Printed on October 20, 2014

Degui Zhi, Ph.D.

Assistant Professor Department of Biostatistics

School of Public Health University of Alabama at Birmingham

Ryals Public Health Bldg 327C

1665 University Blvd. Birmingham, AL 35294-0022

Phone: (205)-975-9192 Fax: (205) 975-2540 Email: dzhi@uab.edu

EDUCATION 2001-2006 Ph.D. in Bioinformatics, University of California, San Diego.

1997-1999 M.Sc. in computer science, National University of Singapore

1993-1997 B.S. in computer science, Peking University (Beijing University)

CURRENT APPOINTMENT 03/2009-present Assistant Professor, Section on Statistical Genetics, Department of

Biostatistics, School of Public Health, University of Alabama at Birmingham

2010-present Associate Scientist, Nutrition Obesity Research Center (NORC), University of Alabama at Birmingham

2014-present Member, Biostatistics Core, Nutrition Obesity Research Center (NORC), University of Alabama at Birmingham

2014-present Member, BTS Consulting Center, Department of Biostatistics, School of Public Health, University of Alabama at Birmingham

RESEARCH INTERESTS KEYWORDS Computational genomics, Statistical genetics, Bioinformatics,

Systems biology, Next-generation sequencing, Epigenetics, Big data, Machine Learning, Genetics epidemiology

PREVIOUS RESEARCH EXPERIENCE

Degui Zhi CV Page 2 of 21

2006-2009 Postdoctoral fellow, Department of Plant and Microbial Biology, University of California, Berkeley.

2001-2006 Research assistant, Department of Computer Science, University of California, San Diego

2004-2006 Visiting research assistant, Burnham Institute, La Jolla, California

2004 Summer visiting student researcher, Max Planck Institute for Molecular Genetics, Berlin, Germany

2001 Summer intern, Arena Pharmaceutical Inc., San Diego

2000-2001 Research assistant, Department of Computer Science and Engineering, University of California, Santa Cruz

1999-2000 Full-time research assistant, Department of Computational Science, National University of Singapore

1997-1999 Graduate student researcher, Department of Computer Science, School of Computing, National University of Singapore

AWARDS Best Paper award, the Science Unbound Foundation, for Best paper by a UAB based investigator in the area of statistical genetics, 2013. NIH Pathway to independence K99/R00, 2007-2012. Outstanding Poster award (4 out of 171), RECOMB, 2007. Travel award, Workshop on Genomic Impact of Eukaryotic Transposable Elements, 2006. Max-Planck-Society fellowship, 2004. First class award (top 10), National Mathematics Olympic, Liaoning Province, China, 1992.

CURRENT RESEARCH GRANT SUPPORT

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NIH/NHGRI R01 HG008115 (Yu, Zhang, & Zhi) 09/10/2014-06/30/2017 $361,108 (Year 1 direct costs) Next-Generation Bioinformatics for Next-Generation Sequencing The goals of this project are to develop an improved computational system for calling of rare genetic variants and haplotypes and for integrating genetic data sets of different compositions and generated by different platforms. Role: co-PI. NIH R01 HL104135 (Arnett) 08/15/2010 – 05/31/2015, Yearly Cost: $924,356. Title: Epigenetic Determinants of Lipid Response to Dietary Fat and Fenofibrate. In this project, we will identify novel epigenetic variations that predict individuals who respond poorly to dietary fat or favorably to fenofibrate which will lead to the development of targeted interventions to more effectively prevent and treat hypertriglyceridemia. Role: co-Investigator. NIH R01 HL055673 (Arnett) 06/01/13 – 04/30/17, First year direct: $626,073. Title: HyperGEN: Genetics of Left Ventricular Hypertrophy. Left ventricular (LV) remodeling and hypertrophy occurs frequently in the general population and is a strong predictor of myocardial infarction, heart failure, and stroke. Using whole exome sequencing, this project will identify novel genes contributing to LV hypertrophy, and evaluate their relevance in a cell-based system to identify new pathways for future treatment. Role: co-Investigator. NIH R01 CA154643 Skibola (PI) 03/01/13 – 04/30/2015 Resequencing and Functional Studies to Identify Casual Gene Variants of Lymphoma

Non-Hodgkin lymphoma (NHL) is the fifth most common cancer in the U.S and will account for over 66,000 newly diagnosed cases and 20,000 deaths in the U.S. and 300,000 cases and 175,000 deaths worldwide in 2010. We will perform genetic studies that will aid in the identification of common genetic variants that cause lymphoma. These studies will increase our understanding of how lymphoma develops in the body and provide new ways to screen, prevent and treat lymphoma.

