Ruping Sun

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Credentials

PhD

Bio

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

Research Summary

Publications

Wang Z, Xia Y, Mills L, Nikolakopoulos AN, Maeser N, Dehm SM, Sheltzer JM, and Sun R. Evolving copy number gains promote tumor expansion and bolster mutational diversification. Nat Commun 15, 2025 (2024). https://doi.org/10.1038/s41467-024-46414-5

Girish V, Lakhani AA, Thompson SL, Scaduto CM, Brown LM, Hagenson RA, Sausville EL, Mendelson BE, Kandikuppa PK, Lukow DA, Yuan ML, Stevens EC, Lee SN, Schukken KM, Akalu SM, Vasudevan A, Zou C, Salovska B, Li W, Smith JC, Taylor AM, Martienssen RA, Liu Y, Sun R, Sheltzer JM. Oncogene-like addiction to aneuploidy in human cancers. Science. 2023 Aug 25;381(6660):eadg4521. doi: 10.1126/science.adg4521.

Sun R and Nikolakopoulos AN.  Elements and evolutionary determinants of genomic divergence between paired primary and metastatic tumors.PLoS Computational Biology, March 17, 2021.https://doi.org/10.1371/journal.pcbi.1008838

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 element. Cell,  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.