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Introduction

My name is Jin Zhang. I received my PhD in Department of Computer Science & Engineering at University of Connecticut under Dr. Yufeng Wu.

I am present a postdoctoral research associate under Dr. Christopher Maher at Washington University in St. Louis.

Education

Aug. 2008 - Dec. 2012   Computer Science & Engineering, University of Connecticut, Storrs

Publications

• 1. INTEGRATE-Neo: A pipeline for Personalized Gene Fusion Neoantigen Discovery [link],

  2. Jin Zhang, Elaine R. Mardis, and Christopher A. Maher

  3. Bioinformatics, advance access, 2016.

  4. Multi-institutional Analysis Shows that Low PCAT-14 Expression Associates with Poor Outcomes in Prostate Cancer [link],

  5. Nicole M. White*, Shuang G. Zhao*, Jin Zhang, Emily B. Rozycki, Ha X. Dang, Sandra D. McFadden, Abdallah M. Eteleeb, Mohammed Alshalalfa, Ismael A. Vergara, Nicholas Erho, Jeffrey M. Arbeit, Robert Jeffrey Karnes, Robert B. Den, Elai Davicioni, and Christopher A. Maher

  6. European Urology, S0302-2838(16)30417-1, 2016.

  7. Comprehensive genomic analysis reveals FLT3 activation and a therapeutic strategy for a patient with relapsed adult B-lymphoblastic leukemia [link],

  8. Malachi Griffith, Obi L. Griffith, Kilannin Krysiak, Zachary L. Skidmore, Matthew J. Christopher, Jeffery M. Klco, Avinash Ramu, Tamara L. Lamprecht, Alex H. Wagner, Katie M. Campbell, Robert Lesurf, Jasreet Hundal, Jin Zhang, Nicholas C. Spies, Benjamin J. Ainscough, David E. Larson, Sharon E. Heath, Catrina Fronick, Shelly O'Laughlin, Robert S. Fulton, Vincent Magrini, Sean McGrath, Scott M. Smith, Christopher A. Miller, Christopher A. Maher, Jacqueline E. Payton, Jason R. Walker, James M. Eldred, Matthew J. Walter, Daniel C. Link, Timothy A. Graubert, Peter Westervelt, Shashikant Kulkarni, John F. DiPersio, Elaine R. Mardis, Richard K. Wilson, Timothy J. Ley

  9. Experimental Hematology, 44(7):603-13, 2016.

  10. A genomic case study of mixed fibrolamellar hepatocellular carcinoma [link],

  11. O. L. Griffith, M. Griffith, K. Krysiak, V. Magrini, A. Ramu, Z. L. Skidmore, J. Kunisaki, R. Austin, S. McGrath, J. Zhang, R. Demeter, T. Graves, J. M. Eldred, J. Walker, D. E. Larson, C. A. Maher, Y. Lin, W. Chapman, A. Mahadevan, R. Miksad, I. Nasser, D. W. Hanto and E. R. Mardis

  12. Annals of Oncology, 27(6):1148-54, 2016.

  13. INTEGRATE: Gene fusion discovery using whole genome and transcriptome data [link],

  14. Jin Zhang, Nicole M. White, Heather K. Schmidt, Robert S. Fulton, Chad Tomlinson, Wesley C. Warren, Richard K. Wilson, and Christopher A. Maher,

  15. Genome Research, 26(1):108-18, 2016.

  16. GINDEL: Accurate Genotype Calling of Insertions and Deletions from Low Coverage Population Sequence Reads [link],

  17. Chong Chu, Jin Zhang, and Yufeng Wu, PLoS One, 25;9(11):e113324, 2014.

  18. cDNA Hybrid Capture Improves Transcriptome Analysis on Low-input and Archived Samples [link],

  19. Christopher R. Cabanski, Vincent Magrini, Malachi Griffith, Obi L. Griffith, Sean McGrath, Jin Zhang, Jason Walker, Amy Ly, Ryan Demeter, Winnie W. Pong, David H. Gutmann, Ramaswamy Govindan, Elaine R. Mardis, and Christopher A. Maher, The Journal of Molecular Diagnostics, 16(4)440-51, 2014.

