I am a researcher interested in applying machine learning and statistics to computational biology, and working as Director  and Professor of the Center for iFlora Bioinformatics at Kunming Institute of Botany, Chinese Academy of Science.

My major research interest concerns the development of statistical and machine learning methods and softwares for computational biology. I am particularly interested in complex biological data modeling, such as high-throughput genomic data, network biology, population genomics and related evolutionary problems. Currently, my research  projects are mainly focus on following topics:

  • Comparative genomics
  • de novo assembly of plant genome
  • Population genomics

All publications

  1. 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,DOI: 10.1038/nprot.2018.033
  2. Julie George*, Jing Shan Lim*, Se Jin Jang, Yupeng Cun(4th/96), … , Roman K. Thomas: Comprehensive genomic profiles of small cell lung cancer. Nature 07/2015; 524(7563), DOI:10.1038/nature14664
  3. Yupeng Cun, Holger Fröhlich: netClass: an R-package for network based, integrative biomarker signature discovery. Bioinformatics01/2014; 30(9)., DOI:10.1093/bioinformatics/btu025
  4. 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
  5. Yupeng Cun, Holger Fröhlich: Integrating Prior Knowledge Into Prognostic Biomarker Discovery based on Network Structure, arxiv.org/abs/1212.3214
  6. 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
  7. Yupeng Cun#, Holger Fröhlich: Biomarker gene signature discovery integrating network knowledge. MPDI Biology, 2012 DOI:10.3390/biology1010005
  8. Julie George, …, Yupeng Cun(28th /68), …, , Roman Thomas*, Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct molecular subtypes of high-grade neuroendocrine lung tumorsNature Communications, | (2018) 9:1048 |DOI: 10.1038/s41467-018-03099-x
  9. Changjun Huang, Yupeng Cun, …, Yong Liu,(2017) Transcriptomic profile of tobacco in response to Tomato zonate spot orthotospovirus infectionVirology Journal :14(1) .2017
  10. Gero Knittel, …, Yupeng Cun (9th/32), …., Christian Reinhardt,  Two mouse models reveal an actionable PARP1 dependence in aggressive chronic lymphocytic leukemiaNature Communications, 2017,DOI: 10.1038/s41467-017-00210-6