. The laboratory's current research mainly includes the following three directions:

1. RNA biology-driven translation regulation mechanisms and evolutionary patterns: This research integrates basic molecular evolution theories, functional genomics, and bioinformatics analysis to explore how RNA editing (such as A-to-I, C-to-U), m6A modification, uORF, and other regulatory mechanisms dynamically control the translation process. We also investigate how the sequence evolution of these elements is linked to functional adaptation. Additionally, we aim to develop AI-based translation efficiency prediction models for the precise design of mRNA stability and translation efficiency. We will further explore the regulatory role of RNA editing and modifications in translation elongation, and how their abnormalities relate to diseases such as cancer and autoimmune disorders.

2. Combining molecular evolution and genomics to analyze the RNA regulatory basis of environmental adaptation: This project uses genomic data and phenotype association analysis of natural Drosophila populations to reveal the critical role of RNA expression regulation and element variation in species' adaptive evolution. It also extends the "evolutionary repair" theory, providing molecular evidence to clarify how natural selection shapes the evolutionary trajectory of RNA regulatory elements.

3. RNA virus evolution and intelligent vaccine design: By combining RNA biology and molecular evolution methods, the laboratory explores the evolutionary trends and driving forces of RNA viruses, such as the novel coronavirus. We are using cutting-edge technologies like artificial intelligence to analyze how the genomic evolution of the novel coronavirus affects its transmission and immune evasion mechanisms. Additionally, we are investigating RNA editing-mediated virus-host translation regulation interactions, unveiling new mechanisms of immune response, and optimizing vaccine antigen design by integrating translation regulation. Our goal is to develop AI and molecular evolution algorithms to optimize viral protein expression sequences and enhance vaccine efficacy.

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.

Genetics
Genetics Track
Molecular Biology

Laboratory Introduction