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Yuji Zhang, PhD

Academic Title:

Associate Professor

Primary Appointment:

Epidemiology & Public Health

Location:

Howard Hall, 109C

Phone (Primary):

410-706-8523

Fax:

410-706-8548

Education and Training

Ph.D. in Computer Engineering, Virginia Polytechnic Institute and State University.

M.S. in Bioinformatics, Southeast University, China.

B.S. in Biomedical Engineering, Southeast University, China.

Biosketch

Dr. Zhang’s research focuses on developing translational informatics approaches to reveal novel human disease mechanisms. She has solid interdisciplinary trainings in bioinformatics and Computer Engineering. Dr. Zhang has years of research experience in integrative analysis of multi-source high-dimensional biological data for novel association discovery between different biological entities (e.g., gene, drug, and gene) under different biological states. In addition, she has extensive collaborative research experience in medical informatics, ontology, software engineering, and biomedical and basic science fields. Her current research mission is to leverage the gap between the analytical needs of arising from multi-source biological “big” data in biomedical research and advanced informatics approaches. As the lead of the bioinformatics core at University of Maryland Greenebaum Comprehensive Cancer Center and University of Maryland School of Medicine, Dr. Zhang has been serving as co-principle investigator/co-investigator leading the bioinformatics and statistical analyses in numerous federal funded research projects including the International Consortium for Prostate Cancer Genetics (ICPCG) and the consortium of Extracellular non-coding RNA biomarker discovery of hepatocellular cancer. She has also been organizing/co-organizing several international workshops in the informatics field since 2012.

Research/Clinical Keywords

Translational Bioinformatics, Network Medicine, Systems Biology, Next Generation Sequencing, Systems Pharmocogenomics, Non Coding RNA mechanisms

Highlighted Publications

  1. Wang J, Zhao L, Ye Y, Zhang Y. Adverse event detection by integrating Twitter data and VAERS. Journal of Biomedical Semantics, 2018 Jun 20; 9:19.
  2. Wang L, Felts SJ, Van Keulen VP, Scheid AD, Block MS, Markovic SN, Pease LR, Zhang Y. Integrative genome-wide analysis of long noncoding RNAs in diverse immune cell types of melanoma patients. Cancer Research, 2018 Jun 12; pii: canres.0529.2018. 
  3. Zhang Y, Shen F, Mojarad MR, Li D, Tao C, Yu Y, Liu S, Liu H. Systematic identification of latent disease-gene relationships from PubMed articles. PLOS ONE, 2018 Jan 16; 13(1): e0191568.
  4. Wang L, Ma X, Xu X, Zhang Y. Systematic identification and characterization of cardiac long intergenic noncoding RNAs in zebrafish. Scientific Reports, 2017 Apr 28;7(1):1250.
  5. Zhang Y, Zhu Q, Liu H. Next generation informatics for big data in precision medicine era. BioData Mining2015 Nov 3;8:34. 
  6. Thibodeau SN, French AJ, McDonnell SK, Cheville J, Middha S, Tillmans L, Riska S, Baheti S, Larson MC, Fogarty Z, Zhang Y, Larson N, Nair A, O’Brien D, Wang L, Schaid DJ. Identification of candidate genes for prostate cancer-risk SNPs utilizing a normal prostate tissue eQTL data set. Nature communications, 2015 Nov 27;6:8653.
  7. Zhang Y, Tao C, Jiang G, Nair AA, Su J, Chute CG, Liu H. Network-based analysis reveals distinct association patterns in a semantic MEDLINE-based drug-disease-gene network. Journal of Biomedical Semantics, 2014 Aug 6;5:33. 
  8. Zhang Y, Tao C, He Y, Kanjamala P, Liu H. Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology. Journal of Biomedical Semantics, 2013 Nov 11;4(1):33.
  9. Wang J, Zhang Y, Marian C, Ressom HW. Identification of aberrant pathways and network activities from high-throughput data. Briefings in Bioinformatics, 2012;13(4):406-19.

