基本信息
刘心 男 博导 其他
电子邮件： liuxin@genomics.cn
通信地址： 广东省深圳市盐田区北山道北山工业区综合楼
邮政编码：
电子邮件： liuxin@genomics.cn
通信地址： 广东省深圳市盐田区北山道北山工业区综合楼
邮政编码：
研究领域
从2009年开始从事基因组相关基础科学研究，主要研究方向为基因组学，群体进化基因组学，生物信息学方向，主要的研究内容包括动植物大基因组组装及进化研究，基于全基因组重测序的群体基因组研究等。以下对本人带领的团队正在开展中的主要科研项目和科研方向做简述。
1、大型动植物基因组。随着基因组技术的不断发展，对更多物种开展全基因组测序成为可能，因此我们加入到了国际大型基因组计划“地球生物基因组”（Earth BioGenome Project）中，负责其中的植物基因组（子项目，万种植物基因组计划，10KP）以及鱼类基因组（子项目，万种鱼类基因组项目，Fish10K）。在这两个项目中，近期已经完成了上百个基因组的测序和组装，我们也在对这些组装好的基因组做进一步的分析，其中具有代表性的已经发表研究文章的物种包括银杏、抹香鲸等。当前，我们正在开展特殊生境植物，深海动植物等物种基因组研究，多个项目处于项目采集、数据产出以及数据分析阶段。
2、动植物比较基因组分析。随着基因组的完成，除了单个基因组能够解决的科学问题之外，通过对比不同物种的基因组，可以进一步阐释生物进化、适应性机制以及特殊性状进化过程等方面。例如，我们正在开展高海拔植物等比较基因组研究，通过大规模基因组的比较分析去寻找高海拔适应性的进化过程和分子机制。我们的比较基因组项目，是同国内外多个研究机构合作开展的。
3、作物群体基因组。测序成本不断降低，对于重要经济物种的群体基因组测序分析成文可能，大规模开展的群体基因组研究，不仅能够直观地反应出作物是如何驯化的，也能够详细地描绘出驯化过程中基因组上发生的变化，而这些变化往往同重要的农艺性状相关。因此，我们正在同国际半干旱作物研究所等机构开展合作，针对鹰嘴豆、花生等重要物种开展大规模重测序研究。
4、基因组分析工具开发。大规模的基因组数据产出需要更加高效的分析软件，同时，更多新的实验技术产出的数据，也需要有新的分析方法。我们对长片段测序数据，正在设计和开发新的分析软件，能够将不同倍型的数据进行分离和分别组装，提高数据利用的效率的同时增加更多的信息。
招生信息
招生方向
动植物基因组：在万种植物基因组、万种鱼类基因组以及作物重测序项目中，对不同物种展开基因组测序和分析，需要学习、了解和应用不同的测序技术，采用多种分析方法，最终通过掌握基因组计划分析方法，在构建基因组图谱的同时，能够从基因组数据中挖掘到同进化以及表型相关的基因组特征，解决物种进化和适应性的问题。 生物信息方法开发：针对长片段测序等新的技术，开发能够用于不同类型、不同物种的测序数据中，开发出能够在基因组研究中广泛应用的分析方法。
教育背景
2009-08--2013-08 香港中文大学 医学科学博士
2005-09--2009-06 北京大学 生命科学专业学士
2005-09--2009-06 北京大学 生命科学专业学士
工作经历
工作简历
2013-08~现在, 深圳华大基因研究院, 研究员
教授课程
阅读与写作
专业英语
专业英语
专利与奖励
奖励信息
（1） 深圳市海外高层次人才（B类）, 市地级, 2015
（2） 深圳市盐田区生物技术高层次人才, 其他, 2014
（2） 深圳市盐田区生物技术高层次人才, 其他, 2014
专利成果
[1] 任丙昭, 欧阳冰洁, 于颖佳, 范广益, 王媚娘, 李新洋, 杨乃波, 刘心. 一种基于噬菌体展示技术开发的ALK纳米抗体及其应用. CN: CN112794914A, 2021-05-14.
[2] 王晨, 黎瀚博, 刘田宾, 刘姗姗, 范广益, 顾颖, 刘心, 徐讯. 一种两栖类动物细胞解离试剂盒. CN: CN111378613A, 2020-07-07.
