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Boyang Zhao

Principal Scientist, Quantalarity Research Group LLC, 2016 - Present

Education
Ph.D. in Computational and Systems Biology, 2016
Massachusetts Institute of Technology

B.S.E. in Biomedical Engineering (Biochemical Concentration), 2011
Minor in Computer Science
College of Engineering
University of Michigan, Ann Arbor

Academic/Research Interests
My current research interest is in quantitative systems pharmacology, in the use of experimental and computational approaches in in vitro and in vivo systems to elucidate mechanisms of drug sensitivity and resistance to enable effective rational drug design.

Publications
* indicates co-first authorship

• Zhao, B.; Rao, Y.; Leighow, S.; O'Brien, E.P.; Gilbert, L.; Pritchard, J.R. A pan-CRISPR analysis of mammalian cell specificity identifies ultra-compact sgRNA subsets for genome-scale experiments. Nat Commun 2022. 13(1):625 [pubmed]
• Petrov, I.; Postadzhiyan, A.; Vasilev, D.; Kasabov, R.; Tokmakova, M.; Nikolov, F.; Istatkov, V.; Zhao, B.; Mutafchiev, D.; and Petkova, R. Familial Hypercholesterolemia Identification Algorithm in Patients with Acute Cardiovascular Events in A Large Hospital Electronic Database in Bulgaria: A Call for Implementation. Advances in Therapy 2021. 3 [pubmed]
• Farmanbar, M.; Ommeren, N., V.; Zhao, B. Semantic search with domain-specific word-embedding and production monitoring in Fintech. In Proceedings of the 28th International Conference on Computational Linguistics: System Demonstrations 2020. 28-33 [pdf]
• Leighow, S., M.; Liu, C.; Inam, H.; Zhao, B.; and Pritchard, J.R. Multi-scale Predictions of Drug Resistance Epidemiology Identify Design Principles for Rational Drug Design. Cell Reports 2020. 30(12), 3951-3963.e4 [pubmed]
• Zhao, B.; Pritchard, J.R. Evolution of the nonsense-mediated decay pathway is associated with decreased cytolytic immune infiltration. PLoS Comput Biol 2019. 15(10), e1007467 [pubmed]
• Zhao, B. Clinical Data extraction and normalization of Cyrillic electronic health records via deep-learning natural language processing. JCO Clin Cancer Inform 2019. 3, 1-9 [pubmed]
• Sun, D.; Dalin, S.; Hemann, M.T.; Lauffenburger, D.A.; Zhao, B. Differential selective pressure alters rate of drug resistance acquisition in heterogeneous tumor populations. Sci Rep 2016. 6, 36198 [pubmed]
• Zhao, B.; Pritchard, J.R. Inherited disease genetics improves the identification of cancer-associated genes. PLoS Genet 2016. 12(6), e1006081 [pubmed]
• Zhao, B.; Sedlak, J.C.; Srinivas, R.; Creixell P.; Pritchard, J.R.; Tidor, B.; Lauffenburger, D.A.; Hemann, M.T. Exploiting temporal collateral sensitivity in tumor clonal evolution. Cell 2016. 165(1), 234-246 [pubmed]
  MIT Spectrum (Spring 2016), lead article in Breakthroughs section, by Leda Zimmerman.
  The Washington Post (March 14) article by Ariana Cha.
• Zhao, B.; Hemann, M.T.; Lauffenburger, D.A. Intratumor heterogeneity alters most effective drugs in designed combinations. Proc Natl Acad Sci.USA 2014. 111(29), 10773-10778 [pubmed]
• Zhao, B.; Pritchard, J.R.; Lauffenburger, D.A.; Hemann, M.T. Addressing genetic tumor heterogeneity through computationally predictive combination therapy. Cancer Discov. 2014, 4(2), 166-74 [pubmed]
  Research Highlight: Jones, B Nat Rev Clin Oncol 11(2), 66 (2014). [pubmed]
  In the Spotlight: Fedele, C. et al. Cancer Discov 4(2), 146-148 (2014). [pubmed]
• He, Y.; Racz, R.; Sayers, S.; Lin, Y.; Todd, T.; Hur, J.; Li, Xi.; Patel, M.; Zhao, B.; Chung, M.; Ostrow, J.; Sylora, A.; Dungarani, P.; Ulysse, G.; Kochhar, K.; Vidri, B.; Strait, K.; Jourdian, G.W.; Xiang, Z. Updates on the web-based VIOLIN vaccine database and analysis system. Nucleic Acids Res. 2014, 42(D1), D1124-D1132 [pubmed]
• Zhao, B.; Pisitkun, T.; Hoffert, J.D.; Knepper, M.A.; Saeed, F. (2012) CPhos: a program to calculate and visualize evolutionarily conserved functional phosphorylation sites. Proteomics, 12(22), 3299-3303. [pubmed]
• Zhao, B.; Knepper, M.A.; Chou, C.L.; Pisitkun, T. (2012) Large-Scale Phosphotyrosine Proteomic Profiling of Rat Renal Collecting Duct Epithelium Reveals Predominance of Proteins Involved in Cell Polarity Determination. Am. J. Physiol. Cell Physiol., 302(1), C27-45. [pubmed]
  Editorial Focus: Ecelbarger, C.M. Am. J. Physiol. Cell Physiol. 302, C16-17 (2012). [pubmed]
• Zhao, B.; O'Brien, P. (2011) Kinetic Mechanism for the Excision of Hypoxanthine by Escherichia coli AlkA and Evidence for Binding to DNA Ends. Biochemistry, 50(20), 4350-4359. [pubmed]
• Feric, M.*; Zhao, B.*; Hoffert, J.D.; Pisitkun, T.; Knepper, M.A. (2011) Large-Scale Phosphoproteomic Analysis of Membrane Proteins in Renal Proximal and Distal Tubule. Am. J. Physiol. Cell Physiol., 300(4), C755-770. [pubmed]
  Editorial Focus: Pluznick, J.L. Am. J. Physiol. Cell Physiol. 300, C752-754 (2011). [pubmed]
• Xiang, Z.; Todd, T.; Ku, K.P.; Kovacic, B.L.; Larson, C.B.; Chen, F.; Hodges, A.P.; Tian, Y; Olenzek, E.A.; Zhao, B.; Colby, L.A.; Rush, H.G.; Gilsdorf, J.R.; Jourdian, G.W.; He, Y. (2008) VIOLIN: Vaccine Investigation and Online Information Network. Nucleic Acids Res., 36, D923-D928. [pubmed]

Curriculum vitae available upon request