Additional Publication Citations

      1. Zhang Y, Zhu J, Sun X, Lu Z. A method of oligonucleotide synthesis optimization.  Biotechnology, 2002;12(4):26-28.
      2. Ressom HW*, Zhang Y*, Xuan J, Wang Y, Clarke R. Inference of gene regulatory networks from time course gene expression data using neural networks and swarm intelligence.  Proceedings of 2006 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology (CIBCB '06). 2006 Sep 28;1-8. (primary author to design the experiment, perform the analysis, and write the manuscript)
      3. Ressom HW*, Zhang Y*, Xuan J, Wang Y, Clarke R. Inferring network interactions using recurrent neural networks and swarm intelligence. Proceedings of the 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBS 2006). 2006 Aug 30;4241-4244. (primary author to design the experiment, perform the analysis, and write the manuscript)
      4. Ressom HW*, Zhang Y*, Xuan J, Wang Y, Clarke R. Integrating multi-source biological data for transcriptional regulatory module discovery. Proceedings of IEEE/NIH Life Science Systems and Applications Workshop 2007 (LISA 2007). 2007 Nov 8;184-187. (primary author to design the experiment, perform the analysis, and write the manuscript)
      5. Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW. Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data. BMC Bioinformatics. 2008 Apr 21;9(1):203.
      6. Zhang Y, Xuan J, de Los Reyes BG, Clarke R, Ressom HW. Network motif-based identification of breast cancer susceptibility genes. Proceedings of the 30th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBS 2008). 2008 Aug 20;5696-5699.
      7. Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW. Reverse engineering module networks by PSO-RNN hybrid modeling. BMC Genomics. 2009 Jul 7;10(1):S15.
      8. Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW. Module-based biomarker discovery for breast cancer. Proceedings of 2010 IEEE International Conference on Bioinformatics & Biomedicine. 2010 Dec 18;352-356.
      9. Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW. Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration. PloS One. 2010 Apr 21;5(4):e10268.
      10. Sun Z, Baheti S, Middha S, Kanwar R, Zhang Y, Li X, Beutler AS, Klee E, Asmann YW, Thompson EA, Kocher JP. SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. Bioinformatics. 2012 Jan 15;28(2):277-278. (participated in determining analytic method, running analyses, and providing statistical interpretation)
      11. Craig TA, Zhang Y, McNulty MS, Middha S, Ketha H, Singh RJ, Magis AT, Funk C, Price ND. Ekker SC, Kumar R. Research resource: whole transcriptome RNA sequencing detects multiple 1alpha, 25-dihydroxyvitamin D(3)-sensitive metabolic pathways in developing zebrafish.  Molecular Endocrinology. 2012 Jun 25;26(9):1630-1642. (determined analytic method, ran analyses, provided statistical interpretation)
      12. Wang J, Zhang Y, Marian C, Ressom HW. Identification of aberrant pathways and network activities from high-throughput data. Briefings in Bioinformatics. 2012 Jan 27;13(4):406-419. (determined analytic method, provided statistical interpretation)
      13. Asmann YW, Middha S, Hossain A, Baheti S, Li Y, Chai HS, Sun Z, Duffy PH, Hadad AA, Nair A, Liu X, Zhang Y, Klee EW, Kalari KR, Kocher JP. TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. Bioinformatics. 2012 Jan 15;28(2):277-278. (determined analytic method, ran analyses, provided statistical interpretation)
      14. Tao C, Zhang Y, Jiang G, Bouamrane MM, Chute CG. Optimizing semantic MEDLINE for translational science studies using semantic web technologies. MIXHS '12 Proceedings of the 2nd international workshop on Managing interoperability and compleXity in health systems. 2012 Oct 29;53-58. (determined analytic method, ran analyses, provided statistical interpretation)
      15. Zhang Y, Li D, Tao C, Shen F, Liu H. An integrative computational approach to identify disease-specific networks from PubMed literature information. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine 2013. 2013 Dec 18;72-75.
