科研成果 |
谢为博,作物遗传改良国家重点实验室固定研究人员(2010-),国家自然科学基金优秀青年科学基金获得者(2019),入选中国科协“青年人才托举工程”(2016),获校研究生指导教师“教书育人奖”(2020)。从事计算基因组学、人工智能生物学等方向的研究,发布了水稻基因组序列变异的功能效应图谱RiceVarMap和植物中首个基于深度学习模型预测基因组序列变异调控效应的网络服务PlantDeepSEA,作为主要设计人员合作开发了全球第一款水稻育种芯片和后续多款育种芯片,被《光明日报》评为2012年度“十大科技瞬间”,获得发明专利3项。主持国家自然科学基金4项,国家863计划专项子课题、十三五重点研发计划课题等3项。发表科学研究论文80余篇,被引用超过6500次,H-index为42。
课题组既有数据分析为主的课题,也有与湿实验结合的课题,欢迎生物、数学、物理和计算机相关专业的青年朋友加入(作为硕博生、博士后和科研助理)。
完整文章列表及引用情况请访问: ORCID http://orcid.org/0000-0002-2768-3572 Google scholar http://scholar.google.com/citations?user=I5zjYOUAAAAJ
主持课题: 国家自然科学基金优秀青年科学基金 水稻基因组学与分子育种,2020-2022 国家自然科学基金面上项目 基于比较基因组和ATAC-seq注释水稻基因组染色质开放区及其序列变异,2018-2021 国家自然科学基金面上项目 整合组学数据剖析水稻籽粒中代谢途径及其调控网络,2016-2019 国家自然科学基金青年基金 基于新一代测序技术的高通量基因分型方法的开发与完善,2012-2014 国家重点研发计划课题 杂种优势预测的新方法和强优势新材料,2016-2020 国家863计划专项子课题 全基因组选择育种技术平台建设,2014-2018 国家863计划专项子课题 水稻组学、资源和生物信息平台的创建,2012-2015 中国科协青年人才托举工程,2015-2017
近年发表的论文:# Equal contribution * Corresponding author
Yu H, Li M, Sandhu J, Sun G, Schnable JC, Walia H, Xie W*, Yu B*, Mower JP*, Zhang C*. Pervasive misannotation of microexons that are evolutionarily conserved and crucial for gene function in plants. Nature Communications, 2022, 13: 820
Zhao H, Li J, Yang L, Qin G, Xia C, Xu X, Su Y, Liu Y, Ming L, Chen L, Xiong L and Xie W*. An inferred functional impact map of genetic variants in rice. Mol Plant, 2021, 14: 1584
Zhao H#, Tu Z#, Liu Y, Zong Z, Li J, Liu H, Xiong F, Zhan J, Hu X, Xie W*. PlantDeepSEA, a deep learning-based web service to predict the regulatory effects of genomic variants in plants. Nucleic Acids Res, 2021, 49: W523
Tang S#, Zhao H#, Lu S, Yu L, Zhang G, Zhang Y, Yang Q, Zhou Y, Wang X, Ma W, Xie W*, Guo L*. Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus. Mol Plant, 2021, 14: 470
Liu C, Tu Y, Liao S, Fu X, Lian X, He Y, Xie W*, Wang G*. Genome-wide association study of flowering time reveals complex genetic heterogeneity and epistatic interactions in rice. Gene, 2021, 770: 145353
Zhu T#, Liao K#, Zhou R#, Xia C, Xie W*. ATAC-seq with unique molecular identifiers improves quantification and footprinting. Commun Biol, 2020, 3: 675
Yao W, Li G, Zhao H, Wang G, Lian X, Xie W*. Exploring the rice dispensable genome using a metagenome-like assembly strategy. Genome Biol, 2015, 16: 187 Featured as "Research Highlight" in Genome Biology "Harvesting rice’s dispensable genome"
Xie W#, Wang G#, Yuan M, Yao W, Lyu K, Zhao H, Yang M, Li P, Zhang X, Yuan J, Wang Q, Liu F, Dong H, Zhang L, Li X, Meng X, Zhang W, Xiong L, He Y, Wang S, Yu S, Xu C, Luo J, Li X, Xiao J, Lian X*, Zhang Q*. Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection. Proc Natl Acad Sci USA, 2015, 112: E5411-E5419 Featured as "Research Highlight" in Nature Plants "Rice breeding: Signature analysis"
Zhao H, Yao W, Ouyang Y, Yang W, Wang G, Lian X, Xing Y, Chen L, Xie W*. RiceVarMap: a comprehensive database of rice genomic variations. Nucleic Acids Res, 2015, 43: D1018-1022
Wang Q#, Xie W#, Xing H, Yan J, Meng X, Li X, Fu X, Xu J, Lian X, Yu S, Xing Y, Wang G*. Genetic Architecture of Natural Variation in Rice Chlorophyll Content Revealed by a Genome-Wide Association Study. Mol Plant, 2015, 8: 946-957
Chen W#, Gao Y#, Xie W#, Gong L#, Lu K#, Wang W, Li Y, Liu X, Zhang H, Dong H, Zhang W, Zhang L, Yu S, Wang G, Lian X*, Luo J*. Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Nat Genet, 2014, 46: 714-721
