NAME: Xiaxia Yu, PHD

eRA COMMONS USER NAME (credential, e.g., agency login):

POSITION TITLE: Research Assistant Professor of Stony Brook Hospital

EDUCATION/TRAINING

A. Personal Statement

I have a broad training and expertise in high dimensional computing and machine learning algorithm development on biomedical data. I have several publications in this area. Recently, I have been working on developing the web-based visualization tools for hospital quality control as well as the decision making team. In this project, I will focus on the software and web-based interactive interface development. My training, expertise, and motivation will be important and necessary to successfully carry out the proposed research project and provide clinical insight for this R21 proposal.

B. Positions and Honors

2014- present             Research Assistant Professor, Department of Biomedical Informatics , Stony Brook University, Stony Brook, NY .

C. Contribution to Science

1. Developing high dimensional data computing algorithms is essential for software development in this project. My research experience and publications have focused on developing classification and feature extraction algorithms on biomedical data. They provided me solid background on algorithm design and software development and deep understanding of high dimensional datasets.

a.    Chang YC, Yu X, Zhang Y, Tie Y, Wang YF, Yashchuk S, Ghosh AK, Harrison RW, Weber IT. Potent antiviral HIV-1 protease inhibitor GRL-02031 adapts to the structures of drug resistant mutants with its P1'-pyrrolidinone ring. Journal of medicinal chemistry. 2012; 55(7):3387-97. NIHMSID: NIHMS363524 PubMed [journal] PMID: 22401672, PMCID: PMC3355519

b.    Shen CH, Tie Y, Yu X, Wang YF, Kovalevsky AY, Harrison RW, Weber IT. Capturing the reaction pathway in near-atomic-resolution crystal structures of HIV-1 protease. Biochemistry. 2012; 51(39):7726-32. NIHMSID: NIHMS407755 PubMed [journal] PMID: 22963370, PMCID: PMC3476052

c.    Yu X, Weber IT, Harrison RW. Sparse Representation for Prediction of HIV-1 Protease Drug Resistance. Proceedings of the ... SIAM International Conference on Data Mining. SIAM International Conference on Data Mining. 2013; 2013:342-349. NIHMSID: NIHMS498373 PubMed [journal] PMID: 24910813, PMCID: PMC4045614

d.    Yu X, Weber IT, Harrison RW. Prediction of HIV drug resistance from genotype with encoded three-dimensional protein structure. BMC genomics. 2014; 15 Suppl 5:S1. PubMed [journal] PMID: 25081370, PMCID: PMC4120140

e.    Yu X, Weber IT, Harrison RW. Identifying representative drug resistant mutants of HIV. BMC bioinformatics. 2015; 16 Suppl 17:S1. PubMed [journal] PMID: 26678327, PMCID: PMC4674865

f.     Park JH, Sayer JM, Aniana A, Yu X, Weber IT, Harrison RW, Louis JM. Binding of Clinical Inhibitors to a Model Precursor of a Rationally Selected Multidrug Resistant HIV-1 Protease Is Significantly Weaker Than That to the Released Mature Enzyme. Biochemistry. 2016; 55(16):2390-400. NIHMSID: NIHMS813828 PubMed [journal] PMID: 27039930, PMCID: PMC5013724

Complete List of Published Work in MyBibliography:

http://www.ncbi.nlm.nih.gov/myncbi/browse/collection/50464350

D. Research Support

Ongoing Research Support

None.