(*Corresponding author; #Co-first author)
SELECTED PUBLICATIONS
7. Xuebo Zhao#, Yafei Guo#, Lipeng Kang, Changbin Yin, Aoyue Bi, Daxing Xu, Zhiliang Zhang, Zhang Jijin, Xiaohan Yang, Jun Xu, Song Xu, Xinyue Song, Ming Zhang, Yiwen Li, Philip Kear, Jing Wang, Zhiyong Liu, Xiangdong Fu,Fei Lu. Population genomics unravels the Holocene history of bread wheat and its relatives.Nature Plants. (2023). doi:10.1038/s41477-023-01367-3
6. Yuanying Peng#,*, Honghai Yan#, Laichun Guo#, Cao Deng#, Chunlong Wang#, Yubo Wang#, Lipeng Kang, Pingping Zhou, Kaiquan Yu, Xiaolong Dong, Xiaomeng Liu, Zongyi Sun, Yun Peng, Jun Zhao, Di Deng, Yinghong Xu, Ying Li, Qiantao Jiang, Yan Li, Liming Wei, Jirui Wang, Jian Ma, Ming Hao, Wei Li, Houyang Kang, Zhengsong Peng, Dengcai Liu, Jizeng Jia, Youliang Zheng, Tao Ma*, Yuming Wei*, Fei Lu*, Changzhong Ren*. Reference genome assemblies reveal the origin and evolution of allohexaploid oat. Nature Genetics. (2022). doi:10.1038/s41588-022-01127-7.
5. Y. Zhou
#, X. Zhao
#, Y. Li, J. Xu, A. Bi, L. Kang, D. Xu, H. Chen, Y. Wang, Y. Wang, S. Liu, C. Jiao, H. Lu, J. Wang, C. Yin, Y. Jiao*,
F. Lu*.
Triticum population sequencing provides insights into wheat adaptation.
Nature Genetics.(2020). doi:10.1038/s41588-020-00722-w.
4. Punna Ramu*, Williams Esuma, Robert Kawuki, Ismail Y Rabbi, Chiedozie Egesi, Jessen V Bredeson, Rebecca S Bart, Janu Verma, Edward S Buckler, Fei Lu*. (2017). Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation. Nature Genetics. doi: 10.1038/ng.3845.
3. Wang J#, Xu J#, Yang X#, Xu S, Zhang M, Lu F*. Boosting the power of transcriptomics by developing an efficient gene expression profiling approach. Plant Biotechnol J. (2021). doi:10.1111/PBI.13706
2. Fei Lu*, Maria C Romay, Jeff C Glaubitz, Peter J Bradbury, Rob J Elshire, Tianyu Wang, Yu Li, Yongxiang Li, Kassa Semagn, Xuecai Zhang, Alvaro G. Hernandez, Mark A. Mikel, Ilya Soifer, Omer Barad, Edward S Buckler*. (2015) High-resolution genetic mapping of maize pan-genome sequence anchors. Nature Communications. DOI:10.1038/ncomms7914.
1. Lu F, Lipka AE, Elshire RJ, Glaubitz JC, Cherney JH, Casler MD, Buckler ES, Costich DE. (2013) Switchgrass genomic diversity, ploidy and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genetics. 9(1): e1003215. (Citation: 675 by 2022-07-19)
PREPRINTS
9. Zhiliang Zhang#, Jijin Zhang#, Lipeng Kang, Xuebing Qiu, Song Xu, Jun Xu, Yafei Guo, Zelin Niu, Beirui Niu, Aoyue Bi, Xuebo Zhao, Daxing Xu, Jing Wang, Changbin Yin, Fei Lu. Structural variation discovery in wheat using PacBio high-fidelity sequencing. bioRxiv. (2023). doi: 10.1101/2023.12.08.570887
8. Aoyue Bi#, Daxing Xu#, Lipeng Kang, Yafei Guo, Xinyue Song, Xuebo Zhao, Jijin Zhang, Zhiliang Zhang, Yiwen Li, Changbin Yin, Jing Wang, Fei Lu. An integrated map of genetic variation from 1,062 wheat genomes. bioRxiv. (2023). doi: 10.1101/2023.03.31.535022
7.