Yu H#, Xie W#, Li J, Zhou F*, Zhang Q*. A whole-genome SNP array (RICE6K) for genomic breeding in rice. Plant Biotechnol J, 2014, 12: 28-37
Chen H#, Xie W#, He H#, Yu H#, Chen W, Li J, Yu R, Yao Y, Zhang W, He Y, Tang X*, Zhou F*, Deng X W*, Zhang Q*. A High-Density SNP Genotyping Array for Rice Biology and Molecular Breeding. Mol Plant, 2014, 7: 541-553
Cai H#,Xie W#, Zhu T, Lian X*. Transcriptome response to phosphorus starvation in rice. Acta Physiol Plant, 2012, 34: 327-341
Xie W, Feng Q, Yua H, Huang X, Zhao Q, Xing Y, Yu S, Han B, Zhang Q*. Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc Natl Acad Sci USA, 2010, 119: 151-164
Wang L#, Xie W#, Chen Y, Tang W, Yang J, Ye R, Liu L, Lin Y, Xu C, Xiao J, Zhang Q*. A dynamic gene expression atlas covering the entire life cycle of rice. Plant J, 2010, 61: 752-766
Xie W, Chen Y, Zhou G, Wang L, Zhang C, Zhang J, Xiao J, Zhu T, Zhang Q*. Single feature polymorphisms between two rice cultivars detected using a median polish method. Theor Appl Genet, 2009, 119: 151-164
Wei J, Xie W, Li R, Wang S, Qu H, Ma R, Zhou X, Jia Z. Analysis of trait heritability in functionally partitioned rice genomes. Heredity (Edinb), 2020, 124: 485-498
Yang J, Chang Y, Qin Y, Chen D, Zhu T, Peng K, Wang H, Tang N, Li X, Wang Y, Liu Y, Li X, Xie W, Xiong L. A lamin-like protein OsNMCP1 regulates drought resistance and root growth through chromatin accessibility modulation by interacting with a chromatin remodeller OsSWI3C in rice. New Phytol, 2020, 227: 65-83
Yao W, Li Y, Xie W, Wang L. Features of sRNA biogenesis in rice revealed by genetic dissection of sRNA expression level. Comput Struct Biotechnol J, 2020, 18: 3207-3216
Chen J, Zhou H, Xie W, Xia D, Gao G, Zhang Q, Wang G, Lian X, Xiao J, He Y. Genome-wide association analyses reveal the genetic basis of combining ability in rice. Plant Biotechnol J, 2019, 17: 2211-2222
Hu X, Xie W, Wu C, Xu S. A directed learning strategy integrating multiple omic data improves genomic prediction. Plant Biotechnol J, 2019, 17: 2011-2020
Jain R, Jenkins J, Shu S, Chern M, Martin JA, Copetti D, Duong PQ, Pham NT, Kudrna DA, Talag J, Schackwitz WS, Lipzen AM, Dilworth D, Bauer D, Grimwood J, Nelson CR, Xing F, Xie W, Barry KW, Wing RA, Schmutz J, Li G, Ronald PC. Genome sequence of the model rice variety KitaakeX. BMC Genomics, 2019, 20: 905
Wang S, Wei J, Li R, Qu H, Chater JM, Ma R, Li Y, Xie W, Jia Z. Identification of optimal prediction models using multi-omic data for selecting hybrid rice. Heredity (Edinb), 2019, 123: 395-406
Dong H, Zhao H, Li S, Han Z, Hu G, Liu C, Yang G, Wang G, Xie W, Xing Y. Genome-wide association studies reveal that members of bHLH subfamily 16 share a conserved function in regulating flag leaf angle in rice (Oryza sativa). Plos Genetics, 2018, 14: 20
Song J, Lei Y, Shu C, Ding Y, Xing F, Liu H, Wang J, Xie W, Zhang J, Chen L. Rice Information GateWay: A Comprehensive Bioinformatics Platform for Indica Rice Genomes. Mol Plant, 2018, 11: 505-507
Sun S, Wang T, Wang L, Li X, Jia Y, Liu C, Huang X, Xie W, Wang X. Natural selection of a GSK3 determines rice mesocotyl domestication by coordinating strigolactone and brassinosteroid signaling. Nature Commun, 2018, 9: 13