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Role: Co-Investigator. NIH/NIA R01 AG033682 Allison (PI) 03/15/10 – 2/28/15 Body Composition, Energetics and Longevity Over 50 million Americans are obese and are therefore predicted to live less long than they would otherwise live. Whether reductions in overall obesity or selected aspects of fatness among obese persons will prolong life remains the subject of active debate and controversy. The proposed research will help provide information to inform that dialogue. Role: Co-Investigator. NIH/NIDDK P30 DK056336 Allison (PI) 06/15/12 – 5/31/17 UAB Nutrition Obesity Research Center

One's nutritional intake can have profound positive or negative consequences on health. So too does obesity, or excess body fat, have profound effects, usually negative, on health, quality of life, and lifespan. Beyond these broad generalities, however, much remains unknown in these domains, and misinformation and superstition abound. Our center advances knowledge on these critical contributors to health and disease through scientific inquiry that is both rigorous and creative. Role: Co-Investigator. NIH/NHLBI P01 HL114470 Thannickal (PI) Therapeutic Targeting of the Myofibroblast in Fibrotic Lung Disease 10/1/13 – 7/31/18 The major goal of this translational program project grant is to develop novel anti-fibrotic therapies targeting myofibroblasts in fibrotic lung disease. Roles: co-Investigator NIH/NHGRI R25 HG006110 (Tiwari) Title: Short Course on Next-Generation Sequencing Technology and Statistical Methods 04/27/11 – 1/31/17 $48,584 (first year direct) To offer an annual short course focused on technological and statistical approaches pertaining to next-generation sequencing applied to complex human disorders and quantitative traits. Role: Co-investigator

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NIH/NCI R01 CA186646 (MPI: Brown/Vachon) Title: Molecular characterization of myeloma and related asymptomatic precursor conditions 07/01/2014-05/31/2019 $551,870 (Year 1 direct costs) The purpose of this study is to identify microRNAs associated with the presence of MM and its asymptomatic precursor states and to characterize the role miRNAs in regulating gene transcription. Role: Co-Investigator.

NIH/NCI R01 AR064820 (Brown) Title: association of genetic and autoantibody signatures with SLE clinical course 08/26/2014-06/30/2019 $482,631 (Year 1 direct costs) The purpose of this study is to characterize complex interactions between variation in DNA sequence and autoantibody profiles with the rate of progression and severity of lupus-associated nephritis and severe organ damage, which are more common among ethnic minorities. Role: Co-Investigator.

SAIC-FREDERICK, INC, NCI Chemical Biology Consortium Task Order S08-221ST TO4aSAIC (Gillespie)

Interrogation of Key Genomic Alterations in Glioblastoma Multiforme (GBM) for Identification of Molecular Pathways Critical to GBM Tumorigenesis and Progression.

04/01/2013 – 11/30/2014

Role: co-Investigator.

USDA/NIFA Proposal #2014-07991 (Liu)

Enhancing Low-Oxygen Tolerance of Catfish Using Genomics and Genetics

09/30/2014-09/29/2016

Role: subcontract-PI.

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SELECTED PENDING RESEARCH GRANT SUPPORT

PAST RESEARCH GRANT SUPPORT NIH R00 RR024163 (Pathway to independence, Independent Phase) Title: Algorithms for protein structural classification and function prediction. 07/15/2009 – 05/31/2014, Yearly Total Cost: $244,046. Role: PI. NIH K99 RR024163 (Pathway to independence, Mentored Phase) Title: Algorithms for protein structural classification and function prediction. 09/15/2007 – 06/30/2009, Yearly Cost: $73,440. Role: PI.

UAB NORC Special ARRA Pilot/Feasibility Grant (Zhi) Title: Differential gene expression of ribosomal proteins and its implication to obesity. 06/01/2010 – 05/31/2011, Yearly Cost: $25,000. Role: PI.

