基本信息
贺飞 男 中国科学院遗传与发育生物学研究所
电子邮件： fhe@genetics.ac.cn
通信地址： 中科院遗传与发育生物学研究所
邮政编码：
电子邮件： fhe@genetics.ac.cn
通信地址： 中科院遗传与发育生物学研究所
邮政编码：
研究领域
小麦抗病基因的挖掘与育种利用可以帮助缩短抗病品种的培育周期。但传统的细胞学手段难以精细鉴定小麦基因组中的外源染色体片段，因此我们无法高效地研究来自亲缘或者远缘物种的抗病基因。2018年以来，一系列小麦及其亲缘物种的基因组项目相继完成，小麦抗病基因的克隆与功能研究面临前所未有的时代契机。本研究组将聚焦抗病基因，以远缘杂交材料为基础，利用组学与计算的手段在基因组层面上系统地解析外源基因在小麦抗病育种中的作用，揭示远缘杂交对于小麦抗病等重要农艺性状的分子与遗传基础，并与育种家合作探索提高小麦抗病育种效率的新思路。
招生信息
欢迎对农业感兴趣，有志于采用基因组学的角度对农作物品种设计提出新方案的学生报考。
招生专业
0710J3-生物信息学
招生方向
农作物与病原菌的协同进化
小麦群体遗传学
农作物病原真菌的基因组进化
小麦群体遗传学
农作物病原真菌的基因组进化
教育背景
2006-09--2011-06 中国农业大学 理学博士 （生物信息学）
2002-09--2006-06 西南大学 理学学士 （生物学）
2002-09--2006-06 西南大学 理学学士 （生物学）
工作经历
工作简历
2016-06~2021-06,堪萨斯州立大学 （美国）, 博士后 (Postdoc Follow)
2015-07~2016-06,伊利诺伊大学厄巴纳-香槟分校 （美国）, 访问学者 (Visiting scholar)
2012-08~2016-06,布鲁克海文国家实验室（美国）, 博士后 (Research Associate)
2011-07~2012-07,纪念斯隆凯特琳癌症中心 （美国）, 博士后 （Research Fellow）
2015-07~2016-06,伊利诺伊大学厄巴纳-香槟分校 （美国）, 访问学者 (Visiting scholar)
2012-08~2016-06,布鲁克海文国家实验室（美国）, 博士后 (Research Associate)
2011-07~2012-07,纪念斯隆凯特琳癌症中心 （美国）, 博士后 （Research Fellow）
教授课程
RNAseq data analysis
出版信息
发表论文
[1] 肖军, 鲁非, 邓娴, 宋显伟, 贺飞, 蒋才富, 刘倩, 赵玉胜, 姜丹华, 傅向东. 植物基因组与表观遗传学研究进展. 植物生理学报[J]. 2023, 第 5 作者59(9): 1665-1693, http://lib.cqvip.com/Qikan/Article/Detail?id=7110724235.
[2] Niu，Jianqing, Ma，Shengwei, Zheng，Shusong, Zhang，Chi, Lu，Yaru, Si, Yaoqi, Tian，Shuiquan, Shi，Xiaoli, Liu，Xiaolin, M. Kashif Naeem, Sun，Hua, Hu，Yafei, Wu， Huilan, Cui，Yan, Chen，Chunlin, Long，Wenbo, Zhang，Yue, Gu，Mengjun, Cui，Man, Lu，Qiao, Zhou，Wenjuan, Peng，Junhua, Akhunov，Eduard, He，Fei, Zhao，Shancen, Ling，Hong-Qing. Whole-genome sequencing of diverse wheat accessions uncovers genetic changes during modern breeding in China and the United States. The Plant Cell[J]. 2023, 第 24 作者 通讯作者
[3] Jordan, Katherine W, He, Fei, de Soto, Monica Fernandez, Akhunova, Alina, Akhunov, Eduard. Differential chromatin accessibility landscape reveals structural and functional features of the allopolyploid wheat chromosomes. GENOME BIOLOGY[J]. 2020, 第 2 作者21(1): http://dx.doi.org/10.1186/s13059-020-02093-1.
[4] He, Fei, Pasam, Raj, Shi, Fan, Kant, Surya, KeebleGagnere, Gabriel, Kay, Pippa, Forrest, Kerrie, Fritz, Allan, Hucl, Pierre, Wiebe, Krystalee, Knox, Ron, Cuthbert, Richard, Pozniak, Curtis, Akhunova, Alina, Morrell, Peter L, Davies, John P, Webb, Steve R, Spangenberg, German, Hayes, Ben, Daetwyler, Hans, Tibbits, Josquin, Hayden, Matthew, Akhunov, Eduard. Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. NATURE GENETICS[J]. 2019, 第 1 作者51(5): 896-+, http://dx.doi.org/10.1038/s41588-019-0382-2.
