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Degui Zhi, Ph.D.

Degui Zhi, Ph.D. Department of Biostatistics
Ryals Public Health Bldg 327L
University of Alabama at Birmingham
Birmingham, AL 35294
Phone: (205) 975-9192
Fax: (205) 975-2540
E-mail: dzhi@uab.edu
Full CV


Dr. Zhi received his Ph.D. in bioinformatics from University of California, San Diego in 2006. He then took his postdoctoral training in computational genomics at the University of California, Berkeley. He joined the Section on Statistical Genetics at the University of Alabama at Birmingham as an assistant professor in 2009. His current research interests include protein function prediction from structure and bioinformatics and statistical genetics problems relating to next-generation sequencing and rare variants.

Publications
 

  • 2013
  • 2012
  • 2011
  • 2010
  • 2007
  • 2006
  • pre 2006
  1. Bertha Hidalgo, Marguerite Irvin, Jin Sha, Degui Zhi, Stella Aslibekyan, Devin Absher, Hemant Tiwari, Edmond Kabagambe, Jose Ordovas and Donna Arnett, "Epigenomewide Association Study of Fasting Measures of Glucose, Insulin, and HOMA-IR in GOLDN", Diabetes, Accepted., 2013, PMCID: in process.
     
  2. Guo-Bo Chen, Nianjun Liu, Yann C Klimentidis, Xiaofeng Zhu, Degui Zhi, Xujing Wang, Xiang-Yang Lou. A unified GMDR method for detecting gene–gene interactions in family and unrelated samples with application to nicotine dependence. Human Genetics, accepted, 2013. [PMID: 24057800] PMCID: in process.
     
  3. Kui Zhang, Degui Zhi*. “Joint haplotype phasing and genotype calling of multiple individuals using haplotype informative reads”. Bioinformatics, accepted, 2013. [PMID: 23943637] [PMCID: PMC3777110]
     
  4. Zhi D, Aslibekyan S, Irvin MR, Claas SA, Borecki IB, Ordovas JM, Absher DM, Arnett DK. SNPs located at CpG sites modulate genome-epigenome interaction. Epigenetics. official journal of the DNA Methylation Society 2013, 8(8). [PMID: 23811543] PMCID: in process.
     
  5. Wan-Yu Lin, Nengjun Yi, Xiang-Yang Lou, Degui Zhi, Kui Zhang, Guimin Gao, Hemant K. Tiwari, and Nianjun Liu “Haplotype Kernel Association Test as a Powerful Method to Identify Chromosomal Regions Harboring Uncommon Causal Variants”, Genetic Epidemiology, Accepted, 2013. [PMID: 23740760] PMCID: in process.
     
  6. Guodong Wu, Degui Zhi*, Pathway-based approaches for sequencing-based genome-wide association studies, Genet Epidemiology, 37, 478-494. [PMID: 23650134] [doi: 10.1002/gepi.21728] PMCID: in process.
     
  7. Samad Jahandideh, Degui Zhi*, “Systematic investigation of predicted effect of nonsynonymous SNPs in human prion protein gene: A molecular modeling and molecular dynamics study”, Journal of Biomolecular Structure & Dynamics, Accepted. 2013. [PMID: 23527686] PMCID: in process.
     

*Senior corresponding author, trainees are underscored

  1. Tonner P, Srinivasasainagendra V, Zhang S, Zhi D*, “Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data”, BMC genomics 13: 412. 2012. [PMCID: PMC3478165]
     
  2. Samad Jahandideh, Vinodh Srinivasasainagendra, Degui Zhi*, “Comprehensive comparative analysis and identification of RNA-binding protein domains: multi-class classification and feature selection”, Journal of Theoretical Biology 2012 312C:65-75. [PMID: 22884576]
     
  3. Wan-Yu Lin, Nengjun Yi, Degui Zhi, Kui Zhang, Guimin Gao, Hemant K. Tiwari, Nianjun Liu, “Haplotype-based methods for detecting uncommon causal variants with common SNPs”. Genet Epidemiol 2012, 36(6):572-582. [PMCID: PMC3513398]
     
  4. Degui Zhi, Ryan Irvin, Charles Gu, Alexander Stoddard, Rachel Lorier, Andrea Matter, D C Rao, Vinodh Srinivasasainagendra, Hemant K Tiwari, Amy Turner, Ulrich Broeckel, Donna K Arnett. " Whole-exome sequencing and an iPSC-derived cardiomyocyte model provides a powerful platform for gene discovery in left ventricular hypertrophy". Frontiers in Applied Genetic Epidemiology, accepted, 2012. [PMID: 22654895] [PMCID: PMC3361011]
     
  5. Hong-Beom Bae, Jaroslaw W. Zmijewski, Jessy S. Deshane, Degui Zhi, Lawrence C. Thompson, Cynthia B. Peterson, David D. Chaplin and Edward Abraham. "Vitronectin inhibits neutrophil apoptosis through activation of integrin associated signaling pathways". American Journal of Respiratory Cell and Molecular Biology, accepted, 2012. [PMID: 22281987] [PMCID: PMC3380283]
     
  6. Degui Zhi, Jihua Wu, Nianjun Liu, and Kui Zhang. Genotype Calling from Next Generation Sequencing Data using Haplotype Information of Reads. Bioinformatics, in press, 2012. [PMID: 22285565] [PMCID: PMC3493122]
     
