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Siming Zhao, PhD

Title(s):
Assistant Professor of Biomedical Data Science

Department(s):
Biomedical Data Science

Education:
2010 B.S. Tsinghua University, Beijing
2015 Ph.D. Yale University, New Haven

Programs:
Norris Cotton Cancer Center
Quantitative Biomedical Sciences

Websites:
https://www.simingzhaolab.org/

Contact Information:


Professional Interests:

Dr. Zhao's research focuses on studying the genetic etiology of human diseases, in particular, cancer. Her lab develops computational methods and tools to analyze large-scale genomic datasets, aiming to translate data into biological insights. Specific areas of interest include modeling of mutation selection in cancer, genotype-phenotype association analysis, integration of multiple types of genomic datasets for disease gene discovery.

Rotations and Thesis Projects:

Methods development for studying mutations in noncoding regions in cancer
Impacts of genetic backgrounds for cancer phenotypes
Causal gene/pathway identification in genome wide association analysis

Biography:

Dr. Zhao completed her PhD in Genetics at Yale University and received post-doctoral training at University of Chicago. She has broad training in genetics, cancer biology, bioinformatics and statistical genetics. In the past, she developed computational methods to study the genetics of cancer and other complex diseases. She also also led the analysis of several cancer whole-exome sequencing projects. She is interested in the roles of genetic variations in cancer and computational methods to translate large-scale genomic data into disease mechanisms.


Selected Publications:

 

Integrated mutational landscape analysis of uterine leiomyosarcomas.
Choi J, Manzano A, Dong W, Bellone S, Bonazzoli E, Zammataro L, Yao X, Deshpande A, Zaidi S, Guglielmi A, Gnutti B, Nagarkatti N, Tymon-Rosario JR, Harold J, Mauricio D, Zeybek B, Menderes G, Altwerger G, Jeong K, Zhao S, Buza N, Hui P, Ravaggi A, Bignotti E, Romani C, Todeschini P, Zanotti L, Odicino F, Pecorelli S, Ardighieri L, Bilguvar K, Quick CM, Silasi DA, Huang GS, Andikyan V, Clark M, Ratner E, Azodi M, Imielinski M, Schwartz PE, Alexandrov LB, Lifton RP, Schlessinger J, Santin AD
Proc Natl Acad Sci U S A. 2021 Apr 13;118(15) pii: e2025182118. doi: 10.1073/pnas.2025182118.
PMID: 33876771

Allele-specific open chromatin in human iPSC neurons elucidates functional disease variants.
Zhang S, Zhang H, Zhou Y, Qiao M, Zhao S, Kozlova A, Shi J, Sanders AR, Wang G, Luo K, Sengupta S, West S, Qian S, Streit M, Avramopoulos D, Cowan CA, Chen M, Pang ZP, Gejman PV, He X, Duan J
Science. 2020 Jul 31;369(6503):561-565. doi: 10.1126/science.aay3983.
PMID: 32732423

Whole-exome sequencing of cervical carcinomas identifies activating ERBB2 and PIK3CA mutations as targets for combination therapy.
Zammataro L, Lopez S, Bellone S, Pettinella F, Bonazzoli E, Perrone E, Zhao S, Menderes G, Altwerger G, Han C, Zeybek B, Bianchi A, Manzano A, Manara P, Cocco E, Buza N, Hui P, Wong S, Ravaggi A, Bignotti E, Romani C, Todeschini P, Zanotti L, Odicino F, Pecorelli S, Donzelli C, Ardighieri L, Angioli R, Raspagliesi F, Scambia G, Choi J, Dong W, Bilguvar K, Alexandrov LB, Silasi DA, Huang GS, Ratner E, Azodi M, Schwartz PE, Pirazzoli V, Stiegler AL, Boggon TJ, Lifton RP, Schlessinger J, Santin AD
Proc Natl Acad Sci U S A. 2019 Nov 5;116(45):22730-22736. doi: 10.1073/pnas.1911385116. Epub 2019 Oct 17.
PMID: 31624127