SAIC-FREDERICK, INC, NCI Chemical Biology Consortium Task order S08-221ST TO4 (Gillespie) Title: Interrogation of Key Genomic Alterations in Glioblastoma Multiforme (GBM) for Identification of Molecular Pathways Critical to GBM Tumorigenesis and Progression. 07/02/2010 – 06/30/2012 Yearly Cost: Role: co-Investigator.

UAB NORC Pilot/Feasibility Grant (Zhi)

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Title: Expression of ribosomal protein genes and pseudogenes in adipose and its implications to obesity 06/01/2011 – 05/31/2013, Yearly Cost: $25,000. Role: PI.

PEER-REVIEWED RESEARCH JOURNAL PUBLICATIONS (*Senior corresponding author or joint co-first author, trainees are underscored) 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. "Cyclosporine-mediated 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.

Degui Zhi CV Page 8 of 21

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: 4129397.

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.

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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: 4076093.

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.

16. Kui Zhang, Degui Zhi*. “Joint haplotype phasing and genotype calling of multiple individuals using haplotype informative reads”. Bioinformatics, 29(19):2427-34, 2013. PMCID: PMC3777110.

17. 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):802-6. PMCID: PMC3883783 [Available on 2014/8/1].

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18. 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, 37(6):560-70, 2013. PMCID: PMC4116485.

19. Guodong Wu, Degui Zhi*, Pathway-based approaches for sequencing-based genome-wide association studies, Genet Epidemiology, 37, 478-494. 2013. PMCID: PMC3856324.

20. 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, 32(2):289-300. 2014. PMC3851017 [Available on 2015/2/1].

21. 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: 3478165.

22. 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. PMCID: PMC3867591.

23. 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: 3513398.

24. 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, 3:92, 2012. PMCID: 3361011.

25. 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, 46(6):790-796, 2012. PMCID: 3380283.

26. Degui Zhi, Jihua Wu, Nianjun Liu, and Kui Zhang. “Genotype Calling from Next Generation Sequencing Data using Haplotype Information of Reads.” Bioinformatics, 1;28(7):938-46, 2012. PMCID: PMC3493122.

27. 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

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28. 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

29. 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

30. Guodong Wu, Nengjun Yi, Devin Absher, and Degui Zhi*. “Statistical Quantification of Methylation Levels by Next-generation Sequencing”. PLoS ONE 6(6): e21034, 2011. PMCID: PMC3115964

31. 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

32. 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: PMC3269888

33. 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. PMCID: PMC3042188

34. N. Yi, and D. Zhi. “Bayesian Analysis of Rare Variants in Genetic Association Studies”, Genetic Epidemiology, 35: 57–69, 2011. PMCID: PMC3200544

35. A. Aleshin, and D. Zhi*. “Recombination-associated sequence homogenization of neighboring Alu elements: signature of nonallelic gene conversion”, Molecular Biology and Evolution, 27 (10): 2300-2311, 2010. PMCID: PMC2950799

36. D. Zhi, M. Shatsky, and S.E. Brenner. “Alignment-Free Local Structural Comparison by Writhe Decomposition”, Bioinformatics 26: 1176-1184, 2010. PMCID: PMC2859133

37. D. Zhi. “Sequence correlation between neighboring Alu instances suggests post-retrotransposition sequence exchange due to Alu gene conversion”, Gene, 390(1-2):117-21, 2007.

38. 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.

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39. D. Zhi, S.S. Krishna, H. Cao, P. Pevzner, and A. Godzik. “Representing and comparing protein structures as paths in three-dimensional space”, BMC Bioinformatics, 7:460, 2006. PMCID: PMC1626488

40. 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.

41. D. Zhi, B. Raphael, A. Price, H. Tang, and P. Pevzner. “Identifying repeat domains in large genomes”, Genome Biology, 7(1):R7, 2006. PMCID: PMC1538870

42. 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.

43. 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. PMCID: PMC525693

44. 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.

45. 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.

BOOK CHAPTERS (*Senior corresponding author, trainees are underscored) 46. Degui Zhi, Kui Zhang, Genotype Calling and Haplotype Phasing from Next

Generation Sequencing Data. In Somnath Datta, and Dan Nettleton (Editors): Statistical Analysis of Next Generation Sequence Data. Springer. 2014.