Xuebo Zhao#, Yafei Guo#, Lipeng Kang, Aoyue Bi, Daxing Xu, Zhiliang Zhang, Zhang Jijin, Xiaohan Yang, Jun Xu, Song Xu, Xinyue Song, Ming Zhang, Yiwen Li, Philip Kear, Jing Wang, Changbin Yin, Zhiyong Liu, Xiangdong Fu,Fei Lu*. Population genomics unravels the Holocene history ofTriticum-Aegilopsspecies.bioRxiv. (2022).doi:10.1101/2022.04.07.487499
6. Zhiliang Zhang#, Jijin Zhang#, Lipeng Kang, Xuebing Qiu, Beirui Niu, Aoyue Bi, Xuebo Zhao, Daxing Xu, Jing Wang, Changbin Yin, Xiangdong Fu, Fei Lu*. Genotyping of structural variation using PacBio high-fidelity sequencing. bioRxiv. (2021). doi:10.1101/2021.10.28.466362
5. Yuanying Peng*, Honghai Yan, Laichun Guo, Cao Deng, Lipeng Kang, Chunlong Wang, Pingping Zhou, Kaiquan Yu, Xiaolong Dong, Jun Zhao, Yun Peng, Xiaomeng Liu, Di Deng, Yinghong Xu, Ying Li, Qiantao Jiang, Yan Li, Liming Wei, Jirui Wang, Jian Ma, Ming Hao, Wei Li, Houyang Kang, Youliang Zheng, Yuming Wei, F. Lu*, Changzhong Ren*. Reference genome assemblies reveal the origin and evolution of allohexaploid oat. Research Square. (2021). doi:10.21203/rs.3.rs-664692/v1
4. X. Zhao, X. Fu, C. Yin*, F. Lu*. Wheat Speciation and Adaptation: Perspectives from Reticulate Evolution. Preprints. (2021). 2021040559
3. Y. Zhou#, X. Zhao#, Y. Li, J. Xu, A. Bi, L. Kang, H. Chen, Y. Wang, Y. Wang, S. Liu, C. Jiao, H. Lu, J. Wang, C. Yin, Y. Jiao*, F. Lu*. Convergence within divergence: insights of wheat adaptation from Triticum population sequencing. bioRxiv. (2020). doi:10.1101/2020.03.21.001362
2. H. Chen, C. Jiao, Y. Wang, Y. Wang, C. Tian, H. Yu, J. Wang, X. Wang, F. Lu, X. Fu, Y. Xue, W. Jiang, H. Ling, H. Lu, Y. Jiao. Comparative Population Genomics of Bread Wheat (Triticum aestivum) Reveals Its Cultivation and Breeding History in China. bioRxiv. (2019). doi:10.1101/519587
1. Punna Ramu*, Williams Esuma, Robert Kawuki, Ismail Y Rabbi, Chiedozie Egesi, Jessen V Bredeson, Rebecca S Bart, Janu Verma, Edward S Buckler, Fei Lu*. (2016). Cassava HapMap: Managing genetic load in a clonal crop species. bioRxiv. doi: http://dx.doi.org/10.1101/077123
ALL PEER-REVIEWED PUBLICATIONS
42. Yafei Guo, Lipeng Kang, Fei Lu. Genetic Insights into Adaptation of Alfalfa. Molecular Plant. (2024). doi: 10.1016/j.molp.2024.06.015
41. Yongxing Chen, Huixin Xiao, Yuange Wang, Wenling Li, Lingchuan Li, Lingli Dong, Xuebo Zhao, Miaomiao Li, Ping Lu, Huaizhi Zhang, Guanghao Guo, Keyu Zhu, Beibei Li, Lei Dong, Peng Chen, Shuming Wu, Yunbo Jiang, Fei Lu, Chengguo Yuan, Zhiyong Liu, Yusheng Zhao, Qiuhong Wu. WPA1 encodes a vWA domain protein that regulates wheat plant architecture. The Crop Journal. (2024). doi: 10.1016/j.cj.2024.05.008
40. Xuelei Lin#, Yongxin Xu#, Dongzhi Wang#, Yiman Yang, Xiaoyu Zhang, Xiaomin Bie, Lixuan Gui, Zhongxu Chen, Yiliang Ding, Long Mao, Xueyong Zhang, Fei Lu, Xiansheng Zhang, Cristobal Uauy, Xiangdong Fu, Jun Xiao. Systemic identification of wheat spike development regulators by integrated multi-omics, transcriptional network, GWAS and genetic analyses. Molecular Plant. (2024). doi: 10.1016/j.molp.2024.01.010
