钱文峰

中国科学院遗传与发育生物学研究所

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  • 钱文峰
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钱文峰博士、研究员、博士生导师 2006年,获北京大学生命科学专业学士学位(指导老师:中国科学院昆明动物所王文研究员); 2012年,获密歇根大学进化生物学专业博士学位(指导老师:张建之教授); 2012年12月起,在遗传与发育生物学研究所任研究员; 2014年入选“青年千人计划”; 2018年获“益海嘉里”优秀导师奖; 2019年入选“优秀青年科学基金”项目。研究方向 特别说明:本课题组不专门做数据库或软件的开发,对学生的数学/计算机能力并没有特别的要求。实验室目前所有成员都是生命科学背景,大多数学生在进入本课题组后才系统学习统计学与计算机编程。 实验室的研究包括生物学大数据的产生及其解读。我们研究的目标是通过高通量实验方法与相应的计算生物学手段认识遗传与进化的基本过程,其中一些研究成果将会对人类健康和农业生产产生积极的影响。具体而言,我们的研究包括以下几个方面: (一)通过ribo-seq等方法检测细胞内核糖体在mRNA上的分配与分布,试图理解翻译对生长与发育过程的调控作用、机制与进化; (二)通过高通量实验构建基因型与表型的对应关系(fitness landscape),试图理解生命在这种对应关系指导下的进化过程; (三)通过定向进化实验实现蛋白质的快速“驯化”(directed evolution),并在此过程中研究蛋白质功能优化的基本规律(evolutionary trajectory); (四)通过体细胞谱系追踪理解多细胞生物的发育过程(cell lineage tracing),特别是理解组织/器官发生与再生的发育来源。课题组成员获奖情况 振声奖学金:吴少欢(2016)、陈思羽(2017) “益海嘉里”优秀博士生奖:陈瑛(2019) 国家奖学金:陈瑛(2019)、段朝瑞(2018)、张宇亮(2018) “益海嘉里”优秀博士后奖:肇涛澜(2017)相关报道与科普文章 《癌症与突变》(https://zhuanlan.zhihu.com/p/49502048) 《突变率的一个新的调控因子》(https://mp.weixin.qq.com/s/TK8xeQxDnNK1mxY2z5jefg) 《不只有A的poly(A)尾》(https://mp.weixin.qq.com/s/K6jlDcv1BJe2g52KglWf4g) 《染色体变异与癌症》(https://mp.weixin.qq.com/s/qe_0StGg_xT1lb_veDo-6Q)读研体会与建议 钱文峰2011年获国家留学基金委“优秀自费留学生奖学金特别优秀奖”后《神州学人》的专栏文章 http://www.chinanews.com/lxsh/2012/09-19/4196713.shtml采访与报道 《九旬院士的17载科教实验:挽起求索科学的“小手”》http://www.sohu.com/a/75801914_160309 《最简细胞:助力打开生命“黑箱”》http://paper.sciencenet.cn/htmlnews/2016/3/341762.shtm发表论文实时更新请见http://qianlab.genetics.ac.cn/publications.html或https://www.ncbi.nlm.nih.gov/pubmed/?term=wenfeng+qian%5Bau%5D或https://scholar.google.com/citations?user=M5ae5GYAAAAJ&hl=en(实验室成员,*共同第一作者,#通讯作者)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.文章解读:《钱文峰研究组发现由DNA复制引起的蛋白质剂量失衡及细胞的应对机制》(http://www.genetics.ac.cn/xwzx/kyjz/201912/t20191206_5450138.html)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(1):189(12 pages).文章解读:《曹晓风与钱文峰研究组合作发现poly(A)尾中鸟嘌呤含量调控翻译的新机制》(http://www.genetics.ac.cn/xwzx/kyjz/201909/t20190909_5378240.html )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)文章解读:《钱文峰研究组合作发现非整倍体细胞增殖缺陷的新机制》(http://www.genetics.ac.cn/xwzx/kyjz/201907/t20190726_5352005.html)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): 580.20. 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).文章解读:《钱文峰研究组发现DNA固有曲率调控局部突变率》(http://www.genetics.ac.cn/xwzx/kyjz/201809/t20180919_5085111.html )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.文章解读:《钱文峰研究组优化单细胞DNA甲基化修饰异质性算法并发布数据库HeteroMeth》(http://www.genetics.ac.cn/xwzx/kyjz/201809/t20180913_5077777.html)18. Y. Yang*, W. Cao*, S. Wu, and W. Qian# (2017) Genetic interaction network as an important determinant of gene order in genome evolution. Molecular Biology and Evolution 34 (12), 3254-3266.文章解读:《钱文峰研究组发现遗传互作网络对染色体上基因顺序的决定作用》(http://www.genetics.ac.cn/xwzx/kyjz/201710/t20171011_4871720.html)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. Science Bulletin 62 (19), 1304-1314.文章解读:《单细胞转录组学研究揭示植物中存在着广泛的单等位基因表达》(http://www.genetics.ac.cn/xwzx/kyjz/201709/t20170929_4866650.html)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. Molecular Biology and Evolution 34 (11), 2944-2958.文章解读:《钱文峰研究组揭示同义密码子对于mRNA水平的调控》(http://www.genetics.ac.cn/xwzx/kyjz/201708/t20170828_4852394.html)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文章解读:《钱文峰研究组和杜茁研究组联合揭示反式剪接的翻译调控功能》(http://www.genetics.ac.cn/xwzx/kyjz/201709/t20170904_4854566.html)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 Computational Biology 13 (6): e1005585.文章解读:《钱文峰研究组发现组蛋白修饰分工调控基因表达水平和基因表达噪音》(http://www.genetics.ac.cn/xwzx/kyjz/201707/t20170705_4822692.html)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. (*, equal contributions)文章解读:《薛勇彪研究组和钱文峰研究组合作在水稻花器官稳态发育的分子机制研究中取得重要进展》(http://www.genetics.cas.cn/xwzx/kyjz/201607/t20160704_4634747.html)12. C. Li, W. Qian, C. J. Maclean and J. Zhang (2016) The fitness landscape of a tRNA gene. Science. 352(6287):837-40Science专文评述Toward a prospective molecular evolution(https://science.sciencemag.org/content/352/6287/769)11. W. Qian, and J. Zhang (2014) Genomic evidence for adaptation by gene duplication. Genome Research 24:1356-1362.10. C. Park, W. Qian, and J. Zhang (2012) Genomic evidence for elevated mutation rates in highly expressed genes. EMBO Reports 13:1123-1129.9. 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, 2:1399-1410.8. 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.Recommended by F1000 (https://f1000.com/prime/718320889)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 108:8725-8730.6. 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 26:425-430. (*, equal contributions)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 42:272-276. (*, equal contributions)Nature Reviews Genetics专文评述Meaningful connections(https://www.nature.com/articles/nrg2756)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).3. W. Qian, and J. Zhang (2009) Protein subcellular relocalization in the evolution of yeast singleton and duplicate genes. Genome Biology and Evolution 1:198-204.2. W. Qian, and J. Zhang (2008) Gene dosage and gene duplicability. Genetics 179:2319-2324.1. W. Qian, and J. Zhang (2008) Evolutionary dynamics of nematode operons: easy come, slow go. Genome Research 18:412-421.Recommended by F1000 (https://f1000.com/prime/1104212)