Manuscript(s) under peer review（*co-first author）：

• Xiguo Yuan, Yuan Zhao, Yang Guo, Linmei Ge, Wei Liu, Shiyu Wen, Qi Li, Zhangbo Wan, Peina Zheng, Tao Guo, Zhida Li, Martin Peifer, Yupeng Cun, COSINE: A Web Server for Clonal and Subclonal Structure Inference and Evolution in Cancer Genomics, 2021, arXiv:2103.15142

Peer reviewed papers: Orcid ID: orcid.org/0000-0002-4241-8099

• 17. Dentro, …., Yupeng Cun(23th), …, Peter Van Loo, 2021 Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes, Cell 184(8), P2239-2254.E39
• 16. Chengli Zhou, Linmei Ge, Yanbu Guo, Dongming Zhou*, Yupeng Cun*. 2021, A comprehensive comparison on current deep learning approaches for plant images classification, 2021 J. Phys.: Conf. Ser. 1873 012002 (IWECAI 2021)  (EI, conference paper).
• 15. 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): 246-249.10.24272/j.issn.2095-8137.2021.014
• 14.Yulia Rubanova, Ruian Shi, Caitlin F. Harrigan, …,Yupeng Cun,…, Quaid Morris(75 total authors), Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig，Nature Communications 11(1):731 DOI: 10.1038/s41467-020-14352-7
• 13. Marek Cmero, Ke Yuan, Cheng Soon Ong, …,Yupeng Cun,…, Geoff Macintyre(75 total authors), Inferring structural variant cancer cell fraction，Nature Communications 11(1):730 DOI: 10.1038/s41467-020-14351-8
• 12. Peter J. Campbell, Gad Getz, Jan O Korbel, …,Yupeng Cun,…, Jiashan Zhang(1318 total authors), Pan-cancer analysis of whole genomes, Nature 578 (7793), 82-93
• 11. Moritz Gerstung, Clemency Jolly, Ignaty Leshchiner, …,Yupeng Cun,…, Peter Van Loo(71 total authors), The evolutionary history of 2,658 cancers, Nature 578 (7793), 122-128
• 10. 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 13,1488–1501 (2018) ，DOI: 10.1038/nprot.2018.033
• 9. Julie George, Vonn Walter, Martin Peifer, Ludmil B. Alexandrov,…, Yupeng Cun(28th /68), …, Reinhard Büttner, David Neil Hayes, Elisabeth Brambilla, Lynnette Fernandez-Cuesta & Roman K. Thomas: Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct molecular subtypes of high-grade neuroendocrine lung tumors, Nature Communications, | (2018) 9:1048 |DOI: 10.1038/s41467-018-03099-x
• 8. Maxime Tarabichi, Iñigo Martincorena, Moritz Gerstung, …., Yupeng Cun, …, David Wedge & Peter Van Loo(79 total authors),Neutral tumor evolution? Nature Genetics(2018)50, 1630–1633
• 7. Gero Knittel,, Tim Rehkämper, Darya Korovkina, Paul Liedgens, Christian Fritz, Alessandro Torgovnick, Yussor Al-Baldawi, Mona Al-Maarri,Yupeng Cun (9th/32), …, Martin Peifer, Reinhard Buettner, Thorsten Persigehl, Christian Reinhardt:  Two mouse models reveal an actionable PARP1 dependence in aggressive chronic lymphocytic leukemia. Nature Communications, 2017，DOI: 10.1038/s41467-017-00210-6
• 6. Changjun Huang, Yupeng Cun, Haiqin Yu, Zhijun Tong, Bingguang Xiao, Zhongbang Song, Bingwu Wang, Yongping Li, Yong Liu,(2017) Transcriptomic profile of tobacco in response to Tomato zonate spot orthotospovirus infection. Virology Journal :14(1) .2017
• 5. 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 07/2015; 524(7563), DOI:10.1038/nature14664
• 4. Yupeng Cun, Holger Fröhlich: netClass: an R-package for network based, integrative biomarker signature discovery. Bioinformatics 01/2014; 30(9)., DOI:10.1093/bioinformatics/btu025
• 3. 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
• 2. 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
• 1. Yupeng Cun, Holger Fröhlich: Biomarker gene signature discovery integrating network knowledge. MPDI Biology, 2012 DOI:10.3390/biology1010005