2024

Chen J^#, Liu C^#, Li W^#, Zhang W, Wang Y, CLARK AG^*, Lu J^* (2024) From sub-Saharan Africa to China: Evolutionary history and adaptation of Drosophila melanogaster revealed by population genomics. Science Advances 10: eadh3425. DOI: 10.1126/sciadv.adh3425 . PDF

Jin K, Tang X, Qian Z, Wu Z, Yang Z, Qian T, Hon C, Lu J^* (2024) Modeling viral evolution: A novel SIRSVIDE framework with application to SARS-CoV-2 dynamics. hLife . DOI: 10.1016/j.hlife.2024.03.006 . PDF

Yao Z^#, Zhang L^#, Duan Y, Tang X^*, Lu J^* (2024) Molecular Insights into the Adaptive Evolution of SARS-CoV-2 Spike Protein. Journal of Infection 106121. DOI: 10.1016/j.jinf.2024.106121 . PDF

Wu C^#, A R^#, Ye S^#, Ye F, Huo W, Lu R, Tang Y, Yang J, Meng X, Tang Y, Chen S, Zhao L, Huang B, Zhang Z, Chen Y, Li D, Wang W, Shan KJ, Lu J^*, Tan W^* (2024) Rapid identification of full-length genome and tracing variations of monkeypox virus in clinical specimens based on mNGS and amplicon sequencing. Virologica Sinica 39(1): 134–143. DOI: 10.1016/j.virs.2023.12.002 . PDF

2023

Shan KJ^#, Wu C^#, Tang X, Lu R, Hu Y^*, Tan W^*, Lu J^* (2023) Molecular evolution of protein sequences and codon usage in monkeypox viruses. Genomics, Proteomics & Bioinformatics qzad003. DOI: 10.1093/gpbjnl/qzad003 . PDF

Wang Y^*, Tang X, Lu J^* (2023) Convergent and divergent evolution of microRNA-mediated regulation in metazoans. Biological Reviews. DOI: 10.1111/brv.13033 . PDF

Hu S^#, Wu C^#, Wu X^#, Ma X, Shu C, Chen Q, Zheng A, Yang H, Lu J^*, Du P^*, Gao GF^*, Wang Q^* (2023) Classification of five SARS-CoV-2 serotypes based on RBD antigenicities. Science Bulletin 68(23): 3003–3012. DOI: 10.1016/j.scib.2023.09.048 . PDF

Ou X^#, Xu G^#, Li P^#, Liu Y^#, Zan F, Liu P, Hu J, Lu X, Dong S, Zhou Y, Mu Z, Wu Z, Wang J, Jin Q, Liu P, Lu J, Wang X^*, Qian Z^* (2023) Host susceptibility and structural and immunological insight of S proteins of two SARS-CoV-2 closely related bat coronaviruses. Cell Discovery 9: 78. DOI: 10.1038/s41421-023-00581-9 . PDF

Wu X^#, Shan KJ^#, Zan F^#, Tang X, Qian Z^*, Lu J^* (2023) Optimization and deoptimization of codons in SARS-CoV-2 and related implications for vaccine development. Advanced Science 10(23): 2205445. DOI: 10.1002/advs.202205445 . PDF

Tang X, Qian Z, Lu X, Lu J^* (2023) Adaptive evolution of the Spike protein in coronaviruses. Molecular Biology and Evolution 40(4): msad089. DOI: 10.1093/molbev/msad089 . PDF

Li P^#, Hu J^#, Liu Y^#, Ou X, Mu Z, Lu X, Zan F, Cao M, Tan L, Dong S, Zhou Y, Lu J, Jin Q, Wang J, Wu Z^*, Zhang Y^*, Qian Z^* (2023) Effect of polymorphism in Rhinolophus affinis ACE2 on entry of SARS-CoV-2 related bat coronaviruses. PLoS Pathogens 19(1): e1011116. DOI: 10.1371/journal.ppat.1011116 . PDF

2022

Qian Z^*, Li P, Tang X, Lu J^* (2022) Evolutionary dynamics of the severe acute respiratory syndrome coronavirus 2 genomes. Medical Review 2(1): 3–22. DOI: 10.1515/mr-2021-0035 . PDF

Ruan Y^#, Hou M^#, Tang X^#, He X, Lu X, Lu J^*, Wu CI^*, Wen H^* (2022) The runaway evolution of SARS-CoV-2 leading to the highly evolved Delta strain. Molecular Biology and Evolution 39(3): msac046. DOI: 10.1093/molbev/msac046 . PDF

