科研项目 (Grant)

  1. 陕西省杰出青年科学基金，基因组信息学，2024JC-JCQN-28，2024.1-2026.12， 50万，主持 （在研）

  2. 国家重点研发计划“前沿生物技术专项”，关键模式生物基因组精细研究及其示范应用，2022YFC3400300，2022.11 - 2027.10，2070万元 个人负责283万元，（在研）

  3. 国家自然科学基金面上项目：基于图模型的跨物种泛基因组构建及模式挖掘算法研究 No. 62172325, 2022.1~2025.12   61万元   主持 （在研）

  4. 国家自然科学基金青年项目：基于网络模型的癌症异常DNA甲基化模块挖掘算法研究 No.61702406  2018.1~2020.12   28万元   主持 （已结题）
  5. 国家科技重大专项，乙肝相关肝癌早期免疫诊断关键技术研发和应用， No. 2018ZX10302205, 1400万 (子课题35万)， 2018.10~2021.12, 骨干 （已结题）
  6. 中国博士后科学基金面上项目：肺癌异常DNA甲基化网络模式挖掘算法研究，2017M623178，5万元   主持 （已结题）
  7. 陕西省博士后项目资助：基于网络的冠心病异常DNA甲基化模块挖掘算法研究，8万元，主持 （已结题）

  8. 国家自然科学基金重点项目: 基于网络模型的癌症相关模式挖掘理论与方法 No.61532014   2016.1~2020.12        主要参与人

  9. 国家自然科学基金重大研究计划-延续项目:基于非编码RNA调控网络的复杂疾病致病模式发现研究 No.91530113  2016.1~2016.12 主要参与人

  10. 国家自然科学基金重大研究计划项目: 复杂疾病恶化过程相关模式发现理论与方法研究  No.91130006   2012.1~2014.12  主要参与人

  11. 国家自然科学基金青年项目: 长非编码RNA功能预测网络模型与算法研究    No.61303118  2014.01~ 2016.12          主要参与人

  12. 中央高校基本科研业务费: 生物大数据相关模式挖掘理论与关键技术及应用 No. BDZ021404  2014.1~2016.12         主要参与人

研究论文 (Publications)

