Principal investigator
Name:
Liye ZhangAssistant Professor , PhD, Assistant Professor
Position:
Affiliation:
School of Life Science and Technology
Honor:
Education Background:
- 2003-2007, Shanghai Jiaotong University, School of Life Science and Technology, B.S.
- 2007-2012, Penn State University (Advisors: Franklin Pugh and Hong Ma), Ph.D.
Working Experience:
- 2012-2017, Boston University School of Medicine (Advisor: Stefano Monti), Postdoc Associate in Computational Biomedicine
- 2017/05-Present, ShanghaiTech University, School of Life Science and Technology, Assistant Professor (TENURE-TRACK)
Group Introduction
Research Area:
Bioinformatics, Genomics, Precision Medicine
Research Interests:
The research of our lab focuses on interpreting the meaning of large biological omics data, especially in the area of precision medicine. The long-term goal of our lab is to derive mathematic models that can explain and predict the biological phenomena, especially in the clinical domain. Currently we are focusing on two major research areas.
1. We are interested in developing DNA/RNA/epigenetics based Biomarkers to characterize subgroups related to disease (mostly cancer for now, but not limited to cancer) subtypes and treatment response, and then understand the underlying biology by integrative analyses and functional validation.
2. We are also interested in long-term collaboration with other labs to elucidate the mechanisms related to human diseases. The data mining and bioinformatics analyses will involve the integration of multi-dimensional omics data and require tailored algorithm/statistical method development, thus providing data-driven hypothesis to facilitate and guide experimental validation. We currently have ongoing collaboration with Ruslan Afasizhev’s lab on understanding the mechanisms of mitochondria transcription regulation and RNA editing in Trypanosoma brucei.
Lab Webpage: https://bioliyezhang.github.io
Representative Publications (*First Author, # Corresponding Author)
- 1. Zhang, Liye#*; Yang, Chih-Sheng; Varelas, Xaralabos; Monti, Stefano#; Zhang, Liye#*; Yang, Chih-Sheng; Varelas, Xaralabos; Monti, Stefano#.Altered RNA editing in 3 ' UTR perturbs microRNA-mediated regulation of oncogenes and tumor-suppressors.SCIENTIFIC REPORTS. 2016. 6.
- 2. Voena, Claudia*; Varesio, Lydia M.; Zhang, Liye; Menotti, Matteo; Poggio, Teresa; Panizza, Elena; Wang, Qi; Minero, Valerio G.; Fagoonee, Sharmila; Compagno, Mara; Altruda, Fiorella; Monti, Stefano; Chiarle, Roberto#.Oncogenic ALK regulates EMT in non-small cell lung carcinoma through repression of the epithelial splicing regulatory protein 1.ONCOTARGET. 2016. 7(22):33316-33330.
- 3. Chapuy, Bjoern*; Roemer, Margaretha G. M.; Stewart, Chip; Tan, Yuxiang; Abo, Ryan P.; Zhang, Liye; Dunford, Andrew J.; Meredith, David M.; Thorner, Aaron R.; Jordanova, Ekaterina S.; Liu, Gang; Feuerhake, Friedrich; Ducar, Matthew D.; Illerhaus, Gerald; Gusenleitner, Daniel; Linden, Erica A.; Sun, Heather H.; Homer, Heather; Aono, Miyuki; Pinkus, Geraldine S.; Ligon, Azra H.; Ligon, Keith L.; Ferry, Judith A.; Freeman, Gordon J.; van Hummelen, Paul; Golub, Todd R.; Getz, Gad; Rodig, Scott J.; de Jong, Daphne; Monti, Stefano; Shipp, Margaret A.#.Targetable genetic features of primary testicular and primary central nervous system lymphomas.BLOOD. 2016. 127(7):869-881.
- 4. Chapuy, Bjoern*; Cheng, Hongwei; Watahiki, Akira; Ducar, Matthew D.; Tan, Yuxiang; Chen, Linfeng; Roemer, Margaretha G. M.; Ouyang, Jing; Christie, Amanda L.; Zhang, Liye; Gusenleitner, Daniel; Abo, Ryan P.; Farinha, Pedro; von Bonin, Frederike; Thorner, Aaron R.; Sun, Heather H.; Gascoyne, Randy D.; Pinkus, Geraldine S.; van Hummelen, Paul; Wulf, Gerald G.; Aster, Jon C.; Weinstock, David M.; Monti, Stefano; Rodig, Scott J.; Wang, Yuzhuo; Shipp, Margaret A.#.Diffuse large B-cell lymphoma patient-derived xenograft models capture the molecular and biological heterogeneity of the disease.BLOOD. 2016. 127(18):2203-2213.
- 5. Hiemer, Samantha E.*; Zhang, Liye; Kartha, Vinay K.; Packer, Trevor S.; Almershed, Munirah; Noonan, Vikki; Kukuruzinska, Maria; Bais, Manish V.; Monti, Stefano; Varelas, Xaralabos#.A YAP/TAZ-Regulated Molecular Signature Is Associated with Oral Squamous Cell Carcinoma.MOLECULAR CANCER RESEARCH. 2015. 13(6):957-968.
- 6. Suematsu, Takuma*; Zhang, Liye; Aphasizheva, Inna; Monti, Stefano; Huang, Lan; Wang, Qi; Costello, Catherine E.; Aphasizhev, Ruslan#.Antisense Transcripts Delimit Exonucleolytic Activity of the Mitochondrial 3 ' Processome to Generate Guide RNAs.MOLECULAR CELL. 2016. 61(3):364-378.
- 7. Aphasizheva, Inna*; Zhang, Liye; Wang, Xiaorong; Kaake, Robyn M.; Huang, Lan; Monti, Stefano; Aphasizhev, Ruslan#.RNA Binding and Core Complexes Constitute the U-Insertion/Deletion Editosome.MOLECULAR AND CELLULAR BIOLOGY. 2014. 34(23):4329-4342.
- 8. Zhang, Liye*; Ma, Hong#; Pugh, B. Franklin#.Stable and dynamic nucleosome states during a meiotic developmental process.GENOME RESEARCH. 2011. 21(6):875-884.
- 9. Rhee, Ho Sung*; Bataille, Alain R.; Zhang, Liye; Pugh, B. Franklin#.Subnucleosomal Structures and Nucleosome Asymmetry across a Genome.CELL. 2014. 159(6):1377-1388.
- 10. Zhang, Liye*; Sement, Francois M.; Suematsu, Takuma; Yu, Tian; Monti, Stefano; Huang, Lan; Aphasizhev, Ruslan; Aphasizheva, Inna#.PPR polyadenylation factor defines mitochondrial mRNA identity and stability in trypanosomes.EMBO JOURNAL. 15 Aug 2017. 36(16):2435-2454.
- 11. Wu, Pin*; Hou, Linjun; Zhang, Yingdong; Zhang, Liye#.Phylogenetic Tree Inference: A Top-Down Approach to Track Tumor Evolution.FRONTIERS IN GENETICS. 07 Feb 2020. 10.
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