39. Botao Ye#, Yangyang Liu#, Ziying Wang#, Liping Shen, Changbin Yin, Kuocheng Shen, Jiaqiang Sun, Xiaowan Xu, Mengjing Sun, Jianhui Wu, Zhonghu He, Xuchang Yu, Fei Lu*, Yuanfeng Hao*, Zifeng Guo*. Genetic basis of geographical differentiation, breeding selection, domestication effects and breeding application for TaJAZ1 in wheat. Journal of Genetics and Genomics. (2024). doi: 10.1016/j.jgg.2024.01.004
38. Liping Shen#, Lili Zhang#, Changbin Yin#, Xiaowan Xu#, Yangyang Liu, Kuocheng Shen, He Wu, Zhiwen Sun, Ke Wang, Zhonghu He, Xueyong Zhang, Chenyang Hao, Jian Hou, Aoyue Bi, Xuebo Zhao, Daxing Xu, Botao Ye, Xuchang Yu, Ziying Wang, Danni Liu, Yuanfeng Hao*, Fei Lu*, Zifeng Guo*. The wheat sucrose synthase gene TaSus1 is a major determinant of grain number per spike. The Crop Journal. (2023). doi: 10.1016/j.cj.2023.11.007
37. Yafei Guo, Fei Lu. The changing colour of carrot. Nature Plants. (2023). doi: 10.1038/s41477-023-01523-9
36. Yangyang Liu#, Jun Chen#, Changbin Yin#, Ziying Wang, He Wu, Kuocheng Shen, Zhiliang Zhang, Lipeng Kang, Song Xu, Aoyue Bi, Xuebo Zhao, Daxing Xu, Zhonghu He, Xueyong Zhang, Chenyang Hao, Jianhui Wu, Yan Gong, Xuchang Yu, Zhiwen Sun, Botao Ye, Danni Liu, Lili Zhang, Liping Shen, Yuanfeng Hao*, Youzhi Ma*, Fei Lu*, Zifeng Guo*. A High-Resolution Genotype–Phenotype Map Identifies the TaSPL17 Controlling Grain Number and Size in Wheat. Genome Biology. (2023). doi: 10.1186/s13059-023-03044-2.
35. Xuebo Zhao, Yafei Guo, Fei Lu. Reply to : Where Was Wheat Domesticated?. Nature Plants. (2023). doi: 10.1038/s41477-023-01468-z
34. Zhaoxu Gao, Jianxin Bian, Fei Lu, Yuling Jiao, Hang He. Triticeae Crop Genome Biology: An Endless Frontier. Frontiers in Plant Science. (2023). doi: 10.3389/FPLS.2023.1222681/BIBTEX
33. Yangyang Liu#, Kuocheng Shen#, Changbin Yin#, Xiaowan Xu#, Xuchang Yu, Botao Ye, Zhiwen Sun, Jiayu Dong, Aoyue Bi, Xuebo Zhao, Daxing Xu, Zhonghu He, Xueyong Zhang, Chenyang Hao, Jianhui Wu6, Ziying Wang, He Wu, Danni Liu, Lili Zhang, Liping Shen, Yuanfeng Hao*, Fei Lu*, Zifeng Guo*. Genetic basis of geographical differentiation and breeding selection for wheat plant architecture traits. Genome Biology. (2023). doi: 10.1186/s13059-023-02932-x
32. Xuebo Zhao#, Yafei Guo#, Lipeng Kang, Changbin Yin, Aoyue Bi, Daxing Xu, Zhiliang Zhang, Zhang Jijin, Xiaohan Yang, Jun Xu, Song Xu, Xinyue Song, Ming Zhang, Yiwen Li, Philip Kear, Jing Wang, Zhiyong Liu, Xiangdong Fu, Fei Lu. Population genomics unravels the Holocene history of bread wheat and its relatives. Nature Plants. (2023). doi:10.1038/s41477-023-01367-3
31. Hao Jiang, Yu Fang, Dong Yan, Si-tong Liu, Jun Wei, Fei-long Guo, Xing-ting Wu, Hong Cao, Chang-bin Yin, Fei Lu, Li-feng Gao & Yong-xiu Liu. (2022). Genome-wide association study reveals a NAC transcription factor TaNAC074 linked to pre-harvest sprouting tolerance in wheat. Theor. Appl. Genet. 135, 3265–3276.
