Ruping Sun

Overview

Ruping Sun

Titles

Research Associate, Stanford University School of Medicine

Lab

Andrea Califano

Ruping Sun is a postdoctoral research scientist in the laboratory of Andrea Califano. The goal of his current research is to identify disease-driver genomic events or patterns by linking genomic changes with transcriptomic changes. One of his particular interests is to study the functional propagation of genomic variants through a ensemble of regulatory networks reversely engineered in the Califano Lab.

Previously, Ruping worked at the Max-Planck Institute for Molecular Genetics in Berlin, Germany, under the supervision of Stefan Haas and Martin Vingron. During his time in Germany, he focused on algorithm design for analyzing next-generation sequencing datasets. Ruping obtained his PhD in Fudan University, Shanghai, China.

Education History

PhD, Fudan University, Shanghai, China

Publications

* indicates equal author contributions

Fernandez-Cuesta L*, Sun R*, Menon R, George J, et al. Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data. Genome Biol. 2015 Jan 5;16:7. 

Fernandez-Cuesta L, Peifer M, Lu X, Sun R, et al. Frequent mutations in chromatin-remodelling genes in pulmonary carcinoids. Nat Commun. 2014 Mar 27;5:3518.

Fernandez-Cuesta L, Plenker D, Osada H, Sun R, et al. CD74-NRG1 fusions in lung adenocarcinoma. Cancer Discov. 2014 Apr;4(4):415-22.

Peifer M, Fernández-Cuesta L, Sos ML, George J, Seidel D, Kasper LH, Plenker D, Leenders F, Sun R, et al. Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer. Nat. Genet. 2012 Oct;44(10):1104-10.

Sun R, Love MI, Zemojtel T, Emde AK, Chung HR, Vingron M, Haas SA. Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads. Bioinformatics. 2012 Apr 1;28(7):1024-5.

Emde AK, Schulz MH, Weese D, Sun R, Vingron M, Kalscheuer VM, Haas SA, Reinert K. Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinformatics. 2012 Mar 1;28(5):619-27.

Love MI, Myšičková A, Sun R, Kalscheuer V, Vingron M, Haas SA. Modeling read counts for CNV detection in exome sequencing data. Stat Appl Genet Mol Biol. 2011 Nov 8;10(1). 

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. 2009 Feb 26;10:93.

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 (Landmark Ed). 2009 Jan 1;14:4058-70.

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. 2008 Oct 1;68(14):1496-509.