[3] 方东明, 陈晓丽, 吴晨雨, 刘欢, 刘心. 基于已知序列确定目标物种中对应序列的方法和系统. CN: CN111128303A, 2020-05-08.
[4] 方东明, 陈晓丽, 吴晨雨, 陈利鹏, 刘欢, 刘心. 对具有已知序列的生物序列进行分析的方法和系统. CN: CN111128305A, 2020-05-08.
[5] 宋跃, 宋波, 符渊, 刘欢, 程时锋, 刘心. 一种高效获取叶绿体DNA测序数据的方法及其应用. CN: CN110042148A, 2019-07-23.
[6] 王晨, 黎瀚博, 刘田宾, 刘姗姗, 范广益, 顾颖, 刘心, 徐讯. 一种两栖类动物细胞解离试剂盒. CN: CN111378613B, 2024-01-09.
[7] 方东明, 陈晓丽, 吴晨雨, 刘欢, 刘心. 基于已知序列确定目标物种中对应序列的方法和系统. CN: CN111128303B, 2023-09-15.
[8] 方东明, 陈晓丽, 吴晨雨, 陈利鹏, 刘欢, 刘心. 对具有已知序列的生物序列进行分析的方法和系统. CN: CN111128305B, 2023-09-22.
[2] 王晨, 黎瀚博, 刘田宾, 刘姗姗, 范广益, 顾颖, 刘心, 徐讯. 一种两栖类动物细胞解离试剂盒. CN: CN111378613A, 2020-07-07.
[3] 方东明, 陈晓丽, 吴晨雨, 刘欢, 刘心. 基于已知序列确定目标物种中对应序列的方法和系统. CN: CN111128303A, 2020-05-08.
[4] 方东明, 陈晓丽, 吴晨雨, 陈利鹏, 刘欢, 刘心. 对具有已知序列的生物序列进行分析的方法和系统. CN: CN111128305A, 2020-05-08.
[5] 宋跃, 宋波, 符渊, 刘欢, 程时锋, 刘心. 一种高效获取叶绿体DNA测序数据的方法及其应用. CN: CN110042148A, 2019-07-23.
[6] 王晨, 黎瀚博, 刘田宾, 刘姗姗, 范广益, 顾颖, 刘心, 徐讯. 一种两栖类动物细胞解离试剂盒. CN: CN111378613B, 2024-01-09.
[7] 方东明, 陈晓丽, 吴晨雨, 刘欢, 刘心. 基于已知序列确定目标物种中对应序列的方法和系统. CN: CN111128303B, 2023-09-15.
[8] 方东明, 陈晓丽, 吴晨雨, 陈利鹏, 刘欢, 刘心. 对具有已知序列的生物序列进行分析的方法和系统. CN: CN111128305B, 2023-09-22.
出版信息
发表论文
[1] Liu Xin. Whole genome resequencing and phenotyping of MAGIC population for high resolution mapping of drought tolerance in chickpea. The Plant Genome[J]. 2023, [2] Li, Ming, Zhang, Rui, Fan, Guangyi, Xu, Wenteng, Zhou, Qian, Wang, Lei, Li, Wensheng, Pang, Zunfang, Yu, Mengjun, Liu, Qun, Liu, Xin, Schartl, Manfred, Chen, Songlin. Reconstruction of the Origin of a Neo-Y Sex Chromosome and Its Evolution in the Spotted Knifejaw, Oplegnathus punctatus. MOLECULAR BIOLOGY AND EVOLUTION[J]. 2021, 38(6): 2615-2626, http://dx.doi.org/10.1093/molbev/msab056.
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[4] Wang, Yayu, Liao, Shuilin, Gai, Yingbao, Liu, Guilin, Jin, Tao, Liu, Huan, Gram, Lone, Strube, Mikael Lenz, Fan, Guangyi, Sahu, Sunil Kumar, Liu, Shanshan, Gan, Shuheng, Xie, Zhangxian, Kong, Lingfen, Zhang, Pengfan, Liu, Xin, Wang, DaZhi. Metagenomic Analysis Reveals Microbial Community Structure and Metabolic Potential for Nitrogen Acquisition in the Oligotrophic Surface Water of the Indian Ocean. FRONTIERS IN MICROBIOLOGY[J]. 2021, 12: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7935530/.
