A*: major contribution with First/Corresponding author; B*: minor contributing author.

2027

• A25. Liuqing Yang⁺, Fang Yang⁺, Chenghao Mei, Wenwen Li, Lin Liu, Jinhua Fan, Xiang Li, Runxiang Yang, Lianhua Ye^*, Yupeng Cun^*, A conserved glycolytic malignant subcluster drives invasive progression through a targetable PPIA-BSG metabolic-immune axis in early lung adenocarcinoma, Theranostics, 2027; 17(1):83-98. doi:10.7150/thno.139927. https://www.thno.org/v17p0083.htm

2026

• A24. Xiaobin Wu⁺, Liuqing Yang⁺, Yepeng Fan⁺, Xiaohuan Li⁺, Xiuyu Shi⁺, Chunfang Dai, Yayan Pang, Jiaojiao Wang, Yupeng Cun*, Zhifang Dong*, Maternal sleep deprivation in late pregnancy alters offspring hippocampal development revealed by single-cell and spatial transcriptomics, Molecular Psychiatry, 2026, DOI: https://www.doi.org/10.1038/s41380-026-03831-w
• A23. Chao Zhang†, Ling Liu†, Ruoyu Deng, Jialing Lv, Chenghao Mei, Wen Zhang, Liuqing Yang, Fang Yang, Runxiang Yang*, Yupeng Cun*, EGFR double-mutant reveals distinct EMT-like malignant and macrophage subtypes engaging COL4A3-CD44 crosstalk in lung adenocarcinoma,Translational Oncology, 2026，https://doi.org/10.1016/j.tranon.2026.102951
• A22. Yue Xie⁺, Li Li⁺, Rong Li, Yihong Sun, Ting Zhou, Yupeng Cun*, Gaohui Zhu*，Longitudinal Single-Cell Transcriptomic Profiling Reveals Dynamic Immune Cell Alterations During Burosumab Therapy in X-Linked Hypophosphatemia, Pediatric Discovery, 2026
• A21. Qiang Chen⁺, Liuqing Yang⁺, Sili Ni⁺, Yihong Sun, Jiwei Li, Yue Xie, Xingang Yuan, Yimin Xie, Yunxuan Zhang, Xiaoyan Luo*, Yupeng Cun*, Hua Wang*, Single-cell RNA Sequencing Discovered Subtypes Associated with Angiogenesis and Propranolol Treatment in Infantile Hemangioma, Genomics, Proteomics & Bioinformatics, 2026;, qzag023
• A20. Yihong Sun⁺, Ningning Chen⁺, Congjie Chen, Weitian Lu, Qian Wan, Tingsong Li*, Yupeng Cun*, Distinctive genetic architecture of infantile epileptic spasms syndrome compared to self-limited infantile epilepsy by trios whole-exome sequencing. Epilepsia Open 2026 doi: 10.1002/epi4.70208
• A19. Jing Song, Xiaomei Song, Yue Xie, Hong Guo*, Yupeng Cun*. MIF-expressing tumor cells mediate immunotherapeutic resistance in esophageal squamous cell carcinoma. Theranostics 2026; 16(3):1613-1629. doi:10.7150/thno.118269

2025

• A18. Ling Hu, Pei-Han Huang, Yi-Gang Song, Shook Ling Low, Guo-Xiong Hu, Shi-Shun Zhou, Lang Li, Yun-Hong Tan, Hong-Hu Meng*, Yu-Peng Cun*, Jie Li*，RAD-seq reveals Cenozoic shifts in the palaeogeographic distribution of Trigonobalanus verticillata across the Indochina Peninsula and Malay Archipelago, Palaeogeography, Palaeoclimatology, Palaeoecology, 2025, http://doi.org/10.1016/j.palaeo.2025.113291
• A17. Shuxin Tang⁺, Jinhua Fan⁺, Yupeng Cun*, Identification of prognostic biomarkers in gene expression profile of neuroblastoma via machine learning, Pediatric Discovery, 2025, doi: 10.1002/pdi3.70009
• A16. Gaohui Zhu⁺, Yue Xie⁺, Li Li, Rong Li, Yihong Sun, Ting Zhou*，Yupeng Cun*, Single-cell RNA sequencing reveals important role of monocytes and macrophages during mucopolysaccharidosis treatment, Scientific Reports 2025. doi:10.1038/s41598-025-97330-7
• A15. Yun Liu#, Xiwen Luo#, Liuqing Yang, Qiang Luo, Xiya Luo, Li Xu, Yating Wang, Yunfei An, Yupeng Cun*, Xuemei Tang*, Single-cell landscape of immunological responses in patients with juvenile idiopathic arthritis, Genes & Diseases 2025, doi:10.1016/j.gendis.2025.101577
• A14. Yi Dai^#, Yilei Wu^#, Dake Zhao*, Yupeng Cun*. Whole-genome sequencing revealed genetic basis of diterpenoid alkaloid difference in Aconitum vilmorinianum, BMC Plant Biology 2025,25:184. doi: 10.1186/s12870-025-06200-x