[5] Xiao, Long, Zhao, Zhiguang, He, Fei, Du, Zhuo. Multivariable regulation of gene expression plasticity in metazoans. OPEN BIOLOGY[J]. 2019, 第 3 作者 通讯作者 9(12): https://doaj.org/article/3e246e053795463481feb3c5f5c8784a.
[6] Jordan, Katherine W, Wang, Shichen, He, Fei, Chao, Shiaoman, Lun, Yanni, Paux, Etienne, Sourdille, Pierre, Sherman, Jamie, Akhunova, Alina, Blake, Nancy K, Pumphrey, Michael O, Glover, Karl, Dubcovsky, Jorge, Talbert, Luther, Akhunov, Eduard D. The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping. PLANT JOURNAL[J]. 2018, 第 3 作者95(6): 1039-1054, http://dx.doi.org/10.1111/tpj.14009.
[7] Arkin, Adam P, Cottingham, Robert W, Henry, Christopher S, Harris, Nomi L, Stevens, Rick L, Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W, Henderson, Matthew L, Riehl, William J, MurphyOlson, Dan, Chan, Stephen Y, Kamimura, Roy T, Kumari, Sunita, Drake, Meghan M, Brettin, Thomas S, Glass, Elizabeth M, Chivian, Dylan, Gunter, Dan, Weston, David J, Allen, Benjamin H, Baumohl, Jason, Best, Aaron A, Bowen, Ben, Brenner, Steven E, Bun, Christopher C, Chandonia, JohnMarc, Chia, JerMing, Colasanti, Ric, Conrad, Neal, Davis, James J, Davison, Brian H, DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N, Fang, Gang, Faria, Jose P, Frybarger, Paul M, Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L, He, Fei, Jain, Rashmi, Joachimiak, Marcin P, Keegan, Kevin P, Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L, Meyer, Folker, Mills, Marissa, Novichkov, Pavel S, Oh, Taeyun, Olsen, Gary J, Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S, Price, Gavin A, Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C, Schatz, Michael C, Seaver, Samuel M D, Shukla, Maulik, Sutormin, Roman A, Syed, Mustafa H, Thomason, James, Tintle, Nathan L, Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, Yu, Dantong. KBase: The United States Department of Energy Systems Biology Knowledgebase. NATURE BIOTECHNOLOGY. 2018, 第 49 作者36(7): 566-569, https://www.webofscience.com/wos/woscc/full-record/WOS:000438082000010.
[8] Qi, Huan, Jiang, Zhenhong, Zhang, Kang, Yang, Shiping, He, Fei, Zhang, Ziding. PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System. GENOMICS PROTEOMICS & BIOINFORMATICS[J]. 2018, 第 5 作者 通讯作者 16(4): 283-293, https://doaj.org/article/0170c3d29aed417aaaf7411146f55f37.
[9] He, Fei, Yoo, Shinjae, Wang, Daifeng, Kumari, Sunita, Gerstein, Mark, Ware, Doreen, Maslov, Sergei. Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis. PLANT JOURNAL[J]. 2016, 第 1 作者86(6): 472-480, https://www.webofscience.com/wos/woscc/full-record/WOS:000380214500003.
[10] Jiang, Zhenhong, Dong, Xiaobao, Li, ZhiGang, He, Fei, Zhang, Ziding. Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection. SCIENTIFIC REPORTS[J]. 2016, 第 4 作者 通讯作者 6: http://dx.doi.org/10.1038/srep35064.
[11] He, Fei, Maslov, Sergei. Pan- and core- network analysis of co-expression genes in a model plant. SCIENTIFIC REPORTS[J]. 2016, 第 1 作者 通讯作者 6: http://dx.doi.org/10.1038/srep38956.
[12] He, Fei, Karve, Abhijit A, Maslov, Sergei, Babst, Benjamin A. Large-Scale Public Transcriptomic Data Mining Reveals a Tight Connection between the Transport of Nitrogen and Other Transport Processes in Arabidopsis. FRONTIERS IN PLANT SCIENCE[J]. 2016, 第 1 作者 通讯作者 7: https://doaj.org/article/1d32427ecdb84b12a340fa2a44e1ad2f.