OTHER PUBLICATIONS 47. Wu H, Wu MC, Zhi D, Santorico SA, Cui X: Statistics for Next Generation

Sequencing - Meeting Report. Front Genet 2012, 3:128. PMCID: PMC3395795.

48. Bairong Shen, Andrew E. Teschendorff, Degui Zhi, and Junfeng Xia: Biomedical Data Integration, Modeling, and Simulation in the Era of Big Data and Translational Medicine - Editorial. BioMed Research International 2014, Volume 2014, Article ID 731546. PMCID: in process.

ABSTRACTS

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1. D. M. Absher, M. R. Irvin, S. Aslibekyan, J. Sha, L. L. Waite, D. Zhi, K. Stanton Thibeault, J. Ordovas, D. K. Arnett. “DNA Methylation at CPT1A is Associated with Triglyceride Levels, BMI and WHR.” Annual Meeting of The American Society of Human Genetics, 2013.

2. W. Yang, U. Broeckel, A. J. Stoddard, D. Zhi, M. R. Irvin, H. K. Tiwari, S. C. Hunt, D. C. Rao, D. K. Arnett, C. C. Gu. “Variable set enrichment analysis of exome sequencing data reveals interesting candidate genes for left ventricular hypertrophy”. Annual Meeting of The American Society of Human Genetics, 2013.

3. Degui Zhi and Kui Zhang. “Joint haplotype phasing and genotype calling of multiple individuals using long-range haplotype informative reads” CSHL Biology of Genomes, 2013.

4. K. Zhang, D. Zhi. “Genotype calling for next-generation sequencing data from multiple populations.” Annual Meeting of The American Society of Human Genetics, 2012.

5. D. Zhi, K. Zhang. “Genotype calling and haplotype inference for next-generation sequencing data incorporating haplotype information in sequencing reads.” Annual Meeting of The American Society of Human Genetics, 2012.

6. N. Liu, W. Lin, N. Yi, D. Zhi, K. Zhang, G. Gao, H. Tiwari. “Haplotype-based methods for detecting uncommon causal variants with common SNPs.” Annual Meeting of The American Society of Human Genetics, 2012.

7. G. Wu, D. Zhi. “Gene-based collapsing methods may not be powerful for pathway-based association analysis for exome sequencing data.” Annual Meeting of The American Society of Human Genetics, 2012.

8. X. Lou, G. Chen, N. Liu, Y. Klimentidis, X. Zhu, D. Zhi, X. Wang. “A unified generalized multifactor reduction method for detecting gene-gene interactions in family and unrelated samples with application to nicotine dependence.” Annual Meeting of The American Society of Human Genetics, 2012.

9. Guodong Wu, Kai Wang, Degui Zhi. “Pathway-based genetic association analysis for exome sequencing data”, Annual Meeting of The American Society of Human Genetics, 2011.

10. Jihua Wu, Guo-Bo Chen, Degui Zhi, Nianjun Liu, and Kui Zhang, “A Hidden Markov Model for Haplotype Inference for Present-Absent Genotype Data Using Previously Identified Haplotype and Haplotype Patterns”, JSM 2011.

11. Nengjun Yi and Degui Zhi. “Bayesian Analysis of Rare Variants with Disparate Effects in Association Studies”, Annual Meeting of ENAR, 2011.

12. Jihua Wu, Guo-bo Chen, Degui Zhi, Nianjun Liu, and Kui Zhang. “A Hidden Markov Model for Haplotype Inference Using Previously Identified Haplotype and Haplotype Patterns”, Annual Meeting of ENAR, 2011.

Degui Zhi CV Page 14 of 21

13. Liyan Gao, Zhide Fang, Kui Zhang, Degui Zhi and Xiangqin Cui. “Length Bias Correction for RNA-seq Data in Gene Set Analyses”, Annual Meeting of ENAR, 2011.

14. D. Zhi, N. Yi,. “Bayesian Analysis of Rare Variants in Genetic Association Studies”, Annual Meeting of The American Society of Human Genetics, 2010.

15. N. Yi, D. Zhi. “Hierarchical Generalized Linear Models For Detecting Rare Variants With Disparate Effects In Association Studies”, Annual Meeting of The American Society of Human Genetics, 2010.

