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Degui Zhi, Ph.D. - Publications

Affiliations: 
University of California, San Diego, La Jolla, CA 
Area:
Bioinformatics, proteomics, mass spectrometry
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47 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Kuo TT, Jiang X, Tang H, Wang X, Bath T, Bu D, Wang L, Harmanci A, Zhang S, Zhi D, Sofia HJ, Ohno-Machado L. iDASH secure genome analysis competition 2018: blockchain genomic data access logging, homomorphic encryption on GWAS, and DNA segment searching. Bmc Medical Genomics. 13: 98. PMID 32693816 DOI: 10.1186/S12920-020-0715-0  0.32
2020 Kim S, Park HJ, Cui X, Zhi D. Collective effects of long-range DNA methylations predict gene expressions and estimate phenotypes in cancer. Scientific Reports. 10: 3920. PMID 32127627 DOI: 10.1038/S41598-020-60845-2  0.314
2019 Naseri A, Holzhauser E, Zhi D, Zhang S. Efficient haplotype matching between a query and a panel for genealogical search. Bioinformatics (Oxford, England). 35: i233-i241. PMID 31510689 DOI: 10.1093/Bioinformatics/Btz347  0.311
2019 Naseri A, Zhi D, Zhang S. Multi-allelic positional Burrows-Wheeler transform. Bmc Bioinformatics. 20: 279. PMID 31167638 DOI: 10.1186/S12859-019-2821-6  0.31
2019 Zhong H, Kim S, Zhi D, Cui X. Predicting gene expression using DNA methylation in three human populations. Peerj. 7: e6757. PMID 31106051 DOI: 10.7717/Peerj.6757  0.306
2019 Geng X, Irvin MR, Hidalgo B, Aslibekyan S, Srinivasasainagendra V, An P, Frazier-Wood AC, Tiwari HK, Dave T, Ryan K, Ordovas JM, Straka RJ, Feitosa MF, Hopkins PN, Borecki I, ... ... Zhi D, et al. An Exome-Wide Sequencing Study of the GOLDN Cohort Reveals Novel Associations of Coding Variants and Fasting Plasma Lipids. Frontiers in Genetics. 10: 158. PMID 30863429 DOI: 10.3389/Fgene.2019.00158  0.353
2019 Wu Z, Yan J, Wang K, Liu X, Guo Y, Zhi D, Ruan J, Zhao Z. The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: genomics with bigger data and wider applications. Bmc Genomics. 20: 80. PMID 30712512 DOI: 10.1186/S12864-018-5369-3  0.354
2019 Zhi D, Zhao Z, Li F, Wu Z, Liu X, Wang K. The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: genomics meets medicine. Bmc Medical Genomics. 12: 20. PMID 30704510 DOI: 10.1186/S12920-018-0448-5  0.314
2018 Geng X, Irvin MR, Hidalgo B, Aslibekyan S, Srinivasasainagendra V, An P, Frazier-Wood A, Tiwari HK, Dave T, Ryan K, Ordovas JM, Straka RJ, Feitosa MF, Hopkins PN, Borecki I, ... ... Zhi D, et al. An exome-wide sequencing study of lipid response to high-fat meal and fenofibrate in Caucasians from the GOLDN cohort. Journal of Lipid Research. PMID 29463568 DOI: 10.1194/Jlr.P080333  0.321
2017 Liu N, Irvin MR, Zhi D, Patki A, Beasley TM, Nickerson DA, Hill CE, Chen J, Kimmel SE, Limdi NA. Influence of common and rare genetic variation on warfarin dose among African-Americans and European-Americans using the exome array. Pharmacogenomics. PMID 28686080 DOI: 10.2217/Pgs-2017-0046  0.307
2017 Ng MCY, Graff M, Lu Y, Justice AE, Mudgal P, Liu CT, Young K, Yanek LR, Feitosa MF, Wojczynski MK, Rand K, Brody JA, Cade BE, Dimitrov L, Duan Q, ... ... Zhi D, et al. Discovery and fine-mapping of adiposity loci using high density imputation of genome-wide association studies in individuals of African ancestry: African ancestry anthropometry genetics consortium. Plos Genetics. 13: e1006719. PMID 28430825 DOI: 10.1371/Journal.Pgen.1006719  0.361
