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Bioinformatics

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Data Analysis

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Genomics


Welcome to Yi's lab!


Team

Yi Wang

Principle Investigator

        西南大学教授,青年千人。2002年浙江大学学士,2005年电子科技大学硕士,2009年重庆大学博士,具有生命科学和信息科学的交叉背景。曾担任企业软件开发工程师,拥有丰富的软件开发经验,三项软件著作权和两项专利的主要贡献者。
        2010年到2017年分别在加州大学戴维斯分校和伯克利分校进行研究和工作,担任生物信息学专家,积累了丰富的组学数据,尤其是基因组数据的分析经验。开发了多个数据库和在线工具,包括植物基因结构比较进化数据库,小麦D基因组物理图谱和全基因组测序项目数据库,同源基因快速比较分析工具,多倍体特异性引物设计和微生物组数据可视化等工具。
        2017年加入西南大学,入职家蚕基因组生物学国家重点实验室,2018年入选千人计划青年项目。目前已发表SCI论文35篇,包括Nucleic Acids Research, Bioinformatics, Nature, PNAS等著名杂志,总影响因子超过150,总引用超过800

Funding

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主持基金项目


西南大学引进人才项目基金,2018-2020


国家青年千人基金,2018-2020


国家自然科学基金面上项目:反转座基因注释工具的开发及在家蚕基因组中的应用,2019-2022

Research

研究方向

Database

开发生物信息数据库

Bioinformatics tools

研究新颖的数据算法与工具

Resequencing analysis

基因组测序分析

Data visualization

生物大数据可视化

Evolution

比较基因组与进化

Pan genome

家蚕及野蚕的泛基因组分析

Tool

已发布的生物信息工具,包括各种数据库,软件,及web在线分析平台

Publication

2018

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

Xu L, Naylor D, Dong Z, Simmons T, Pierroz G, Hixson KK, Kim YM, Zink EM, Engbrecht KM, Wang Y, et al. 2018. Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria. Proc Natl Acad Sci USA 115 (18), E4284-E4293.

Huo N, Zhu T, Altenbach S, Dong L, Wang Y, Mohr T, Liu Z, Dvorak J, Luo MC, Gu YQ. 2018. Dynamic Evolution of α-Gliadin Prolamin Gene Family in Homeologous Genomes of Hexaploid Wheat. Sci Rep 8 (1), 5181.

Huo N, Zhang S, Zhu T, Dong L, Wang Y, Mohr T, Hu T, Liu Z, Dvorak J, Luo MC, et al. 2018. Gene duplication and evolution dynamics in the homeologous regions harboring multiple prolamin and resistance gene families in hexaploid wheat. Frontiers in plant science 9.

2017

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

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

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

Luo MC, Gu YQ, Puiu D, Wang H, Twardziok SO, Deal KR, Huo N, Zhu T, Wang L, Wang Y … Dvorak, J. 2017. Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature 551: 498-502.

Huo NX, Dong LL, Zhang SL, Wang Y, Zhu TT, Mohr T, Altenbach S, Liu ZY, Dvorak J, Anderson OD et al. 2017. 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 92: 571-583.

2016

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

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

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

Bassi FM, Ghavami F, Hayden MJ, Wang Y, Forrest KL, Kong S, Dizon R, Michalak de Jimenez MK, Meinhardt SW, Mergoum M et al. 2016. Fast-forward genetics by radiation hybrids to saturate the locus regulating nuclear-cytoplasmic compatibility in Triticum. Plant Biotechnol J 14: 1716-1726.

Dong L, Huo N, Wang Y, Deal K, Wang D, Hu T, Dvorak J, Anderson OD, Luo MC, Gu YQ. 2016. Rapid evolutionary dynamics in a 2.8-Mb chromosomal region containing multiple prolamin and resistance gene families in Aegilops tauschii. Plant J 87: 495-506.

