1、基因组变异与精准医学

    遗传变异不仅是人类表型变化的基础，也是疾病易感性的基础。根据发生突变的碱基数目，遗传变异可分为单核苷酸多态性（SNP）和结构变异。SNP和串联重复序列曾被认为是人类遗传变异最主要的形式，但最新的研究表明基因组结构变异广泛存在于健康和病患人体中，影响着基因的表达和表型的变化，甚至引发疾病或增加复杂性状疾病的发病风险。近年来，以基因组测序为核心技术的精准医学研究成为大家关注的热点，基因突变信息的识别是精准医学的核心关键技术。然而，目前对海量基因组数据中遗传变异，尤其是结构变异的挖掘算法远未成熟。

    我们重点关注基因组结构变异挖掘中的关键性问题（如结构变异中断点的精准定位、重复序列区域附近的结构变异识别等），提出新的计算方法，建立较为完善的统计学模型及质量评估标准，以便快速、准确的从海量数据中挖掘出基因组结构变异。随着高通量测序技术的进步以及越来越多的个人基因组数据的出现，深度挖掘和分析其中的遗传变异，将对我们深入理解复杂性状疾病的分子机制、鉴定易感基因和认识遗传变异和疾病表型的关系具有重要意义。

2、环形非编码RNA组学

    近年来，环形RNA（circular RNAs）成为非编码RNA领域一个新的研究热点。与现有的线性非编码RNA分子不同，环形RNA是一类由线性RNA通过3’，5’-磷酸二酯键将两端相连而形成的RNA环状分子。然而由于计算方法及研究手段的限制，目前只发现少部分环形RNA并且绝大多数无法了解其功能。尤其是目前对更多环形RNA功能的探知和验证仍需要更多新颖的理论假说和大量的实验验证。但在此之前，能否从海量的RNA测序数据中高效识别环形RNA及其不同形式的转录本，成为后续功能验证及表达调控机制研究的重要前提。

    我们针对环形RNA研究中的关键计算生物学问题开展研究，建立新的环形剪接位点预测工具（CIRI）。借助于CIRI，我们发现来源于内含子和基因间区的环形RNA约占所有环形RNA的12-20%。我们还发现及实验证实了仅在环形RNA中表达的片段（ICFs，intronic/intergenic circRNA fragments），并对其特征进行了描述。这些ICF的存在，提示环形RNA不仅仅是线性转录产物的副产物，而是作为一种非编码RNA，与编码RNA有着不同的形成机制。我们结合断点识别和最大似然估计算法，实现对各可变剪接丰度的准确估计以及全长序列组装与重建，为后续研究环形RNA的形成及可变剪接机制提供了重要的方法学工具。

3、宏基因组技术与人体健康

    微生物广泛存在于各种生态环境中，与我们的生产、生活及自身健康密切相关。基于高通量测序的宏基因组学技术，已成为研究微生物群落组成、结构及功能最主要的技术手段。然而受高通量测序技术的限制，宏基因组研究中所利用的实验技术和计算方法遇到了很多困难。如何对缺乏参考序列的海量混合测序片段进行拼接和组装，这是所有宏基因组学研究面临的首要问题。此外，相对于研究基础较多的人体微生物组，新环境下宏基因组的研究更缺乏有效的实验和计算手段。

    我们针对宏基因组研究的关键问题，重点开发基于单细胞测序技术的宏基因组拼接、序列归类和注释等方面的算法和工具。利用功能基因组学和代谢组学技术，研究人体口腔和肠道微生物组，揭示不同病理条件下微生物群落结构的组成、代谢功能及其变化规律。整合基因组学、计算生物学和系统生物学的研究手段，了解人类健康、生物被膜形成机制以及宿主与致病菌的相互作用等科学问题。

欢迎具有计算机科学、统计学和生物信息学背景的考生报考！

071007-遗传学
071021-生物信息学
071022-基因组学

计算生物学
基因组学

2001-07--2006-06   中国科学院海洋研究所   博士
1997-09--2001-06   青岛海洋大学   学士

   

2010-09~现在, 中国科学院北京生命科学研究院, 研究员
2006-07~2010-09,美国宾州州立大学, 博士后

2020-11-01-今,Journal of Genetics and Genomics, 编委
2020-09-01-今,遗传, 副主编
2019-03-01-今,Medicine in Microecology, 副主编
2016-01-01-今,Hereditas, 编委
2015-01-01-今,Briefings in Bioinformatics, 编委
2014-06-30-今,Genomics, Proteomics & Bioinformatics, 副主编

生物信息学
实用生物信息学（1）:高通量测序数据分析技术
生态基因组学
生物统计及生物信息学
高通量测序数据分析技术
医学遗传学与基因组学
医学遗传学与人类基因组学
基因组学和生物信息学前沿系列讲座
基因组学前沿

   

（1） 中国科学院优秀博士学位论文, , 部委级, 2007
（2） 中国科学院院长特别奖, , 部委级, 2006

[1] 王金锋, 赵方庆. 检测口腔细菌的物质在诊断妊娠糖尿病中的应用. CN: CN112442531A, 2021-03-05.