Yang M, Lu K, Zhao FJ, Xie W, Ramakrishna P, Wang G, Du Q, Liang L, Sun C, Zhao H, Zhang Z, Liu Z, Tian J, Huang XY, Wang W, Dong H, Hu J, Ming L, Xing Y, Wang G, Xiao J, Salt DE, Lian X. Genome-Wide Association Studies Reveal the Genetic Basis of Ionomic Variation in Rice. Plant Cell, 2018, 30: 2720-2740
Zhu C, Peng Q, Fu D, Zhuang D, Yu Y, Duan M, Xie W, Cai Y, Ouyan Y, Lian X, Wu C. The E3 Ubiquitin Ligase HAF1 Modulates Circadian Accumulation of EARLY FLOWERING3 to Control Heading Date in Rice under Long-Day Conditions. Plant Cell, 2018, 30: 2352-2367
Wang Q, Zhao H, Jiang J, Xu J, Xie W, Fu X, Liu C, He Y, Wang G. Genetic Architecture of Natural Variation in Rice Nonphotochemical Quenching Capacity Revealed by Genome-Wide Association Study. Frontiers in Plant Science, 2017, 8: 13
Zhou H, Li P, Xie W, Hussain S, Li Y, Xia D, Zhao H, Sun S, Chen J, Ye H, Hou J, Zhao D, Gao G, Zhang Q, Wang G, Lian X, Xiao J, Yu S, Li X, He Y. Genome-wide Association Analyses Reveal the Genetic Basis of Stigma Exsertion in Rice. Mol Plant, 2017, 10: 634-644
Bai X, Zhao H, Huang Y, Xie W, Han Z, Zhang B, Guo Z, Yang L, Dong H, Xue W, Li G, Hu G, Hu Y, Xing Y. Genome-Wide Association Analysis Reveals Different Genetic Control in Panicle Architecture Between Indica and Japonica Rice. Plant Genome, 2016, 9:
Dong H, Zhao H, Xie W, Han Z, Li G, Yao W, Bai X, Hu Y, Guo Z, Lu K, Yang L, Xing Y. A Novel Tiller Angle Gene, TAC3, together with TAC1 and D2 Largely Determine the Natural Variation of Tiller Angle in Rice Cultivars. PLoS Genet, 2016, 12: e1006412
Jin M, Liu H, He C, Fu J, Xiao Y, Wang Y, Xie W, Wang G, Yan J. Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation. Sci Rep, 2016, 6: 18936
Magwa RA, Zhao H, Yao W, Xie W, Yang L, Xing Y, Bai X. Genomewide association analysis for awn length linked to the seed shattering gene qSH1 in rice. J Genet, 2016, 95: 639-646
Ouyang Y, Li G, Mi J, Xu C, Du H, Zhang C, Xie W, Li X, Xiao J, Song H, Zhang Q. Origination and Establishment of a Trigenic Reproductive Isolation System in Rice. Mol Plant, 2016, 9: 1542-1545
Zhang J, Chen L, Sun S, Kudrna D, Copetti D, Li W, Mu T, Jiao W, Xing F, Lee S, Talag J, Song J, Du B, Xie W, Luo M, Maldonado C, Goicoechea J, Xiong L, Wu C, Xing Y, Zhou DX, Yu S, Zhao Y, Wang G, Yu Y, Luo Y, Hurtado B, Danowitz A, Wing R, Zhang Q. Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data. Sci Data, 2016, 3: 160076
Zhang J, Chen L, Xing F, Kudrna D, Yao W, Copetti D, Mu T, Li W, Song J, Xie W, Lee S, Talag J, Shao L, An Y, Zhang C, Ouyang Y, Sun S, Jiao W, Lv F, Du B, Luo M, Maldonado C, Goicoechea J, Xiong L, Wu C, Xing Y, Zhou D, Yu S, Zhao Y, Wang G, Yu Y, Luo Y, Zhou Z, Hurtado B, Danowitz A, Wing R, Zhang Q. Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. Proc Natl Acad Sci USA, 2016, 113: E5163-5171
Wu J, Feng F, Lian X, Teng X, Wei H, Yu H, Xie W, Yan M, Fan P, Li Y, Ma X, Liu H, Yu S, Wang G, Zhou F, Luo L, Mei H. Genome-wide Association Study (GWAS) of mesocotyl elongation based on re-sequencing approach in rice. BMC Plant Biol, 2015, 15:218
Zhang L, Mao D, Xing F, Bai X, Zhao H, Yao W, Li G, Xie W, Xing Y. Loss of function of OsMADS3 via the insertion of a novel retrotransposon leads to recessive male sterility in rice (Oryza sativa). Plant Sci, 2015, 238:188-97