Tiwari VK, Heesacker A, Riera-Lizarazu O, Gunn H, Wang S, Wang Y, Gu YQ, Paux E, Koo DH, Kumar A et al. 2016. A whole-genome, radiation hybrid mapping resource of hexaploid wheat. Plant J 86: 195-207.

1Valdes Franco JA, Collier R, Wang Y, Huo N, Gu Y, Thilmony R, Thomson JG. 2016. Draft Genome Sequence of Agrobacterium rhizogenes Strain NCPPB2659. Genome Announc 4.

2015

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

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

Kumar A, Seetan R, Mergoum M, Tiwari VK, Iqbal MJ, Wang Y, Al-Azzam O, Simkova H, Luo MC, Dvorak J et al. 2015. Radiation hybrid maps of the D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes. BMC Genomics 16: 800.

Pearce S, Vazquez-Gross H, Herin SY, Hane D, Wang Y, Gu YQ, Dubcovsky J. 2015. WheatExp: an RNA-seq expression database for polyploid wheat. BMC Plant Biol 15: 299.

2014

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

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

Wang Y, Wang Y, Zhou K, Hong A. 2014. Constructing regulatory networks to identify biomarkers for insulin resistance. Gene 539: 68-74.

Zhu M, Chen G, Zhou S, Tu Y, Wang Y, Dong T, Hu Z. 2014. 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 55: 119-135.

2013

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

Dong T, Hu Z, Deng L, Wang Y, Zhu M, Zhang J, Chen G. 2013. A tomato MADS-box transcription factor, SlMADS1, acts as a negative regulator of fruit ripening. Plant Physiol 163: 1026-1036.

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

Luo MC, Gu YQ, You FM, Deal KR, Ma Y, Hu Y, Huo N, Wang Y, Wang J, Chen S et al. 2013. 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 110: 7940-7945.

2008-2012

Dong L, Huo N, Wang Y, Deal K, Luo MC, Wang D, Anderson OD, Gu YQ. 2012. Exploring the diploid wheat ancestral A genome through sequence comparison at the high-molecular-weight glutenin locus region. Mol Genet Genomics 287: 855-866.

Kumar A, Simons K, Iqbal MJ, de Jimenez MM, Bassi FM, Ghavami F, Al-Azzam O, Drader T, Wang Y, Luo MC et al. 2012. Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor Aegilops tauschii. BMC Genomics 13: 597.

Belknap WR, Wang Y, Huo N, Wu J, Rockhold DR, Gu YQ, Stover E. 2011. Characterizing the citrus cultivar Carrizo genome through 454 shotgun sequencing. Genome 54: 1005-1015.

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

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

Yang Y, Hu Z, Liu Z, Wang Y, Chen X, Chen G. 2009. High human GLUT1, GLUT2, and GLUT3 expression in Schizosaccharomyces pombe. Biochemistry (Mosc) 74: 75-80.

Wang Y, Chen G, Yang Y, Hu Z, Chen X. 2008. A systems biology analysis of protein-protein interactions in the APOBEC family. Life Sci 83: 521-530.

Position

欢迎具有计算机背景,生物学背景的同学报考本实验的硕士研究生和博士研究生,同时也欢迎具有生物信息学,计算生物学背景的博士来本实验室进行博士后研究。

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硕士博士研究生


本团队每年招收硕士生4名,博士生1-2名

对每名学生按照其基础提供相应的培养方式

鼓励学生的创造性思维

培养学生的编程和数据分析能力

培养学生独立进行科研的能力


博士后


在站期间的福利待遇将按照西南大学有关政策执行。
全职博士后薪酬待遇分别为100万元、60万元、30万元,每月薪酬由基本工资(2300元/月)、生活补贴(4700元/月)、科研补贴(5000元/月)组成,每年发放绩效津贴(分为I、II、III类)。考核表现优异者优先留校。

Contact Us

TEL: 023-68251683

FAX: 023-68251128

E-mail:yiwang28@swu.edu.cn

Address: State Key Laboratory of Silkworm Genome Biology,Southwest University,Chongqing 400716,China