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Quantitative Sciences

The study of biostatistics, bioinformatics, systems biology and genomics focuses on developing and applying statistical and mathematical models in close collaboration with biomedical researchers. The mission of the Program in Quantitative Sciences is to train researchers who will contribute to biomedical research by developing new methods for the design and analysis of research studies and by formulating mathematical models of biologic systems, thereby contributing to our understanding of cancer biology and disease processes. The Quantitative Sciences Program currently has around 50 students and 70 faculty.

Alumni 

2021 Graduates
Chen, Jiun-Sheng (Dr. Chad Huff)
Srinivasan, Sanjana (Dr. Giulio Draetta)

2020 Graduates
Ramesh, Naveen (Dr. Nick Navin)
Lenoir, Walter (Dr. Traver Hart)
Davis, Alexander (Dr. Nick Navin)
Zhou, Yanhong (Dr. J. Jack Lee) 

2019 Graduates
Yang, Jie (Dr. Erik Sulman)
Xia, Fang (Dr. Xuelin Huang)
Sivakumar, Smruthy (Dr. Paul Scheet) 

2018 Graduates
Zhang, Youyi (Dr. Jeffrey Morris)
Liu, Yihua (Dr. Paul Scheet)
Zhou, Heng (Dr. Ying Yuan)

Alumni Publications

Alexander Davis

Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer.
Leung ML, Davis A, Gao R, Casasent A, Wang Y, Sei E, Vilar E, Maru D, Kopetz S, Navin NE.
Genome Res. 2017 Aug;27(8):1287-1299. doi: 10.1101/gr.209973.116. Epub 2017 May 25.
PMID: 28546418 

*Tumor evolution: Linear, branching, neutral or punctuated?
Davis A, Gao R, Navin N.
Biochim Biophys Acta. 2017 Apr;1867(2):151-161. doi: 10.1016/j.bbcan.2017.01.003. Epub 2017 Jan 19. Review.
PMID:28110020

Punctuated copy number evolution and clonal stasis in triple-negative breast cancer.
Gao R, Davis A, McDonald TO, Sei E, Shi X, Wang Y, Tsai PC, Casasent A, Waters J, Zhang H, Meric-Bernstam F, Michor F, Navin NE.
Nat Genet. 2016 Oct;48(10):1119-30. doi: 10.1038/ng.3641. Epub 2016 Aug 15.
PMID:27526321

*Computing tumor trees from single cells.
Davis A, Navin NE.
Genome Biol. 2016 May 26;17(1):113. doi: 10.1186/s13059-016-0987-z.
PMID: 27230879

Walter Frank Lenoir

network of human functional gene interactions from knockout fitness screens in cancer cells
Eiru Kim, Merve Dede, Walter F Lenoir, Gang Wang, Sanjana Srinivasan, Medina Colic, Traver Hart
Life Sci Alliance. 2019 Apr; 2(2): e201800278. Published online 2019 Apr 12. doi: 10.26508/lsa.201800278
PMCID: PMC6464042

*PICKLES: the database of pooled in-vitro CRISPR knockout library essentiality screens.
Lenoir WF, Lim TL, Hart T.
Nucleic Acids Res. 2018 Jan 4;46(D1):D776-D780. doi: 10.1093/nar/gkx993.
PMID: 29077937

DNA polymerase ι compensates for Fanconi anemia pathway deficiency by countering DNA replication stress
Rui Wang, Walter F. Lenoir, Chao Wang, Dan Su, Megan McLaughlin, Qianghua Hu, Xi Shen, Yanyan Tian, Naeh Klages-Mundt, Erica Lynn, Richard D. Wood, Junjie Chen, Traver Hart, Lei Li
Proceedings of the National Academy of Sciences Dec 2020, 202008821; DOI: 10.1073/pnas.2008821117

Yihua Liu

*Identification of thresholds for dichotomizing DNA methylation data.
Liu Y, Ji Y, Qiu P.
EURASIP J Bioinform Syst Biol. 2013 Jun 6;2013(1):8. doi: 10.1186/1687-4153-2013-8.
PMID: 23742247

Naveen Ramesh

*Decoding the evolutionary response to prostate cancer therapy by plasma genome sequencing
Ramesh N, Sei E, Tsai PC, Bai S, Zhao Y, Troncoso P, Corn PG, Logothetis C, Zurita AJ, Navin NE. Decoding the evolutionary response to prostate cancer therapy by plasma genome sequencing. Genome Biol. 2020 Jul 6;21(1):162. doi: 10.1186/s13059-020-02045-9
PMID: 32631448; PMCID: PMC7336456

Smruthy Sivakumar

TBX2 subfamily suppression in lung cancer pathogenesis: a high-potential marker for early detection.
Khalil AA, Sivakumar S, Lucas FAS, McDowell T, Lang W, Tabata K, Fujimoto J, Yatabe Y, Spira A, Scheet P, Nemer G, Kadara H.
Oncotarget. 2017 Aug 4;8(40):68230-68241. doi: 10.18632/oncotarget.19938. eCollection 2017 Sep 15.
PMID: 28978111

*Genomic Landscape of Atypical Adenomatous Hyperplasia Reveals Divergent Modes to Lung Adenocarcinoma.
Sivakumar S, Lucas FAS, McDowell TL, Lang W, Xu L, Fujimoto J, Zhang J, Futreal PA, Fukuoka J, Yatabe Y, Dubinett SM, Spira AE, Fowler J, Hawk ET, Wistuba II, Scheet P, Kadara H.
Cancer Res. 2017 Nov 15;77(22):6119-6130. doi: 10.1158/0008-5472.CAN-17-1605. Epub 2017 Sep 26.
PMID: 28951454

Rapid and powerful detection of subtle allelic imbalance from exome sequencing data with hapLOHseq.
San Lucas FA, Sivakumar S, Vattathil S, Fowler J, Vilar E, Scheet P.
Bioinformatics. 2016 Oct 1;32(19):3015-7. doi: 10.1093/bioinformatics/btw340. Epub 2016 Jun 10.
PMID: 27288500

Youyi Zhang

Radiomic analysis in prediction of Human Papilloma Virus status.
Yu K, Zhang Y, Yu Y, Huang C, Liu R, Li T, Yang L, Morris JS, Baladandayuthapani V, Zhu H.
Clin Transl Radiat Oncol. 2017 Nov 6;7:49-54. doi: 10.1016/j.ctro.2017.10.001. eCollection 2017 Dec.
PMID: 29594229


Heng Zhou

*Accuracy, Safety, and Reliability of Novel Phase I Trial Designs.
Zhou H, Yuan Y, Nie L.
Clin Cancer Res. 2018 Apr 16. pii: clincanres.0168.2018. doi: 10.1158/1078-0432.CCR-18-0168. [Epub ahead of print]
PMID: 29661774

*BOP2: Bayesian optimal design for phase II clinical trials with simple and complex endpoints.
Zhou H, Lee JJ, Yuan Y.
Stat Med. 2017 Sep 20;36(21):3302-3314. doi: 10.1002/sim.7338. Epub 2017 Jun 7.
PMID: 28589563