2017 Hedman ÅK, Mendelson MM, Marioni RE, Gustafsson S, Joehanes R, Irvin MR, Zhi D, Sandling JK, Yao C, Liu C, Liang L, Huan T, McRae AF, Demissie S, Shah S, et al. Epigenetic Patterns in Blood Associated With Lipid Traits Predict Incident Coronary Heart Disease Events and Are Enriched for Results From Genome-Wide Association Studies. Circulation. Cardiovascular Genetics. 10. PMID 28213390 DOI: 10.1161/Circgenetics.116.001487  0.356
2016 Day K, Waite LL, Alonso A, Irvin MR, Zhi D, Thibeault KS, Aslibekyan S, Hidalgo B, Borecki IB, Ordovas JM, Arnett DK, Tiwari HK, Absher DM. Heritable DNA Methylation in CD4+ Cells among Complex Families Displays Genetic and Non-Genetic Effects. Plos One. 11: e0165488. PMID 27792787 DOI: 10.1371/Journal.Pone.0165488  0.334
2016 Geng X, Liu S, Yao J, Bao L, Zhang J, Li C, Wang R, Sha J, Zeng P, Zhi D, Liu Z. A Genome Wide Association Study Identifies Multiple Regions Associated with Head Size in Catfish. G3 (Bethesda, Md.). PMID 27558670 DOI: 10.1534/G3.116.032201  0.315
2016 Dai H, Wu G, Wu M, Zhi D. An Optimal Bahadur-Efficient Method in Detection of Sparse Signals with Applications to Pathway Analysis in Sequencing Association Studies. Plos One. 11: e0152667. PMID 27380176 DOI: 10.1371/Journal.Pone.0152667  0.326
2016 Das M, Sha J, Hidalgo B, Aslibekyan S, Do AN, Zhi D, Sun D, Zhang T, Li S, Chen W, Srinivasan SR, Tiwari HK, Absher D, Ordovas JM, Berenson GS, et al. Association of DNA Methylation at CPT1A Locus with Metabolic Syndrome in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) Study. Plos One. 11: e0145789. PMID 26808626 DOI: 10.1371/Journal.Pone.0145789  0.302
2016 Ma Y, Follis JL, Smith CE, Tanaka T, Manichaikul AW, Chu AY, Samieri C, Zhou X, Guan W, Wang L, Biggs ML, Chen YI, Hernandez DG, Borecki I, Chasman DI, ... ... Zhi D, et al. Interaction of methylation-related genetic variants with circulating fatty acids on plasma lipids: a meta-analysis of 7 studies and methylation analysis of 3 studies in the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium. The American Journal of Clinical Nutrition. PMID 26791180 DOI: 10.3945/Ajcn.115.112987  0.329
2015 Joshi PK, Esko T, Mattsson H, Eklund N, Gandin I, Nutile T, Jackson AU, Schurmann C, Smith AV, Zhang W, Okada Y, Stančáková A, Faul JD, Zhao W, Bartz TM, ... ... Zhi D, et al. Directional dominance on stature and cognition in diverse human populations. Nature. 523: 459-62. PMID 26131930 DOI: 10.1038/Nature14618  0.34
2015 Demerath EW, Guan W, Grove ML, Aslibekyan S, Mendelson M, Zhou YH, Hedman ÅK, Sandling JK, Li LA, Irvin MR, Zhi D, Deloukas P, Liang L, Liu C, Bressler J, et al. Epigenome-wide association study (EWAS) of BMI, BMI change and waist circumference in African American adults identifies multiple replicated loci. Human Molecular Genetics. PMID 25935004 DOI: 10.1093/Hmg/Ddv161  0.304
2015 Tran NT, Aslibekyan S, Tiwari HK, Zhi D, Sung YJ, Hunt SC, Rao DC, Broeckel U, Judd SE, Muntner P, Kent ST, Arnett DK, Irvin MR. PCSK9 variation and association with blood pressure in African Americans: preliminary findings from the HyperGEN and REGARDS studies. Frontiers in Genetics. 6: 136. PMID 25904937 DOI: 10.3389/Fgene.2015.00136  0.319
