王  翊

中国致公党党员，教授，博士生导师

国家重要人才计划青年项目入选者

第三批“重庆市学术技术带头人”

一、个人简历

1998-2002，浙江大学计算数学与应用软件专业学习，获理学学士学位。

2002-2005，电子科技大学生物医学工程专业学习，获工学硕士学位；研究方向：基于生物信息学进行基因药物筛选及疾病预警微系统研究。

2005-2009，重庆大学生物医学工程专业学习，获理学博士学位；研究方向：基于生物大数据进行植物基因组与功能研究。

2009-2010，重庆诺京生物信息技术有限公司上班，任职软件工程师；主要工作：生物大数据平台的开发和高效共享；帮助企业获得三项软件著作权和两项专利。

2009-2010，重庆大学，博士后；研究方向：基于生物大数据进行植物基因组分析、系统发育与进化研究。

2010-2015，加州大学戴维斯分校 ，博士后；研究方向：植物全基因组及功能分析、系统发育与进化研究，生物组学大数据分析平台、在线浏览数据库工具的开发。

2015-2017，加州大学伯克利分校，Associate Specialist；研究方向：植物全基因组及功能分析、系统发育与进化研究，生物组学大数据分析平台和在线浏览数据库工具的开发。

2017-至今，西南大学家蚕基因组生物学国家重点实验室，前沿交叉学科研究院生物学研究中心，教授；面向本科生和研究生讲授《生物学前沿导论(双语)》、《生物组学大数据》、《基因组与生物信息学》、《生命科学前沿》等课程。

二、研究方向

1. 以近年来高度发展的“生物学大数据”为契机，利用优质的生物信息学数据处理方法、算法和软件体系和多样化的分析手段，切实推动生命科学发展。将生物多组学大数据分析技术与基因组功能、个体发育与物种进化相结合，解析生命体背后的遗传密码，揭秘生物漫长而有趣的进化之旅。基于海量的生物多组学大数据，发展具有国际先进水平的多组学大数据分析处理策略，建立重要性状的基因组及蛋白质组等多组学整合数据库，构建高效精准的分子辅助育种的生物信息技术体系，促进以大数据为支持的，包括家蚕、蜘蛛、小麦、水稻等在内的多种物种的基础研究和生物育种发展。

2. 目前的研究重点：1）人工智能（深度学习、机器学习）在生物多组学大数据中的应用研究；2）基因组与泛基因组研究，解析个体发育与物种进化；3）单细胞与表观基因组研究，解析重要基因功能和细胞命运；4）生物组学大数据分析平台、在线数据库浏览工具等的开发和应用。

三、主持及参加项目

1. 主持国家自然科学基金面上项目、联合基金重点项目，中央高校科研项目等多个国家级项目；重庆市、西南大学引进人才项目等多个项目，参与科技部重点研发项目，国家自然科学基金重点项目、重庆市创新团体等国家级、省部级项目。

2. 指导学生参加国家级、市级比赛项目，学生获得：

    第十七届“挑战杯”课外学术科技作品竞赛重庆选拔赛特等奖、重庆市优秀本科生毕业论文，作为西南大学唯一学术论文代表入围第十四届全国大学生创新创业年会学术论文（全国仅199篇），提名第十三届中国青少年科技创新奖等。学生获国家奖学金、校候光炯奖学金、优秀研究生干部、五好研究生、先进个人、优秀党员、研究生优秀科技成果、实验室“科研标兵”等数十人次。

四、主要学术成果

1、参编《中国养蚕学》。

2、研发了PIECE、OrthoVenn、RetroScan、SilkDB 3.0、GSP、MetaCoMET等10余个生物信息学软件或数据平台。

    （1）. RetroScan：快速、便捷进行反转座子Retrocopy分析和注释的工具软件

（https://github.com/Vicky123wzy/RetroScan）

    （2）. SilkDB 3.0：家蚕多组学遗传信息在线数据库

（https://silkdb.bioinfotoolkits.net）

   （3）. OrthoVenn 1/2/3: 多物种同源基因比较和分析的在线数据库

（https://orthovenn2.bioinfotoolkits.net）

   （4）. NetVenn：多组基因集合的相互作用分析及在线注释工具

（http://probes.pw.usda.gov/NetVenn 或 http://wheat.pw.usda.gov/NetVenn）

  （5）. MetaCoMET：在线发现、注释和可视化分析微生物核心OUT的浏览器工具

（http://probes.pw.usda.gov/MetaCoMET 或 http://aegilops.wheat.ucdavis.edu/MetaCoMET）

 （6）. PlantRGDB：植物反转座基因分析数据库

（http://probes.pw.usda.gov/plantrgdb 或 http://aegilops.wheat.ucdavis.edu/plantrgdb）