Wang J, Yao W, Zhu D, Xie W, Zhang Q. Genetic basis of sRNA quantitative variation analyzed using an experimental population derived from an elite rice hybrid. Elife, 2015, 4: e04250
Yang Z, Ma H, Hong H, Yao W, Xie W, Xiao J, Li X, Wang S. Transcriptome-based analysis of mitogen-activated protein kinase cascades in the rice response to Xanthomonas oryzae infection. Rice (N Y), 2015, 8: 4
Zhang L, Li Q, Dong H, He Q, Liang L, Tan C, Han Z, Yao W, Li G, Zhao H, Xie W, Xing Y. Three CCT domain-containing genes were identified to regulate heading date by candidate gene-based association mapping and transformation in rice. Sci Rep, 2015, 5: 7663
Peng B, Kong H, Li Y, Wang L, Zhong M, Sun L, Gao G, Zhang Q, Luo L, Wang G, Xie W, Chen J, Yao W, Peng Y, Lei L, Lian X, Xiao J, Xu C, Li X, He Y. OsAAP6 functions as an important regulator of grain protein content and nutritional quality in rice. Nat Commun, 2014, 5: 4847
Songyikhangsuthor K, Guo Z, Wang N, Zhu X, Xie W, Mou T, Xiong L. Natural variation in the sequence of SNAC1 and its expression level polymorphism in rice Germplasms under drought stress. J Genet Genomics, 2014, 41: 609-612
Wang J, Yu H, Weng X, Xie W, Xu C, Li X, Xiao J, Zhang Q. An expression quantitative trait loci-guided co-expression analysis for constructing regulatory network using a rice recombinant inbred line population. J Exp Bot, 2014, 65: 1069-1079
Wang K, Cui K, Liu G, Xie W, Yu H, Pan J, Huang J, Nie L, Shah F, Peng S. Identification of quantitative trait loci for phosphorus use efficiency traits in rice using a high density SNP map. BMC Genet, 2014, 15: 1276
Yang W, Guo Z, Huang C, Duan L, Chen G, Jiang N, Fang W, Feng H, Xie W, Lian X, Wang G, Luo Q, Zhang Q, Liu Q, Xiong L. Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice. Nat Commun, 2014, 5: 5087
Li Y, Fan C, Xing Y, Yun P, Luo L, Yan B, Peng B, Xie W, Wang G, Li X, Xiao J, Xu C, He Y. Chalk5 encodes a vacuolar H(+)-translocating pyrophosphatase influencing grain chalkiness in rice. Nat Genet, 2014, 46: 398-404
Wang J, Yu H, Weng X, Xie W, Xu C, Li X, Xiao J, Zhang Q. An expression quantitative trait loci-guided co-expression analysis for constructing regulatory network using a rice recombinant inbred line population. J Exp Bot, 2014, 65: 1069-1079
Tan C, Han Z, Yu H, Zhan W, Xie W, Chen X, Zhao H, Zhou F, Xing Y. QTL scanning for rice yield using a whole genome SNP array. J Genet Genomics, 2013, 40: 629-638
Yan W, Liu H, Zhou X, Li Q, Zhang J, Lu L, Liu T, Zhang C, Zhang Z, Shen G, Yao W, Chen H, Yu S, Xie W, Xing Y. Natural variation in Ghd7.1 plays an important role in grain yield and adaptation in rice. Cell Res, 2013, 23: 969-971
Cai H, Xie W, Lian X. Comparative Analysis of Differentially Expressed Genes in Rice Under Nitrogen and Phosphorus Starvation Stress Conditions. Plant Molecular Biology Reporter, 2013, 31: 160-173
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Ding J, Shen J, Mao H, Xie W, Li X, Zhang Q. RNA-directed DNA methylation is involved in regulating photoperiod-sensitive male sterility in rice. Mol Plant, 2012, 5: 1210-1216
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Jiang Y, Cai Z, Xie W, Long T, Yu H, Zhang Q. Rice functional genomics research: Progress and implications for crop genetic improvement. Biotechnol Adv, 2012, 30:1059-1070