[13] Wang, Daifeng, He, Fei, Maslov, Sergei, Gerstein, Mark. DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks. PLOS COMPUTATIONAL BIOLOGY[J]. 2016, 第 2 作者12(10): https://doaj.org/article/309e52bc73054fbab5801d434f060718.
[14] Du, Zhuo, Santella, Anthony, He, Fei, Tiongson, Michael, Bao, Zhirong. De Novo Inference of Systems-Level Mechanistic Models of Development from Live-Imaging-Based Phenotype Analysis. CELL[J]. 2014, 第 3 作者156(1-2): 359-372, http://dx.doi.org/10.1016/j.cell.2013.11.046.
[15] He, Fei, Zhou, Yuan, Zhang, Ziding. Deciphering the Arabidopsis Floral Transition Process by Integrating a Protein-Protein Interaction Network and Gene Expression Data. PLANT PHYSIOLOGY[J]. 2010, 第 1 作者153(4): 1492-1505, https://www.webofscience.com/wos/woscc/full-record/WOS:000280566000005.
[16] He, Fei, Zhang, Yan, Chen, Hao, Zhang, Ziding, Peng, YouLiang. The prediction of protein-protein interaction networks in rice blast fungus. BMC GENOMICS[J]. 2008, 第 1 作者 通讯作者 9(1): 519-519, https://doaj.org/article/9e9f7a68d3274ef09e0532883da88624.
[2] Niu，Jianqing, Ma，Shengwei, Zheng，Shusong, Zhang，Chi, Lu，Yaru, Si, Yaoqi, Tian，Shuiquan, Shi，Xiaoli, Liu，Xiaolin, M. Kashif Naeem, Sun，Hua, Hu，Yafei, Wu， Huilan, Cui，Yan, Chen，Chunlin, Long，Wenbo, Zhang，Yue, Gu，Mengjun, Cui，Man, Lu，Qiao, Zhou，Wenjuan, Peng，Junhua, Akhunov，Eduard, He，Fei, Zhao，Shancen, Ling，Hong-Qing. Whole-genome sequencing of diverse wheat accessions uncovers genetic changes during modern breeding in China and the United States. The Plant Cell[J]. 2023, 第 24 作者 通讯作者
[3] Jordan, Katherine W, He, Fei, de Soto, Monica Fernandez, Akhunova, Alina, Akhunov, Eduard. Differential chromatin accessibility landscape reveals structural and functional features of the allopolyploid wheat chromosomes. GENOME BIOLOGY[J]. 2020, 第 2 作者21(1): http://dx.doi.org/10.1186/s13059-020-02093-1.
[4] He, Fei, Pasam, Raj, Shi, Fan, Kant, Surya, KeebleGagnere, Gabriel, Kay, Pippa, Forrest, Kerrie, Fritz, Allan, Hucl, Pierre, Wiebe, Krystalee, Knox, Ron, Cuthbert, Richard, Pozniak, Curtis, Akhunova, Alina, Morrell, Peter L, Davies, John P, Webb, Steve R, Spangenberg, German, Hayes, Ben, Daetwyler, Hans, Tibbits, Josquin, Hayden, Matthew, Akhunov, Eduard. Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. NATURE GENETICS[J]. 2019, 第 1 作者51(5): 896-+, http://dx.doi.org/10.1038/s41588-019-0382-2.
[5] Xiao, Long, Zhao, Zhiguang, He, Fei, Du, Zhuo. Multivariable regulation of gene expression plasticity in metazoans. OPEN BIOLOGY[J]. 2019, 第 3 作者 通讯作者 9(12): https://doaj.org/article/3e246e053795463481feb3c5f5c8784a.
[6] Jordan, Katherine W, Wang, Shichen, He, Fei, Chao, Shiaoman, Lun, Yanni, Paux, Etienne, Sourdille, Pierre, Sherman, Jamie, Akhunova, Alina, Blake, Nancy K, Pumphrey, Michael O, Glover, Karl, Dubcovsky, Jorge, Talbert, Luther, Akhunov, Eduard D. The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping. PLANT JOURNAL[J]. 2018, 第 3 作者95(6): 1039-1054, http://dx.doi.org/10.1111/tpj.14009.