  1. Yang Gao#, Xiaofei Yang#, Hao Chen#, Xinjiang Tan#, Zhaoqing Yang#, Lian Deng#, ..., Yan Lu*, Jiayou Chu*, Kai Ye*, Shuhua Xu*. A pangenome reference of 36 Chinese populations. Nature, 619 (7968), 112–121 (2023). https://doi.org/10.1038/s41586-023-06173-7 （并列一作）
  2. Li Guo#, Thilo Winzer#, Xiaofei Yang#, Yi Li#, Zemin Ning#, Zhesi He, Roxana Teodor, Ying Lu, Tim A. Bowser, Ian A. Graham*, Kai Ye*, The opium poppy genome and morphinan production, Science, 2018, 362(6412): 343-347. 10.1126/science.aat4096 (并列一作)
  3. Xiaofei Yang#, Shenghan Gao#, Li Guo#, Bo Wang, Yanyan Jia, Jian Zhou, Yizhuo Che, Peng Jia, Jiadong Lin, Tun Xu, Jianyong Sun, Kai Ye*. Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway. Nature Communications, 2021, 12, 6030 (2021). https://doi.org/10.1038/s41467-021-26330-8. (IF= 17.69, WOS引用：；Google引用 22)
  4. Xiaofei Yang, Gaoyang Zheng, Peng Jia, Songbo Wang, Kai Ye, Pindel-TD: a tandem duplication detector based on a pattern growth approach, Genomics, Proteomics & Bioinformatics, 2024;, qzae008, https://doi.org/10.1093/gpbjnl/qzae008
  5. Xiaofei Yang, Xixi Zhao, Shoufang Qu, Peng Jia, Bo Wang, Shenghan Gao, Tun Xu, Wenxin Zhang, Jie Huang*, Kai Ye*, Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing, Fundamental Research, 2022, 2(6): 946-953, https://doi.org/10.1016/j.fmre.2022.02.005. 
  6. Bo Wang, Ningxin Dang, Xiaofei Yang*, Shuhua Xu*, Kai Ye*, The human pangenome reference: the beginning of a new era for genomics, Science Bulletin, 2023, 68(14):1484-1487. https://doi.org/10.1016/j.scib.2023.06.014. (共同通讯)
  7. Shenghan Gao*, Xiaofei Yang*#, Hongtao Guo, Xixi Zhao, Bo Wang, Kai Ye#, HiCAT: a tool for automatic annotation of centromere structure. Genome Biology 24, 58 (2023). https://doi.org/10.1186/s13059-023-02900-5 (共同通讯)
  8. Shenghan Gao*, Xiaofei Yang*#, Jianyong Sun, Xixi Zhao, Bo Wang, Kai Ye#, IAGS: Inferring Ancestor Genome Structure under a wide range of evolutionary scenarios, Molecular Biology and Evolution, 2022, 39(3): msac041., https://doi.org/10.1093/molbev/msac041 (共同通讯)
  9. Bo Wang, Xiaofei Yang*, Yanyan Jia, Yu Xu, Peng Jia, Ningxin Dang, Songbo Wang, Tun Xu, Xixi Zhao, Shenghan Gao, Quanbin Dong, Kai Ye*. High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads. Genomics, Proteomics & Bioinformatics 20 (2022) 4–13, https://doi.org/10.1016/j.gpb.2021.08.003. (共同通讯，高被引，封面)
  10. Tun Xu, Xiaofei Yang*, Yanyan Jia, Zihang Li, Guangbo Tang, Xiujuan Li, Bo Wang, Tingjie Wang, Jiadong Lin, Li Guo, Kai Ye*, A global survey of the transcriptome of the opium poppy (Papaver somniferum) based on single-molecule long-read isoform sequencing. The Plant Journal, 2022, 110(2):607-620, https://doi.org/10.1111/tpj.15689. (共同通讯)
  11. Tingjie Wang, Ningxin Dang, Guangbo Tang, Zihang Li, Xiujuan Li, Bingyin Shi, Zhong Xu, Lei Li, Xiaofei Yang*, Chuanrui Xu*, Kai Ye*, Integrating bulk and single-cell RNA sequencing reveals cellular heterogeneity and immune infiltration in hepatocellular carcinoma. Molecular Oncology, 2022, 16(11):2195-2213, https://doi.org/10.1002/1878-0261.13190 (共同通讯)
  12. Jiadong Lin#; Xiaofei Yang#; Walter Kosters; Tun Xu; Yanyan Jia; Songbo Wang; Qihui Zhu; Mallory Ryan; Li Guo; Chengsheng Zhang; The Human Genome Structural Variation Consortium; Charles Lee; Scott E. Devine; Evan E. Eichler; Kai Ye*; Mako: a graph-based pattern growth approach to detect complex structural variants, Genomics Proteomics & Bioinformatics, 2022, 20(1):205-218, https://doi.org/10.1016/j.gpb.2021.03.007. (并列一作)
  13. Xiaofei Yang#, Shenghan Gao#, Tun Xu#, Bo Wang, Yanyan Jia, Kai Ye*. Reply to “Subgenome-aware analyses suggest a reticulate allopolyploidization origin in three Papaver genomes”. Nature Communications, 2023, 14(1):2203. https://doi.org/10.1038/s41467-023-37940-9. 
  14. Xiaofei Yang#; Shenghan Gao#; Tingjie Wang#; Boyu Yang; Ningxin Dang; Kai Ye*. gCAnno: a graph-based single cell type annotation method. BMC Genomics, 2020, 21(1):823. https://doi.org/10.1186/s12864-020-07223-4. 
  15. Xiaofei Yang, Tun Xu, Peng Jia, Han Xia, Li Guo, Lei Zhang, Kai Ye, Transportation, germs, culture: a dynamic graph model of COVID-19 outbreak, Quantitative Biology, 2020, 8(3): 238–244, https://doi.org/10.1007/s40484-020-0215-4.
