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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
 

  • 2014
  • 2013
  • 2012
  • 2011
  • 2010
  • 2007
  • 2006
  • pre 2006
  1. Degui Zhi, Aditi Shendre, Rebecca Scherzer, Marguerite R Irvin, Rodney T Perry, Shawn Levy, Donna K Arnett, Carl Grunfeld, Sadeep Shrestha. “Deep Sequencing of RYR3 gene identifies rare and common variants associated with increased carotid intima-media thickness (cIMT) in HIV-infected individuals”. Accepted pending minor revision at Journal of Human Genetics, 2014. PMCID, in process
     
  2. Jianguo Chen, Anna Zmijewska, Degui Zhi and Roslyn B. Mannon. "Cyclosporinemediated allograft fibrosis is associated with micro-rna 21 through akt signaling." Transplant International, 2014. PMCID, in process
     
  3. Christine F. Skibola, Sonja I. Berndt, Joseph Vijai, Lucia Conde, Zhaoming Wang, Meredith Yeager, Paul I.W. de Bakker, Brenda M. Birmann, Claire M. Vajdic, Jia-Nee Foo, Paige M. Bracci, Roel C.H. Vermeulen, Susan L. Slager, Silvia de Sanjose, Sophia S. Wang, Martha S. Linet, Gilles Salles, Qing Lan, Gianluca Severi, Henrik Hjalgrim, Tracy Lightfoot, Mads Melbye, Jian Gu, Hervé Ghesquières, Brian K. Link, Lindsay M. Morton, Elizabeth A. Holly, Alex Smith, Lesley F. Tinker, Lauren R. Teras, Anne Kricker, Nikolaus Becker, Mark P. Purdue, John J. Spinelli, Yawei Zhang, Graham G. Giles, Paolo Vineis, Alain Monnereau, Kimberly A. Bertrand, Demetrius Albanes, Anne Zeleniuch-Jacquotte, Attilio Gabbas, Charles C. Chung, Laurie Burdett, Amy Hutchinson, Charles Lawrence, Rebecca Montalvan, Liming Liang, Jinyan Huang, Baoshan Ma, Jianjun Liu, Hans-Olov Adami, Bengt Glimelius, Yuanqing Ye, Grzegorz S. Nowakowski, Ahmet Dogan, Carrie A. Thompson, Thomas M. Habermann, Anne J. Novak, Mark Liebow, Thomas E. Witzig, George J. Weiner, Maryjean Schenk, Patricia Hartge, Anneclaire J. De Roos, Wendy Cozen, Degui Zhi, Nicholas K. Akers, Jacques Riby, Martyn T. Smith, Mortimer Lacher, Danylo J. Villano, Ann Maria, Eve Roman, Eleanor Kane, Rebecca D. Jackson, Kari E. North, W. Ryan Diver, Jenny Turner, Bruce K. Armstrong, Yolanda Benavente, Paolo Boffetta, Paul Brennan, Lenka Foretova, Marc Maynadie, Anthony Staines, James McKay, Angela R. Brooks-Wilson, Tongzhang Zheng, Theodore R. Holford, Saioa Chamosa, Rudolph Kaaks, Rachel S. Kelly, Bodil Ohlsson, Ruth C. Travis, Elisabete Weiderpass, Jacqueline Clavel, Edward Giovannucci, Peter Kraft, Jarmo Virtamo, Patrizio Mazza, Pierluigi Cocco, Maria Grazia Ennas, Brian C.H. Chiu, Joseph F. Fraumeni, Alexandra Nieters, Kenneth Offit, Xifeng Wu, James R. Cerhan, Karin E. Smedby, Stephen J. Chanock, Nathaniel Rothman. "Genome-wide Association Study Identifies Five Susceptibility Loci for Follicular Lymphoma outside the HLA Region." Am J Hum Genet 95(4): 462-471, 2014. PMCID, in process.
     