   

[1] Li, Zhanzhan, Zhang, Bing, Wang, Ning, Zuo, Zhenqiang, Wei, Hong, Zhao, Fangqing. A novel peptide protects against diet-induced obesity by suppressing appetite and modulating the gut microbiota. GUT[J]. 2023, 72(4): 686-698, http://dx.doi.org/10.1136/gutjnl-2022-328035.
[2] He, Ruiqiao, Zhu, Junjie, Ji, Peifeng, Zhao, Fangqing. SEVtras delineates small extracellular vesicles at droplet resolution from single-cell transcriptomes. Nature Methods[J]. 2023, [3] Hou, Lingling, Zhang,Jinyang, Zhao, Fangqing. Full-length circular RNA profiling by nanopore sequencing and CIRI-long. Nature Protocols[J]. 2023, [4] Wengbing Chen, Yupeng Geng, Bing Zhang, Ying Yan, Fangqing Zhao, Miao Miao. Stop or not: genome-wide profiling of reassigned stop codons in ciliates. Molecular Biology and Evolution[J]. 2023, 40(4): msad064-, [5] Wu, Wanying, Zhao, Fangqing, Zhang, Jinyang. circAtlas 3.0: a gateway to 3 million curated vertebrate circular RNAs based on a standardized nomenclature scheme.. Nucleic Acids Research[J]. 2023, [6] Chen, LingLing, Bindereif, Albrecht, Bozzoni, Irene, Chang, Howard Y Y, Matera, A Gregory, Gorospe, Myriam, Hansen, Thomas B B, Kjems, Jorgen, Ma, XuKai, Pek, Jun Wei, Rajewsky, Nikolaus, Salzman, Julia, Wilusz, Jeremy E E, Yang, Li, Zhao, Fangqing. A guide to naming eukaryotic circular RNAs. NATURE CELL BIOLOGY. 2023, [7] Zuo, Zhenqiang, Zhao, Fangqing. Gut microbiota-targeted interventions: from conventional approaches to genetic engineering. SCIENCE BULLETIN[J]. 2023, 68(12): 1231-1234, http://dx.doi.org/10.1016/j.scib.2023.05.018.
[8] Yi Liu, Huimin Fan, Yonghui Shao, Jing Zhang, Zhenqiang Zuo, Jinfeng Wang, Fangqing Zhao, Libin Jiang. Gut microbiota dysbiosis associated with different types of demyelinating optic neuritis in patients. MULTIPLE SCLEROSIS AND RELATED DISORDERS. 2023, 72: http://dx.doi.org/10.1016/j.msard.2023.104619.
[9] Chen, Yamao, Zhou, Shengyu, Li, Ming, Zhao, Fangqing, Qi, Ji. STEEL enables high-resolution delineation of spatiotemporal transcriptomic data. BRIEFINGS IN BIOINFORMATICS[J]. 2023, 24(2): http://dx.doi.org/10.1093/bib/bbad068.
[10] Zhou, Tian, Xiao, Liwen, Zhao, Fangqing. MAMI: a comprehensive database of mother-infant microbiome and probiotic resources. Nucleic Acids Research[J]. 2023, [11] Guangping Huang, Wenyu Shi, Le Wang, Qingyue Qu, Zhenqiang Zuo, Jinfeng Wang, Fangqing Zhao, Fuwen Wei. PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation. MICROBIOME[J]. 2023, 11(1): 1-15, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10559513/.
[12] Xiao, Liwen, Zhao, Fangqing. Microbial transmission, colonization and succession: from pregnancy to infancy. GUT[J]. 2023, [13] Bo Tang, Li Tang, Wei He, Xingyu Jiang, Changjiang Hu, Yicheng Li, Yang Zhang, Kun Pang, Yuanyuan Lei, Shengpeng Li, Shuang Liu, Sumin Wang, Min Yang, Zhongjun Li, Fangqing Zhao, Shiming Yang. Correlation of gut microbiota and metabolic functions with the antibody response to the BBIBP-CorV vaccine. CELL REPORTS MEDICINE[J]. 2022, 3(10): http://dx.doi.org/10.1016/j.xcrm.2022.100752.
[14] Zhao, Yuanyuan, Zhang, Bing, Ma, Yiming, Zhao, Fuqiang, Chen, Jianan, Wang, Bingzhi, Jin, Hua, Zhou, Fulai, Guan, Jiawei, Zhao, Qian, Wang, Hongying, Liu, Qian, Zhao, Fangqing, Wang, Xia. Colorectal Cancer Patient-Derived 2D and 3D Models Efficiently Recapitulate Inter- and Intratumoral Heterogeneity. ADVANCED SCIENCE[J]. 2022, 9(22): http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000804684600001.