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[6] Zhao, Hansheng, Sun, Shuai, Ding, Yulong, Wang, Yue, Yue, Xianghua, Du, Xiao, Wei, Qiang, Fan, Guangyi, Sun, Huayu, Lou, Yongfeng, Yang, Huanming, Wang, Jian, Xu, Xun, Li, Lichao, Yang, Kebin, Xu, Hao, Wang, Jiongliang, Zhu, Chenglei, Wang, Sining, Shan, Xuemeng, Hou, Yinguang, Wang, Yu, Fei, Benhua, Liu, Xin, Jiang, Zehui, Gao, Zhimin. Analysis of 427 genomes reveals moso bamboo population structure and genetic basis of property traits. NATURE COMMUNICATIONS[J]. 2021, 12(1): http://dx.doi.org/10.1038/s41467-021-25795-x.
[7] Guo, Lidong, Xu, Mengyang, Wang, Wenchao, Gu, Shengqiang, Zhao, Xia, Chen, Fang, Wang, Ou, Xu, Xun, Seim, Inge, Fan, Guangyi, Deng, Li, Liu, Xin. SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme. BMC BIOINFORMATICS[J]. 2021, 22(1): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7993450/.
[8] Wei, Tong, van Treuren, Rob, Liu, Xinjiang, Zhang, Zhaowu, Chen, Jiongjiong, Liu, Yang, Dong, Shanshan, Sun, Peinan, Yang, Ting, Lan, Tianming, Wang, Xiaogang, Xiong, Zhouquan, Liu, Yaqiong, Wei, Jinpu, Lu, Haorong, Han, Shengping, Chen, Jason C, Ni, Xuemei, Wang, Jian, Yang, Huanming, Xu, Xun, Kuang, Hanhui, van Hintum, Theo, Liu, Xin, Liu, Huan. Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce. NATURE GENETICS[J]. 2021, 53(5): 752-+, http://dx.doi.org/10.1038/s41588-021-00831-0.
[9] Chengcheng Shi, Jianwei Chen, Qijin Ge, Jiahui Sun, Wenjie Guo, Jie Wang, Ling Peng, Qiwu Xu, Guangyi Fan, Wenwei Zhang, Xin Liu. Draft Genomes and Comparative Analysis of Seven Mangrove Rhizosphere-Associated Fungi Isolated From Kandelia obovata and Acanthus ilicifolius. FRONTIERS IN FUNGAL BIOLOGY[J]. 2021, 2: https://doaj.org/article/2aef4d7e01224182896fb3552d1600c5.
[10] Xu, Mengyang, Guo, Lidong, Du, Xiao, Li, Lei, Peters, Brock A, Deng, Li, Wang, Ou, Chen, Fang, Wang, Jun, Jiang, Zhesheng, Han, Jinglin, Ni, Ming, Yang, Huanming, Xu, Xun, Liu, Xin, Huang, Jie, Fan, Guangyi. Accurate haplotype-resolved assembly reveals the origin of structural variants for human trios. BIOINFORMATICS[J]. 2021, 37(15): 2095-2102, http://dx.doi.org/10.1093/bioinformatics/btab068.
[11] Sjostedt, Evelina, Zhong, Wen, Fagerberg, Linn, Karlsson, Max, Mitsios, Nicholas, Adori, Csaba, Oksvold, Per, Edfors, Fredrik, Limiszewska, Agnieszka, Hikmet, Feria, Huang, Jinrong, Du, Yutao, Lin, Lin, Dong, Zhanying, Yang, Ling, Liu, Xin, Jiang, Hui, Xu, Xun, Wang, Jian, Yang, Huanming, Bolund, Lars, Mardinoglu, Adil, Zhang, Cheng, von Feilitzen, Kalle, Lindskog, Cecilia, Ponten, Fredrik, Luo, Yonglun, Hokfelt, Tomas, Uhlen, Mathias, Mulder, Jan. An atlas of the protein-coding genes in the human, pig, and mouse brain. SCIENCE[J]. 2020, 367(6482): 1090-+, https://www.webofscience.com/wos/woscc/full-record/WOS:000520018400034.