16. G. Wu, N. Yi, D. Absher, D. Zhi. “Quantification of Methylation Levels by Next-generation Sequencing”, Annual Meeting of The American Society of Human Genetics, 2010.

17. Guodong Wu, Nengjun Yi, Devin Absher, and Degui Zhi. “Bayesian Hierarchical Models for Quantifying Methylation Levels by Next-generation Sequencing”, Annual Meeting of ENAR, 2010.

18. D. Zhi, and N. Liu. “Bayesian network model for SNP calling in shallow sequencing with haplotype based prior”, Annual Meeting of The American Society of Human Genetics, 2009.

19. A. Aleshin, and D. Zhi*. “ Recombination-associated sequence homogenization of neighboring Alu elements—The signature of nonallelic gene conversion”, CSHL Biology of Genomes, 2008.

TEACHING 2014, UAB BST776 Statistical Methods for Genetic Analysis II

Role: Guest lecturer on pathway-based association analysis. Role: Guest lecturer on epigenetics.

2013, NHGRI SHORT COURSE ON NEXT-GENERATION SEQUENCING: TECHNOLOGY AND STATISTICAL METHODS, UAB, Birmingham, AL.

Role: Course instructor on Variant calling and assembly from NGS data. 2013, UAB BST775 Statistical Methods for Genetic Analysis I

Role: Redesign the course with updated contents. Role: Course master.

2013, NIGMS SHORT COURSE ON STATISTICAL GENETICS AND GENOMICS, UAB, Birmingham, AL.

Role: Course instructor on Software demonstration of genotype imputation. Role: Course instructor on Software demonstration of exome sequence data analysis.

Degui Zhi CV Page 15 of 21

Role: Course instructor on Genotype calling from NGS data. 2012, NHGRI SHORT COURSE ON NEXT-GENERATION SEQUENCING: TECHNOLOGY AND STATISTICAL METHODS, UAB, Birmingham, AL.

Role: Course instructor on Assembling NGS data. 2012, NIGMS SHORT COURSE ON STATISTICAL GENETICS AND GENOMICS, UAB, Birmingham, AL.

Role: Course instructor on Software demonstration of exome sequence data analysis.

2012, UAB BST612 Intermediate Statistical Analysis Role: Course master.

2012, UAB GBS722 Bioinformatics Course Role: gave 1 guest lecture.

2011, UAB BST795 Faculty Research Area Seminar Role: gave 1 guest lecture.

2011, NIGMS SHORT COURSE ON STATISTICAL GENETICS AND GENOMICS, UAB, Birmingham, AL.

Role: Course instructor on Software demonstration of exome sequence data analysis.

2011, UAB BST695 Special Topics in Statistical Genomics Role: Course master.

2010, UAB BST676 Genomic Data Analysis Role: gave 2 Guest lectures on Next-generation sequencing data analyses.

2004, UCSD BENG202 Bioinformatics II: Sequence and Structure Analysis—Methods and Applications.

Role: Teaching assistant, co-designed the course materials, which is adopted as online companion materials for the textbook published by the course instructor.

CONTINUING EDUCATION ON TEACHING 2014, UAB Center for Teaching & Learning, Creating Learning Objectives for

Design & Assessment 2014, UAB Center for Teaching & Learning, Developing a Teaching Philosophy

that Can Be Easily Articulated 2014, UAB Center for Teaching & Learning, Maximizing the First Day of Class 2014, UAB Center for Teaching & Learning, Getting the best results from IDEA

Degui Zhi CV Page 16 of 21

CONFERENCE AND INVITED TALKS Inferring genotypes and haplotypes from Next-generation sequencing data. Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, Nov, 2014.

Next-generation bioinformatics for next-generation sequencing: genotype calling and haplotype phasing. Department of Computer and Information Sciences, University of Alabama at Birmingham, Birmingham, AL, Oct, 2014.

Genotype calling from NGS data: incorporating haplotype information in reads. NGS workshop, International Conference on Intelligent Biology and Medicine (ICIBM), Nashville, TN, August, 2013

From genetics to epigenetics. Sino-US summer school for translational biomedical informatics (3S-TBI2013) Suzhou, Jiangsu Province, China, June, 2013.

Genotype calling and haplotype inference from next-generation sequencing data. HitSEQ SIG of ISMB, Long Beach, CA, July, 2012.