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^* (2022) VarEPS: an evaluation and prewarning system of known and virtual variations of SARS-CoV-2 genomes. Nucleic Acids Research 50(D1): D888–D897. DOI: 10.1093/nar/gkab921 . PDF

Duan Y, Tang X, Lu J^* (2022) Evolutionary driving forces of A-to-I editing in metazoans. WIREs RNA 13: e1666. DOI: 10.1002/wrna.1666 . PDF

2021

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 alerts potential ecological risks. Zoological Research 42(6): 833–843. DOI: 10.24272/j.issn.2095-8137.2021.334 . PDF

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 398(10308): 1299–1303. DOI: 10.1016/S0140-6736(21)02020-1 . PDF

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 64: 1560–1563. DOI: 10.1007/s11427-021-1972-1 . PDF

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 8(8): nwab073. DOI: 10.1093/nsr/nwab073 . PDF

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 38(7): 2930–2945. DOI: 10.1093/molbev/msab083 . PDF

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. DOI: 10.1038/s41467-021-21394-y . PDF

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 66(22): 2297–2311. DOI: 10.1016/j.scib.2021.02.012 . PDF

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 49(8): e44. DOI: 10.1093/nar/gkab010 . PDF

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 . PDF

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 . PDF

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 . PDF

2020

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: 1608–1611. DOI: 10.1007/s11427-020-1764-2 . PDF

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. DOI: 10.1093/nsr/nwaa036 . PDF

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 20: 14. DOI: 10.1186/s12862-020-1580-3 . PDF

Wang Y^#, Zhang H^#, Lu J^* (2020) Recent advances in ribosome profiling for deciphering translational regulation. Methods 176: 46–54. DOI: 10.1016/j.ymeth.2019.05.011 . PDF

2019

Wu C, Lu J^* (2019) Diversification of transposable elements in arthropods and its impact on genome evolution. Genes 10(5): 338. DOI: 10.3390/genes10050338 . PDF

Zhang H^#, Wang Y^#, Lu J^* (2019) Function and evolution of upstream ORFs in eukaryotes. Trends in Biochemical Sciences 44(9): 782–794. DOI: 10.1016/j.tibs.2019.03.002 . PDF

Dou S^#, Wang Y^#, Lu J^* (2019) Metazoan tsRNAs: biogenesis, evolution and regulatory functions. Non-Coding RNA 5(1): 18. DOI: 10.3390/ncrna5010018 . PDF

2018

Zhang H^#, Dou S^#, He F, Luo J, Wei L, 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. DOI: 10.1371/journal.pbio.2003903 . PDF

Zhang H^#, Wang Y^#, Li J, Chen H, He X, Zhang H, Liang H^*, Lu J^* (2018) Biosynthetic energy cost for amino acids decreases in cancer evolution. Nature Communications 9: 4124. DOI: 10.1038/s41467-018-06461-1 . PDF

Luo S^#, He F^#, Luo J^#, Dou S^#, Wang Y^#, Guo A, 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. DOI: 10.1093/nar/gky189 . PDF

Luo J^#, Wang Y^#, Yuan J^#, Zhao Z, Lu J^* (2018) MicroRNA duplication accelerates the recruitment of new targets during vertebrate evolution. RNA 24(6): 787–802. DOI: 10.1261/rna.062752.117 . PDF

Duan Y^#, Dou S^#, Zhang H^#, Wu C, Wu M, 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. DOI: 10.1093/molbev/msx274 . PDF

2017

Duan Y^#, Dou S^#, Luo S^#, Zhang H, Lu J^* (2017) Adaptation of A-to-I RNA editing in Drosophila. PLoS Genetics 13(3): e1006648. DOI: 10.1371/journal.pgen.1006648 . PDF

Luo S, Lu J^* (2017) Silencing of transposable elements by piRNAs in Drosophila: an evolutionary perspective. Genomics, Proteomics & Bioinformatics 15(3): 164–176. DOI: 10.1016/j.gpb.2017.01.006 . PDF

2016

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. DOI: 10.1038/ncomms11012 . PDF

Wang Y, Luo J, Zhang H, Lu J^* (2016) MicroRNAs in the same clusters evolve to coordinately regulate functionally related genes. Molecular Biology and Evolution 33(9): 2232–2247. DOI: 10.1093/molbev/msw089 . PDF