2015 Geng X, Sha J, Liu S, Bao L, Zhang J, Wang R, Yao J, Li C, Feng J, Sun F, Sun L, Jiang C, Zhang Y, Chen A, Dunham R, ... Zhi D, et al. A genome-wide association study in catfish reveals the presence of functional hubs of related genes within QTLs for columnaris disease resistance. Bmc Genomics. 16: 196. PMID 25888203 DOI: 10.1186/S12864-015-1409-4  0.307
2015 Zhi D, Liu N, Zhang K. On the design and analysis of next-generation sequencing genotyping for a cohort with haplotype-informative reads. Methods (San Diego, Calif.). 79: 41-6. PMID 25644447 DOI: 10.1016/J.Ymeth.2015.01.016  0.339
2015 Zhi D, Shendre A, Scherzer R, Irvin MR, Perry RT, Levy S, Arnett DK, Grunfeld C, Shrestha S. Deep sequencing of RYR3 gene identifies rare and common variants associated with increased carotid intima-media thickness (cIMT) in HIV-infected individuals. Journal of Human Genetics. 60: 63-7. PMID 25500725 DOI: 10.1038/Jhg.2014.104  0.337
2014 Aslibekyan S, Wiener HW, Wu G, Zhi D, Shrestha S, de Los Campos G, Vazquez AI. Estimating proportions of explained variance: a comparison of whole genome subsets. Bmc Proceedings. 8: S102. PMID 25519356 DOI: 10.1186/1753-6561-8-S1-S102  0.353
2014 Cerhan JR, Berndt SI, Vijai J, Ghesquières H, McKay J, Wang SS, Wang Z, Yeager M, Conde L, de Bakker PI, Nieters A, Cox D, Burdett L, Monnereau A, Flowers CR, ... ... Zhi D, et al. Genome-wide association study identifies multiple susceptibility loci for diffuse large B cell lymphoma. Nature Genetics. 46: 1233-8. PMID 25261932 DOI: 10.1038/Ng.3105  0.307
2014 Wu J, Chen GB, Zhi D, Liu N, Zhang K. 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. PMID 25161663 DOI: 10.3389/Fgene.2014.00267  0.315
2014 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. 15: 534-42. PMID 25101798 DOI: 10.1038/Gene.2014.47  0.307
2014 Aslibekyan S, Dashti HS, Tanaka T, Sha J, Ferrucci L, Zhi D, Bandinelli S, Borecki IB, Absher DM, Arnett DK, Ordovas JM. PRKCZ methylation is associated with sunlight exposure in a North American but not a Mediterranean population. Chronobiology International. 31: 1034-40. PMID 25075435 DOI: 10.3109/07420528.2014.944266  0.332
2014 Irvin MR, Zhi D, Joehanes R, Mendelson M, Aslibekyan S, Claas SA, Thibeault KS, Patel N, Day K, Jones LW, Liang L, Chen BH, Yao C, Tiwari HK, Ordovas JM, et al. Epigenome-wide association study of fasting blood lipids in the Genetics of Lipid-lowering Drugs and Diet Network study. Circulation. 130: 565-72. PMID 24920721 DOI: 10.1161/Circulationaha.114.009158  0.317
2014 Frazier-Wood AC, Aslibekyan S, Absher DM, Hopkins PN, Sha J, Tsai MY, Tiwari HK, Waite LL, Zhi D, Arnett DK. Methylation at CPT1A locus is associated with lipoprotein subfraction profiles. Journal of Lipid Research. 55: 1324-1330. PMID 24711635 DOI: 10.1194/Jlr.M048504  0.342
2014 Chen GB, Liu N, Klimentidis YC, Zhu X, Zhi D, Wang X, Lou XY. A unified GMDR method for detecting gene-gene interactions in family and unrelated samples with application to nicotine dependence. Human Genetics. 133: 139-50. PMID 24057800 DOI: 10.1007/S00439-013-1361-9  0.304
