在研项目：

1. 2025-2029，基于序列到图像转换策略的基因组序列计算框架构建，国家自然科学基金委重点项目，负责人
2. 2022-2027，关键模式生物基因组精细研究及其示范应用，科技部重点研发专项，负责人
3. 2022-2026，国家杰出青年科学基金（生物信息学），国家自然科学基金委，负责人

结题项目：

1. 2021-2024，肿瘤微卫星不稳定计算方法及其应用，国家自然科学基金委面上项目，负责人
2. 2018-2020，精准医学大数据的有效挖掘与关键信息技术研发，国家重点研发计划，子课题负责人
3. 2017-2020，中国人群多组学参比数据库与分析系统建设，国家重点研发计划，项目骨干
4. 2017-2020，基因组复杂变异的检测算法和应用，国家自然科学基金委面上项目，负责人

科研论文：

1. Peisen Sun, Stephen J Bush, Songbo Wang, Peng Jia, Mingxuan Li, Tun Xu, Pengyu Zhang, Xiaofei Yang, Chengyao Wang, Linfeng Xu, Tingjie Wang, Kai Ye. (2025). STMiner: gene-centric spatial transcriptomics for deciphering tumor tissues. Cell Genomics, Feb 12;5(2):100771.
2. Dan Xu, Mengyao Guo, Xin Xu, Gan Luo, Yaxin Liu, Stephen J Bush, Chengyao Wang, Tun Xu, Wenxin Zeng, Chongbing Liao, Qingxia Wang, Wei Zhao, Wenying Zhao, Yuezhuangnan Liu, Shanshan Li, Shuangshuang Zhao, Yaming Jiu, Nathalie Sauvonnet, Wuyuan Lu, Philippe J Sansonetti, Kai Ye. (2025). Shigella infection is facilitated by interaction of human enteric α-defensin 5 with colonic epithelial receptor P2Y11. Nature Microbiology, 10(2):509-526.
3. Bo Wang, Peng Jia, Shenghan Gao, Huanhuan Zhao, Gaoyang Zheng, Linfeng Xu, Kai Ye. (2025). Long and Accurate: How HiFi Sequencing is Transforming Genomics. Genomics, Proteomics & Bioinformatics, qzaf003.
4. Shenghan Gao, Yimeng Zhang, Stephen J Bush, Bo Wang, Xiaofei Yang, Kai Ye. (2024). Centromere Landscapes Resolved from Hundreds of Human Genomes. Genomics Proteomics Bioinformatics, Oct 18:qzae071.
5. Wang, S., Ye, K. (2024). Deep-learning based representation and recognition for genome variants – From SNVs to structural variants. National Science Review, nwae335.
6. Gao, S., Jia, Y., Guo, H., Xu, T., Wang, B., Bush, S.J., Wan, S., Zhang, Y., Yang, X., Ye, K. (2024). The centromere landscapes of four karyotypically diverse Papaver species provide insights into chromosome evolution and speciation. Cell Genomics, 100626.
7. Wang, B., Jia, Y., Dang, N., Yu J., …, Ma, W., Ye, K. (2024). Near telomere-to-telomere genome assemblies of two Chlorella species unveil the composition and evolution of centromeres in green algae. BMC Genomics, 25, 356.
8. Wang, S., Lin, J., Jia, P., Xu, T., Li, X., Liu, Y., Xu, D., Bush, S.J., Meng, D., Ye, K. (2024). De novo and somatic structural variant discovery with SVision-pro. Nature Biotechnology, Mar 22.
9. Jia P., Yang X., Yang X., Wang T., Xu Y., Ye K., (2024). MSIsensor-RNA: Microsatellite Instability Detection for Bulk and Single-cell Gene Expression Data, Genomics, Proteomics & Bioinformatics, qzae004.
10. Jia, P., Dong, L., Yang, X., Wang, B., Bush, S.J., Wang, T., …, Lv, Y., Wang, J., Ye, K. (2023). Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet. Genome Biology, 24(1):277.
11. Xu, Y., Bush, S.J., Yang, X., Xu, L., Wang, B., Ye, K. (2023). Evolutionary analysis of conserved non-coding elements subsequent to whole-genome duplication in opium poppy. The Plant Journal, 116(6):1804-1824.
12. Wang, B., Dang, N., Yang, X., Xu, S., & Ye, K. (2023). The human pangenome reference: the beginning of a new era for genomics. Science Bulletin, 68(14), 1484-1487.
13. Lin, J., Jia, P., Wang, S., Kosters, W., & Ye, K. (2023). Comparison and benchmark of structural variants detected from long read and long-read assembly. Briefings in Bioinformatics, 24(4), bbad188.
14. Jia, Y., Xu, Y., Wang, B., Guo, L., Guo, M., Che, X., & Ye, K. (2023). The tissue-specific chromatin accessibility landscape of Papaver somniferum. Frontiers in Genetics, 14.
15. How-Kit, A., & Ye, K. (2023). Editorial: Microsatellite and microsatellite instability. Frontiers in Genetics, 14.
16. Gao, Y., Yang, X., Chen, H., Tan, X., Yang, Z., Deng, L., . . . Ye, K., Xu, S.(2023). A pangenome reference of 36 Chinese populations. Nature, 619(7968), 112-121.
17. Gao, S., Yang, X., Guo, H., Zhao, X., Wang, B., & Ye, K. (2023). HiCAT: a tool for automatic annotation of centromere structure. Genome Biology, 24(1), 58.
18. Ye, K. (2022). A commentary of “the intersection of archaeology and genomics: Sparking the advances in cognitive human society”: 10 remarkable discoveries from 2020 in Nature. Fundamental Research, 2(2), 339-340.
19. Yang, X., Zhao, X., Qu, S., Jia, P., Wang, B., Gao, S., . . . Ye, K. (2022). Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing. Fundamental Research, 2(6), 946-953.
20. Xu, T., Yang, X., Jia, Y., Li, Z., Tang, G., Li, X., . . . Ye, K. (2022). A global survey of the transcriptome of the opium poppy (Papaver somniferum) based on single-molecule long-read isoform sequencing. The Plant Journal, 110(2), 607-620.
