Liye Zhang    Assistant Professor, PI
InstituteSchool of Life Science and Technology
Research AreaBioinformatics, Genomics, Precision Medicine

2003-2007 B.S. in Biotechnology, Shanghai Jiaotong University, School of Life Science and Technology
2007-2012 Ph.D. in Cell and Developmental Biology, Penn State University (Advisors: Franklin Pugh and Hong Ma)
2012-2017 Postdoc Associate in Computational Biomedicine, Boston University School of Medicine (Advisor: Stefano Monti)
2017.5 to Present: Assistant Professor, PI at ShanghaiTech University, School of Life Science and Technology

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:

Selected Publications

Cancer Genomics

·  Liye Zhang*(Co-corresponding author), Chih-Cheng Yang, Xaralabos Varelas, Stefano Monti*.Altered A-to-I RNA editing in 3' UTR perturbs microRNA-mediated regulation of oncogenes and tumor suppressor genes.Scientific Reports2016 Mar 16; 6:23226 (pdf)

·  Claudia Voena*, Lydia Varesio*,Liye Zhang* (Co-first author), Matteo Menotti, Teresa Poggio, Elena Panizza, Qi Wang, Valerio Minero, Shamila Fagonee, Mara Compagno, Fiorella Altruda, Stefano Monti, Roberto Chiarle.Oncogenic ALK regulates EMT in Non-Small Cell Lung Carcinoma through repression of the epithelial splicing regulatory protein 1.Oncotarget2016 May 31;7(22):33316-30. (pdf)

·  Bjoern Chapuy, Margaretha Roemer, Chip Stewart, Yuxiang Tan, Ryan Abo,Liye Zhang, et al, Stefano Monti, Margaret Shipp.Targetable genetic features of primary testicular and primary central nervous system lymphomas. Blood2016 Feb 18; 127 (7):869-881 (pdf)

·  Bjoern Chapuy, Hongwei Cheng, Akira Watahiki, Matthew Ducar, Daniel Gusenleitner, Linfeng Chen, Margaretha Roemer, Jing Quyang, Amanda Christie,Liye Zhang et al, Margaret Shipp.Diffuse Large B-cell Lymphoma Patient-derived Xenograft Models Capture the Molecular and Biologic Heterogeneity of the Disease.(E-published in Blood)(pdf)

·  Samantha Hiemer,Liye Zhang, Vinay Kartha, Munirah Almershed, Stefano Monti, Maria Kukuruzinska, Xaralabos Varelas.A YAP/TAZ-regulated transcriptional signature associated with Oral Squamous Cell Carcinoma.Molecular Cancer Research. 2015 Jun; 13(6): 957-968 (pdf)

Pathogen Trypanosoma Mitochondrial transcription regulation and RNA editing

·  Takuma Suematsu*,Liye Zhang*(Co-first author), Inna Aphasizheva, Stefano Monti, Lan Huang, Catherine Costello, Ruslan Aphasizhev.Antisense Transcripts Impede Uridylation-induced Exonucleolytic Degradation to Generate Guide RNAs.Molecular Cell2016 Feb 4; 61 (3): 364-378 (pdf)

·  Inna Aphasizheva*,Liye Zhang*(Co-first author), Xiaorong Wang, Robyn Kaake, Lan Huang, Stefano Monti and Ruslan Aphasizhev.RNA binding and core complexes constitute the u-insertion/deletion editosome.Molecular and Cellular Biology2014 Dec 1; 34(23): 4329-42 (pdf)

Epigenetics/Chromatin Regulation

·  Liye Zhang, Hong Ma, Frank Pugh.Stable and dynamic nucleosome states during a meiotic developmental process.Genome Research2011 Jun; 21(6): 875-884. (pdf)

·  Ho Sung Rhee, Alain R. Bataille,Liye Zhang, Benjamin F Pugh.Subnucleosomal Structures and Nucleosome Asymmetry Across a Genome.Cell2014 Dec 4; 159(6): 1377-1388 (pdf)