This is Ruping Sun. A Bioinformatician and Geneticist, who does data driven modelling, visualization and bias collection/correction in the field of Cancer Genomics/Transcriptomics. Here posted my research activities and some thoughts in Cancer Bioinformatics and Genomic Data Science. I am currently a research associate in Dr. Curtis' Lab, the Department of Genetics and Medicine at Stanford University. My current work involves dissecting Intra-Tumor Heterogeneity (ITH) using Multi-Region, Longitudinal and Single-Cell sampling of clinical tumor samples. I am interested in unraveling following,
- Can various types of somatic mutations inform clonal composition and growth patterns?
- Does genetic background shape somatic evolution in human cancers and how?
- Propagation of genetic variants onto epi-genetic networks that in turn impacts genetics.
- Better ways to perform visualization analysis for Cancer research.
- Can biases in sequencing oriented research be utilized to strengthen our conclusions?
Our ability to answer these questions depends on not only technology advancement but also the development of better suited algorithms. Hence I devoted myself in constructing relevant computational tools, such as
Breakpointer for using sequencing artifacts to enhance SV detection,
TRUP for a thorough RNA-seq analysis, and more recently
VAP for mutation detection in multi region sequencing of tumor specimen.