Genotype calling and haplotype inference from next-generation sequencing data. Emory University, Atlanta, GA, March, 2012.

Haplotype/genotype calling and Exome sequencing for rare Mendelian disease, 2 day conference on STATISTICAL ANALYSES FOR NEXT GENERATION SEQUENCING, Birmingham, AL, Sep, 2011.

Genotype calling for next-gen sequencing data, UAB Research Computing Day, Birmingham, AL, Sep, 2011.

Statistical power of exome sequencing for rare diseases, NextGen-UAB Symposium, Birmingham, AL, May, 2011.

Bayesian Analysis of Rare Variants with Disparate Effects in Association Studies, Annual Meeting of ENAR, Miami, FL, March, 2011.

Bayesian Hierarchical Models for Quantifying Methylation Levels by Next-generation Sequencing, Annual Meeting of ENAR, New Orleans, LA, March, 2010.

Protein structural comparison, classification, and function prediction in the structural genomics era, University of Tennessee, Knoxville, TN, February, 2009.

A sequence alignment-based optimization framework for the inference of nontrivial protein domain architecture and ancient homology, Tongji University, Shanghai, China, December, 2008.

Repeat, Repeat, Repeat (Analysis of genomic repeats), Beijing Genome Institute, Shenzhen, Guangdong, China, December, 2008.

Degui Zhi CV Page 17 of 21

A sequence alignment-based optimization framework for the inference of nontrivial protein domain architecture and ancient homology, Computational Systems Biology Seminar, University of Georgia, Athens, GA, July, 2008.

Beyond Sequence Alignment: An optimization framework for the inference of nontrivial protein domain architecture and ancient homology, Section on Statistical Genetics, School of Public Health, University of Alabama, Birmingham, AL, July, 2008.

An optimization framework for the inference of nontrivial protein domain architecture and ancient homology, University of Tennessee, Knoxville, TN, April, 2008.

Alignment-free local structural comparison by Writhe decomposition, Workshop on Algorithms in Bioinformatics (WABI), Philadelphia, PA, September, 2007.

Comparative genomics analysis of Alu gene conversions, 1st International Conference and Workshop on Genomic Impact of Eukaryotic Transposable Elements, Asilomar, CA, April, 2006.

Resolving difference between nearly identical repeats in fragment assembly, RECOMB satellite meeting on DNA sequencing and characterizations, Stanford, CA, May, 2002.

PhD COMMITTEE CHAIR Guodong Wu BST 2009-2014

Current position: Biostatistician, Lovelace Respiratory Research Institute

MS STUDENT CHAIR Guodong Wu BST 2011

PHD DISSERTATION COMMITTEE Celeste Yang BST 2013 Aditi Shendre EPI 2014- Lindsay Jones BST 2014- Anh N Do EPI 2014- Rachel Brewer Nutrition 2014-

MS DISSERTATION COMMITTEE Peng Li BST 2011 Ngan Thanh Tran EPI 2014

STUDENT ADVISOR

Degui Zhi CV Page 18 of 21

Dongning He BST MS 2013- Dongmei Sun BST MSPH 2013-

OTHER STUDENT MENTOR Xin Geng UAB's NIGMS-funded Bursary Award for short course

2013 Aditi Shendre UAB's NIGMS-funded Bursary Award for short course

2013 Yue Pan UAB's NIGMS-funded Bursary Award for short course 2012 Nirmal Choradia MD student intern 2011 Shravan Gopal Graduate student research 2009 Hua Zhong Graduate student research 2009 Alexey Aleshin Undergrad student research 2007

POSTDOCTORAL FELLOW MENTOR Kirk Williams (co-mentor with David Allison) 2009-2011 Samad Jahandideh 2010-2012 Curtis Holliman (co-mentor with Hemant Tiwari) 2011-2014

EDITORIAL BOARD Academic editor, PLOS ONE 2013- Editorial board member, Computational Biology Journal 2012- Review editor, Frontiers in Bioinformatics and Computational Biology 2011- Review editor, Frontiers in Evolutionary and Population Genetics 2011- Review editor, Frontiers in Epigenetics 2011- Review editor, Frontiers in Statistical Genetics and Methodology 2010-

