(2014-)

(*, equal contributions; #, corresponding authors)

43. Y. Liu *, B. Jiao* ,W. Qian*# (2024) Synthetic Gene Drives in Plants: Development Strategies, Potential Applications, and Ethical Considerations. Modern Agriculture 2024; 2:e30 [https://doi.org/10.1002/moda.30] [PDF]

42. Y. Liu *, B. Jiao , J. Champer, W. Qian# (2024) Overriding Mendelian inheritance in Arabidopsis with a CRISPR toxin-antidote gene drive that impairs pollen germination. Nat. Plants. doi: 10.1038/s41477-024-01692-1. Epub ahead of print. PMID: 38886523.[PDF]

42-1. P. Neve, L. Barrett.(2024) Driving evolution in wild plants. Nat. Plants. https://doi.org/10.1038/s41477-024-01723-x [PDF]

41. W. Yu*, S. Zhang*, S. Zhao, L.-G Chen, J. Cao, H. Ye, J. Yan, Q. Zhao, B. Mo, Y. Wang, Y. Jiao, Y. Ma, X. Huang, W. Qian# & J. Dai#.(2024) Designing a synthetic moss genome using GenoDesigner. Nat. Plants. DOI: 10.1038/s41477-024-01693-0 [PDF]

40. L.-G Chen*, T. Lan*, S. Zhang*, M. Zhao*, G. Luo, Y. Gao, Y. Zhang, Q. Du, H. Lu, B. Li, B. Jiao, Z. Hu, Y. Ma, Q. Zhao, Y. Wang#, W. Qian#, J. Dai#, Y. Jiao# (2024) A designer synthetic chromosome fragment functions in moss. Nat. Plants 10(2):228-239. [PDF]

39. J. Wang*, G. Zhang*, W. Qian#, and K. Li# (2023) Decoding the Heterogeneity and Specialized Function of Translation Machinery Through Ribosome Profiling in Yeast Mutants of Initiation Factors. Adv. Biol. (Weinh) 8(2):e2300494. [PDF]

38. J. Kong*, S. Zhang, W. Qian, K. Li# (2023) Synonymous somatic mutations that alter proximal out-of-frame downstream ATGs are associated with aberrant gene expression levels in cancer cells. J. Genet. Genomics 50(6):447-449.. [PDF]

37. B. Sun*, Y. Wang*, Q. Yang*, H. Gao, H. Niu, Y. Li, Q. Ma, Q. Huan, W. Qian#, and B. Ren# (2023) A high-resolution transcriptomic atlas depicting nitrogen fixation and nodule development in soybean. J. Integr. Plant Biol. 00: 1-17 [PDF]

36. K. Li*, J. Kong*, S. Zhang*, T. Zhao, and W. Qian# (2022) Distance-dependent inhibition of translation initiation by downstream out-of-frame AUGs is consistent with a Brownian ratchet process of ribosome scanning. Genome Biology. 23, 254 [PDF]

35. C. Wei*, K.-J Shan*, W. Wang*, S. Zhang, Q. Huan#, and W. Qian# (2021) Evidence for a mouse origin of the SARS-CoV-2 Omicron variant. Journal of Genetics and Genomics. 48, 1111-1121 [PDF]

34. K.-J Shan*, C. Wei*, Y. Wang, Q. Huan#, and W. Qian# (2021) Host-specific asymmetric accumulation of mutation types reveals that the origin of SARS-CoV-2 is consistent with a natural process. The Innovation. 2, 100159 [PDF] Highlighted in One Health Collection by Cell Press

33. W. Luo*, Q. Huan*, Y. Xu, W. Qian, K. Chong#, and J. Zhang# (2021) Integrated global analysis reveals a vitamin E-vitamin K1 sub-network, downstream of COLD1, underlying rice chilling tolerance divergence. Cell Report. 36, 109397 [PDF]

32. Q. Zhang, Z. Wang, W. Zhang, Q. Wen, X. Li, J. Zhou, X. Wu, Y. Guo, Y. Liu, C. Wei, W. Qian, Y. Tian# (2021) The memory of neuronal mitochondrial stress is inherited transgenerationally via elevated mitochondrial DNA levels. Nature Cell Biology. [PDF]