      16. Leonard B, Hart SN, Burns MB, Carpenter MA, Temiz NA, Rathore A, Isaksson Vogel R, Nikas JB, Law EK, Brown WL, Li Y, Zhang Y, Maurer MJ, Oberg AL, Cunningham JM, Shridhar V, Bell DA, April C, Bently D, Bibikova M, Cheetham RK, Fan JB, Grocock R, Humphray S, Kingsbury Z, Peden J, Chien J, Swisher EM, Hartmann LC, Kalli KR, Goode EL, Sicotte H, Kaufmann SH, & Harris RS APOBEC3B upregulation and genomic mutation patterns in serous ovarian carcinoma. Cancer Research. 2013 Dec 15;73(24):7222-7231. (determined analytic method, ran analyses, provided statistical interpretation)
      17. Hart SN, Therneau TM, Zhang Y, Poland GA, Kocher JP. Calculating sample size estimates for RNA sequencing data. Journal of Computational Biology. 2013 Dec 1;20(12):970-978. (determined analytic method, ran analyses, provided statistical interpretation)
      18. Zhang Y, Tao C, He Y, Kanjamala P, Liu H. Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology. Journal of Biomedical Semantics. 2013 Nov 11;4(1):33.
      19. Sun Z, Asmann YW, Nair A, Zhang Y, Wang L, Kalari KR, Bhagwate AV, Baker TR, Carr, JM, Kocher JP, Perez EA, Thompson EA. Impact of library preparation on downstream analysis and interpretation of RNA-Seq data: comparison between Illumina PolyA and NuGEN Ovation protocol. PloS One. 2013 Aug 19;8(8):e71745. (determined analytic method, ran analyses, provided statistical interpretation)
      20. Pugazhenthi S, Zhang Y, Bouchard R, & Mahaffey G. (2013). Induction of an inflammatory loop by interleukin-1 beta and tumor necrosis factor-alpha involves NF- kappa B and STAT-1 in differentiated human neuroprogenitor cells. PloS One, 8(7), e69585. (determined analytic method, ran analyses, provided statistical interpretation)
      21. Zhang Y, Tao C, He Y, Kanjamala P, Liu H. Analysis of vaccine-related networks using Semantic MEDLINE and the vaccine ontology. Proceedings of the Workshop of Vaccine and Drug Ontology Studies (VDOS 2013), in conjunction with the International Conference on Biomedical Ontologies (ICBO). 2013 July 8-9, Montreal, Qc, Canada.
      22. Zhang Y, Xuan J, Clarke R, Ressom HW. Module-based breast cancer classification. International Journal of Data Mining and Bioinformatics. 2013;7(3):284-302.
      23. Zhang Y, Tao C. Network Analysis of Cancer-focused Association Network Reveals Distinct Network Association Patterns. Cancer Informatics. 2014;13(Suppl 3):45.
      24. Tao C, Wu P, Zhang Y. Linked vaccine adverse event data representation from VAERS for biomedical informatics research. PAKDD 2014: Trends and Applications in Knowledge Discovery and Data Mining (Part of the Lecture Notes in Computer Science book series). 2014 May 13;652-661.
      25. Craig, TA*, Zhang Y*, Magisc AT, Funk CC, Price ND, Ekker, SC, Kumar R. Detection of 1,25-Dihydroxyvitamin D-regulated miRNAs in zebrafish by whole transcriptome sequencing. Zebrafish. 2014 Jun1;11(3):207-218. (*co-first authorship)
      26. Zhang Y, Tao C, Jiang G, Nair A, Su J, Chute CG, Liu H. Network-based analysis reveals distinct association patterns in a Semantic MEDLINE-based Drug-Disease-Gene network. Journal of Biomedical Semantics. 2014 Aug 6;5(1):33.
      27. Zhang Y. Network-based analysis of time series RNA-seq gene expression data by integrating the interactome and gene ontology information. Proceedings of 2014 8th International Conference on Systems Biology (ISB). 2014 Oct 24;201-209.
      28. Zhu Q, Liu H, Zhang Y, Wang J. Evidence based computational drug repositioning candidate screening pipeline design: case study. Proceedings of 2014 8th International Conference on Systems Biology (ISB). 2014 Oct 24;210-218. (determined analytic method, ran analyses, provided statistical interpretation)
      29. Wang L, Chen J, Wang C, Uusküla-Reimand L, Chen K, Medina-Rivera A, Young E, Zimmermann M, Yan H, Sun Z, Zhang Y, Wu S, Huang H, Wilson MD, Kocher JP, Li W. MACE: model based analysis of ChIP-exo. Nucleic Acids Research. 2014, Nov 10;42(20):e156-e156. (determined analytic method, ran analyses, provided statistical interpretation)
      30. Tao C, Yu P, Luo Y, Zhang Y. Linked vaccine adverse event data from VAERS for biomedical data analysis and longitudinal studies. BioData Mining. 2014 Dec 31;7(1):36.
