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

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
• B9. L Yin, X Xu, B Conacher, Y Lin, GL Carrillo, Yupeng Cun, MA Fox, X Lu, H Xie, Elevated EGR1 binding at enhancers in excitatory neurons correlates with neuronal subtype-specific epigenetic regulation BMC Biology. 2025, 23 (1), 251

2024

• B8. WT He, DX Li, JH Fan, ZY Yao, Yupeng Cun, ZF Dong, Maternal sleep deprivation disrupts glutamate metabolism in offspring rats. . Zoological Research 2024, 45 (6), 1221
• 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)
• B7. Hongfei Ge, Tengyuan Zhou, Chao Zhang, Yupeng Cun, Weixiang Chen, Yang Yang, Qian Zhang, Huanhuan Li, Jun Zhong, Xuyang Zhang, Hua Feng, Rong Hu, Targeting ASIC1a promotes neural progenitor cell migration and neurogenesis in ischemic stroke. Research, 2023

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)
• B6.Ye Liu, Xiaolin Ji, Ying Liu, Dan Li, Yupeng Cun, Ye Zhang, Ruixin Wang, Yanling Hao, Shuo Wang, Chunying Chen, Yiming Shao. A D-peptide-based HIV gelatinous combination vaccine improves therapy in ART-delayed macaques of chronic infection. Nano Today, 2022

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