  （7）. PIECE 1.0/2.0：植物基因结构比较和进化分析数据库

（http://probes.pw.usda.gov/piece 或 http://aegilops.wheat.ucdavis.edu/piece）

  （8）. GSP：多倍体基因组特异引物在线设计图形化工具

（https://github.com/bioinfogenome/GSP）

 （9）. AIM：植物基因组模块相互作用分析数据库

（http://probes.pw.usda.gov/AIM）

3、以通信或第一作者在Nature Communications、Nucleic Acids Research、Briefings in Bioinformatics、Bioinformatics等国际知名期刊上发表高水平论文20余篇，入选ESI高被引论文两篇。在Nature、PNAS等杂志上参与发表文章20余篇。全部文章总引用3200多次，h-index 23。

1. Hu W, Jia A, Ma S, Zhang G, Wei Z, Lu F, Luo Y, Zhang Z, Sun J, Yang T, Xia T, Li Q, Yao T, Zheng J, Jiang Z, Xu Z, Xia Q, Wang Y(*). A molecular atlas reveals the tri-sectional spinning mechanism of spider dragline silk. Nat Commun. 2023 Feb 15; 14(1):837.

2. Wei Z, Sun J, Li Q, Yao T, Zeng H, Wang Y(*). RetroScan: An Easy-to-Use Pipeline for Retrocopy Annotation and Visualization. Front Genet. 2021 Aug 16; 12:719204.

3. Jia A, Xu L, Wang Y(*). Venn diagrams in bioinformatics. Brief Bioinform. 2021 Sep 2; 22(5):bbab108.

4. Zeng H, Chen X, Li H, Zhang J, Wei Z, Wang Y(*). Interpopulation differences of retroduplication variations (RDVs) in rice retrogenes and their phenotypic correlations. Comput Struct Biotechnol J. 2021 Jan 5; 19:600-611.

5. Fang Lu, Zhaoyuan Wei#, Yongjiang Luo, Hailong Guo, Guoqing Zhang, Qingyou Xia, Yi Wang(*). SilkDB 3.0: visualizing and exploring multiple levels of data for silkworm. Nucleic Acids Res, 2019, 10, 23, pii: gkz919.

6. Ling, Xu; Zhaobin, Dong; Lu, Fang; Yongjiang, Luo; Zhaoyuan, Wei; Hailong, Guo; Guoqing, Zhang;Yong Q, Gu; Devin, Coleman-Derr; Qingyou, Xia; Yi, Wang(*), OrthoVenn2: a web server for wholegenome comparison and annotation of orthologous clusters across multiple species, Nucleic Acids Res, 2019.5.4, 47(W1): W52~W58.  

7. Wang, Yi(*), PlantRGDB: A Database of Plant Retrocopied Genes, Plant Cell Physiol, 2017.1.22, 1(58): e2~e2.

8. Valdes Franco JA, Wang Y, Huo N, Ponciano G, Colvin HA, McMahan CM, Gu YQ, Belknap WR et al. Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes. BMC genomics. 2018, 19 (1), 271.  

9. Wang Y, Xu L, Thilmony R, You FM, Gu YQ, Coleman-Derr D.  PIECE 2.0: an update for the plant gene structure comparison and evolution database. Nucleic Acids Res. 2017, 45: 1015-1020.

10. Wang Y. PlantRGDB: A Database of Plant Retrocopied Genes. Plant Cell Physiol.  2017, 58: e2.  

11. Liu Y#, Wang Y#, Guo F, Zhan L, Mohr T, Cheng P, Huo N, Gu R, Pei D, Sun J et al. Deep sequencing and transcriptome analyses to identify genes involved in secoiridoid biosynthesis in the Tibetan medicinal plant Swertia mussotii. Sci Rep. 2017, 7: 43108.

12. Wang Y, Tiwari VK, Rawat N, Gill BS, Huo N, You FM, Coleman-Derr D, Gu YQ. GSP: a web-based platform for designing genome-specific primers in polyploids. Bioinformatics.2016, 32: 2382-2383.  

13. Wang Y, Xu L, Gu YQ, Coleman-Derr D. MetaCoMET: a web platform for discovery and visualization of the core microbiome. Bioinformatics. 2016, 32: 3469-3470.

14. Xie J#, Huo N#, Zhou S#, Wang Y#, Guo G, Deal K, Ouyang S, Liang Y, Wang Z, Xiao L et al. Sequencing and Comparative Analyses of Aegilops Tauschii Chromosome Arm 3DS Reveal Rapid Evolution of Triticeae Genomes. Journal of Genetics and Genomics. 2016, 44: 51-61.