  16. Xiaofei Yang, Wan-Ping Lee, Kai Ye, Charles Lee. One reference genome is not enough [J]. Genome Biology, 2019, 20(1): 104. https://doi.org/10.1186/s13059-019-1717-0. 
  17. Xiaofei Yang, Lin Gao†, Shihua Zhang†. Comparative pan-cancer DNA methylation analysis reveals cancer common and specific patterns, Briefings in Bioinformatics, 2017, 18(5):761-773. doi: 10.1093/bib/bbw063. 
  18. Xiaofei Yang, Xiaojian Shao, Lin Gao†, Shihua Zhang†. Systematic DNA methylation analysis of multiple cell lines reveals common and specific patterns within and across tissues of origin[J]. Human Molecular Genetics, 2015, 24(15): 4374-4384. https://doi.org/10.1093/hmg/ddv172. 
  19. Xiaofei Yang, Lin Gao†, Xingli Guo, Xinhua Shi, Hao Wu, Fei Song, Bingbo Wang. A network based method for analysis of lncRNA-disease associations and prediction of lncRNAs implicated in diseases[J]. PLoS One, 2014, 9(1): e87797. doi: 10.1371/journal.pone.0087797
  20. Xiaofei Yang, Xiaojian Shao, Lin Gao, et al. Comparative DNA methylation analysis to decipher common and cell type-specific patterns among multiple cell types[J]. Briefings in Functional Genomics, 2016, 15(6):399-407. doi: 10.1093/bfgp/elw013. 
  21. Bo Wang, Yanyan Jia, Ningxin Dang, Jie Yu, Stephen J. Bush, Shenghan Gao, Wenxi He, Sirui Wang, Hongtao Guo, Xiaofei Yang, Weimin Ma & Kai Ye, Near telomere-to-telomere genome assemblies of two Chlorella species unveil the composition and evolution of centromeres in green algae. BMC Genomics 25, 356 (2024). https://doi.org/10.1186/s12864-024-10280-8
  22. Jiadong Lin#, Songbo Wang#, Peter A. Audano, Deyu Meng, Jacob I. Flores, Walter Kosters, Xiaofei Yang, Peng Jia, Tobias Marschall, Christine R. Beck, Kai Ye*, SVision: a deep learning approach to resolve complex structural variants. Nature Methods, 2022, https://doi.org/10.1038/s41592-022-01609-w. (IF = 47.99，WOS引用：1；Google引用3)
  23. Peng Jia*, Lianhua Dong*, Xiaofei Yang, Bo Wang, Stephen J. Bush, Tingjie Wang, Jiadong Lin, Songbo Wang, Xixi Zhao, Tun Xu, Yizhuo Che, Ningxin Dang, Luyao Ren, Yujing Zhang, Xia Wang, Fan Liang, Yang Wang, Jue Ruan, Han Xia, Yuanting Zheng, Leming Shi, Yi Lv#, Jing Wang# & Kai Ye#. Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet. Genome Biol 24, 277 (2023). https://doi.org/10.1186/s13059-023-03116-3
  24. Peng Jia, Xuanhao Yang, Xiaofei Yang, Tingjie Wang, Yu Xu, Kai Ye, MSIsensor-RNA: Microsatellite Instability Detection for Bulk and Single-cell Gene Expression Data, Genomics, Proteomics & Bioinformatics, 2024;, qzae004, https://doi.org/10.1093/gpbjnl/qzae004
  25. Yizhuo Che, Xiaofei Yang, Peng Jia, Tingjie Wang, Dan Xu, Tianxue Guo, Kai Ye*, D2 Plot, a Matrix of DNA Density and Distance to Periphery, Reveals Functional Genome Regions. Advanced Science, 2022, doi.org/10.1002/advs.202202149. (IF = 17.52，WOS引用：0；Google引用0)
  26. Tingjie Wang#, Chuanrui Xu#, Zhijing Zhang, Hua Wu, Xiujuan Li, Yu Zhang, Nan Deng, Ningxin Dang, Guangbo Tang, Xiaofei Yang, Bingyin Shi, Zihang Li, Lei Li*, Kai Ye*. Cellular heterogeneity and transcriptomic profiles during intrahepatic cholangiocarcinoma initiation and progression, Hepatology, 2022, doi:10.1002/hep.32483 (封面，IF = 17.30，WOS引用：2；Google引用3)
  27. Ye Li, Tao Li, Lili Zhao, Yiheng Zhang, Xiaoya Wang, Yulun Wu, Ziwei Lu, Jialiang Lu, Meijuan Dang, Heying Wang, Yating Jian, Xiaoyun Lu, Xiaofei Yang, Songhua Fan, Lei Zhang, Yu Jiang, Guogang Luo, Guilian Zhang. Platelet distribution width: A significant predictor of poor outcome after mechanical thrombectomy[J]. Journal of Stroke and Cerebrovascular Diseases, 2022, 31(3): 106273. (IF = 2.68，WOS引用：0；Google引用0)
  28. Yiheng Zhang, Dayu Zhu, Tao Li, Xiaoya Wang, Lili Zhao, Xiaofei Yang, Meijuan Dang, Ye Li, Yulun Wu, Ziwei Lu, Jialiang Lu, Yating Jian, Heying Wang, Lei Zhang, Xiaoyun Lu, Ziyu Shen, Hong Fan, Wenshan Cai, Guilian Zhang. Detection of acute ischemic stroke and backtracking stroke onset time via machine learning analysis of metabolomics[J]. Biomedicine & Pharmacotherapy, 2022, 155: 113641. (IF = 7.42，WOS引用：0；Google引用1)
  29. Tingjie Wang, Chuanrui Xu, Dan Xu, Xiaofei Yang, Yaxin Liu, Xiujuan Li, Zihang Li, Ningxin Dang, Yi Lv, Zhijing Zhang, Lei Li, Kai Ye. Integrating cell interaction with transcription factors to obtain a robust gene panel for prognostic prediction and therapies in cholangiocarcinoma[J]. Frontiers in Genetics, 2022, 13. (IF = 4.77，WOS引用：0；Google引用0)