  4. James R Cerhan, Sonja I Berndt, Joseph Vijai, Hervé Ghesquières, James McKay, Sophia S Wang, Zhaoming Wang, Meredith Yeager, Lucia Conde, Paul I W de Bakker, Alexandra Nieters, David Cox, Laurie Burdett, Alain Monnereau, Christopher R Flowers, Anneclaire J De Roos, Angela R Brooks-Wilson, Qing Lan, Gianluca Severi, Mads Melbye, Jian Gu, Rebecca D Jackson, Eleanor Kane, Lauren R Teras, Mark P Purdue, Claire M Vajdic, John J Spinelli, Graham G Giles, Demetrius Albanes, Rachel S Kelly, Mariagrazia Zucca, Kimberly A Bertrand, Anne Zeleniuch-Jacquotte, Charles Lawrence, Amy Hutchinson, Degui Zhi, Thomas M Habermann, Brian K Link, Anne J Novak, Ahmet Dogan, Yan W Asmann, Mark Liebow, Carrie A Thompson, Stephen M Ansell, Thomas E Witzig, George J Weiner, Amelie S Veron, Diana Zelenika, Hervé Tilly, Corinne Haioun, Thierry Jo Molina, Henrik Hjalgrim, Bengt Glimelius, Hans-Olov Adami, Paige M Bracci, Jacques Riby, Martyn T Smith, Elizabeth A Holly, Wendy Cozen, Patricia Hartge, Lindsay M Morton, Richard K Severson, Lesley F Tinker, Kari E North, Nikolaus Becker, Yolanda Benavente, Paolo Boffetta, Paul Brennan, Lenka Foretova, Marc Maynadie, Anthony Staines, Tracy Lightfoot, Simon Crouch, Alex Smith, Eve Roman, W Ryan Diver, Kenneth Offit, Andrew Zelenetz, Robert J Klein, Danylo J Villano, Tongzhang Zheng, Yawei Zhang, Theodore R Holford, Anne Kricker, Jenny Turner, Melissa C Southey, Jacqueline Clavel, Jarmo Virtamo, Stephanie Weinstein, Elio Riboli, Paolo Vineis, Rudolph Kaaks, Dimitrios Trichopoulos, Roel C H Vermeulen, Heiner Boeing, Anne Tjonneland, Emanuele Angelucci, Simonetta Di Lollo, Marco Rais, Brenda M Birmann, Francine Laden, Edward Giovannucci, Peter Kraft, Jinyan Huang, Baoshan Ma, Yuanqing Ye, Brian C H Chiu, Joshua Sampson, Liming Liang, Ju-Hyun Park, Charles C Chung, Dennis D Weisenburger, Nilanjan Chatterjee, Joseph F Fraumeni Jr, Susan L Slager, Xifeng Wu, Silvia de Sanjose, Karin E Smedby, Gilles Salles, Christine F Skibola, Nathaniel Rothman & Stephen J Chanock. "Genome-wide association study identifies multiple susceptibility loci for diffuse large B cell lymphoma." Nature Genetics. 2014. Accepted. PMCID: in process.
     
  5. Stella Aslibekyan, Hassan S Dashti, Toshiko Tanaka, Jin Sha, Luigi Ferrucci, Degui Zhi, Stefania Bandinelli, Ingrid B Borecki, Devin M Absher, Donna K Arnett, Jose M Ordovas. "PRKCZ methylation is associated with sunlight exposure in a North American but not a Mediterranean population." Chronobiol Int: 1-7, 2014. PMCID: in process.
     