30. Jun Xiao, Bao Liu, Yingyin Yao, Zifeng Guo, Haiyan Jia, Lingrang Kong, Aimin Zhang, Wujun Ma, Zhongfu Ni, Shengbao Xu, Fei Lu, Yuannian Jiao, Wuyun Yang, Xuelei Lin, Silong Sun, Zefu Lu, Lifeng Gao, Guangyao Zhao, Shuanghe Cao, Qian Chen, Kunpu Zhang, Mengcheng Wang, Meng Wang, Zhaorong Hu, Weilong Guo, Guoqiang Li, Xin Ma, Junming Li, Fangpu Han, Xiangdong Fu, Zhengqiang Ma, Daowen Wang, Xueyong Zhang, Hong-Qing Ling, Guangmin Xia, Yiping Tong, Zhiyong Liu, Zhonghu He, Jizeng Jia & Kang Chong. (2022). Wheat genomic study for genetic improvement of traits in China. Sci. China Life Sci. 2022 659 65, 1718–1775.
29. Yuanying Peng#,*, Honghai Yan#, Laichun Guo#, Cao Deng#, Chunlong Wang#, Yubo Wang#, Lipeng Kang, Pingping Zhou, Kaiquan Yu, Xiaolong Dong, Xiaomeng Liu, Zongyi Sun, Yun Peng, Jun Zhao, Di Deng, Yinghong Xu, Ying Li, Qiantao Jiang, Yan Li, Liming Wei, Jirui Wang, Jian Ma, Ming Hao, Wei Li, Houyang Kang, Zhengsong Peng, Dengcai Liu, Jizeng Jia, Youliang Zheng, Tao Ma*, Yuming Wei*, Fei Lu*, Changzhong Ren*. Reference genome assemblies reveal the origin and evolution of allohexaploid oat. Nature Genetics. (2022). doi:10.1038/s41588-022-01127-7.
28. Yuange Wang#, Fei Du#, Jian Wang, Ke Wang, Caihuan Tian, Xiaoquan Qi, Fei Lu, Xigang Liu, Xingguo Ye, and Yuling Jiao*. Improving bread wheat yield through modulating an unselected AP2/ERF gene. Nature Plants. (2022). doi:10.1038/s41477-022-01197-9.
27. Xiaofei Yang, Haopeng Yu, Wenqing Sun, Ling Ding, Ji Li, Jitender Cheema, Ricardo Ramirez-Gonzalez, Xuebo Zhao, Azahara C. Martín, Fei Lu, Bao Liu, Cristobal Uauy, Yiliang Ding & Huakun Zhang. Wheat in vivo RNA structure landscape reveals a prevalent role of RNA structure in modulating translational subgenome expression asymmetry. Genome Biology. (2021). doi: 10.1186/s13059-021-02549-y
26. Zhang, X.*, Zhu, Y., Kremling, K.A.G., Romay, M.C., Bukowski, R., Sun, Q., Gao, S., Buckler, E.S., Lu, F.*. Genome‑wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact. Theor. Appl. Genet.. (2021). doi:10.1007/s00122-021-03965-1
25. Wang J#, Xu J#, Yang X#, Xu S, Zhang M, Lu F*. Boosting the power of transcriptomics by developing an efficient gene expression profiling approach. Plant Biotechnol J. (2021). doi:10.1111/PBI.13706
24. X. Zhao, X. Fu, C. Yin*, F. Lu*. Wheat Speciation and Adaptation: Perspectives from Reticulate Evolution. aBiotech. (2021). doi:10.1007/s42994-021-00047-0
23. H. Zhai, C. Jiang, Y. Zhao, S. Yang, Y. Li, K. Yan, S. Wu, B. Luo, Y. Du, H. Jin, X. Liu, Y. Zhang,
F. Lu, M. Reynolds, X. Ou, W. Qiao, Z. Jiang, T. Peng, D. Gao, W. Hu, J. Wang, H. Gao, G. Yin, K. Zhang, G. Li, D. Wang,
Wheat heat tolerance is impaired by heightened deletions in the distal end of 4AL chromosomal arm.