[15] Wu, Wanying, Zhang, Jinyang, Cao, Xiaofei, Cai, Zhengyi, Zhao, Fangqing. Exploring the cellular landscape of circular RNAs using full-length single-cell RNA sequencing. NATURE COMMUNICATIONS[J]. 2022, 13(1): https://doaj.org/article/179871cb334a40029f8356b265a1bf14.
[16] Zhang, Bing, Hou, Lina, Qi, Hongli, Hou, Lingling, Zhang, Tiancheng, Zhao, Fangqing, Miao, Miao. An Extremely Streamlined Macronuclear Genome in the Free-Living Protozoan Fabrea salina. MOLECULAR BIOLOGY AND EVOLUTION[J]. 2022, 39(4): http://dx.doi.org/10.1093/molbev/msac062.
[17] Xiao, Liwen, Zhang, Fengyi, Zhao, Fangqing. Large-scale microbiome data integration enables robust biomarker identification. Nature Computational Science[J]. 2022, [18] Li, Zhanzhan, Zhang, Bing, Wang, Ning, Zuo, Zhenqiang, Wei, Hong, Zhao, Fangqing. A novel peptide protects against diet-induced obesity by suppressing appetite and modulating the gut microbiota. GUT. 2022, [19] Chen, Shuai, Cao, Xiaofei, Zhang, Jinyang, Wu, Wanying, Zhang, Bing, Zhao, Fangqing. circVAMP3 Drives CAPRIN1 Phase Separation and Inhibits Hepatocellular Carcinoma by Suppressing c-Myc Translation. ADVANCED SCIENCE[J]. 2022, 9(8): http://dx.doi.org/10.1002/advs.202103817.
[20] Xiaobing Wang, Kun Pang, Jinfeng Wang, Bing Zhang, Zhenwei Liu, Saisai Lu, Xin Xu, Lingxiao Zhu, Zihao Zhou, Miaomiao Niu, Jianxia Gao, Jianmin Li, Fangqing Zhao, Jinyu Wu. Microbiota dysbiosis in primary Sjögren’s syndrome and the ameliorative effect of hydroxychloroquine. CELL REPORTS. 2022, 40(11): http://dx.doi.org/10.1016/j.celrep.2022.111352.
[21] Yang, Jing, Hou, Lingling, Wang, Jinfeng, Xiao, Liwen, Zhang, Jinyang, Yin, Nanlin, Yao, Su, Cheng, Kun, Zhang, Wen, Shi, Zhonghua, Wang, Jing, Jiang, Hai, Huang, Nana, You, Yanxia, Lin, Mingmei, Shang, Ruiyan, Wei, Yuan, Zhao, Yangyu, Zhao, Fangqing. Unfavourable intrauterine environment contributes to abnormal gut microbiome and metabolome in twins. GUT[J]. 2022, 71(12): 2451-2462, http://dx.doi.org/10.1136/gutjnl-2021-326482.
[22] He, Ruiqiao, Li, Pan, Wang, Jinfeng, Cui, Bota, Zhang, Faming, Zhao, Fangqing. The interplay of gut microbiota between donors and recipients determines the efficacy of fecal microbiota transplantation. GUT MICROBES[J]. 2022, 14(1): https://doaj.org/article/a7346cd527034fbb89c63796cd7c49ee.
[23] Chen, Shuai, Zhang,Jinyang, Zhao, Fangqing. Screening Linear and Circular RNA Transcripts from Stress Granules. Genomics, Proteomics & Bioinformatics[J]. 2022, [24] Yu, You, Zhang, Bing, Ji, Peifeng, Zuo, Zhenqiang, Huang, Yongxi, Wang, Ning, Liu, Chang, Liu, ShuangJiang, Zhao, Fangqing. Changes to gut amino acid transporters and microbiome associated with increased E/I ratio in Chd8(+/-) mouse model of ASD-like behavior. NATURE COMMUNICATIONS[J]. 2022, 13(1): http://dx.doi.org/10.1038/s41467-022-28746-2.
[25] Xiaoai Zhang, Qingzhi Zhai, Jinfeng Wang, Xiuling Ma, Bo Xing, Hang Fan, Zhiying Gao, Fangqing Zhao, Wei Liu. Variation of the Vaginal Microbiome During and after Pregnancy in Chinese Women. GENOMICS, PROTEOMICS & BIOINFORMATICS[J]. 2022, http://dx.doi.org/10.1016/j.gpb.2021.08.013.
[26] Yu, You, Zhao, Fangqing. Microbiota-gut-brain axis in autism spectrum disorder. JOURNAL OF GENETICS AND GENOMICSnull. 2021, 48(9): 755-762, http://dx.doi.org/10.1016/j.jgg.2021.07.001.