  6. J. Wu, G. B. Chen, D. Zhi, N. Liu and K. Zhang. "A hidden Markov model for haplotype inference for present-absent data of clustered genes using identified haplotypes and haplotype patterns." Frontiers in genetics 5: 267, 2014. [PMCID: PMC4129397]
     
  7. Shendre A, Wiener HW, Zhi D, Vazquez AI, Portman MA, Shrestha S. High-density Genotyping of Immune Loci in Kawasaki Disease and IVIG Treatment Response in European-American Case-parent Trio Study. Genes and Immunity, accepted, 2014. PMCID: in process
     
  8. Stella Aslibekyan, Howard W. Wiener, Guodong Wu, Degui Zhi, Sadeep Shrestha, Gustavo de los Campos, Ana Ines Vazquez. “Estimating Proportions of Explained Variance: a Comparison of Whole Genome Subsets”. BMC Proceedings 2014, 8(Suppl 1):S102. 2014. PMCID: in process.
     
  9. Marguerite R. Irvin*, Degui Zhi*, Roby Joehanes*, Michael Mendelson*, Stella Aslibekyan, Steven A. Claas, Krista S. Thibeault, Nikita Patel, Kenneth Day, Lindsay Waite Jones, Liming Liang, Brian H. Chen, Chen Yao, Hemant K. Tiwari, Jose M. Ordovas, Daniel Levy, Devin Absher, Donna K. Arnett. Epigenome-wide association study of fasting blood lipids in the Genetics of Lipid Lowering Drugs and Diet Network Study, Circulation 130(7): 565-572, 2014. PMCID, in process.
     
  10. Marguerite R. Irvin; Degui Zhi; Stella Aslibekyan; Steven A Claas; Devin M. Absher; Jose M. Ordovas; Hemant K. Tiwari; Steve Watkins; Donna K. Arnett. Genomics of post-prandial lipidomic phenotypes in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) Study, PLoS One. 6;9(6):e99509, 2014. [PMCID: PMC4048279]
     
  11. Chacko BKK, P.A.,Ravi, S, Benavides, G.A., Mitchell, T., Dranka, B.P., Ferrick, D., Singal, A.K., Ballinger, S.W., Bailey, S.M., Hardy, R.W., Jianhua Zhang, J, Zhi, D., and Darley-Usmar, V.M. The Bioenergetic Health Index: A New Concept in Mitochondrial Translational Research. Clin Sci (Lond) 127(6): 367-373, 2014. PMCID, in process.
     
  12. Frazier-Wood, A.C.*, Aslibekyan, S.*, Absher, D.M., Hopkins, P.N., Sha, J., Tsai, M.Y., Tiwari, H.K., Waite, L., Zhi, D., & Arnett, D.K., "Methylation at CPT1A locus is associated with lipoprotein subfraction profiles." J Lipid Res 55(7): 1324-1330, 2014. [PMCID: PMC4076093]
     
  13. Aditi Shendre, Marguerite R Irvin, Bradley E Aouizerat, Howard W Wiener, Ana I Vazquez, Kathryn Anastos, Jason Lazar, Chenglong Liu, Roksana Karim, Nita A Limdi, Mardge H Cohen, Elizabeth T. Golub, Degui Zhi, Robert C Kaplan, Sadeep Shrestha, “RYR3 gene variants in subclinical atherosclerosis among HIV-infected women in the Women’s Interagency HIV Study (WIHS)”, Atherosclerosis 233(2): 666- 672, 2014. [PMCID: PMC3965606]
     
  14. Bertha Hidalgo, Marguerite Irvin, Jin Sha, Degui Zhi, Stella Aslibekyan, Devin Absher, Hemant Tiwari, Edmond Kabagambe, Jose Ordovas and Donna Arnett, "Epigenome-wide Association Study of Fasting Measures of Glucose, Insulin, and HOMA-IR in GOLDN", Diabetes, 63(2):801-7. 2014. [PMCID: PMC3968438]
     
  15. 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." Hum Genet 133(2): 139-150, 2014. [PMCID: PMC3947150].
     
  1. 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.
     
  2. Kui Zhang, Degui Zhi*. “Joint haplotype phasing and genotype calling of multiple individuals using haplotype informative reads”. Bioinformatics, accepted, 2013. [PMID: 23943637] [PMCID: PMC3777110]
     
  3. 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.
     
  4. 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.
     
  5. 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.
     
  6. 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]