[7] Arkin, Adam P, Cottingham, Robert W, Henry, Christopher S, Harris, Nomi L, Stevens, Rick L, Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W, Henderson, Matthew L, Riehl, William J, MurphyOlson, Dan, Chan, Stephen Y, Kamimura, Roy T, Kumari, Sunita, Drake, Meghan M, Brettin, Thomas S, Glass, Elizabeth M, Chivian, Dylan, Gunter, Dan, Weston, David J, Allen, Benjamin H, Baumohl, Jason, Best, Aaron A, Bowen, Ben, Brenner, Steven E, Bun, Christopher C, Chandonia, JohnMarc, Chia, JerMing, Colasanti, Ric, Conrad, Neal, Davis, James J, Davison, Brian H, DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N, Fang, Gang, Faria, Jose P, Frybarger, Paul M, Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L, He, Fei, Jain, Rashmi, Joachimiak, Marcin P, Keegan, Kevin P, Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L, Meyer, Folker, Mills, Marissa, Novichkov, Pavel S, Oh, Taeyun, Olsen, Gary J, Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S, Price, Gavin A, Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C, Schatz, Michael C, Seaver, Samuel M D, Shukla, Maulik, Sutormin, Roman A, Syed, Mustafa H, Thomason, James, Tintle, Nathan L, Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, Yu, Dantong. KBase: The United States Department of Energy Systems Biology Knowledgebase. NATURE BIOTECHNOLOGY. 2018, 第 49 作者36(7): 566-569, https://www.webofscience.com/wos/woscc/full-record/WOS:000438082000010.
[8] Qi, Huan, Jiang, Zhenhong, Zhang, Kang, Yang, Shiping, He, Fei, Zhang, Ziding. PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System. GENOMICS PROTEOMICS & BIOINFORMATICS[J]. 2018, 第 5 作者 通讯作者 16(4): 283-293, https://doaj.org/article/0170c3d29aed417aaaf7411146f55f37.
[9] He, Fei, Yoo, Shinjae, Wang, Daifeng, Kumari, Sunita, Gerstein, Mark, Ware, Doreen, Maslov, Sergei. Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis. PLANT JOURNAL[J]. 2016, 第 1 作者86(6): 472-480, https://www.webofscience.com/wos/woscc/full-record/WOS:000380214500003.
[10] Jiang, Zhenhong, Dong, Xiaobao, Li, ZhiGang, He, Fei, Zhang, Ziding. Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection. SCIENTIFIC REPORTS[J]. 2016, 第 4 作者 通讯作者 6: http://dx.doi.org/10.1038/srep35064.
[11] He, Fei, Maslov, Sergei. Pan- and core- network analysis of co-expression genes in a model plant. SCIENTIFIC REPORTS[J]. 2016, 第 1 作者 通讯作者 6: http://dx.doi.org/10.1038/srep38956.
[12] He, Fei, Karve, Abhijit A, Maslov, Sergei, Babst, Benjamin A. Large-Scale Public Transcriptomic Data Mining Reveals a Tight Connection between the Transport of Nitrogen and Other Transport Processes in Arabidopsis. FRONTIERS IN PLANT SCIENCE[J]. 2016, 第 1 作者 通讯作者 7: https://doaj.org/article/1d32427ecdb84b12a340fa2a44e1ad2f.
[13] Wang, Daifeng, He, Fei, Maslov, Sergei, Gerstein, Mark. DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks. PLOS COMPUTATIONAL BIOLOGY[J]. 2016, 第 2 作者12(10): https://doaj.org/article/309e52bc73054fbab5801d434f060718.
[14] Du, Zhuo, Santella, Anthony, He, Fei, Tiongson, Michael, Bao, Zhirong. De Novo Inference of Systems-Level Mechanistic Models of Development from Live-Imaging-Based Phenotype Analysis. CELL[J]. 2014, 第 3 作者156(1-2): 359-372, http://dx.doi.org/10.1016/j.cell.2013.11.046.
[15] He, Fei, Zhou, Yuan, Zhang, Ziding. Deciphering the Arabidopsis Floral Transition Process by Integrating a Protein-Protein Interaction Network and Gene Expression Data. PLANT PHYSIOLOGY[J]. 2010, 第 1 作者153(4): 1492-1505, https://www.webofscience.com/wos/woscc/full-record/WOS:000280566000005.
[16] He, Fei, Zhang, Yan, Chen, Hao, Zhang, Ziding, Peng, YouLiang. The prediction of protein-protein interaction networks in rice blast fungus. BMC GENOMICS[J]. 2008, 第 1 作者 通讯作者 9(1): 519-519, https://doaj.org/article/9e9f7a68d3274ef09e0532883da88624.
科研活动
参与会议
（1）Exome sequencing highlights the role of wild relative introgression in shaping the adaptive landscape of the wheat genome 2020-01-11