  30. Peter Ebert#; Peter A. Audano#; Qihui Zhu#; Bernardo Rodriguez-Martin#; ... Jiadong Lin; Xiaofei Yang; Kai Ye; ...; Charles Lee*; Jan O. Korbel*; Tobias Marschall*; Evan E. Eichler*; Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science, 2021: eabf7117. (高被引，IF = 63.83，WOS引用：127；Google引用255)
  31. Wan-Ping Lee#, Qihui Zhu#, Xiaofei Yang, Silvia Liu, Eliza Cerveira, Mallory Ryan, Adam Mil-Homens, Lauren Bellfy, Kai Ye, Chengsheng Zhang*, and Charles Lee*. JAX-CNV: A whole genome sequencing-based algorithm for copy number detection at clinical grade level. Genomics, Proteomics & Bioinformatics (2022), https://doi.org/10.1016/j.gpb.2021.06.003. (IF=7.691，WOS引用：0；Google引用 1)
  32. Yongyong Kang, Xinchao Ji, Li Guo, Han Xia, Xiaofei Yang, Zhen Xie, Xiaodan Shi, Rui Wu, Dongyun Feng, Chen Wang, Min Chen, Wenliang Zhang, Hong Wei, Yuanlin Guan, Kai Ye, Gang Zhao. Cerebrospinal Fluid from Healthy Pregnant Women Does Not Harbor a Detectable Microbial Community. Microbiology spectrum, 2021, 9(3), e00769-21. (IF=9.04，WOS引用：3；Google引用 4)
  33. Rundong Li, Pinghui Wang*, Jiongli Zhu, Junzhou Zhao, Jia Di, Xiaofei Yang, Kai Ye. “Building Fast and Compact Sketches for Approximately Multi-Set Multi-Membership Querying”. SIGMOD 2021. (CCF Rank A), https://doi.org/10.1145/3448016.3452829 (WOS引用：0；Google引用 1)
  34. Yue Wang, Yufeng Liu, Xiaofei Yang, Hui Guo, Jiadong Lin, Jinkui Yang, Mingqian He, Jingya Wang, Xiaomei Liu, Tingting Shi, Liping Wu, Chengsheng Zhang, Kai Ye, Bingyin Shi. Predicting the early risk of ophthalmopathy in Graves’ disease patients using TCR repertoire[J]. Clinical and translational medicine, 2020, 10(7): e218. (IF=8.55，WOS引用：2；Google引用 2)
  35. Peng. Jia, Xiaofei Yang, Li. Guo, Bowen. Liu, Jiadong. Lin, Hao. Liang, Jianyong. Sun, Chengsheng Zhang, Kai Ye, MSIsensorpro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability, Genomics, Proteomics & Bioinformatics 2020 Feb; 18(1): 65-71, doi: https://doi.org/10.1016/j.gpb.2020.02.001 (IF=7.69，WOS引用：21；Google引用 32)
  36. Bowen Liu, Xiaofei Yang, Tingjie Wang, Jiadong Lin, Yongyong Kang, Peng Jia, Kai Ye. MEpurity: estimating tumor purity using DNA methylation data[J]. Bioinformatics, 2019 Dec 15; 35(24): 5298-5300, doi.org/10.1093/bioinformatics/btz555. (IF=6.93，WOS引用：4；Google引用 5)
  37. YongYong Kang, Xiaofei Yang, Jiadong Lin, Kai Ye. PVTree: A Sequential Pattern Mining Method for Alignment Independent Phylogeny Reconstruction [J]. Genes, 2019, 10(2): 73. (IF=4.14，WOS引用：4；Google引用 5)
  38. Kai Ye, Li Guo, Xiaofei Yang, et al, Split-Read Indel and Structural Variant Calling Using PINDEL, Methods in molecular biology (Clifton, N.J.) 1833:95-105, July 2018, DOI: 10.1007/978-1-4939-8666-8_7. (WOS引用：12；Google引用 17)
  39. Xiaoke Ma, Liang Yu, Peizhuo Wang, Xiaofei Yang. Discovering DNA methylation patterns for long non-coding RNAs associated with cancer subtypes [J]. Computational biology and chemistry, 2017, 69: 164-170. (IF=3.74，WOS引用：24；Google引用 25)
  40. Xingli Guo, Lin Gao, Qi Liao, Hui Xiao, Xiaoke Ma, Xiaofei Yang, et al. Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks[J]. Nucleic Acids Research, 2013, 41(2): e35-e35. (IF=19.16，WOS引用：150；Google引用 186)
  41. Hao Wu, Lin Gao, Feng Li, Fei Song, Xiaofei Yang, et al. Identifying overlapping mutated driver pathways by constructing gene networks in cancer[J]. BMC Bioinformatics, 2015, 16(Suppl 5): S3. (IF=3.33，WOS引用：15；Google引用 24)
  42. Hao Wu, Lin Gao, Jihua Dong, Xiaofei Yang. Detecting overlapping protein complexes by rough-fuzzy clustering in protein-protein interaction networks[J]. PloS One, 2014, 9(3): e91856. (IF=3.75，WOS引用：19；Google引用 52)
  43. Xingli Guo, Lin Gao, Chunshui Wei, Xiaofei Yang, et al. A computational method based on the integration of heterogeneous networks for predicting disease-gene associations[J]. PLoS One, 2011, 6(9): e34171.  (IF=3.75，WOS引用：20；Google引用 33)
  44. Feng Li, Lin Gao, Xiaoke Ma, Xiaofei Yang. Detection of driver pathways using mutated gene network in cancer [J]. Molecular BioSystems, 2016,12, 2135-2141. (IF=3.34，WOS引用：7；Google引用 10)
  45. 郭杏莉, 高琳*, 刘永轩, 党合萱, 王羽, 杨晓飞, et al. 长非编码 RNA 生物特征研究与分析. 科学通报, 2013, 58(27): 2779-2786; 