      31. Shih Y, Zhang Y, Ding Y, Ross CA, Li H, Olson TM, Xu X. The Cardiac transcriptome and dilated cardiomyopathy genes in zebrafish. Circulation: Cardiovascular Genetics. 2015 Apr;8(2):261-269. (determined analytic method, ran analyses, provided statistical interpretation)
      32. Felts SJ, Van Keulen VP, Scheid AD, Allen KS, Bradshaw RK, Jen J, Peikert T, Middha S, Zhang Y, Block MS, Markovic SN, & Pease LR. Gene expression patterns in CD4+ peripheral blood cells in healthy subjects and stage IV melanoma patients. Cancer Immunology & Immunotherapy. 2015 Nov 1;64(11):1437-1447. (determined analytic method, ran analyses, provided statistical interpretation)
      33. Zhang Y. Network analysis reveals stage-specific changes in zebrafish embryo development using time course whole transcriptome profiling and prior biological knowledge. BioData Mining. 2015 Aug 28;8(1):26.
      34. Zhang Y, Yu P, & Tao C. Identification of sex-associated network patterns in vaccine-adverse event association network in VAERS. Journal of Biomedical Semantics. 2015 Aug 19;6(1):33.
      35. Thibodeau SN, French AJ, McDonnell SK, Cheville J, Middha S, Tillmans L, Riska S, Baheti S, Larson MC, Fogarty Z, Zhang Y, Larson N, Nair A, O’Brien D, Wang L, Schaid DJ. Identification of candidate genes for prostate cancer-risk SNPs utilizing a normal prostate tissue eQTL data set. Nature Communications. 2015 Nov 27;6:8653. (Data analysis, manuscript writing). (determined analytic method, ran analyses, provided statistical interpretation)
      36. Zhang Y, Zhu Q, Liu H. Next generation informatics for big data in precision medicine era. BioData Mining. 2015 Nov 3;8(1):34.
      37. Fan L, Peng G, Sahgal N, Fazli L, Gleave M, Zhang Y, Hussain A, Qi J. Regulation of c-Myc expression by the histone demethylase JMJD1A is essential for prostate cancer cell growth and survival. Oncogene. 2016 May 12;35(19):2441-52. (determined analytic method, ran analyses, provided statistical interpretation)
      38. Dong D, Zhang Y, Reece EA, Wang L, Harman CR, Yang P. microRNA expression profiling and functional annotation analysis of their targets modulated by oxidative stress during embryonic heart development in diabetic mice. Reproductive Toxicology. 2016 Oct 31;11(65):365-374. (determined analytic method, ran analyses, provided statistical interpretation)
      39. Jackson IL, Zhang Y, Bentzen S, Hu J, Zhang C, Katz BP, Vujaskovic Z. Pathophysiological mechanisms underlying phenotypic differences in pulmonary radioresponse among murine strains. Scientific Reports. 2016 Nov 15;6:36579. (determined analytic method, ran analyses, provided statistical interpretation)
      40. Wang L, Ma X, Xu X, Zhang Y. Systematic identification and characterization of cardiac long intergenic noncoding RNAs in zebrafish. Scientific Reports. 2017 Apr 28;7(1):1250.
      41. Kaczanowska S, Joseph AM, Guo J, Tsai AK, Lasola JJ, Younger K, Zhang Y, Gonzales CV, Davila E. A synthetic CD8α:MyD88 coreceptor enhances CD8+ T-cell responses to weakly immunogenic and lowly expressed tumor antigens. Cancer Research. 2017 Dec 15; 77(24):7049-7058. (determined analytic method, ran analyses, provided statistical interpretation)
      42. Zhang Y, Shen F, Mojarad MR, Li D, Tao C, Yu Y, Liu S, Liu H. Systematic identification of latent disease-gene relationships from PubMed articles. PLOS ONE. 2018 Jan 16; 13(1): e0191568.
      43. Scheid AD, Keulen V, Felts SJ, Neier SC, Middha S, Nair AA, Techentin RW, Gilbert BK, Jen J, Neuhauser C, Zhang Y, Pease LR. Gene expression signatures characterized by longitudinal stability and interindividual variability delineate baseline phenotypic groups with distinct responses to immune stimulation. The Journal of Immunology. 2018 Mar 1; 200(5):1917-1928. (determined analytic method, ran analyses, provided statistical interpretation)
      44. Wang L, Felts SJ, Van Keulen VP, Scheid AD, Block MS, Markovic SN, Pease LR, Zhang Y. Integrative genome-wide analysis of long noncoding RNAs in diverse immune cell types of melanoma patients. Cancer Research. 2018 Jun 12; pii: canres.0529.2018. doi: 10.1158/0008-5472.CAN-18-0529. [Epub ahead of print]
      45. Wang J, Zhao L, Ye Y, Zhang Y. Adverse event detection by integrating Twitter data and VAERS. Journal of Biomedical Semantics. 2018 Jun 20; 9:19.