21. Wang, T., Xu, C., Zhang, Z., Wu, H., Li, X., Zhang, Y., . . . Ye, K. (2022). Cellular heterogeneity and transcriptomic profiles during intrahepatic cholangiocarcinoma initiation and progression. Hepatology, 76(5).
22. Wang, T., Xu, C., Xu, D., Yang, X., Liu, Y., Li, X., . . . Ye, K. (2022). Integrating cell interaction with transcription factors to obtain a robust gene panel for prognostic prediction and therapies in cholangiocarcinoma. Frontiers in Genetics, 13.
23. Wang, T., Dang, N., Tang, G., Li, Z., Li, X., Shi, B., . . . Ye, K. (2022). Integrating bulk and single-cell RNA sequencing reveals cellular heterogeneity and immune infiltration in hepatocellular carcinoma. Molecular Oncology, 16(11), 2195-2213.
24. Wang, B., Yang, X., Jia, Y., Xu, Y., Jia, P., Dang, N., . . . Ye, K. (2022). High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads. Genomics, Proteomics & Bioinformatics, 20(1), 4-13.
25. Lin, J., Yang, X., Kosters, W., Xu, T., Jia, Y., Wang, S., . . . Ye, K. (2022). Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants. Genomics, Proteomics & Bioinformatics, 20(1), 205-218.
26. Lin, J., Wang, S., Audano, P. A., Meng, D., Flores, J. I., Kosters, W., . . . Ye, K. (2022). SVision: a deep learning approach to resolve complex structural variants. Nature Methods, 19(10), 1230-1233.
27. Gao, S., Yang, X., Sun, J., Zhao, X., Wang, B., & Ye, K. (2022). IAGS: Inferring Ancestor Genome Structure under a Wide Range of Evolutionary Scenarios. Molecular Biology and Evolution, 39(3), msac041.
28. Dang, X., Kang, Y., Wang, X., Cao, W., Li, M., He, Y., . . . Ye, K., Xu, D. (2022). Frequent exacerbators of chronic obstructive pulmonary disease have distinguishable sputum microbiome signatures during clinical stability. Frontiers in Microbiology, 13.
29. Che, Y., Yang, X., Jia, P., Wang, T., Xu, D., Guo, T., & Ye, K. (2022). D2 Plot, a Matrix of DNA Density and Distance to Periphery, Reveals Functional Genome Regions. Advanced Science, 9(30), 2202149.
30. Yang, X., Gao, S., Guo, L., Wang, B., Jia, Y., Zhou, J., . . . Ye, K. (2021). Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway. Nature Communications, 12(1), 6030.
31. Wang, Y., Chen, Z., Wang, T., Guo, H., Liu, Y., Dang, N., . . . Ye, K., Shi, B. (2021). A novel CD4+ CTL subtype characterized by chemotaxis and inflammation is involved in the pathogenesis of Graves’ orbitopathy. Cellular & Molecular Immunology, 18(3), 735-745.
32. Kang, Y., Ji, X., Guo, L., Xia, H., Yang, X., Xie, Z., . . . Ye, K., Zhao, G. (2021). Cerebrospinal Fluid from Healthy Pregnant Women Does Not Harbor a Detectable Microbial Community. Microbiology Spectrum, 9(3), e00769-00721.
33. Ebert, P., Audano, P. A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M. J., . . . Eichler, E. E. (2021). Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science, 372(6537), eabf7117.
34. Yang, X., Gao, S., Wang, T., Yang, B., Dang, N., & Ye, K. (2020). gCAnno: a graph-based single cell type annotation method. BMC Genomics, 21(1), 823.
35. Xie, F., Zhang, J., Wang, J., Reuben, A., Xu, W., Yi, X., . . . Ye, K., Cheng, C., Xia, T. (2020). Multifactorial Deep Learning Reveals Pan-Cancer Genomic Tumor Clusters with Distinct Immunogenomic Landscape and Response to Immunotherapy. Clinical Cancer Research, 26(12), 2908-2920.
36. Wang, Y., Liu, Y., Yang, X., Guo, H., Lin, J., Yang, J., . . . Ye, K., Shi, B. (2020). Predicting the early risk of ophthalmopathy in Graves’ disease patients using TCR repertoire. Clinical and Translational Medicine, 10(7), e218.
37. Wang, B., Yu, H., Jia, Y., Dong, Q., Steinberg, C., Alabouvette, C., . . . Ye, K., Ma, J., Guo, L. (2020). Chromosome-Scale Genome Assembly of Fusarium oxysporum Strain Fo47, a Fungal Endophyte and Biocontrol Agent. Molecular Plant-Microbe Interactions®, 33(9), 1108-1111.
38. Guo, L., Ye, K., & Wang, L. (2020). Chromosome-Scale Genome Assembly of Talaromyces rugulosus W13939, a Mycoparasitic Fungus and Promising Biocontrol Agent. Molecular Plant-Microbe Interactions®, 33(12), 1446-1450.
39. Jia, P., Yang, X., Guo, L., Liu, B., Lin, J., Liang, H., . . . Ye, K. (2020). MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability. Genomics, Proteomics & Bioinformatics, 18(1), 65-71.
40. Guo, L., Ji, M., & Ye, K. (2020). Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum. BMC Genomics, 21(1), 179.
41. Fokkens, L., Guo, L., Dora, S., Wang, B., Ye, K., Sánchez-Rodríguez, C., & Croll, D. (2020). A Chromosome-Scale Genome Assembly for the Fusarium oxysporum Strain Fo5176 To Establish a Model Arabidopsis-Fungal Pathosystem. G3 Genes|Genomes|Genetics, 10(10), 3549-3555.