[27] Zhang, Jinyang, Zhao, Fangqing. Characterizing Circular RNAs Using Nanopore Sequencing. TRENDS IN BIOCHEMICAL SCIENCES. 2021, 46(9): 785-786, http://dx.doi.org/10.1016/j.tibs.2021.06.002.
[28] Zhang, Jinyang, Hou, Lingling, Zuo, Zhenqiang, Ji, Peifeng, Zhang, Xiaorong, Xue, Yuanchao, Zhao, Fangqing. Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long. NATURE BIOTECHNOLOGY[J]. 2021, 39(7): 836-845, http://dx.doi.org/10.1038/s41587-021-00842-6.
[29] Wang, Jinfeng, Li, Zhanzhan, Ma, Xiuling, Du, Lifeng, Jia, Zhen, Cui, Xue, Yu, Liqun, Yang, Jing, Xiao, Liwen, Zhang, Bing, Fan, Huimin, Zhao, Fangqing. Translocation of vaginal microbiota is involved in impairment and protection of uterine health. NATURE COMMUNICATIONS[J]. 2021, 12(1): http://dx.doi.org/10.1038/s41467-021-24516-8.
[30] Zhang, Jinyang, Zhao, Fangqing. Reconstruction of circular RNAs using Illumina and Nanopore RNA-seq datasets. METHODS[J]. 2021, 196: 17-22, http://dx.doi.org/10.1016/j.ymeth.2021.03.017.
[31] Meng, Yao, Xiao, Liwen, Chen, Wenbing, Zhao, Fangqing, Zhao, Xiang. An efficient metatranscriptomic approach for capturing RNA virome and its application to SARS-CoV-2. JOURNAL OF GENETICS AND GENOMICSnull. 2021, 48(9): 860-862, http://dx.doi.org/10.1016/j.jgg.2021.08.005.
[32] Xiao, Liwen, Wang, Jinfeng, Zheng, Jiayong, Li, Xiaoqing, Zhao, Fangqing. Deterministic transition of enterotypes shapes the infant gut microbiome at an early age. GENOME BIOLOGY[J]. 2021, 22(1): http://dx.doi.org/10.1186/s13059-021-02463-3.
[33] Zheng, Yi, Zhao, Fangqing. Visualization of circular RNAs and their internal splicing events from transcriptomic data. BIOINFORMATICS[J]. 2020, 36(9): 2934-2935, https://www.webofscience.com/wos/woscc/full-record/WOS:000537450900046.
[34] 赵方庆. CircAltas: an integrated resource of one million highly confident circular RNAs from 1070 vertebrate transcriptomes.. Genome Biology. 2020, [35] Wu, Wanying, Ji, Peifeng, Zhao, Fangqing. CircAtlas: an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes. GENOME BIOLOGY[J]. 2020, 21(1): http://dx.doi.org/10.1186/s13059-020-02018-y.
[36] Jia, Na, Wang, Jinfeng, Shi, Wenqiang, Du, Lifeng, Sun, Yi, Zhan, Wei, Jiang, JiaFu, Wang, Qian, Zhang, Bing, Ji, Peifeng, BellSakyi, Lesley, Cui, XiaoMing, Yuan, TingTing, Jiang, BaoGui, Yang, WeiFei, Lam, Tommy TsanYuk, Chang, QiaoCheng, Ding, ShuJun, Wang, XianJun, Zhu, JinGuo, Ruan, XiangDong, Zhao, Lin, Wei, JiaTe, Ye, RunZe, Que, Teng Cheng, Du, ChunHong, Zhou, YuHao, Cheng, Jing Xia, Dai, PeiFang, Guo, WenBin, Han, XiaoHu, Huang, EnJiong, Li, LianFeng, Wei, Wei, Gao, YuChi, Liu, JingZe, Shao, HongZe, Wang, Xin, Wang, ChongCai, Yang, TianCi, Huo, QiuBo, Li, Wei, Chen, HaiYing, Chen, ShenEn, Zhou, LingGuo, Ni, XueBing, Tian, JunHua, Sheng, Yue, Liu, Tao, Pan, YuSheng, Xia, LuoYuan, Li, Jie, Zhao, Fangqing, Cao, WuChun, Tick Genome Microbiome Consortium. Large-Scale Comparative Analyses of Tick Genomes Elucidate Their Genetic Diversity and Vector Capacities. CELL[J]. 2020, 182(5): 1328-+, http://dx.doi.org/10.1016/j.cell.2020.07.023.
[37] Zhang, Jinyang, Chen, Shuai, Yang, Jingwen, Zhao, Fangqing. Accurate quantification of circular RNAs identifies extensive circular isoform switching events. NATURE COMMUNICATIONS[J]. 2020, 11(1): http://dx.doi.org/10.1038/s41467-019-13840-9.
[38] Wang, Jinfeng, Jia, Zhen, Zhang, Bing, Peng, Lei, Zhao, Fangqing. Tracing the accumulation of in vivo human oral microbiota elucidates microbial community dynamics at the gateway to the GI tract. GUTnull. 2020, 69(7): 1355-1356, https://www.webofscience.com/wos/woscc/full-record/WOS:000569655200025.