GUEST EDITORIAL ACTIVITY Guest editor, Research Topic: Identification of rare genetic variants contributing to human diseases. Frontiers in Genetics, 2014 Guest editor, Biomedical Data Integration, Modeling, and Simulation in the Era of Big Data and Translational Medicine. BioMed Research International 2014

Degui Zhi CV Page 19 of 21

JOURNAL AND CONFERENCE REFEREES Advances in Bioinformatics 2009 American Journal of Clinical Nutrition 2014 Bioinformatics 2006, 2007, 2008, 2009, 2009, 2010, 2011, 2013, 2013, 2013 BMC Bioinformatics 2012, 2013 BMC Genetics 2012 Computational and Mathematical Methods in Medicine 2013 Computational Statistics and Data Analysis 2009, 2010 European Conferences on Computational Biology (ECCB) 2006 European Journal of Clinical Investigation 2011 Frontiers in Genetics 2011, 2013, 2014 Genes 2010 Genetic Epidemiology 2012, 2013 Genetics Research 2012 Genome Research 2011 Human Genetics 2012 Human Heredity 2010 International Journal of Obesity 2014 Int’l Conf. on Research in Computational Molecular Biology (RECOMB) 2005 Journal of Biomedicine and Biotechnology 2010 Journal of Computational and Graphical Statistics 2012 Journal of Medical Genetics 2012 Journal of Obesity 2012 Molecular Biology and Evolution 2009 Molecular Systems Biology 2008 Nature Biotechnology 2011(co-review) Nature Communications 2013 Nature Methods 2011 Nucleic Acids Research 2007, 2011 PLOS ONE, 2012, 2013 Respiratory Research, 2013

REVIEWS OF RESEARCH GRANTS

Degui Zhi CV Page 20 of 21

Ad hoc reviewer, NIH IAR Reviewer Challenge Grants Panel ZRG1 PSE-C/J (58) R 2009

Reviewer, Italian Ministry of Health Researchers Call 2010, 2011, 2013 Ad hoc Statistical reviewer, NIH MGB Section 2010 Reviewer, Tuskegee/UAB partnership pilot grant 2010 Reviewer, Portuguese Foundation for Science and Technology, Diagnostic,

Therapies and Public Health Evaluation Panel, 2012 Reviewer, Kansas City Area Life Sciences Institute (KCALSI) Patton Trust Grant

Program, 2012 Reviewer, NIH RFA-RM-14-001: Computational Analyses Exploiting Reference

Epigenomic Maps [ZRG1 IMST-R (51) R] study section panel 2014 Reviewer, NIH K99/R00 Grants Panel ZGM1 TWD-Y (KR) 2014 2014

PROFESSINAL MEMBERSHIPS International Society of Computational Biology (ISCB), 2006-present Sigma Xi, 2007-present Reuter Insight Expert, 2008-present American Society of Human Genetics, 2008-present American Association for the Advancement of Science, 2007-present

COMMITTEE AND LOCAL SERVICES Co-Leader, SSG Journal Club, Biostatistics Department, SOPH, UAB, 2009 - Member, Admission Committee, Biostatistics Department, SOPH, UAB, 2009-2010, 2012- Member, SSG curriculum committee, Biostatistics Department, SOPH, UAB, 2010 Member, SSG overseas connection task force, Biostatistics Department, SOPH,

UAB, 2010 Member, SSG Professional Development Workshop Organization Committee,

Biostatistics Department, SOPH, UAB, 2010 Member, UAB Research Computing Day Program Committee, 2011 Alternate Senate, UAB faculty senate, 2011 – 2013 Member, UAB faculty senate finance committee, 2011 – 2013 Grader, UAB Department of Biostatistics comprehensive exams, 2014 Member, SOPH UWIRC review committee, UAB 2014 Leader, SSG Journal Club, Biostatistics Department, SOPH, UAB, 2014 -

Degui Zhi CV Page 21 of 21

CONFERENCE ORGANIZATION Member, UAB Research Computing Day Program Committee, 2011

Co-investigator, Workshop on next-generation sequencing data analysis, 2011, (NIH R13 grant funded, PI: Cui)

Co-Investigator, Short Course on next-generation sequencing data analysis, 2011-2014, (NIH R25 grant funded, PI: Tiwari)

Session Chair, Next-generation sequencing data analysis, ENAR, 2011.