2013 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. 8: 802-6. PMID 23811543 DOI: 10.4161/Epi.25501  0.332
2013 Lin WY, Yi N, Lou XY, Zhi D, Zhang K, Gao G, Tiwari HK, Liu N. Haplotype kernel association test as a powerful method to identify chromosomal regions harboring uncommon causal variants. Genetic Epidemiology. 37: 560-70. PMID 23740760 DOI: 10.1002/Gepi.21740  0.357
2013 Wu G, Zhi D. Pathway-based approaches for sequencing-based genome-wide association studies. Genetic Epidemiology. 37: 478-94. PMID 23650134 DOI: 10.1002/Gepi.21728  0.389
2012 Zhi D, Chen R. Statistical guidance for experimental design and data analysis of mutation detection in rare monogenic mendelian diseases by exome sequencing. Plos One. 7: e31358. PMID 22348076 DOI: 10.1371/Journal.Pone.0031358  0.332
2012 Zhi D, Wu J, Liu N, Zhang K. Genotype calling from next-generation sequencing data using haplotype information of reads. Bioinformatics (Oxford, England). 28: 938-46. PMID 22285565 DOI: 10.1093/Bioinformatics/Bts047  0.343
2011 Chen W, Gao X, Wang J, Sun C, Wan W, Zhi D, Liu N, Chen X, Gao G. Evaluation of association tests for rare variants using simulated data sets in the Genetic Analysis Workshop 17 data. Bmc Proceedings. 5: S86. PMID 22373475 DOI: 10.1186/1753-6561-5-S9-S86  0.311
2011 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-variant effects. Plos Genetics. 7: e1002382. PMID 22144906 DOI: 10.1371/Journal.Pgen.1002382  0.317
2011 Wu G, Yi N, Absher D, Zhi D. Statistical quantification of methylation levels by next-generation sequencing. Plos One. 6: e21034. PMID 21698242 DOI: 10.1371/Journal.Pone.0021034  0.324
2011 Yi N, Zhi D. Bayesian analysis of rare variants in genetic association studies. Genetic Epidemiology. 35: 57-69. PMID 21181897 DOI: 10.1002/Gepi.20554  0.358
2010 Aleshin A, Zhi D. Recombination-associated sequence homogenization of neighboring Alu elements: signature of nonallelic gene conversion. Molecular Biology and Evolution. 27: 2300-11. PMID 20453015 DOI: 10.1093/Molbev/Msq116  0.376
2007 Zhi D, Keich U, Pevzner P, Heber S, Tang H. Correcting base-assignment errors in repeat regions of shotgun assembly. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 4: 54-64. PMID 17277413 DOI: 10.1109/Tcbb.2007.1005  0.691
2007 Zhi D. Sequence correlation between neighboring Alu instances suggests post-retrotransposition sequence exchange due to Alu gene conversion. Gene. 390: 117-21. PMID 17134854 DOI: 10.1016/J.Gene.2006.09.030  0.341
2006 Zhi D, Krishna SS, Cao H, Pevzner P, Godzik A. Representing and comparing protein structures as paths in three-dimensional space. Bmc Bioinformatics. 7: 460. PMID 17052359 DOI: 10.1186/1471-2105-7-460  0.463
2006 Jones NC, Zhi D, Raphael BJ. AliWABA: alignment on the web through an A-Bruijn approach. Nucleic Acids Research. 34: W613-6. PMID 16845083 DOI: 10.1093/Nar/Gkl288  0.542
2006 Zhi D, Raphael BJ, Price AL, Tang H, Pevzner PA. Identifying repeat domains in large genomes. Genome Biology. 7: R7. PMID 16507140 DOI: 10.1186/Gb-2006-7-1-R7  0.513
2004 Raphael B, Zhi D, Tang H, Pevzner P. A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Research. 14: 2336-46. PMID 15520295 DOI: 10.1101/Gr.2657504  0.524
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