Xiaoju (Ju) Zhang

• Skilled in using Python and R to process and analyze large, multi-dimensional genomic data and C++ to develop RNA structure predicting software under Unix environment.
• Proficient in statistics, Genomic bioinformatics, molecular structure modeling and simulation algorithm development.
• Experience in whole genome data (GWAS) association study and population genetics case-control study.
• Experience with Blast+, PDB, SWISS-PROT, Genebank, Rfam, and Gene ontology analysis.
• Five years of bench experiment experience in human genetics and influenza biochemistry; six years of computational experiment experience in RNA structural biology and yeast genomics.
• Excellent presentation and communication skills using native Chinese Mandarin and English fluencies.

University of Rochester, Rochester, NY
Ph.D. Chemistry, Focus on RNA Computational Biology, Expected May 2015

University of Oklahoma Health Sciences, Center Oklahoma City, OK
M.S. Biochemistry, Focus on Influenza Virology, May 2008

Shanghai Jiao Tong University, Shanghai, China
M.S. Human Genetics, May 2005

Sichuan University, Chengdu, China
B.S. Biochemistry, June 2001

University of Rochester, Rochester, NY
PhD Researcher August 2009 - Present

• Investigated yeast tRNA’s decay with large RNA-Seq data through sequence/structure analyses using R and python.
• Constructed gene alignment across 5 yeast species from chromosome sequences using Blast+ and BioPython.
• Built Monte Carlo simulation tool with C++ to determine RNA folding pathways.
• Conducted study of tRNA modifications function by molecular dynamics computational simulations.
• Wrote pipeline to compute RNA folding free energy and predict secondary structure with C++ and Python.
• Designed DNA riboswitch sensing ATP binding and introduced a C++/python pipeline to design riboswitch based on DNA/RNA folding free energy model.

Teaching Assistant of General Chemistry September 2008 – January 2010

• Guided undergraduate laboratory for 2 semesters, total 100 students of 5 classes.
• Lectured weekly workshop on course materials for 1 semester, total 40 students of 3 classes.
• Awarded Sherman Clarke Fellowship twice for outstanding academic records and excellent teaching performance.

University of Oklahoma Health Sciences Center, Oklahoma City, OK
Lab Tech Assistant December 2007 - May 2008 Dec. 2007 - June 2008

• Cultured and maintained influenza virus in mammalian cell lines.
  
• Assessed antibody quantity versus quality after influenza
  vaccination with ELISA assay.

Masters Researcher September 2005 - November 2007

• Isolated influenza hemagglutin receptors from mammalian cell membrane
• Examined gylco-pattern of influenza hemagglutin receptors with mass spectrum (MS).

Shanghai Jiao Tong University, Shanghai, China
Master Researcher September 2002 - May 2005

• Mapped Dowling-Degos disease to chromosome 17p13.3, locating the gene causing a genetic dermatology disease.

• Conducted association study of ApoD gene and schizophrenia, and excluded risk factor of ApoD gene for schizophrenia in Chinese Han population.

  Collaborative Projects and Outcomes

  University of Rochester Rochester, NY Rochester, NY
  Project Collaborator August 2012 - Present

• Collaborated with yeast functional genomics groups located in Rochester and Seattle on investigation of the determinants of tRNA function and decay in yeast with large RNA-Seq data.

• Collaborated with a yeast genetic group in Rochester on study of inhibitory codon pair function and conservation.

• Collaborated with a chemistry lab and a life sciences software company located in Maryland to develop DNA riboswitch design platform.

• Collected, analyzed, and presented sequencing analysis results in weekly conference calls.

RNA Society, 2012-present
International Society for Computational Biology (ISCB), 2014-present

Vice president of Oklahoma City Scholars & Students Association, 2006-2007
Sherman Clarke Fellowship, University of Rochester, 2009-2011

• Zhang, X.; Walker, R. C.; Phizicky, E. M.; Mathews, D. H., The influence of sequence and covalent modifications on yeast tRNA dynamics. Journal of Chemical Theory and Computation 2014.
• Guy, M. P.; Young, D. L.; Payea, M. J.; Zhang, X.; Kon, Y.; Dean, K. M.; Grayhack, E. J.; Mathews, D. H.; Fields, S.; Phizicky, E. M., Identification of the determinants of tRNA function and susceptibility to rapid tRNA decay by high-throughput in vivo analysis. Genes & development 2014, 28, 1721-1732.
• Feng, J.; Gulati, U.; Zhang, X.; Keitel, W. A.; Thompson, D. M.; James, J. A.; Thompson, L. F.; Air, G. M., Antibody quantity versus quality after influenza vaccination. Vaccine 2009, 27, 6358-6362.
  
• Zhang, X.; Li, D.; Duan, S.; Duan, Y.; Chen, Q.; Li, X.; Liu, Z.; He, L., Analysis of the Association between Apolipoprotein D and Schizophrenia. Neuropsychobiology 2006, 54, 40-44.
• Li, C.-R.; Xing, Q.-H.; Zhang, X.-J.; Ma, H.-J.; Wang, D.-G.; Feng, G.-Y.; Zhu, W.-Y., A gene locus responsible for reticulate pigmented anomaly of the flexures maps to chromosome 17p13. 3. Journal of investigative dermatology 2006, 126, 1297-1301.
• Duan, S.; Xu, Y.; Chen, W.; Zhang, X., Feng, G., He, L., No association between the promoter variants of tumor necrosis factor alpha (TNF-α) and schizophrenia in Chinese Han population. Neuroscience letters 2004, 366, 139-143.