31. Y. Wang*, Q. Huan*#, K. Li, W. Qian# (2021) Single-cell transcriptome atlas of the leaf and root of rice seedlings. Journal of Genetics and Genomics. [PDF]

30. Q. Wang, Q. Su, J. Nian, J. Zhang, M. Guo, G. Dong, J. Hu, R. Wang, C. Wei, G. Li, W. Wang, H. Guo, S. Lin, W. Qian, X. Xie, Q. Qian, F. Chen# and J. Zuo# (2021) The Ghd7 Transcription Factor Represses the ARE1 Expression to Enhance Nitrogen Utilization and Grain Yield in Rice. Molecular Plant. 14, 1-12 [PDF]

29. C. Wei*, Y.-M. Chen*, Y. Chen# and W. Qian# (2021) The Missing Expression Level-Evolutionary Rate Anticorrelation in Viruses Does Not Support Protein Function as a Main Constraint on Sequence Evolution. Genome Biol. Evol. 13, 4 [PDF]

28. W. Qian# and J. Zhang# (2021) Codon usage bias and nuclear mRNA concentration: Correlation vs. causation. Proc. Natl. Acad. Sci. USA. 118, No. 20 e2104714118 [PDF]

27. T. Zhao*#, Y.-M. Chen*, Y. Li*, J. Wang, S. Chen, N. Gao# and W. Qian# (2021) Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding. Genome Biology. 22, 16 [PDF]

26. T. Zhao*#, S. Zhang*, and W. Qian# (2020) Cis-regulatory mechanisms and biological effects of translation elongation. Yi Chuan. 2020 Jul. 20;42(7):613-631. [PDF]

25. Y. Chen, K.-J. Shan, and W. Qian# (2020) Asians do not exhibit elevated expression or unique genetic polymorphisms for ACE2, the cell-entry receptor of SARS-CoV-2. Preprints. doi : 10.20944/preprints202002.0258.v2 [PDF]

24. Y. Chen* #, K. Li*, X. Chu, L.B. Carey,and W. Qian# (2019) Synchronized replication of genes encoding the same protein complex in fast-proliferating cells. Genome Research. 29, 1929-1938. [PDF]

23. T. Zhao*, Q. Huan*, J. Sun*, C. Liu*, X. Hou, X. Yu, I. Silverman, Y. Zhang,B. Gregory, C. Liu, W. Qian# and X. Cao#(2019) Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency. Genome Biology. 20, 189 [PDF]

22. Y. Chen, S. Chen, K. Li, Y. Zhang, X. Huang, T. Li, S. Wu, Y. Wang, L.B. Carey# and W. Qian# (2019) Overdosage of balanced protein complexes reduces proliferation rate in aneuploid cells. Cell Systems. 9, 129-142 e125. (Featured Article) [PDF] Peer Review from Angelika Amon [PDF]

21. J. Zhou, X. Wang, M. Wang, Y. Chang, F. Zhang, Z. Ban, R. Tang, Q. Gan, S. Wu, Y. Guo, Q. Zhang, F. Wang, L. Zhao, Y. Jing , W. Qian , G. Wang, W. Guo# , C. Yang# (2018) The lysine catabolite saccharopine impairs development by disrupting mitochondrial homeostasis. The Journal of Cell Biology. 218 (2): 580 (18 pages).[PDF]

20. C. Duan*, Q. Huan*, X. Chen*, S. Wu, L.B. Carey, X. He and W. Qian# (2018) Reduced intrinsic DNA curvature leads to increased mutation rate. Genome Biology. 19(1):132 (18 pages).[PDF]

19. Q. Huan*, Y. Zhang*, S. Wu, and W. Qian# (2018) HeteroMeth: A Database of Cell-to-cell Heterogeneity in DNA Methylation. Genomics, Proteomics & Bioinformatics.16 (4), 234-243. [PDF]