Detailed modeling of positive selection improves detection of cancer driver genes.
Zhao S, Liu J, Nanga P, Liu Y, Cicek AE, Knoblauch N, He C, Stephens M, He X
Nat Commun. 2019 Jul 30;10(1):3399. doi: 10.1038/s41467-019-11284-9. Epub 2019 Jul 30.
PMID: 31363082

A Statistical Framework for Mapping Risk Genes from De Novo Mutations in Whole-Genome-Sequencing Studies.
Liu Y, Liang Y, Cicek AE, Li Z, Li J, Muhle RA, Krenzer M, Mei Y, Wang Y, Knoblauch N, Morrison J, Zhao S, Jiang Y, Geller E, Ionita-Laza I, Wu J, Xia K, Noonan JP, Sun ZS, He X
Am J Hum Genet. 2018 Jun 7;102(6):1031-1047. doi: 10.1016/j.ajhg.2018.03.023. Epub 2018 May 10.
PMID: 29754769

Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs.
Ward MC, Zhao S, Luo K, Pavlovic BJ, Karimi MM, Stephens M, Gilad Y
Elife. 2018 Apr 12;7 pii: e33084. doi: 10.7554/eLife.33084. Epub 2018 Apr 12.
PMID: 29648536

Mutational landscape of uterine and ovarian carcinosarcomas implicates histone genes in epithelial-mesenchymal transition.
Zhao S, Bellone S, Lopez S, Thakral D, Schwab C, English DP, Black J, Cocco E, Choi J, Zammataro L, Predolini F, Bonazzoli E, Bi M, Buza N, Hui P, Wong S, Abu-Khalaf M, Ravaggi A, Bignotti E, Bandiera E, Romani C, Todeschini P, Tassi R, Zanotti L, Odicino F, Pecorelli S, Donzelli C, Ardighieri L, Facchetti F, Falchetti M, Silasi DA, Ratner E, Azodi M, Schwartz PE, Mane S, Angioli R, Terranova C, Quick CM, Edraki B, Bilguvar K, Lee M, Choi M, Stiegler AL, Boggon TJ, Schlessinger J, Lifton RP, Santin AD
Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):12238-12243. Epub 2016 Oct 10.
PMID: 27791010

Dual CCNE1/PIK3CA targeting is synergistic in CCNE1-amplified/PIK3CA-mutated uterine serous carcinomas in vitro and in vivo.
Cocco E, Lopez S, Black J, Bellone S, Bonazzoli E, Predolini F, Ferrari F, Schwab CL, Menderes G, Zammataro L, Buza N, Hui P, Wong S, Zhao S, Bai Y, Rimm DL, Ratner E, Litkouhi B, Silasi DA, Azodi M, Schwartz PE, Santin AD
Br J Cancer. 2016 Jul 26;115(3):303-11. doi: 10.1038/bjc.2016.198. Epub 2016 Jun 28.
PMID: 27351214

Genomic characterization of sarcomatoid transformation in clear cell renal cell carcinoma.
Bi M, Zhao S, Said JW, Merino MJ, Adeniran AJ, Xie Z, Nawaf CB, Choi J, Belldegrun AS, Pantuck AJ, Kluger HM, Bilguvar K, Lifton RP, Shuch B
Proc Natl Acad Sci U S A. 2016 Feb 23;113(8):2170-5. doi: 10.1073/pnas.1525735113. Epub 2016 Feb 10.
PMID: 26864202

Landscape of somatic single-nucleotide and copy-number mutations in uterine serous carcinoma.
Zhao S, Choi M, Overton JD, Bellone S, Roque DM, Cocco E, Guzzo F, English DP, Varughese J, Gasparrini S, Bortolomai I, Buza N, Hui P, Abu-Khalaf M, Ravaggi A, Bignotti E, Bandiera E, Romani C, Todeschini P, Tassi R, Zanotti L, Carrara L, Pecorelli S, Silasi DA, Ratner E, Azodi M, Schwartz PE, Rutherford TJ, Stiegler AL, Mane S, Boggon TJ, Schlessinger J, Lifton RP, Santin AD
Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):2916-21. doi: 10.1073/pnas.1222577110. Epub 2013 Jan 28.
PMID: 23359684

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