42. Yang, X., Lee, W.-P., Ye, K., & Lee, C. (2019). One reference genome is not enough. Genome Biology, 20(1), 104.
43. Liu, B., Yang, X., Wang, T., Lin, J., Kang, Y., Jia, P., & Ye, K. (2019). MEpurity: estimating tumor purity using DNA methylation data. Bioinformatics, 35(24), 5298-5300.
44. Kang, Y., Yang, X., Lin, J., & Ye, K. (2019). PVTree: A Sequential Pattern Mining Method for Alignment Independent Phylogeny Reconstruction. Genes, 10(2).
45. Guo, L., & Ye, K. (2019). Mapping Genome Variants Sheds Light on Genetic and Phenotypic Differentiation in Chinese. Genomics, Proteomics & Bioinformatics, 17(3), 226-228.
46. Guo, L., Winzer, T., Yang, X., Li, Y., Ning, Z., He, Z., . . . Ye, K. (2018). The opium poppy genome and morphinan production. Science, 362(6412), 343-347.
47. Ye, K., Wang, J., Jayasinghe, R., Lameijer, E.-W., McMichael, J. F., Ning, J., . . . Ding, L. (2016). Systematic discovery of complex insertions and deletions in human cancers. Nature Medicine, 22(1), 97-104.
48. Kroon, M., Lameijer, E. W., Lakenberg, N., Hehir-Kwa, J. Y., Thung, D. T., Slagboom, P. E., . . . Ye, K. (2016). Detecting dispersed duplications in high-throughput sequencing data using a database-free approach. Bioinformatics, 32(4), 505-510.
49. Hehir-Kwa, J. Y., Marschall, T., Kloosterman, W. P., Francioli, L. C., Baaijens, J. A., Dijkstra, L. J., . . .Ye, K., Guryev, V. (2016). A high-quality human reference panel reveals the complexity and distribution of genomic structural variants. Nature Communications, 7(1), 12989.
50. Sudmant, P. H., Rausch, T., Gardner, E. J., Handsaker, R. E., Abyzov, A., Huddleston, J., . . . The Genomes Project, C. (2015). An integrated map of structural variation in 2,504 human genomes. Nature, 526(7571), 75-81.
51. Kloosterman, W. P., Francioli, L. C., Hormozdiari, F., Marschall, T., Hehir-Kwa, J. Y., Abdellaoui, A., . . . Ye, K., Guryev, V. (2015). Characteristics of de novo structural changes in the human genome. Genome research, 25(6), 792-801.
52. Auton, A., Abecasis, G. R., Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., . . . National Eye Institute, N. I. H. (2015). A global reference for human genetic variation. Nature, 526(7571), 68-74.
53. Niu, B., Ye, K., Zhang, Q., Lu, C., Xie, M., McLellan, M. D., . . . Ding, L. (2014). MSIsensor: microsatellite instability detection using paired tumor-normal sequence data. Bioinformatics, 30(7), 1015-1016.
54. Ye, K., Beekman, M., Lameijer, E.-W., Zhang, Y., Moed, M. H., van den Akker, E. B., . . . Slagboom, P. E. (2013). Aging as Accelerated Accumulation of Somatic Variants: Whole-Genome Sequencing of Centenarian and Middle-Aged Monozygotic Twin Pairs. Twin Research and Human Genetics, 16(6), 1026-1032.
55. Zhang, Y., Lameijer, E.-W., t Hoen, P. A. C., Ning, Z., Slagboom, P. E., & Ye, K. (2012). PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data. Bioinformatics, 28(4), 479-486.
56. McVean, G. A., Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., . . . University of, G. (2012). An integrated map of genetic variation from 1,092 human genomes. Nature, 491(7422), 56-65.
57. Mills, R. E., Walter, K., Stewart, C., Handsaker, R. E., Chen, K., Alkan, C., . . . Genomes, P. (2011). Mapping copy number variation by population-scale genome sequencing. Nature, 470(7332), 59-65.
58. Ye, K., Jia, Z., Wang, Y., Flicek, P., & Apweiler, R. (2010). Mining Unique-m Substrings from Genomes. J Proteomics Bioinform (0974-276X (Print)).
59. Durbin, R. M., Altshuler, D., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., . . . The Translational Genomics Research, I. (2010). A map of human genome variation from population-scale sequencing. Nature, 467(7319), 1061-1073.
60. Ye, K., Schulz, M. H., Long, Q., Apweiler, R., & Ning, Z. (2009). Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics, 25(21), 2865-2871.
61. Ye, K., Vriend, G., & Ijzerman, A. P. (2008). Tracing evolutionary pressure. Bioinformatics, 24(7), 908-915.
62. Ye, K., Anton Feenstra, K., Heringa, J., Ijzerman, A. P., & Marchiori, E. (2008). Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting. Bioinformatics, 24(1), 18-25.
63. Ye, K., Kosters, W. A., & Ijzerman, A. P. (2007). An efficient, versatile and scalable pattern growth approach to mine frequent patterns in unaligned protein sequences. Bioinformatics, 23(6), 687-693.
64. Ye, K., Lameijer, E.-W. M., Beukers, M. W., & Ijzerman, A. P. (2006). A two-entropies analysis to identify functional positions in the transmembrane region of class A G protein-coupled receptors. Proteins: Structure, Function, and Bioinformatics, 63(4), 1018-1030.