[12] Wang, Sibo, Li, Linzhou, Li, Haoyuan, Sahu, Sunil Kumar, Wang, Hongli, Xu, Yan, Xian, Wenfei, Song, Bo, Liang, Hongping, Cheng, Shifeng, Chang, Yue, Song, Yue, Cebi, Zehra, Wittek, Sebastian, Reder, Tanja, Peterson, Morten, Yang, Huanming, Wang, Jian, Melkonian, Barbara, van de Peer, Yves, Xu, Xun, Wong, Gane KaShu, Melkonian, Michael, Liu, Huan, Liu, Xin. Genomes of early-diverging streptophyte algae shed light on plant terrestrialization. NATURE PLANTS[J]. 2020, 6(2): 95-+, [13] Sun, Shuai, Wang, Yue, Zeng, Wenhong, Du, Xiao, Li, Lei, Hong, Xiaoning, Huang, Xiaoyun, Zhang, He, Zhang, Mengqi, Fan, Guangyi, Liu, Xin, Liu, Shanshan. The genome of Mekong tiger perch (Datnioides undecimradiatus) provides insights into the phylogenetic position of Lobotiformes and biological conservation. SCIENTIFIC REPORTS[J]. 2020, 10(1): http://dx.doi.org/10.1038/s41598-020-64398-2.
[14] Han, Kai, Shi, Chengcheng, Li, Liangwei, Seim, Inge, Lee, Simon MingYuen, Xu, Xun, Yang, Huanming, Fan, Guangyi, Liu, Xin. Lineage-specific evolution of mangrove plastid genomes. PLANT GENOME[J]. 2020, 13(2): http://dx.doi.org/10.1002/tpg2.20019.
[15] Liu, Jin, Shi, Cong, Shi, ChengCheng, Li, Wei, Zhang, QunJie, Zhang, Yun, Li, Kui, Lu, HuiFang, Shi, Chao, Zhu, SiTao, Xiao, ZaiYun, Nan, Hong, Yue, Yao, Zhu, XunGe, Wu, Yu, Hong, XiaoNing, Fan, GuangYi, Tong, Yan, Zhang, Dan, Mao, ChangLi, Liu, YunLong, Hao, ShiJie, Liu, WeiQing, Lv, MeiQi, Zhang, HaiBin, Liu, Yuan, Hutang, GeRan, Wang, JinPeng, Wang, JiaHao, Sun, YingHuai, Ni, ShuBang, Chen, WenBin, Zhang, XingCai, Jiao, YuanNian, Eichler, Evan E, Li, GuoHua, Liu, Xin, Gao, LiZhi. The Chromosome-Based Rubber Tree Genome Provides New Insights into Spurge Genome Evolution and Rubber Biosynthesis. MOLECULAR PLANT[J]. 2020, 13(2): 336-350, http://lib.cqvip.com/Qikan/Article/Detail?id=7101522865.
[16] YunPeng Zhao, Guangyi Fan, PingPing Yin, Shuai Sun, Ning Li, Xiaoning Hong, Gang Hu, He Zhang, FuMin Zhang, JingDan Han, YaJun Hao, Qiwu Xu, Xianwei Yang, Wenjie Xia, Wenbin Chen, HanYang Lin, Rui Zhang, Jiang Chen, XiaoMing Zheng, Simon MingYuen Lee, Joongku Lee, Koichi Uehara, Jian Wang, Huanming Yang, ChengXin Fu, Xin Liu, Xun Xu, Song Ge, 张富民. Resequencing 545 ginkgo genomes across the world reveals the evolutionary history of the living fossil. NATURE COMMUNICATIONS[J]. 2019, 10(1): 1-10, http://dx.doi.org/10.1038/s41467-019-12133-5.
[17] Li, Chang, Tan, Xiaoxuan, Bai, Jie, Xu, Qiwu, Liu, Shanshan, Guo, Wenjie, Yu, Cong, Fan, Guangyi, Lu, Yishan, Zhang, He, Yang, Huanming, Chen, Jianwei, Liu, Xin. A survey of the sperm whale (Physeter catodon) commensal microbiome. PEERJ[J]. 2019, 7: https://doaj.org/article/f40c514608654306b7ca6fa991eb8b36.
