Selected Publications

Academic Article

Year Title Altmetric
2016 Gravidas with class III obesity: evaluating the abdominal skin microbiota above and below the panniculus*Journal of Maternal-Fetal and Neonatal Medicine.  29:3312-3316. 2016
2016 The Bioenergetic Health Index is a sensitive measure of oxidative stress in human monocytesRedox Biology.  8:43-50. 2016
2016 Genetically predicted longer telomere length is associated with increased risk of B-cell lymphoma subtypesHuman Molecular Genetics.  25:1663-1676. 2016
2016 Oxidative modifications of protein tyrosyl residues are increased in plasma of human subjects with interstitial lung diseaseAmerican Journal of Respiratory and Critical Care Medicine.  193:861-866. 2016
2016 APOL1 nephropathy risk variants are associated with altered high-density lipoprotein profiles in African AmericansNephrology Dialysis Transplantation.  31:602-608. 2016
2016 Meta-analysis of genome-wide association studies discovers multiple loci for chronic lymphocytic leukemiaNature Communications.  7. 2016
2016 Vaginal Microbiota in Pregnancy: Evaluation Based on Vaginal Flora, Birth Outcome, and RaceAmerican Journal of Perinatology.  33:401-408. 2016
2016 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 consortiumAmerican Journal of Clinical Nutrition.  103:567-578. 2016
2016 A genome-wide study of lipid response to fenofibrate in Caucasians: A combined analysis of the GOLDN and ACCORD studiesPharmacogenetics -London-.  26:324-333. 2016
2016 Association of DNA Methylation at CPT1A Locus with Metabolic Syndrome in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) StudyPLoS ONE.  11:e0145789. 2016
2015 Defining the effects of storage on platelet bioenergetics: The role of increased proton leakBBA - Molecular Basis of Disease.  1852:2525-2534. 2015
2015 Use of ECMO in the management of severe acute respiratory distress syndrome: A survey of academic medical centers in the United StatesASAIO Journal.  61:556-563. 2015
2015 Epigenome-wide association study (EWAS) of BMI, BMI change and waist circumference in African American adults identifies multiple replicated lociHuman Molecular Genetics.  24:4464-4479. 2015
2015 Directional dominance on stature and cognition in diverse human populationsNature.  523:459-462. 2015
2015 A genome-wide association study in catfish reveals the presence of functional hubs of related genes within QTLs for columnaris disease resistanceBMC Genomics.  16. 2015
2015 Cyclosporine-mediated allograft fibrosis is associated with micro-RNA-21 through AKT signalingTransplant International.  28:232-245. 2015
2015 Decreased Bioenergetic Health Index in monocytes isolated from the pericardial fluid and blood of post-operative cardiac surgery patientsBioscience Reports.  35. 2015
2015 Deep sequencing of RYR3 gene identifies rare and common variants associated with increased carotid intima-media thickness (cIMT) in HIV-infected individualsJournal of Human Genetics.  60:63-67. 2015
2015 Epigenome-wide study identifies novel methylation loci associated with body mass index and waist circumferenceObesity Research.  23:1493-1501. 2015
2015 Lipid changes due to fenofibrate treatment are not associated with changes in DNA methylation patterns in the GOLDN studyFrontiers in Genetics.  6. 2015
2015 On the design and analysis of next-generation sequencing genotyping for a cohort with haplotype-informative readsMethods.  79:41-46. 2015
2015 PCSK9 variation and association with blood pressure in African Americans: Preliminary findings from the HyperGEN and REGARDS studiesFrontiers in Genetics.  6. 2015
2014 High-density genotyping of immune loci in Kawasaki disease and IVIG treatment response in European-American case-parent trio studyGenes and Immunity.  15:534-542. 2014
2014 Genome-wide association study identifies multiple susceptibility loci for diffuse large B cell lymphomaNature Genetics.  46:1233-1238. 2014
2014 Epigenome-wide association study of fasting blood lipids in the genetics of lipid-lowering drugs and diet network studyCirculation.  130:565-572. 2014
2014 Estimating proportions of explained variance: A comparison of whole genome subsetsBMC Proceedings.  8. 2014
2014 Genomics of post-prandial lipidomic phenotypes in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) studyPLoS ONE.  9. 2014