已授权专利：

1. 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，中国发明，2020.10.9，ZL201810813090.4，（专利权人：一附院）
2. 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，中国发明，2020-11-10，ZL201811408606.2 （专利权人：西安交通大学）
3. 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，中国发明，2020-6-19，ZL201811641480.4 （专利权人：西安交通大学）
4. 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，中国发明，2021-4-30，ZL202110485740.9
5. 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， ZL202010081979.5
6. 叶凯，蔺佳栋，王松渤，杨晓飞，一种基于深度学习的基因组结构变异检测系统及方法，中国发明，2021-09-29，ZL202111156180.9
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，中国发明，2020-2-26，ZL202010121579.2
8. 叶凯，梁皓，杨晓飞，杨帆，贾鹏，郭立，基于外显子测序数据的拷贝数变异检测方法及系统、终端和存储介质，中国发明，2020-01-14，ZL 202010038141.8
9. 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，中国发明，2019-12-24，ZL201911347153.2

学术专著：

1. Ye, Kai; Guo, Li; Yang, Xiaofei; Lamijer, Eric-Wubbo; Raine, Keiran; Ning, Zemin; Split-Read Indel and Structural Variant Calling Using PINDEL, Humana Press, New York, NY, 2018.
2. Ye, Kai; Ning, Zemin; Detecting Break Points of Insertions and Deletions from Paired-end Short Reads, Caister Academic Press, 2014.