                                                                                              Grants and Contracts

                                                                                              R01CA214783                                                Dorgan (PI)                                                                                         

                                                                                              04/01/18-03/31/21

                                                                                              Title: Early life exposures and breast density in young women                    

                                                                                              Goal: Identifying early life metabolic influences on adult breast density, one of the strongest known breast cancer risk factors.

                                                                                              Role: Co-Investigator

                                                                                               

                                                                                              R01CA224696                                                Njar (PI)                                                                                             

                                                                                              03/01/18-02/28/23

                                                                                              Title: Development of next generation galeterone analogs for prostate cancer therapy

                                                                                              Goal: Producing a more efficacious novel agent against all forms of prostate cancer, including metastatic and drug-resistant diseases for eventual clinical evaluation.

                                                                                              Role: Co-Investigator

                                                                                               

                                                                                              VA Merit Research Award                             Gartenhaus (PI)                                                                                   

                                                                                              07/01/15-06/30/19

                                                                                              Title: Lymphoma development in the elderly: Perturbed posttranscriptional regulation

                                                                                              Goal: Investigating underlying mechanism(s) for the increased rate of lymphoma in our aged population by studying the function of ATM kinase, the major cellular sensor to DNA damage, and downstream targets.

                                                                                              Role: Co-Investigator

                                                                                               

                                                                                              R01DK083243                                                Yang (PI)                                                                                           

                                                                                              03/01/16-02/29/20

                                                                                              Title: Apoptotic mechanism of maternal diabetes-induced neural tube defects

                                                                                              Goal: Investigating the underlying mechanism(s) of maternal diabetes-induced neural tube defects.

                                                                                              Role: Co-Investigator

                                                                                               

                                                                                              P30CA13274                                                  Cullen (PI)                                                                                       

                                                                                              08/01/16-07/30/21     

                                                                                              University of Maryland Cancer Center Support Grant                       

                                                                                              Goal: Providing infrastructure support to the University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center.

                                                                                              Role: Co-Investigator

                                                                                               

                                                                                              R01AR069572                                                 Petri (PI)                                                                                   

                                                                                              09/10/16-07/31/21      

                                                                                              HOPKINS LUPUS COHORT                 

                                                                                              Goal: Determining predictors of noncalcified plaque changes over time using the Hopkins Lupus Cohort, a unique 27 year, 2300 SLE patient longitudinal cohort.

                                                                                              Role: Co-Investigator

                                                                                               

                                                                                              U24HL134763                                                 Terrin (PI)                                                                                   

                                                                                              09/20/16-05/33/23      

                                                                                              PCTC Administrative Coordinating Center                  

                                                                                              Goal: Providing the administrative infrastructure to organize interactions and facilitate collaborations between PCTC investigators.

                                                                                              Role: Co-Investigator

                                                                                               

                                                                                              R01CA207913                                                Davila (PI)                                                                                   

                                                                                              04/01/17-03/31/22     

                                                                                              Augmenting T Cell Activity to Weak Tumor Antigens and Reversing Myeloid Cell-mediated T Cell Inhibition             

                                                                                              Goal: Developing a novel approach for treating established melanoma tumors by enhancing cytotoxic T cell responses towards weakly immunogenic and lowly expressed tumor antigens including neoantigens.

                                                                                              Role: Co-Investigator

                                                                                               

                                                                                              R01HL134368                                                 Yang (PI)                                                                                         

                                                                                              07/01/17-04/30/21

                                                                                              Title: MicroRNA-suppressed mitochondrial fusion in mediating the teratogenicity of maternal diabetes leading to heart defects

                                                                                              Goal: Investigating the underlying mechanism(s) of miRNA-mediated teratogenicity.

                                                                                              Role: Co-Investigator