15. Wang Y, Coleman-Derr D, Chen G, Gu YQ. OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res. 2015, 43: W78-84.    

16. Wang Y#, Drader T#, Tiwari VK, Dong L, Kumar A, Huo N, Ghavami F, Iqbal MJ, Lazo GR, Leonard J et al. Development of a D genome specific marker resource for diploid and hexaploid wheat. BMC Genomics. 2015, 16: 646.

17. Wang Y, Thilmony R, Gu YQ. NetVenn: an integrated network analysis web platform for gene lists. Nucleic Acids Res. 2014, 42: W161-166.

18. Wang Y, Thilmony R, Zhao Y, Chen G, Gu YQ. AIM: a comprehensive Arabidopsis interactome module database and related interologs in plants. Database (Oxford). 2014, bau117.

19. Wang Y, You FM, Lazo GR, Luo MC, Thilmony R, Gordon S, Kianian SF, Gu YQ. PIECE: a database for plant gene structure comparison and evolution. Nucleic Acids Res. 2013, 41: D1159-1166.

20. Wang Y, Hu Z, Yang Y, Chen X, Chen G. Genome-wide identification, phylogeny, and expression analysis of the SBP-box gene family in grapevine. Russ J Plant Physl+. 2010, 57: 273-282.

21. Wang Y, Hu Z, Yang Y, Chen X, Chen G. Function annotation of an SBP-box gene in Arabidopsis based on analysis of co-expression networks and promoters. Int J Mol Sci. 2009, 10: 116-132.

22. Wang Y, Chen G, Yang Y, Hu Z, Chen X. A systems biology analysis of protein-protein interactions in the APOBEC family. Life Sci, 2008.10, 83(15-16): 521-30.

23. Valdes Franco JA, Wang Y, Huo N, Ponciano G, Colvin HA, McMahan CM, Gu YQ, Belknap WR. Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes, BMC genomics, 2018.4.19, 19(1): 271.

24. Xu L, Naylor D, Dong Z, Simmons T, Pierroz G, Hixson KK, Kim YM, Zink EM, Engbrecht KM, Wang Y, Gao C, DeGraaf S, Madera MA, Sievert JA, Hollingsworth J, Birdseye D, Scheller HV, Hutmacher R, Dahlberg J, Jansson C, Taylor JW, Lemaux PG, Coleman-Derr D. Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria, Proc Natl Acad Sci USA, 2018.5.1, 115 (18): E4284-E4293.

25. Huo N, Zhu T, Altenbach S, Dong L, Wang Y, Mohr T, Liu Z, Dvorak J, Luo MC, Gu YQ. Dynamic Evolution of α-Gliadin Prolamin Gene Family in Homeologous Genomes of Hexaploid Wheat, Sci Rep, 2018.3.26, 8(1): 5181.

26. Huo N, Zhang S, Zhu T, Dong L, Wang Y, Mohr T, Hu T, Liu Z, Dvorak J, Luo MC, Wang D, Lee JY, Altenbach S, Gu YQ. Gene duplication and evolution dynamics in the homeologous regions harboring multiple prolamin and resistance gene families in hexaploid wheat, Frontiers in plant science, 2018.3.23, 9:673.

27. Luo MC, Gu YQ, Puiu D, Wang H, Twardziok SO, Deal KR, Huo N, Zhu T, Wang L, Wang Y, McGuire PE, Liu S, Long H, Ramasamy RK, Rodriguez JC, Van SL, Yuan L, Wang Z, Xia Z, Xiao L, Anderson OD, Ouyang S, Liang Y, Zimin AV, Pertea G, Qi P, Bennetzen JL, Dai X, Dawson MW, Müller HG, Kugler K, Rivarola-Duarte L, Spannagl M, Mayer KFX, Lu FH, Bevan MW, Leroy P, Li P, You FM, Sun Q, Liu Z, Lyons E, Wicker T, Salzberg SL, Devos KM, Dvořák J. Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature, 2017.11.23, 551: 498-502.

28. Huo NX, Dong LL, Zhang SL, Wang Y, Zhu TT, Mohr T, Altenbach S, Liu ZY, Dvorak J, Anderson OD, Luo MC, Wang D, Gu YQ. New insights into structural organization and gene duplication in a 1.75-Mb genomic region harboring the -gliadin gene family in Aegilops tauschii, the source of wheat D genome, Plant Journal, 2017.11, 92: 571-583.

29. Bassi FM, Ghavami F, Hayden MJ, Wang Y, Forrest KL, Kong S, Dizon R, Michalak de Jimenez MK, Meinhardt SW, Mergoum M,Gu YQ, Kianian SF. Fast-forward genetics by radiation hybrids to saturate the locus regulating nuclear-cytoplasmic compatibility in Triticum, Plant Biotechnol J, 2016.8, 14(8): 1716-1726.