2024

• A13.Jinhua Fan, Shuxin Tang, Xiangru Kong,  Yupeng Cun*. Integrating multi-omics data reveals neuroblastoma subtypes in the tumor microenvironment, Life Sciences, 2024, (359), 123236. doi: 10.1016/j.lfs.2024.123236
• A12. Fang Yang^#, Jinhua Fan^#, Runxiang Yang* and Yupeng Cun*. Integrative analysis of blood transcriptome profiles in small-cell lung cancer patients for identification of novel chemotherapy resistance-related biomarkers, Frontiers in Immunology 2024,15:1338162. doi: 10.3389/fimmu.2024.1338162
• A11. Hao-Tian Wang^# , Long Zhao^#,Li-Qin Yang, Ming-Xia Ge, Xing-Li Yang, Zong-Liang Gao, Yu-Peng Cun*, Fu-Hui Xiao*, Qing-Peng Kong*, Scrutiny of genome-wide somatic mutation profiles in centenarians identifies the key genomic regions for human longevity,  Aging Cell, 2024, 24 (1) e13916. DOI: 10.1111/acel.13916 (中文介绍)

2023

• A10. Dake Zhao+, Ya Zhang+, Huanxing Ren, …, Jue Ruan, Suiyun Chen*, Diqiu Yu*. Multi-omics analysis reveals the evolutionary origin of diterpenoid alkaloid biosynthesis pathways in Aconitum. Yupeng Cun*, Journal of Integrative Plant Biology 2023, DOI: 10.1111/jipb.13565 (中文介绍)

2022

• A9. Ling Hu, Xin-Gui Le, Shi-Shun Zhou, Can-Yu Zhang, Yun-Hong Tan, Qiang Ren, Hong-Hu Meng*, Yupeng Cun*, and Jie Li*. Conservation Significance of the Rare and Endangered Tree Species, Trigonobalanus doichangensis  (Fagaceae)，Diversity 14, no. 8: 666. 9 (中文介绍)
• A8. Xi-Guo Yuan, Yuan Zhao, Yang Guo, Lin-Mei Ge, Wei Liu, Shi-Yu Wen, Qi Li, Zhang-Bo Wan, Pei-Na Zheng, Tao Guo, Zhi-Da Li, Martin Peifer, Yu-Peng Cun. COSINE: A web server for clonal and subclonal structure inference and evolution in cancer genomics. Zoological Research, (2022) 43(1): 75-77. (中文介绍)

2021

• A7. Yu-Fang Mao, Xi-Guo Yuan*, Yu-Peng Cun*. A novel machine learning approach (svmSomatic) to distinguish somatic and germline mutations using next-generation sequencing data. Zoological Research, (2021), 42(2): 246-249.
• A6.Chengli Zhou, Linmei Ge, Yanbu Guo, Dongming Zhou*, Yupeng Cun*. A comprehensive comparison on current deep learning approaches for plant images classification, (2021) J. Phys.: Conf. Ser. 1873 012002 (IWECAI 2021)  (EI, conference paper).
• B5. Dentro, …., Yupeng Cun(23th), ..., Peter Van Loo, Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes, 2021 Cell 184(8), P2239-2254.E39,

2020

• B4. Moritz Gerstung, …,Yupeng Cun,…, Peter Van Loo(71 total authors). The evolutionary history of 2,658 cancers, Nature 578 (7793), 122-128

2018

• A5. Yupeng Cun*, Tsun-Po Yang*, Viktor Achter*, Ulrich Lang, Martin Peifer, Copy number analysis and inference of subclonal populations in cancer genomes using Sclust. Nature Protocols, (2018)
• B3.Julie George, …,Yupeng Cun(28th/68), …; Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct molecular subtypes of high-grade neuroendocrine lung tumors; 2018, Nature Communications, 9(1048)

2017

• B2. Gero Knittel, …, Yupeng Cun (9th/32)…, Two mouse models reveal an actionable PARP1 dependence in aggressive chronic lymphocytic leukemia. 2017, Nature Communications; 8(153)

2015

• B1. Julie George*, Jing Shan Lim*, Se Jin Jang, Yupeng Cun(4th/96), …, Reinhard Büttner, Stefan A. Haas, Elisabeth Brambilla, Martin Peifer, Julien Sage & Roman K. Thomas, Comprehensive genomic profiles of small cell lung cancer.  Nature，2015; 524(7563),

2014

• A4. Yupeng Cun, Holger Fröhlich. netClass: an R-package for network based, integrative biomarker signature discovery, Bioinformatics, 2014; 30(9)., DOI: 10.1093/bioinformatics/btu025

2013

• A3 Yupeng Cun, Holger Fröhlich, Network and data integration for biomarker signature discovery via network smoothed T-statistics.  PLoS ONE，2013; 8(9):e73074., DOI: 10.1371/journal.pone.0073074

2012

• A2. Yupeng Cun, Holger Fröhlich..Prognostic gene signatures for patient stratification in breast cancer: accuracy, stability and interpretability of gene selection approaches using prior knowledge on protein-protein interactions.  BMC Bioinformatics  2012; 13:69. DOI:10.1186/1471-2105-13-69
• A1. Yupeng Cun, Holger Fröhlich, Biomarker gene signature discovery integrating network knowledge, Biology, 2012 DOI: 10.3390/biology1010005