Sun, Ruping

Research Interests:

• microRNA-mediated RNA-RNA regulation
• transcriptome analysis using RNA-seq data
• genomic variations <-> diseases/phenotypes
• cancer systems biology
• computational methods in Next Generation Sequencing

Short Vita:

• 2009.11-today:
  Postdoctoral researcher in department of computational molecular biology at the Max-Planck-Institute for Molecular Genetics.
  Currently I am studying the cancer transcriptome using RNA-seq data. Ongoing projects also include detecting structural variants from genomic resequencing data and microRNA-mediated RNA-RNA regulation. My research work is mainly supervised by Stefan Haas and Martin Vingron.
• 2002-2008:
  Ph.D candidate in the subject of human and medical molecular genetics. I was studying in state key laboratory of genetic engineering, Institute of Genetics, Fudan University, Shanghai, supervised by professor Yao Li and Yumin Mao.
  My Dissertation "Meta-analysis of Microarray Datasets" discusses the strategies in meta-analysis of static and time-series microarray datasets, as well as the application of these strategies to study gene regulation with the help of other genomic information.
• Before 2002:
  Undergraduate Courses in School of Life Sciences, Fudan University, Shanghai.

Publications:

• Sun R, Love MI, Zemojtel T, Emde AK, Chung HR, Vingron M, Haas SA. (2012)
  Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads.
  Bioinformatics, epub. [PubMed]
• Emde AK, Schulz MH, Weese D, Sun R, Vingron M, Kalscheuer VM, Haas SA, Reinert K. (2012)
  Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS.
  Bioinformatics, epub. [PubMed]
• Love MI, Mysickova A, Sun R, Kalscheuer V, Vingron M; Haas SA. (2011)
  Modeling Read Counts for CNV Detection in Exome Sequencing Data.
  Statistical Applications in Genetics and Molecular Biology: Vol. 10: Iss. 1, Article 52. [Journal Link]
• Sun R., Fu X., Li Y., Xie Y., Mao Y.
  Global gene expression analysis reveals reduced abundance of putative microRNA targets in human prostate tumours,
  BMC Genomics ,Vol.10, 2009, p.93. [PubMed]
• Sun R., Fu X., Guo F., Ma Z., Goulbourne C., Jiang M., Li Y., Xie Y., Mao Y.
  A strategy for meta-analysis of short time series microarray datasets,
  Front. Biosci., vol.14, 2009, p.4058-4070. [PubMed]
• Jiang M., Li M., Fu X., Huang Y., Qian H., Sun R., Mao Y., Xie Y., Li Y.
  Simultaneously detection of genomic and expression alterations in prostate cancer using cDNA microarray,
  Prostate, vol.68, n.14, 2008, p.1496-1509. [PubMed]
• Sun L., Huang S., Wu Q., Gu S., Fu X., Yu K., Lu F., Ji C., Feng C., Sun R., Xie Y., Mao Y
  Identification of genes differentially regulated by transcription factor, AP-2delta,
  Front. Biosci., vol.12, 2007, p.1699-1706. [PubMed]
• Li X., Ji C., Gu J., Xu J., Jin Z., Sun L., Zou X., Lin Y., Sun R., Wang P., Gu S., Mao Y.
  Molecular cloning and characterization of AAAS-V2, a novel splice variant of human AAAS,
  Mol. Biol. Rep., vol.32, n.2, 2005, p.127-131. [PubMed]

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