Zhang C, Wang J, Xie W, Zhou G, Long M, Zhang Q. Dynamic programming procedure for searching optimal models to estimate substitution rates based on the maximum-likelihood method. Proc Natl Acad Sci USA, 2011, 108: 7860-7865
Yu H, Xie W, Wang J, Xing Y, Xu C, Li X, Xiao J, Zhang Q. Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers. PLoS ONE, 2011, 6: e17595
Wang J, Yu H, Xie W, Xing Y, Yu S, Xu C, Li X, Xiao J, Zhang Q. A global analysis of QTLs for expression variations in rice shoot at early seedling stage. Plant J, 2010, 63: 1063-1074
Zhao X, Huang J, Yu H, Wang L,Xie W. Genomic survey, characterization and expression profile analysis of the peptide transporter family in rice (Oryza sativa). BMC Plant Biol, 2010, 10: 92
Zhou Y, Cao Y, Huang Y, Xie W, Xu C, Li X, Wang S. Multiple gene loci affecting genetic background-controlled disease resistance conferred by R gene Xa3/Xa26in rice. Theor Appl Genet, 2009, 120: 127-138
Ye S, Wang L, Xie W, Wan B, Li X, Lin Y. Expression profile of calcium-dependent protein kinase (CDPKs) genes during the whole lifespan and under phytohormone treatment conditions in rice (Oryza sativa ssp. indica). Plant Mol Biol, 2009, 70: 311-325
Qiu X, Xie W, Lian X, Zhang Q. Molecular analyses of the rice glutamate dehydrogenasegene family and their response to nitrogen and phosphorous deprivation. Plant Cell Rep, 2009, 28: 1115-1126
Qiu D, Xiao J, Xie W, Cheng H, Li X, Wang S. Exploring transcriptional signalling mediated by OsWRKY13, a potential regulator of multiple physiological processes in rice. BMC Plant Biol, 2009, 9: 74
Ouyang Y, Chen J, Xie W, Wang L, Zhang Q. Comprehensive sequence and expression profile analysis of Hsp20gene family in rice. Plant Mol Biol, 2009, 70: 341-357
Chen J, Ouyang Y, Wang L, Xie W, Zhang Q. Aspartic proteases gene family in rice: Gene structure and expression, predicted protein features and phylogenetic relation. Gene, 2009, 442: 108-118
Qiu D, Xiao J, Xie W, Liu H, Li X, Xiong L, Wang S. Rice gene network inferred from expression profiling of plants overexpressing OsWRKY13, a positive regulator of disease resistance. Mol Plant, 2008, 1: 538-551
Nuruzzaman M, Gupta M, Zhang C, Wang L, Xie W, Xiong L, Zhang Q, Lian X. Sequence and expression analysis of the thioredoxin protein gene family in rice. Mol Genet Genomics, 2008, 280: 139-151
Nayidu N K, Wang L, Xie W, Zhang C, Fan C, Lian X, Zhang Q, Xiong L. Comprehensive sequence and expression profile analysis of PEX11 gene family in rice. Gene, 2008, 412: 59-70
Gupta M, Qiu X, Wang L, Xie W, Zhang C, Xiong L, Lian X, Zhang Q. KT/HAK/KUP potassium transporters gene family and their whole-life cycle expression profile in rice (Oryza sativa). Mol Genet Genomics, 2008, 280: 437-452
Fang Y, You J, Xie K, Xie W, Xiong L. Systematic sequence analysis and identification of tissue-specific or stress-responsive genes of NAC transcription factor family in rice. Mol Genet Genomics, 2008, 280: 547-563
已批准专利:
周发松,谢为博,喻辉辉,李菁,张启发. 一种水稻全基因组SNP芯片及其应用. 专利号:201210055775
周发松,陈浩东,谢为博,何航,喻辉辉,唐晓艳,李菁,周君莉,何予卿,陈伟,张启发,邓兴旺. 水稻全基因组育种芯片及其应用. 专利号:201380056318
谢为博,张启发,练兴明,王功伟. 一种基于受选择位点指数评估动植物品种育种潜力的方法及其应用. 专利号:201510551134
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