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

2026

• A20. Distinctive genetic architecture of infantile epileptic spasms syndrome compared to self-limited infantile epilepsy by trios whole-exome sequencing. Yihong Sun⁺, Ningning Chen⁺, Congjie Chen, Weitian Lu, Qian Wan, Tingsong Li*, Yupeng Cun*, Epilepsia Open 2026 doi: 10.1002/epi4.70208
• A19.MIF-expressing tumor cells mediate immunotherapeutic resistance in esophageal squamous cell carcinoma. Jing Song, Xiaomei Song, Yue Xie, Hong Guo*, Yupeng Cun*. Theranostics 2026; 16(3):1613-1629. doi:10.7150/thno.118269.

2025

• A18. RAD-seq reveals Cenozoic shifts in the palaeogeographic distribution of Trigonobalanus verticillata across the Indochina Peninsula and Malay Archipelago, 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*，Palaeogeography, Palaeoclimatology, Palaeoecology, 2025, http://doi.org/10.1016/j.palaeo.2025.113291
• A17. Identification of prognostic biomarkers in gene expression profile of neuroblastoma via machine learning, Shuxin Tang⁺, Jinhua Fan⁺, Yupeng Cun*, Pediatric Discovery, 2025, doi: 10.1002/pdi3.70009
• A16. Single-cell RNA sequencing reveals important role of monocytes and macrophages during mucopolysaccharidosis treatment, Gaohui Zhu⁺, Yue Xie⁺, Li Li, Rong Li, Yihong Sun, Ting Zhou* & Yupeng Cun*, Scientific Reports 2025. doi:10.1038/s41598-025-97330-7
• A15. Single-cell landscape of immunological responses in patients with juvenile idiopathic arthritis, Yun Liu^#, Xiwen Luo^#, Liuqing Yang, Qiang Luo, Xiya Luo, Li Xu, Yating Wang, Yunfei An, Yupeng Cun*, Xuemei Tang*, Genes & Diseases 2025, doi:10.1016/j.gendis.2025.101577
• A14. Whole-genome sequencing revealed genetic basis of diterpenoid alkaloid difference in Aconitum vilmorinianum, Yi Dai^#, Yilei Wu^#, Dake Zhao*, Yupeng Cun*, BMC Plant Biology 2025,25:184. doi: 10.1186/s12870-025-06200-x
• B9. Elevated EGR1 binding at enhancers in excitatory neurons correlates with neuronal subtype-specific epigenetic regulation L Yin, X Xu, B Conacher, Y Lin, GL Carrillo, Yupeng Cun, MA Fox, X Lu, H Xie. BMC Biology. 2025, 23 (1), 251

2024

• B8. Maternal sleep deprivation disrupts glutamate metabolism in offspring rats. WT He, DX Li, JH Fan, ZY Yao, Yupeng Cun, ZF Dong. Zoological Research 2024, 45 (6), 1221
• A13. Integrating multi-omics data reveals neuroblastoma subtypes in the tumor microenvironment, Jinhua Fan, Shuxin Tang, Xiangru Kong,  Yupeng Cun*, Life Sciences, 2024, (359), 123236. doi: 10.1016/j.lfs.2024.123236
• A12. Integrative analysis of blood transcriptome profiles in small-cell lung cancer patients for identification of novel chemotherapy resistance-related biomarkers, Fang Yang^#, Jinhua Fan^#, Runxiang Yang* and Yupeng Cun*, Frontiers in Immunology 2024,15:1338162. doi: 10.3389/fimmu.2024.1338162
• A11. Scrutiny of genome-wide somatic mutation profiles in centenarians identifies the key genomic regions for human longevity, 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*,  Aging Cell, 2024, 24 (1) e13916. DOI: 10.1111/acel.13916 (中文介绍)

2023

• A10. Multi-omics analysis reveals the evolutionary origin of diterpenoid alkaloid biosynthesis pathways in Aconitum. Dake Zhao+, Ya Zhang+, Huanxing Ren, …, Jue Ruan, Suiyun Chen*, Diqiu Yu*, Yupeng Cun*, Journal of Integrative Plant Biology 2023, DOI: 10.1111/jipb.13565 (中文介绍)
• B7. Targeting ASIC1a promotes neural progenitor cell migration and neurogenesis in ischemic stroke. Hongfei Ge, Tengyuan Zhou, Chao Zhang, Yupeng Cun, Weixiang Chen, Yang Yang, Qian Zhang, Huanhuan Li, Jun Zhong, Xuyang Zhang, Hua Feng, Rong Hu, Research, 2023

2022

• A9. Conservation Significance of the Rare and Endangered Tree Species, Trigonobalanus doichangensis  (Fagaceae)，Ling Hu, Xin-Gui Le, Shi-Shun Zhou, Can-Yu Zhang, Yun-Hong Tan, Qiang Ren, Hong-Hu Meng*, Yupeng Cun*, and Jie Li*. Diversity 14, no. 8: 666. 9 (中文介绍)
• A8. COSINE: A web server for clonal and subclonal structure inference and evolution in cancer genomics. 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. Zoological Research, (2022) 43(1): 75-77. (中文介绍)
• B6. A D-peptide-based HIV gelatinous combination vaccine improves therapy in ART-delayed macaques of chronic infection. Ye Liu, Xiaolin Ji, Ying Liu, Dan Li, Yupeng Cun, Ye Zhang, Ruixin Wang, Yanling Hao, Shuo Wang, Chunying Chen, Yiming Shao. Nano Today, 2022

2021

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

2020

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

2018

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

2017

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

2015

• B1. Comprehensive genomic profiles of small cell lung cancer. 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, Nature，2015; 524(7563),

2014

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

2013

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

2012

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