[39] Zheng, Yi, Ji, Peifeng, Chen, Shuai, Hou, Lingling, Zhao, Fangqing. Reconstruction of full-length circular RNAs enables isoform-level quantification. GENOME MEDICINE[J]. 2019, 11(1): https://doaj.org/article/19379e7aaebd4476b9d9ba07aa48ca28.
[40] Ji, Peifeng, Wu, Wanying, Chen, Shuai, Zheng, Yi, Zhou, Lin, Zhang, Jinyang, Cheng, Hao, Yan, Jin, Zhang, Shaogeng, Yang, Penghui, Zhao, Fangqing. Expanded Expression Landscape and Prioritization of Circular RNAs in Mammals. CELL REPORTS[J]. 2019, 26(12): 3444-+, http://dx.doi.org/10.1016/j.celrep.2019.02.078.
[41] 赵方庆. Tracing the accumulation of in vivo human oral microbiota elucidates microbial community dynamics at the gateway to the gastrointestinal tract. Gut. 2019, [42] He, Ming, Wang, Jinfeng, Fan, Xinpeng, Liu, Xiaohui, Shi, Wenyu, Huang, Ning, Zhao, Fangqing, Miao, Miao. Genetic basis for the establishment of endosymbiosis in Paramecium. ISME JOURNAL[J]. 2019, 13(5): 1360-1369, [43] Cao, Yuanwei, Sun, Wen, Wang, Jinfeng, Sheng, Gang, Xiang, Guanghai, Zhang, Tongtong, Shi, Wenyu, Li, Chun, Wang, Yanli, Zhao, Fangqing, Wang, Haoyi. Argonaute proteins from human gastrointestinal bacteria catalyze DNA-guided cleavage of single- and double-stranded DNA at 37 degrees C. CELL DISCOVERYnull. 2019, 5: http://dx.doi.org/10.1038/s41421-019-0105-y.
[44] Xu, Yuan, Zhao, Fangqing. Single-cell metagenomics: challenges and applications. PROTEIN & CELL[J]. 2018, 9(5): 501-510, http://lib.cqvip.com/Qikan/Article/Detail?id=675367376.
[45] Yuan Xu, Fangqing Zhao. Single-cell metagenomics: challenges and applications. 蛋白质与细胞：英文版[J]. 2018, 9(5): 501-510, http://lib.cqvip.com/Qikan/Article/Detail?id=675367376.
[46] Gao, Yuan, Zhao, Fangqing. Computational Strategies for Exploring Circular RNAs. TRENDS IN GENETICSnull. 2018, 34(5): 389-400, http://dx.doi.org/10.1016/j.tig.2017.12.016.
[47] Gao, Yuan, Zhang, Jinyang, Zhao, Fangqing. Circular RNA identification based on multiple seed matching. BRIEFINGS IN BIOINFORMATICS[J]. 2018, 19(5): 803-810, http://dx.doi.org/10.1093/bib/bbx014.
[48] Zhou, Lin, Zhao, Fangqing. Prioritization and functional assessment of noncoding variants associated with complex diseases. GENOME MEDICINE[J]. 2018, 10(1): http://dx.doi.org/10.1186/s13073-018-0565-y.
[49] Fangqing Zhao. Mining the hidden treasures from canid genomes. NATIONAL SCIENCE REVIEW. 2018, 6(1): 124-124, [50] Wang, Jinfeng, Zheng, Jiayong, Shi, Wenyu, Du, Nan, Xu, Xiaomin, Zhang, Yanming, Ji, Peifeng, Zhang, Fengyi, Jia, Zhen, Wang, Yeping, Zheng, Zhi, Zhang, Hongping, Zhao, Fangqing. Dysbiosis of maternal and neonatal microbiota associated with gestational diabetes mellitus. GUT[J]. 2018, 67(9): 1614-1625, [51] Peifeng Ji, Yanming Zhang, Jinfeng Wang, Fangqing Zhao. MetaSort untangles metagenome assembly by reducing microbial community complexity. NATURE COMMUNICATIONS[J]. 2017, 8(1): https://doaj.org/article/848e7faf7be0413696f7c8d9de4c4b4c.
[52] Teng, Huajing, Zhang, Yaohua, Shi, Chengmin, Mao, Fengbiao, Cai, Wanshi, Lu, Liang, Zhao, Fangqing, Sun, Zhongsheng, Zhang, Jianxu. Population Genomics Reveals Speciation and Introgression between Brown Norway Rats and Their Sibling Species. MOLECULAR BIOLOGY AND EVOLUTION[J]. 2017, 34(9): 2214-2228, https://www.webofscience.com/wos/woscc/full-record/WOS:000408307400008.