  7. Degui Zhi, and Rui Chen. "Statistical guidance for experimental design and data analysis of mutation detection in rare monogenic Mendelian diseases by exome sequencing". PLoS ONE, 2012;7(2):e31358, 2012. [PMCID: PMC3277495]
     
  8. Christine W. Duarte, Christopher D. Willey, Degui Zhi, Xiangqin Cui, Jacqueline J. Harris, Laura Kelly Vaughan, Tapan Mehta, Raymond O. McCubrey, Nikolai N. Khodarev, Ralph R. Weichselbaum, and G. Yancey Gillespie. Expression signature of IFN/STAT1 signaling genes predicts poor survival outcome in Glioblastoma Multiforme in a subtype-specific manner. PLoS ONE, 7(1):e29653, 2012. [PMCID: PMC3252343]
     
  1. Yi N, Liu N, Zhi D, Li J: Hierarchical Generalized Linear Models for Multiple Groups of Rare and Common Variants: Jointly Estimating Group and Individual-Variants Effects. PLoS Genetics 7(12): e1002382, 2011. [PMCID: PMC3228815]
     
  2. Guodong Wu, Nengjun Yi, Devin Absher, and Degui Zhi*. "Statistical Quantification of Methylation Levels by Next-generation Sequencing". PLoS ONE 6(6): e21034, 2011. *Senior Corresponding author. *Senior Corresponding author. [PMCID: PMC3115964]
     
  3. Wenan Chen, Xi Gao, Jiexun Wang, Chuanyu Sun, Wen Wan, Degui Zhi, Nianjun Liu, Xiangning Chen, Guimin Gao. "An Evaluation of Association Tests for Rare Variants by Using Simulated datasets in the GAW17 Data". BMC Proceedings, 5(Suppl 9):S86, 2011. [PMCID: PMC3287927]
     
  4. Boshao Zhang, Degui Zhi, Kui Zhang, Guimin Gao, David Allison, Nianjun Liu. "Practical Consideration of Genotype Imputation: Sample Size, Window Size, Reference Choice and Untyped Rate", Statistics and Its Interface, 4(3): 339-352, 2011.. [PMCID: PMC3287927]
     
  5. Liyan Gao, Zhide Fang, Kui Zhang, Degui Zhi, and Xiangqin Cui. "Length Bias Correction for RNA-seq Data in Gene Set Enrichment Analyses", Bioinformatics, 27(5):662-9, 2011. [PMID: 21252076] [PMCID: PMC3042188]
     
  6. N. Yi, and D. Zhi. "Bayesian Analysis of Rare Variants in Genetic Association Studies", Genetic Epidemiology, 35: 57–69, 2011.. [PMID: 21181897] [PMCID: PMC3200544] [DOI: 10.1002/gepi.20554]
     
  1. A. Aleshin, and D. Zhi*. “Recombination-associated sequence homogenization of neighboring Alu elements: signature of nonallelic gene conversion”, Accepted at Molecular Biology and Evolution. 2010. 27(10):2300-11.*Senior Corresponding author. [PMID: 20453015] [DOI: 10.1093/molbev/msq116]
     
  2. D. Zhi, M. Shatsky, and S.E. Brenner. “Alignment-Free Local Structural Comparison by Writhe Decomposition”, Bioinformatics. 2010. 26: 1176-1184. [DOI: 10.1093/bioinformatics/btq127]
     
  1. D. Zhi. “Sequence correlation between neighboring Alu instances suggests postretrotransposition sequence exchange due to Alu gene conversion”, Gene, 390(1- 2):117-21, 2007. [PMID: 17134854]
     
  2. D. Zhi, U. Keich, P. Pevzner, S. Heber, and H. Tang. “Correcting base-assignment errors in repeat regions of shotgun assembly”, IEEE Transactions of Computational Biology and Bioinformatics, 4(1):54-64, 2007. [PMID: 17277413]
     
  1. D. Zhi, S.S. Krishna, H. Cao, P. Pevzner, and A. Godzik. “Representing and comparing protein structures as curves in three-dimensional space”, BMC Bioinformatics, 7:460, 2006. [PMID: 17052359] [DOI: 10.1186/1471-2105-7-460]
     
  2. N. Jones, D. Zhi, and B. Raphael. “AliWABA: Alignment on the Web through an A-Bruijn Approach”, Nucleic Acid Research, Webserver issue, 34: W613-W616, 2006. [PMID: 16845083]
     
  3. D. Zhi, B. Raphael, A. Price, H. Tang, and P. Pevzner. “Identifying repeat domains in large genomes”, Genome Biology, 7(1):R7, 2006. [PMID: 16507140]
     
  4. S. Roepcke, D. Zhi, M. Vingron, and P. Arndt. “Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters”, Gene, 365:48-56. 2006. [PMID: 16343812]
     
  1. B. Raphael, D. Zhi, H. Tang, and P. Pevzner. “A Novel method for multiple alignment of sequences with repeated and shuffled elements”, Genome Research, 14: 2336-46, 2004. [PMID: 15520295]
     
  2. X. Chen, Z.L. Ji, D.G. Zhi, and Y.Z. Chen. “CLiBE: a database of computed ligand binding energy for ligand/receptor complexes”, Computers & Chemistry. 26(6): 661- 6, 2002. [PMID: 12385480]
     
  3. Y.Z. Chen, and D.G. Zhi. “Ligand-protein inverse docking and its potential use in computer search of putative protein targets of a drug”, Proteins, 43(2): 217-26, 2001. [PMID: 11276090]