30. Dong L, Huo N, Wang Y, Deal K, Wang D, Hu T, Dvorak J, Anderson OD, Luo MC, Gu Y. Rapid evolutionary dynamics in a 2.8-Mb chromosomal region containing multiple prolamin and resistance gene families in Aegilops tauschii, Plant J, 2016.9, 87(5): 495-506.

31. Tiwari VK, Heesacker A, Riera-Lizarazu O, Gunn H, Wang S, Wang Y, Gu YQ, Paux E, Koo DH, Kumar A,  Luo MC, Lazo G, Zemetra R, Akhunov E, Friebe B, Poland J, Gill BS, Kianian S, Leonard JM. A whole-genome, radiation hybrid mapping resource of hexaploid wheat, Plant J, 2016.4, 86(2): 195-207.

32. Valdes Franco JA, Collier R, Wang Y, Huo N, Gu Y, Thilmony R, Thomson JG. Draft Genome Sequence of Agrobacterium rhizogenes Strain NCPPB2659, Genome Announc, 2016.7.28, 4(4).

33. Kumar A, Seetan R, Mergoum M, Tiwari VK, Iqbal MJ, Wang Y, Al-Azzam O, Simkova H, Luo MC, Dvorak J,  Gu YQ, Denton A, Kilian A, Lazo GR, Kianian SF. Radiation hybrid maps of the D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes, BMC Genomics, 2016.10.16, 16: 800.

34. Pearce S, Vazquez-Gross H, Herin SY, Hane D, Wang Y, Gu YQ, Dubcovsky J. WheatExp: an RNA-seq expression database for polyploid wheat, BMC Plant Biol, 2015.12.24, 15: 299.

35. Yang Y, Wang Y, Zhou K, Hong A. Constructing regulatory networks to identify biomarkers for insulin resistance, Gene, 2014.4.10, 539(1): 68-74.

36. Zhu M, Chen G, Zhou S, Tu Y, Wang Y, Dong T, Hu Z. A new tomato NAC (NAM/ATAF1/2/CUC2) transcription factor, SlNAC4, functions as a positive regulator of fruit ripening and carotenoid accumulation, Plant Cell Physiol, 2014.1, 55(1):119-35.

37. Dong T, Hu Z, Deng L, Wang Y, Zhu M, Zhang J, Chen G. A tomato MADS-box transcription factor, SlMADS1, acts as a negative regulator of fruit ripening, Plant Physiol, 2013.10, 163(2): 1026-36.

38. Liu Y, Huo N, Dong L, Wang Y, Zhang S, Young HA, Feng X, Gu YQ. Complete chloroplast genome sequences of Mongolia medicine Artemisia frigida and phylogenetic relationships with other plants, PLoS One, 2013, 8(2): e57533.

39. Luo MC, Gu YQ, You FM, Deal KR, Ma Y, Hu Y, Huo N, Wang Y, Wang J, Chen S, Jorgensen CM, Zhang Y, McGuire PE, Pasternak S, Stein JC, Ware D, Kramer M, McCombie WR, Kianian SF, Martis MM, Mayer KF, Sehgal SK, Li W, Gill BS, Bevan MW, Simková H, Dolezel J, Weining S, Lazo GR, Anderson OD, Dvorak J. A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor, Proc Natl Acad Sci USA, 2013.5.7, 110(19): 7940-5.,

40. Dong L, Huo N, Wang Y, Deal K, Luo MC, Wang D, Anderson OD, Gu YQ. Exploring the diploid wheat ancestral A genome through sequence comparison at the high-molecular-weight glutenin locus region, Mol Genet Genomics, 2012.12, 287(11-12): 855-866.

41. Kumar A, Simons K, Iqbal MJ, de Jimenez MM, Bassi FM, Ghavami F, Al-Azzam O, Drader T, Wang Y, Luo MC, Gu YQ, Denton A, Lazo GR, Xu SS, Dvorak J, Kianian PM, Kianian SF. Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor Aegilops tauschii, BMC Genomics, 2012.11.5, 13: 597.

42. Belknap WR, Wang Y, Huo N, Wu J, Rockhold DR, Gu YQ, Stover E. Characterizing the citrus cultivar Carrizo genome through 454 shotgun sequencing, Genome, 2011.12, 54(12): 1005-1015.

43.Yang Y, Hu Z, Liu Z, Wang Y, Chen X, Chen G. High human GLUT1, GLUT2, and GLUT3 expression in Schizosaccharomyces pombe, Biochemistry (Mosc), 2009.6, 74(1): 75-80.

五、学术兼职

1. iMeta青年编委，Frontiers of Plant Science专刊编委

2. Bioinformatics等多个生物信息学期刊审稿人

3. 重庆市生物信息学会理事、农林信息学专委会委员

联系方式：

通讯地址：重庆市北碚区天生路2号西南大学南区科技楼211室

邮编：400715

Email：yiwang28@swu.edu.cn