Ruping Sun, PhD

Assistant Professor, Department of Laboratory Medicine and Pathology

Ruping Sun

Contact Info

ruping@umn.edu

Office Phone 612-626-5675

Mailing Address:
Masonic Cancer Research Ctr
2812A (Campus Delivery Code)
1st Floor Mailroom CCRB
2231 6th St SE
Minneapolis, MN 55455

Postdoctoral Research Fellowship, Department of Systems Biology, Columbia University, 2013-2015

Postdoctoral Research Fellowship, Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 2009-2011

PhD, Institute of Genetics, Fudan University, Shanghai, 2009


Summary

Sun Lab Website

Dr. Sun is a computational geneticist with a PhD degree in genetics His research focus is on the translational genomics of solid tumors in conjunction with the Masonic Cancer Center.

Sun has developed considerable expertise in algorithm design and statistical analysis of (epi)genetic sequencing data, as well as in the computational modeling of cancer, such as gene regulatory circuits and cellular automata models. For example, he pioneered research linking intra-tumor heterogeneity with underlying tumor growth dynamics using a data-driven modeling approach of multi-region sequencing (MRS) of solid tumors. He also first introduced regional-assembly into fusion transcript prediction and identified CD74-NRG1 as a potential target of the deadly invasive mucinous subtype of lung cancer. The unique experiences and quantitative training have equipped Sun to initiate a team effort to computationally decompose and model tumor heterogeneity, connecting the multiple facets of tumor evolutionary patterns to clinical features. His group will innovate algorithms and computational methods that advance a mechanistic understanding of tumor evolution and that are broadly utilized by the cancer bioinformatics community.

Understanding the underlying mechanisms behind the initiation, clonal expansion and progression of human cancers requires collaborative teamwork, in Sun's view. Mentoring trainees and teaching courses is a particular interest of his. The future of the fast-moving field of cancer bioinformatics will depend on the ability of students to develop analytical skills and a broader mindset for critical thinking.

Sun Lab Website

Expertise

Bioinformatics; Computational genomics of solid tumors

Research

Research Methods/Techniques

Translational genomics of solid tumors; Algorithm design and statistical analysis of (epi)genetic sequencing data; Computational modeling; Multi-region sequencing (MRS); Next generation sequencing (NGS)

Publications

Z Hu, J Ding, Z Ma, R Sun, JA Seoane, JS Shaffer, CJ Suarez...  Quantitative evidence for early metastatic seeding in colorectal cancer.  Nat Genet. 51(7): 1113-1122, 2019. doi: 10.1038/s41588-019-0423-x. Epub 2019 Jun 17.

SW Cho, J Xu, R Sun, MR Mumbach, AC Carter, YG Chen, KE Yost, J Kim, ...   Promoter of lncRNA gene PVT1 is a tumor-suppressor DNA boundary elementCell,  173 (6), 1398-1412, 2018. e22

Ruping Sun, Zheng Hu, Andrea Sottoriva, Trevor A Graham, Arbel Harpak, Zhicheng Ma, Jared M Fischer, Darryl Shibata & Christina Curtis, Between-region genetic divergence reflects the mode and tempo of tumor evolution. Nature Genetics, 49: 1015–1024, 2017.

Z Hu, R Sun, C Curtis.  A population genetics perspective on the determinants of intra-tumor heterogeneity.  Biochimica et Biophysica Acta (BBA)-Reviews on Cancer 1867 (2), 109-126, 2017.

Lynnette Fernandez-Cuesta*, Ruping Sun*, Roopika Menon, Julie George, Susanne Lorenz, Leonardo A Meza-Zepeda, Martin Peifer, Dennis Plenker, Johannes M Heuckmann, Frauke Leenders, et. al., Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data. Genome Biology, 16(1): 7, 2015. (*: equal contribution)

L Fernandez-Cuesta, M Peifer, J George, A De Reynies, R Sun, ...Genomic characterization of large-cell neuroendocrine lung tumors.  Journal of Thoracic Oncology 10 (9), S185-S185, 2015.

L Fernandez-Cuesta, D Plenker, H Osada, R Sun, R Menon, F Leenders, ...   CD74–NRG1 fusions in lung adenocarcinoma.  Cancer discovery 4 (4), 415-422, 2014

L Fernandez-Cuesta, M Peifer, X Lu, R Sun, L Ozreti?, D Seidel, T Zander, ... Frequent mutations in chromatin-remodelling genes in pulmonary carcinoids.  Nature communications 5, 3518, 2014.