专利/软件著作权

  1. 杨晓飞; 孙雨；叶凯，蔺佳栋，段明哲，郭立；面向生物大数据的流式传输与变异实时挖掘系统及方法，2023.9.29，中国，ZL201911347153.2 (专利)

  2. 杨晓飞; 卜楠; 叶凯; 蔺佳栋; 梁皓; 郭立 ; 一种基于二代测序数据的反转相关复杂变异检测方法, 2020-2-6, 中国, ZL202010081979.5 （专利）

  3. 杨晓飞; 魏宏; 叶凯 ; 多组学融合剪接位点的识别方法及系统、设备和存储介质, 2021-4-30, 中国, ZL202110485740.9 (专利)

  4. 杨晓飞；宗宇；叶凯；基于深度学习模型集成的基因组调控元件识别软件[简称：iGRE-MI] V1.0,, 2023SR0535651,原始取得，全部权利，2023-03-20（软件著作权）

  5. 叶凯; 贾鹏; 杨晓飞; 刘博文; 康永永; 梁皓 ; 一种基于基因组测序的微卫星不稳定性检测系统及方法, 2020-6-19, 中国, ZL201811641480.4 (专利)

  6. 叶凯; 康永永; 杨晓飞; 贾鹏; 蔺佳栋; 郭立 ; 一种基于序列模式挖掘算法的系统发生树构建方法, 2020-11-10, 中国, ZL201811408608.2 (专利)

  7. 叶凯; 杨帆; 杨晓飞; 蔺佳栋; 梁皓; 郭立 ; 一种基于模式增长算法的基因变异检测方法, 2020-2-26, 中国, ZL202010121579.2 (专利)

  8. 施秉银; 王悦; 刘宇峰; 叶凯; 杨晓飞; 蔺佳栋 ; T细胞数据处理方法及装置, 2020-10-9, 中国, ZL201810813090.4 (专利)

  9. 刘宇峰; 王悦; 施秉银; 叶凯; 蔺佳栋; 杨晓飞 ; 免疫组库统计量构建软件V1.0, 2018SR715465, 原始取得, 全部权利, 2018-5-19 (软件著作权)