[18] Sunil Kumar Sahu, Min Liu, Anna Yssel, Robert Kariba, Samuel Muthemba, Sanjie Jiang, Bo Song, Prasad S Hendre, Alice Muchugi, Ramni Jamnadass, ShuMin Kao, Jonathan Featherston, Nyree J C Zerega, Xun Xu, Huanming Yang, Allen Van Deynze, Yves Van de Peer, Xin Liu, Huan Liu. Draft Genomes of Two Artocarpus Plants, Jackfruit ( A. heterophyllus ) and Breadfruit ( A. altilis ). GENES[J]. 2019, 11(1): https://doaj.org/article/3cae4049f05a4cdb91e7606e425529f0.
[19] Mu, Weixue, Yang, Ting, Liu, Xin. The complete plastid genomes of four species from Brassicales. MITOCHONDRIAL DNA PART B-RESOURCES[J]. 2019, 4(1): 124-125, http://dx.doi.org/10.1080/23802359.2018.1536480.
[20] Liu Huan. The Genomes of Early-diverging streptophyte green algae shed light on the dawn of plant terrestrialization. Nature Plants. 2019, [21] Fan, Guangyi, Zhang, Yaolei, Liu, Xiaochuan, Wang, Jiahao, Sun, Zeguo, Sun, Shuai, Zhang, He, Chen, Jianwei, Lv, Meiqi, Han, Kai, Tan, Xiaoxuan, Hu, Jie, Guan, Rui, Fu, Yuanyuan, Liu, Shanshan, Chen, Xi, Xu, Qiwu, Qin, Yating, Liu, Longqi, Bai, Jie, Wang, Ou, Tang, Jingbo, Lu, Haorong, Shang, Zhouchun, Wang, Bo, Hu, Guohai, Zhao, Xia, Zou, Yan, Chen, Ao, Gong, Meihua, Zhang, Wenwei, Lee, Simon M Y, Li, Songhai, Liu, Junnian, Li, Zhen, Lu, Yishan, Sabir, Jamal S M, Sabir, Mumdooh J, Khan, Muhummadh, Hajrah, Nahid H, Yin, Ye, Kristiansen, Karsten, Yang, Huanming, Wang, Jian, Xu, Xun, Liu, Xin. The first chromosome-level genome for a marine mammal as a resource to study ecology and evolution. MOLECULAR ECOLOGY RESOURCES[J]. 2019, 19(4): 944-956, http://dx.doi.org/10.1111/1755-0998.13003.
[22] Varshney, Rajeev K, Thudi, Mahendar, Roorkiwal, Manish, He, Weiming, Upadhyaya, Hari D, Yang, Wei, Bajaj, Prasad, Cubry, Philippe, Rathore, Abhishek, Jian, Jianbo, Doddamani, Dadakhalandar, Khan, Aamir W, Garg, Vanika, Chitikineni, Annapurna, Xu, Dawen, Gaur, Pooran M, Singh, Narendra P, Chaturvedi, Sushil K, Nadigatla, Gangarao V P R, Krishnamurthy, Lakshmanan, Dixit, G P, Fikre, Asnake, Kimurto, Paul K, Sreeman, Sheshshayee M, Bharadwaj, Chellapilla, Tripathi, Shailesh, Wang, Jun, Lee, SukHa, Edwards, David, Polavarapu, Kavi Kishor Bilhan, Penmetsa, R Varma, Crossa, Jose, Nguyen, Henry T, Siddique, Kadambot H M, Colmer, Timothy D, Sutton, Tim, von Wettberg, Eric, Vigouroux, Yves, Xu, Xun, Liu, Xin. Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits. NATURE GENETICS[J]. 2019, 51(5): 857-+, http://dx.doi.org/10.1038/s41588-019-0401-3.
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科研活动
科研项目
（ 1 ） 对澳门红树林植物内生菌多样性及其代谢物的研究, 主持, 国家级, 2017-01--2019-12
（ 2 ） 中国万种植物生命之树-生态保护与生物多样性进化研究, 主持, 省级, 2015-09--2018-08
（ 2 ） 中国万种植物生命之树-生态保护与生物多样性进化研究, 主持, 省级, 2015-09--2018-08
参与会议
（1）Constructing reference genomes for bamboo species 世界竹藤大会2018 2018-06-26
（2）High quality plant and animal genome assemblies using the BGISEQ-500 Sequencing Platform 第26届动植物基因组大会 2018-01-15
（2）High quality plant and animal genome assemblies using the BGISEQ-500 Sequencing Platform 第26届动植物基因组大会 2018-01-15