  20. Endocrine-Therapy-Resistant ESR1 Variants Revealed by Genomic Characterization of Breast-Cancer-Derived Xenografts [link],

  21. Shunqiang Li, Dong Shen, Jieya Shao, Robert Crowder, Wenbin Liu, Aleix Prat, Xiaping He, Shuying Liu, Jeremy Hoog, Charles Lu, Li Ding, Obi L. Griffith, Christopher Miller, Dave Larson, Robert S. Fulton, Michelle Harrison, Tom Mooney, Joshua F. McMichael, Jingqin Luo, Yu Tao, Rodrigo Goncalves, Christopher Schlosberg, Jeffrey F. Hiken, Laila Saied, Cesar Sanchez, Therese Giuntoli, Caroline Bumb, Crystal Cooper, Robert T. Kitchens, Austin Lin, Chanpheng Phommaly, Sherri R. Davies, Jin Zhang, Megha Shyam Kavuri, Donna McEachern, Yi Yu Dong, Cynthia Ma, Timothy Pluard, Michael Naughton, Ron Bose, Rama Suresh, Reida McDowell, Loren Michel, Rebecca Aft, William Gillanders, Katherine DeSchryver, Richard K. Wilson, Shaomeng Wang, Gordon B. Mills, Ana Gonzalez-Angulo, John R. Edwards, Christopher Maher, Charles M. Perou, Elaine R. Mardis, and Matthew J. Ellis, Cell Reports, 4(6), 2013.

  22. Computational approaches for finding long insertions and deletions with next generation sequencing data ,

  23. Jin Zhang, Chong Chu, and Yufeng Wu, in I. Mandoiu, editor, Computational Methods for Next Generation Sequencing Data Analysis, Wiley Book Series on Bioinformatics, 2013.

  24. A synchronization detection approach for identifying rare mutations underlying common disease ,

  25. Jiayin Wang, Xuanping Zhang, Yanqin Liu, Jin Zhang, and Yufeng Wu, 5th International Conference on Bioinformatics and Computational Biology (Honolulu, HI, Mar. 2013)

  26. A probabilistic method for identifying rare variants underlying complex traits [link],

  27. Jiayin Wang, Zhongmeng Zhao, Zhi Cao, Aiyuan Yang and Jin Zhang, BMC Genomics 14(Suppl 1):S11, 2013.

  28. An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data [link],

  29. Jin Zhang Jiayin Wang and Yufeng Wu, BMC Bioinformatics, 13(Suppl 6):S6, 2012.

  30. Part of the paper has been presented at Second Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (Barcelona, Spain, Apr. 2012)

  31. SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data [link],

  32. Jin Zhang and Yufeng Wu, Bioinformatics, 27(23), 3228-3234, 2011.

  33. Identifying Interacting SNPs with Parallel Fish-Agent based Logic Regression [link],

  34. Jiayin Wang, Jin Zhang and Yufeng Wu, Proceedings of 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2011. (Orlando, FL, Feb. 2011)

  35. Haplotype Inference from Short Sequence Reads Using a Population Genealogical History Model [link],

  36. Jin Zhang and Yufeng Wu, in proceedings of Pacific Symposium on Biocomputing: 288-299, 2011. (Big Island, HI, Jan. 2011)

Software

INTEGRATE-Neo

INTEGRATE

SVseq2

SVseq

HapReads

Awards

Graduate PreDoctoral Fellowship, Computer Science & Engineering Department, UConn, 2012

Doctoral Dissertation Fellowship, UConn, Spring 2012

RECOMB 2012 Travel Fellowship

ISBRA 2011 Travel Fellowship

PSB 2011 NIH travel award

Graduate PreDoctoral Fellowship, Computer Science & Engineering Department, UConn, 2009

Contact Information

Email:          jzhang (AT) genome.wustl.edu; jin.zhang (AT) engineer.uconn.edu