18. Y. Yang*, W. Cao*, S. Wu, and W. Qian# (2017) Genetic interaction network as an important determinant of gene order in genome evolution. Mol Biol Evol 34 (12), 3254-3266.[PDF]

17. Y. Han*, X. Chu*, H. Yu, Y.-K. Ma, X.-J. Wang, W. Qian#, and Y. Jiao# (2017) Single-cell transcriptome analysis reveals widespread monoallelic gene expression in individual rice mesophyll cells. Sci Bull 62 (19), 1304-1314. [PDF]

16. S. Chen, K. Li, W. Cao, J. Wang, T. Zhao, Q. Huan, Y.-F. Yang, S. Wu, and W. Qian# (2017) Codon-resolution analysis reveals a direct and context-dependent impact of individual synonymous mutations on mRNA level. Mol Biol Evol 34 (11), 2944-2958.[PDF]

15. Y. Yang*, X. Zhang*, X. Ma*, T. Zhao*,Q. Sun, Q. Huan, S. Wu, Z. Du#, and W. Qian# (2017) Trans-splicing enhances translational efficiency in C. elegans. Genome Research. 27(9):1525-1535[PDF]

14. S. Wu*,# , K. Li*, Y. Li, T. Zhao, T. Li, Y. Yang, W. Qian# (2017) Independent regulation of gene expression level and noise by histone modifications. PLoS Comput Biol 13 (6): e1005585. [PDF]

13. B. Zhang*, S. Wu*, Y. Zhang, T. Xu, F. Guo, H. Tang, X. Li, P. Wang, W. Qian, and Y. Xue (2016) A high temperature-dependent mitochondrial lipase EXTRA GLUME1 promotes floral phenotypic robustness against temperature fluctuation in rice (Oryza sativa L.). PLoS Genetics 12 (7): e1006152.[PDF]

12. C. Li, W. Qian, C. J. Maclean and J. Zhang (2016) The fitness landscape of a tRNA gene. Science 352 (6287): 837-40. [PDF]

11. W. Qian, and J. Zhang (2014) Genomic evidence for adaptation by gene duplication. Genome Research 24: 1356-1362. [PDF]

 

(2008-2012)

10. C. Park, W. Qian, and J. Zhang (2012) Genomic evidence for elevated mutation rates in highly expressed genes. EMBO Reports 13: 1123-1129. [PDF]

9. W. Qian, D. Ma, C. Xiao, Z. Wang, and J. Zhang (2012) The genomic landscape and evolutionary resolution of antagonistic pleiotropy in yeast. Cell Reports, 2: 1399-410. [PDF]

8. W. Qian, J.-R. Yang, N. M. Pearson, C. Maclean, and J. Zhang (2012) Balanced codon usage optimizes eukaryotic translational efficiency. PLoS Genetics 8 (3): e1002603. [PDF]

7. W. Qian, X. He, E. Chan, H. Xu, and J. Zhang (2011) Measuring the evolutionary rate of protein-protein interaction. Proc. Natl. Acad. Sci. USA 108: 8725-30. [PDF]

6. W. Qian*, B.-Y. Liao*, A. Y.-F. Chang, and J. Zhang (2010) Maintenance of duplicate genes and their functional redundancy by reduced expression. Trends in Genetics 26: 425-30. (*, equal contributions) [PDF]

5. X. He*, W. Qian*, Z. Wang*, Y. Li, and J. Zhang (2010) Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks. Nature Genetics 42: 272-6. (*, equal contributions) [PDF]

4. Z. Zhang, W. Qian, and J. Zhang (2009) Positive selection for elevated gene expression noise in yeast. Molecular Systems Biology 5: 299 (12 pages). [PDF]

3. W. Qian, and J. Zhang (2009) Protein subcellular relocalization in the evolution of yeast singleton and duplicate genes. Genome Biology and Evolution 1: 198-204. [PDF]

2. W. Qian, and J. Zhang (2008) Gene dosage and gene duplicability. Genetics 179: 2319-2324. [PDF]

1. W. Qian, and J. Zhang (2008) Evolutionary dynamics of nematode operons: easy come, slow go. Genome Research 18: 412-421. [PDF]