Publications

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

In the Oven

  • 1. Xin Fang, Yupeng Cun, Dongmei Li, Linlin Wang, Huanxing Ren, Yanni Chen, Boting Li, Hongyu Tang, Junmian Tian, Xiaohan Tang, Yuan-wen Duan, Jiajia Wang, Mao Sun, Shuai Liu, Xiaolong Li, Junbo Yang, Yongping Yang, Yingtong Di*, Xiaojiang Hao*,Euphorbia peplus genome and characterization of BAHD enzymes involved in Euphorbia diterpenoid biosynthesis. 2022 (under review)
  • 2. Yang Guo, Shuzhen Wang, Liang Chang, Kun Xie, Xiguo Yuan*, Yupeng Cun*, Inferencing subclonal structure via an elastic-net penalty in bulk cancer genomic data. 2022 (under review)

Major contribution papers

  1. 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.
  2. 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, 101353(42)
  3. Dentro, …., Yupeng Cun(23th), …, Peter Van Loo, Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes, Cell (2021) 184(8), P2239-2254.E39
  4. Yulia Rubanova, Ruian Shi, Caitlin F. Harrigan, …,Yupeng Cun,…, Quaid Morris(75 total authors), Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSigNature Communications (2021) 11(1):731
  5. 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.
  6. 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).
  7. Marek Cmero, Ke Yuan, Cheng Soon Ong, …,Yupeng Cun,…, Geoff Macintyre(75 total authors), Inferring structural variant cancer cell fractionNature Communications(2020) 11(1):730
  8. Peter J. Campbell, Gad Getz, Jan O Korbel, …,Yupeng Cun,…, Jiashan Zhang(1318 total authors), Pan-cancer analysis of whole genomes, Nature (2020) 578 (7793), 82-93
  9. Moritz Gerstung, Clemency Jolly, Ignaty Leshchiner, …,Yupeng Cun,…, Peter Van Loo(71 total authors), The evolutionary history of 2,658 cancers, Nature (2020) 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(2018)
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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. Nature2015; 524(7563),
  16. Yupeng Cun, Holger Fröhlich: netClass: an R-package for network based, integrative biomarker signature discovery. Bioinformatics2014; 30(9)., DOI:10.1093/bioinformatics/btu025
  17. Yupeng Cun, Holger Fröhlich: Network and data integration for biomarker signature discovery via network smoothed T-statistics. PLoS ONE2013; 8(9):e73074., DOI:10.1371/journal.pone.0073074
  18. 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
  19. Yupeng Cun, Holger Fröhlich: Biomarker gene signature discovery integrating network knowledge. MPDI Biology, 2012 DOI:10.3390/biology1010005