Plant Biotechnol. J. (2020).
doi: https://doi.org/10.1111/pbi.13529
22. Y. Zhou#, X. Zhao#, Y. Li, J. Xu, A. Bi, L. Kang, D. Xu, H. Chen, Y. Wang, Y. Wang, S. Liu, C. Jiao, H. Lu, J. Wang, C. Yin, Y. Jiao*, F. Lu*. Triticum population sequencing provides insights into wheat adaptation. Nature Genetics. (2020). doi:10.1038/s41588-020-00722-w
21. Chunzhi Zhang, Pei Wang, Die Tang, Zhongmin Yang, Fei Lu, Jianjian Qi, Nilesh R. Tawari, Yi Shang, Canhui Li & Sanwen Huang. The genetic basis of inbreeding depression in potato. Nature Genetics. (2019). doi:10.1038/s41588-018-0319-1
20. Lian, Q., Tang, D., Bai, Z., Qi, J.,Lu, F., Huang, S., Zhang, C. (2019) Acquisition of deleterious mutations during potato polyploidization.J Integr Plant Biol61: 7– 11
19. Springer Nathan M., Anderson Sarah N., Andorf Carson M., Ahern Kevin R., Bai Fang, Barad Omer, Barbazuk W. Brad, Bass Hank W., Baruch Kobi, Ben-Zvi Gil, Buckler Edward S., Bukowski Robert, Campbell Michael S., Cannon Ethalinda K. S., Chomet Paul, Dawe R. Kelly, Davenport Ruth, Dooner Hugo K., Du Limei He, Du Chunguang, Easterling Katherine A., Gault Christine, Guan Jiahn-Chou, Hunter Charles T., Jander Georg, Jiao Yinping, Koch Karen E., Kol Guy, Köllner Tobias G., Kudo Toru, Li Qing, Lu Fei, Mayfield-Jones Dustin, Mei Wenbin, McCarty Donald R., Noshay Jaclyn M., Portwood John L., Ronen Gil, Settles A. Mark, Shem-Tov Doron, Shi Jinghua, Soifer, Ilya, Stein Joshua C., Stitzer Michelle C., Suzuki Masaharu, Vera Daniel L., Vollbrecht Erik, Vrebalov Julia T., Ware Doreen, Wei Sharon, Wimalanathan, Kokulapalan, Woodhouse Margaret R., Xiong Wenwei, Brutnell Thomas P.The maize W22 genome provides a foundation for functional genomics and transposon biology. Nature Genetics. (2018). doi:10.1038/s41588-018-0158-0
18. Sun Silong, Zhou Yingsi, Chen Jian, Shi Junpeng, Zhao Haiming, Zhao Hainan, Song Weibin, Zhang Mei, Cui Yang, Dong Xiaomei, Liu Han, Ma Xuxu, Jiao Yinping, Wang Bo, Wei Xuehong, Stein Joshua C., Glaubitz Jeff C., Lu Fei, Yu Guoliang, Liang Chengzhi, Fengler Kevin, Li Bailin, Rafalski Antoni, Schnable Patrick S., Ware Doreen H., Buckler Edward S., Lai Jinsheng. Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nature Genetics. (2018). doi:10.1038/s41588-018-0182
17. Karl A. G. Kremling, Shu-Yun Chen, Mei-Hsiu Su, Nicholas K. Lepak, M. Cinta Romay, Kelly L. Swarts, Fei Lu, Anne Lorant, Peter J. Bradbury & Edward S. Buckler. (2018). Dysregulation of expression correlates with rare-allele burden and fitness loss in maize. Nature. doi:10.1038/nature25966
16. Punna Ramu*, Williams Esuma, Robert Kawuki, Ismail Y Rabbi, Chiedozie Egesi, Jessen V Bredeson, Rebecca S Bart, Janu Verma, Edward S Buckler, Fei Lu*. (2017). Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation. Nature Genetics. doi: 10.1038/ng.3845
15. Candice N. Hirsch, Cory D. Hirsch, Alex B. Brohammer, Megan J. Bowman, Ilya Soifer, Omer Barad, Doron Shem-Tov, Kobi Baruch, Fei Lu, Alvaro G. Hernandez, Christopher J. Fields, Chris L. Wright, Klaus Koehler, Nathan Springer, Edward Buckler, C. Robin Buell, Natalia de Leon, Shawn M. Kaeppler, Kevin L. Childs, Mark Mikel. (2016). Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize. The Plant Cell. doi:10.1105/tpc.16.00353