2015

Yu F^{#, *}, Lu J^#, Liu X^#, Gazave E, Chang D, Raj S, Hunter-Zinck H, Blekhman R, Arbiza L, Van Hout C, Morrison A, Johnson AD, Bis J, Cupples LA, Psaty BM, Muzny D, Yu J, Gibbs RA, Keinan A, Clark AG, Boerwinkle E^* (2015) Population genomics analyses of 962 whole genomes of humans reveal natural selection in non-coding regions. PLoS One 10(3): e0121644. DOI: 10.1371/journal.pone.0121644 . PDF

Zhang X, Zhu Y, Liu X, Hong X, Xu Y, Zhu P, Shen Y, Ji Y, Wen X, Zhang C, Zhao Q, Wang Y, Lu J, Guo H^* (2015) Suppression of endogenous gene silencing by bidirectional cytoplasmic RNA decay in Arabidopsis. Science 348(6230): 120–123 DOI: 10.1126/science.aaa2618 . PDF

2014

Ye K^*, Lu J, Ma F, Keinan A, Gu Z^* (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. DOI: 10.1073/pnas.1403521111 . PDF

2013

Ye K^*, Lu J, Raj SM, Gu Z^* (2013) Human expression QTLs are enriched in signals of environmental adaptation. Genome Biology and Evolution 5(9): 1689–1701. DOI: 10.1093/gbe/evt124 . PDF

2012

Lu J^*, Clark AG^* (2012) Impact of microRNA regulation on variation in human gene expression. Genome Research 22: 1243–1254. DOI:10.1101/gr.132514.111 . PDF

2011

Zhou R^#, Ling S^#, Zhao W^#, Osada N, Chen S, Zhang M, He Z, Bao H, Zhong C, Zhang B, Lu X, Turissini D, Duke NC, Lu J^*, Shi S^*, 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): 2833–2842. DOI: 10.1093/molbev/msr102 . PDF

2010

Lu J, Clark AG^* (2010) Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila. Genome Research 20(2): 212–227. DOI: 10.1101/gr.095406.109 . PDF

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(29): 12935–12940. DOI: 10.1073/pnas.1007591107 . PDF

2008

Wu Q^#, Kim YC^#, Lu J, Xuan Z, Chen J, Zheng Y, Zhou T, Zhang MQ, Wu CI, Wang SM^* (2008) Poly A- transcripts expressed in HeLa cells. PLoS One 3(7): e2803. DOI: 10.1371/journal.pone.0002803 . PDF

Lu J, Shen Y, Wu Q, Kumar S, He B, Carthew RW, Wang SM^*, Wu CI^* (2008) The birth and death of microRNA genes in Drosophila. Nature Genetics 40(3): 351–355. DOI: 10.1038/ng.73 . PDF

Lu J, Fu Y, Kumar S, Shen Y, Zeng K, Xu A, Carthew R, Wu CI^* (2008) Adaptive evolution of newly emerged micro-RNA genes in Drosophila. Molecular Biology and Evolution 25(5): 929–938. DOI: 10.1093/molbev/msn040 . PDF

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(17): 6362–6367. DOI: 10.1073/pnas.0711774105 . PDF

2007

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(7167): 203–218. DOI: 10.1038/nature06341 . PDF (Lu J is a coauthor of this paper)

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(7): 2271–2276. DOI: 10.1073/pnas.0610385104 . PDF

2006

Tang T^#, Lu J^#, Huang J, He J, McCouch SR, Shen Y, Kai Z, Purugganan MD, Shi S^*, Wu CI^* (2006) Genomic variation in rice: genesis of highly polymorphic linkage blocks during domestication. PLoS Genetics 2(11): e199. DOI: 10.1371/journal.pgen.0020199 . PDF

Lu J^#, Tang T^#, Tang H, Huang J, Shi S^*, Wu CI^* (2006) The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication. Trends in Genetics 22(3): 126–131. DOI: 10.1016/j.tig.2006.01.004 . PDF

2005 and before

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(11): 4063–4067. DOI: 10.1073/pnas.0500436102 . PDF

Tang H, Wyckoff GJ, Lu J, Wu CI^* (2004) A universal evolutionary index for amino acid changes. Molecular Biology and Evolution 21(8): 1548–1556. DOI: 10.1093/molbev/msh158 . PDF

Lu J, Li WH, Wu CI^* (2003) Comment on "Chromosomal speciation and molecular divergence-accelerated evolution in rearranged chromosomes". Science 302(5647): 988. DOI: 10.1126/science.1088277 . PDF