[53] 赵方庆. The combination of direct and paired link graphs boosts repetitive genome assembly. Nucleic Acids Research. 2017, [54] Zhang, Yanming, Ji, Peifeng, Wang, Jinfeng, Zhao, Fangqing. RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes. NUCLEIC ACIDS RESEARCH[J]. 2016, 44(10): e99-e99, https://www.webofscience.com/wos/woscc/full-record/WOS:000379754600009.
[55] Nie, Yong, Zhao, JieYu, Tang, YueQin, Guo, Peng, Yang, Yunfeng, Wu, XiaoLei, Zhao, Fangqing. Species Divergence vs. Functional Convergence Characterizes Crude Oil Microbial Community Assembly. FRONTIERS IN MICROBIOLOGY[J]. 2016, 7: https://doaj.org/article/178f9aa151334ca7ade735cb58a14269.
[56] Peng, Gongxin, Ji, Peifeng, Zhao, Fangqing. A novel codon-based de Bruijn graph algorithm for gene construction from unassembled transcriptomes. GENOME BIOLOGY[J]. 2016, 17: http://dx.doi.org/10.1186/s13059-016-1094-x.
[57] Zhang, Zhigang, Xu, Dongming, Wang, Li, Hao, Junjun, Wang, Jinfeng, Zhou, Xin, Wang, Weiwei, Qiu, Qiang, Huang, Xiaodan, Zhou, Jianwei, Long, Ruijun, Zhao, Fangqing, Shi, Peng. Convergent Evolution of Rumen Microbiomes in High-Altitude Mammals. CURRENT BIOLOGY[J]. 2016, 26(14): 1873-1879, http://dx.doi.org/10.1016/j.cub.2016.05.012.
[58] Wang, Jinfeng, Gao, Yuan, Zhao, Fangqing. Phage-bacteria interaction network in human oral microbiome. ENVIRONMENTAL MICROBIOLOGY[J]. 2016, 18(7): 2143-2158, http://dx.doi.org/10.1111/1462-2920.12923.
[59] Gao, Yuan, Wang, Jinfeng, Zheng, Yi, Zhang, Jinyang, Chen, Shuai, Zhao, Fangqing. Comprehensive identification of internal structure and alternative splicing events in circular RNAs. NATURE COMMUNICATIONS[J]. 2016, 7(1): https://doaj.org/article/93096215f89a432a93d7cb77e31c1101.
[60] Gao, Yuan, Wang, Jinfeng, Zhao, Fangqing. CIRI: an efficient and unbiased algorithm for de novo circular RNA identification. GENOME BIOLOGY[J]. 2015, 16(1): http://www.corc.org.cn/handle/1471x/2374326.
[61] Chen, Xiao, Zhao, Xiaolu, Liu, Xiaohui, Warren, Alan, Zhao, Fangqing, Miao, Miao. Phylogenomics of non-model ciliates based on transcriptomic analyses. PROTEIN & CELL[J]. 2015, 6(5): 373-385, http://lib.cqvip.com/Qikan/Article/Detail?id=664784215.
[62] Zhao, Hui, Zhao, Fangqing. BreakSeek: a breakpoint-based algorithm for full spectral range INDEL detection. NUCLEIC ACIDS RESEARCH[J]. 2015, 43(14): 6701-6713, http://dx.doi.org/10.1093/nar/gkv605.
[63] Ye, Naihao, Zhang, Xiaowen, Miao, Miao, Fan, Xiao, Zheng, Yi, Xu, Dong, Wang, Jinfeng, Zhou, Lin, Wang, Dongsheng, Gao, Yuan, Wang, Yitao, Shi, Wenyu, Ji, Peifeng, Li, Demao, Guan, Zheng, Shao, Changwei, Zhuang, Zhimeng, Gao, Zhengquan, Qi, Ji, Zhao, Fangqing. Saccharina genomes provide novel insight into kelp biology. NATURE COMMUNICATIONS[J]. 2015, 6: http://dx.doi.org/10.1038/ncomms7986.
[64] Liu, Jiemeng, Wang, Haifeng, Yang, Hongxing, Zhang, Yizhe, Wang, Jinfeng, Zhao, Fangqing, Qi, Ji. Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms. NUCLEIC ACIDS RESEARCH[J]. 2013, 41(1): https://www.webofscience.com/wos/woscc/full-record/WOS:000312889900003.
[65] Guan, Xiangyu, Wang, Jinfeng, Zhao, Hui, Wang, Jianjun, Luo, Ximing, Liu, Fei, Zhao, Fangqing. Soil bacterial communities shaped by geochemical factors and land use in a less-explored area, Tibetan Plateau. BMC GENOMICS[J]. 2013, 14: http://dx.doi.org/10.1186/1471-2164-14-820.