14. Williams Esuma, Liezel Herselman, Maryke Tine Labuschagne, Punna Ramu, Fei Lu, Yona Baguma, Edward S. Buckler, Robert Sezi Kawuki. (2016). Genome-wide association mapping of provitamin A carotenoid content in cassava. Euphytica. DOI: 10.1007/s10681-016-1772-5
13. Li, Y.-x., Li, C., Bradbury, P. J., Liu, X., Lu, F., Romay, M. C., Glaubitz, J. C., Wu, X., Peng, B., Shi, Y., Song, Y., Zhang, D., Buckler, E. S., Zhang, Z., Li, Y. and Wang, T. (2016), Identification of genetic variants associated with maize flowering time using an extremely large multi-genetic background population. Plant J. doi:10.1111/tpj.13174
12. Fei Lu*, Maria C Romay, Jeff C Glaubitz, Peter J Bradbury, Rob J Elshire, Tianyu Wang, Yu Li, Yongxiang Li, Kassa Semagn, Xuecai Zhang, Alvaro G. Hernandez, Mark A. Mikel, Ilya Soifer, Omer Barad, Edward S Buckler*. (2015) High-resolution genetic mapping of maize pan-genome sequence anchors. Nature Communications. DOI:10.1038/ncomms7914
11. Guillaume P. Ramstein, Alexander E. Lipka, Fei Lu, Denise E. Costich, Jerome H. Cherney, Edward S. Buckler and Michael D. Casler. (2015) Genome-Wide Association Study Based on Multiple Imputation with Low-Depth Sequencing Data: Application to Biofuel Traits in Reed Canarygrass. G3: Genes | Genomes | Genetics. DOI: 10.1534/g3.115.017533
10. Glaubitz JC, Casstevens TM, Lu F, Harriman J, Elshire RJ, Sun Q, Buckler ES. (2014) TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline. PLoS ONE 9(2): e90346.
9. Lipka AE, Lu F, Cherney JH, Buckler ES, Casler MD, and Costich DE (2014). “Accelerating the switchgrass (Panicum virgatum L.) breeding cycle using genomic selecting approaches”. PLoS ONE 9(11), e112227.
8. Lu F, Lipka AE, Elshire RJ, Glaubitz JC, Cherney JH, Casler MD, Buckler ES, Costich DE. (2013) Switchgrass genomic diversity, ploidy and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genetics 9(1):e1003215.
7. Abhijit Sanyal#, Ammiraju S.S.Jetty#, Fei Lu#, Yeisoo Yu Teri Rambo, Jennifer Currie, Kristi Kollura, Hye-Ran Kim, Jinfeng Chen, Jianxin Ma, Phillip San Miguel, Mingsheng Chen, Rod A. Wing and Scott A. Jackson. (2010). Orthologous comparisons of the Hd1 region across genera reveal Hd1 gene lability within diploid Oryza species and disruptions to microsynteny in sorghum. MOL BIOL EVOL. DOI:10.1093/molbev/msq133
6. Jetty S.S. Ammiraju, Chuanzhu Fan, Yeisoo Yu, Xiang Song, Karen A. Cranston, Ana Clara Pontaroli, Fei Lu, Abhijit Sanyal, Ning Jiang, Teri Rambo, Jennifer Currie, Kristi Collura, Jayson Talag, Jeffrey L. Bennetzen, Mingsheng Chen, Scott Jackson, Rod A. Wing. (2010). Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza. The Plant Journal. DOI: 10.1111/j.1365-313X.2010.04251.x
5. Lu, F.#, Ammiraju, J. S.#, Sanyal, A.#, Zhang, S.#, Song, R., Chen, J.#, Li, G., Sui, Y., Song, X., Cheng, Z., de Oliveira, A. C., Bennetzen, J. L.,Jackson, S., Wing, R. A., and Chen, M. (2009). Comparative sequence analysis of the MONOCULM1 orthologous regions in fourteen Oryza genomes. Proc Natl Acad Sci USA. 106(6):2071-6.