[66] Wang, Jinfeng, Qi, Ji, Zhao, Hui, He, Shu, Zhang, Yifei, Wei, Shicheng, Zhao, Fangqing. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. SCIENTIFIC REPORTS[J]. 2013, 3: https://www.webofscience.com/wos/woscc/full-record/WOS:000318893700001.
[67] Shen, Xin, Tian, Mei, Meng, Xueping, Liu, Huilian, Cheng, Hanliang, Zhu, Changbao, Zhao, Fangqing. Complete mitochondrial genome of Membranipora grandicella (Bryozoa: Cheilostomatida) determined with next-generation sequencing: The first representative of the suborder Malacostegina. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS[J]. 2012, 7(3): 248-253, http://dx.doi.org/10.1016/j.cbd.2012.03.003.
[68] Zhou, Linglin, Li, Xueying, Liu, Qi, Zhao, Fangqing, Wu, Jinyu. Small RNA transcriptome investigation based on next-generation sequencing technology. JOURNAL OF GENETICS AND GENOMICSnull. 2011, 38(11): 505-513, http://sciencechina.cn/gw.jsp?action=detail.jsp&internal_id=4391431&detailType=1.
[69] 赵方庆. A new scheme to identify and visualize structural variations from paired-end mapping data. Nucleic Acids Res. 2011, [70] Zhu, Erle, Zhao, Fangqing, Xu, Gang, Hou, Huabin, Zhou, LingLin, Li, Xiaokun, Wu, Jinyu, 孙中生, Xiaokun Li, Jinyu Wu. mirTools: microRNA profiling and discovery based on high-throughput sequencing. NUCLEIC ACIDS RESEARCH[J]. 2010, 38(1): W392-W397, http://dx.doi.org/10.1093/nar/gkq393.
[71] Hou HB, Zhao FQ, Zhou LL, Zhu EL, Teng HJ, Li XK, Bao QY, Wu JY, 孙中生, Jinyu Wu. MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation. NUCLEIC ACIDS RESEARCH[J]. 2010, 38(5): W732-W736, http://dx.doi.org/10.1093/nar/gkq302.
[72] Zhao, Fangqing, Hou, Huabin, Bao, Qiyu, Wu, Jinyu. PGA4genomics for comparative genome assembly based on genetic algorithm optimization. GENOMICS[J]. 2009, 94(4): 284-286, http://dx.doi.org/10.1016/j.ygeno.2009.06.006.
[73] Zhao, Fangqing, Qi, Ji, Schuster, Stephan C. Tracking the past: Interspersed repeats in an extinct Afrotherian mammal, Mammuthus primigenius. GENOME RESEARCH[J]. 2009, 19(8): 1384-1392, http://dx.doi.org/10.1101/gr.091363.109.
[74] Chi, Xiaoyuan, Yang, Qingli, Zhao, Fangqing, Qin, Song, Yang, Yu, Shen, Junjun, Lin, Hanzhi. Comparative Analysis of Fatty Acid Desaturases in Cyanobacterial Genomes. COMPARATIVE AND FUNCTIONAL GENOMICS[J]. 2008, http://ir.qdio.ac.cn/handle/337002/1586.
[75] 赵方庆. A novel pheromone trail-based genetic algorithm for comparative genome assembly. Nucleic Acids Res. 2008, [76] Liang ChengWei, Zhao FangQing, Qin Song, Tan CongPing, Wei Wei, Meng ChunXiao. Molecular cloning and characterization of phytoene synthase gene from a unicellular green alga Haematococcus pluvialis. PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS[J]. 2006, 33(9): 854-860, http://www.corc.org.cn/handle/1471x/2378913.
[77] Liang ChengWei, Zhao FangQing, Qin Song, Tan CongPing, Wei Wei, Meng ChunXiao. Molecular cloning and characterization of phytoene synthase gene from a unicellular green alga Haematococcus pluvialis. PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS[J]. 2006, 33(9): 854-860, http://www.corc.org.cn/handle/1471x/2378913.
[78] Bo Tang, Li Tang, Wei He, Xingyu Jiang, Changjiang Hu, Yicheng Li, Yang Zhang, Kun Pang, Yuanyuan Lei, Shengpeng Li, Shuang Liu, Sumin Wang, Min Yang, Zhongjun Li, Fangqing Zhao, Shiming Yang. Correlation of gut microbiota and metabolic functions with the antibody response to the BBIBP-CorV vaccine. CELL REPORTS MEDICINE. http://dx.doi.org/10.1016/j.xcrm.2022.100752.

   

（ 1 ） 计算基因组学交叉合作研究团队, 主持, 部委级, 2013-01--2015-12
（ 2 ） 遗传变异与选择对基因组编码区与非编码区作用模式的比较, 主持, 国家级, 2016-01--2018-12
（ 3 ） 高通量技术与大数据分析在生物安全中的应用研究, 主持, 国家级, 2016-07--2018-12
（ 4 ） 非模式生物基因组遗传变异的识别算法和进化基因组计算平台的建立, 主持, 国家级, 2012-01--2014-12
（ 5 ） 环形非编码RNA组学的关键计算方法研究, 主持, 国家级, 2017-01--2019-12
（ 6 ） 基于配对及家系测序数据的基因组结构变异的识别, 主持, 国家级, 2017-01--2020-12
（ 7 ） 生物信息学, 主持, 国家级, 2018-01--2020-12
（ 8 ） 北京市自然科学杰出青年基金项目, 主持, 省级, 2018-11--2021-12
（ 9 ） 生物信息学, 主持, 国家级, 2021-01--2025-12
（ 10 ） **（涉密）, 主持, 国家级, 2019-12--2022-12
（ 11 ） RNA动态结构及多维相互作用研究, 主持, 国家级, 2020-01--2022-12
（ 12 ） 精准医学大数据的有效挖掘与关键信息技术研发, 主持, 国家级, 2018-06--2020-12
（ 13 ） 单细胞转录组数据中环形RNA精准解析技术, 主持, 国家级, 2022-01--2026-12

已指导学生

周慧玥  硕士研究生  071007-遗传学  

郑毅  硕士研究生  071007-遗传学  

冀培丰  博士研究生  071007-遗传学  

赵辉  硕士研究生  071007-遗传学  

彭公信  博士研究生  071007-遗传学  

高远  博士研究生  071007-遗传学  

史文聿  博士研究生  071007-遗传学  

周琳  博士研究生  071007-遗传学  

吴婉莹  硕士研究生  071007-遗传学  

贾震  博士研究生  071007-遗传学  

马秀伶  硕士研究生  071007-遗传学  

郑毅  博士研究生  071007-遗传学  

现指导学生

陈帅  博士研究生  071007-遗传学  

肖百川  硕士研究生  071007-遗传学  

张金阳  博士研究生  071007-遗传学  

何睿乔  硕士研究生  071007-遗传学  

李占占  博士研究生  071007-遗传学  

张丰驿  硕士研究生  085238-生物工程  

王宁  硕士研究生  071007-遗传学  

吴婉莹  博士研究生  071007-遗传学  

张冰  博士研究生  071007-遗传学  

肖力文  博士研究生  071007-遗传学