4. Ammiraju, J. S.#, Lu, F.#, Sanyal, A.#, Yu, Y., Song, X., Jiang, N., Pontaroli, A. C., Rambo, T., Currie, J., Collura, K., Talag, J., Fan, C., Goicoechea, J. L., Zuccolo, A., Chen, J., Bennetzen, J. L., Chen, M., Jackson, S., and Wing, R. A. (2008). Dynamic Evolution of Oryza Genomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set. The Plant Cell 10.1105/tpc.1108.063727
3. Lukas A. Mueller, René Klein Lankhorst, Steven D. Tanksley, James J. Giovannoni, Ruth White, Julia Vrebalov, Zhangjun Fei, Joyce van Eck, Robert Buels, Adri A. Mills, Naama Menda, Isaak Y. Tecle, Aureliano Bombarely, Stephen Stack, Suzanne M. Royer, Song-Bin Chang, Lindsay A. Shearer, Byung Dong Kim, Sung-Hwan Jo, Cheol-Goo Hur, Doil Choi, Chang-Bao Li, Jiuhai Zhao, Hongling Jiang, Yu Geng, Yuanyuan Dai, Huajie Fan, Jinfeng Chen, Fei Lu, et al. (2009). A Snapshot of the Emerging Tomato Genome Sequence. The Plant Genome. 10.3835/plantgenome2008.08.0005: 78-92
2. Li C-B, Zhao JH, Jiang HL, Geng Y, Dai YY, Fan HJ, Zhang DF, Chen JF, Lu F, Shi JF, Sun SH, Chen JJ, Yan XH, Lu C, Chen MS, Cheng ZK, Ling HQ, Wang Y, Xue YB, Li C. (2008). A snapshot of the Chinese SOL Project. Journal of Genomics and Genetics. 35: 387-390
1. Chen JF, Lu F, Chen SS, Tao SH. Significant positive correlation between the recombination rate and GC content in the human pseudoautosomal region. Genome (2006) 49:413–419.
软件开发
Xiaohan Yang, Jun Xu, Song Xu, Fei Lu. SiPAS-tools. (2022).
Bioinformatic toolkits of RNA-seq data.
7.
Fei Lu. FastCall 2. (2021).
Superfast variant calling and genotyping software for whole genome shotgun (WGS) data.
6.
Fei Lu. HapScanner. (2020).
5.
Fei Lu. Toolkits Integrated for Genetic and Evolutionary Research (TIGER). (2020).
Java-based code packages and tools developed in the lab to conduct efficient analysis on genetics and evolution.
4.
Jun Xu, Fei Lu. SiPAS-Profiler. (2019).
Gene expression profiling software using raw RNA-seq data.
3.
Fei Lu. FastCall. (2016).
Super-fast variant caller for whole genome shotgun (WGS) sequencing data. It works for diploid species, including both inbreds and outcrossers.
2.
Fei Lu, Jeff Glaubitz, Terry Casstevens, Qi Sun, Robert Bukowski, Katie Hyma, Ed Buckler. TASSEL 5.0 Pan-genome Atlas (PanA) pipeline. (2014).
PanA combines genetic mapping and machine learning to produces millions of genetic anchor for the genome of a species.
1.
Fei Lu, Jeff Glaubitz, James Harriman, Terry Casstevens, Rob Elshire. TASSEL 3.0 Universal Network Enabled Analysis Kit (UNEAK) pipeline. (2012).
A reference genome free SNP calling pipeline.