2014 A unified GMDR method for detecting gene-gene interactions in family and unrelated samples with application to nicotine dependenceHuman Genetics.  133:139-150. 2014
2014 Epigenome-wide association study of fasting measures of glucose, insulin, and homa-ir in the genetics of lipid lowering drugs and diet network studyDiabetes.  63:801-807. 2014
2014 Systematic investigation of predicted effect of nonsynonymous SNPs in human prion protein gene: A molecular modeling and molecular dynamics studyJournal of Biomolecular Structure and Dynamics.  32:289-300. 2014
2014 A hidden markov model for haplotype inference for present-absent data of clustered genes using identified haplotypes and haplotype patternsFrontiers in Genetics.  5. 2014
2014 Biomedical data integration, modeling, and simulation in the era of big data and translational medicineBioMed Research International.  2014. 2014
2014 Differential gene expression landscape of co-existing cervical pre-cancer lesions using RNA-seqFrontiers in Oncology.  4. 2014
2014 Genome-wide association study identifies five susceptibility loci for follicular lymphoma outside the HLA regionAmerican Journal of Human Genetics.  95:462-471. 2014
2014 Methylation at CPT1A locus is associated with lipoprotein subfraction profi lesJournal of Lipid Research.  55:1324-1330. 2014
2014 PRKCZ methylation is associated with sunlight exposure in a North American but not a Mediterranean populationChronobiology International.  31:1034-1040. 2014
2014 RYR3 gene variants in subclinical atherosclerosis among HIV-infected women in the Women's Interagency HIV Study (WIHS)Atherosclerosis.  233:666-672. 2014
2014 The Bioenergetic Health Index: a new concept in mitochondrial translational research.Clinical Science.  127:367-373. 2014
2013 Haplotype kernel association test as a powerful method to identify chromosomal regions harboring uncommon causal variantsGenetic Epidemiology.  37:560-570. 2013
2013 Pathway-Based Approaches for Sequencing-Based Genome-Wide Association StudiesGenetic Epidemiology.  37:478-494. 2013
2013 Joint haplotype phasing and genotype calling of multiple individuals using haplotype informative readsComputer applications in the biosciences : CABIOS.  29:2427-2434. 2013
2013 SNPs located at CpG sites modulate genome-epigenome interactionEpigenetics.  8:802-806. 2013
2012 Statistics for next generation sequencing - Meeting reportFrontiers in Genetics.  3. 2012
2012 Whole-exome sequencing and an iPSC-derived cardiomyocyte model provides a powerful platform for gene discovery in left ventricular hypertrophyFrontiers in Genetics.  3. 2012
2012 Comprehensive comparative analysis and identification of RNA-binding protein domains: Multi-class classification and feature selectionJournal of Theoretical Biology.  312:65-75. 2012
2012 Haplotype-Based Methods for Detecting Uncommon Causal Variants With Common SNPsGenetic Epidemiology.  36:572-582. 2012
2012 Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq dataBMC Genomics.  13. 2012
2012 Vitronectin inhibits neutrophil apoptosis through activation of integrin-associated signaling pathwaysAmerican Journal of Respiratory Cell and Molecular Biology.  46:790-796. 2012
2012 Genotype calling from next-generation sequencing data using haplotype information of readsComputer applications in the biosciences : CABIOS.  28:938-946. 2012
2012 Statistical guidance for experimental design and data analysis of mutation detection in rare monogenic Mendelian diseases by exome sequencingPLoS ONE.  7. 2012
2012 Expression signature of IFN/STAT1 signaling genes predicts poor survival outcome in glioblastoma multiforme in a subtype-specific mannerPLoS ONE.  7. 2012
2011 Hierarchical generalized linear models for multiple groups of rare and common variants: Jointly estimating group and Individual-Variant effectsPLoS Genetics.  7. 2011
2011 Practical consideration of genotype imputation: Sample size, window size, reference choice, and untyped rateStatistics and Its Interface.  4:339-352. 2011
2011 Statistical quantification of methylation levels by next-generation sequencingPLoS ONE.  6. 2011
2011 Length bias correction for RNA-seq data in gene set analysesComputer applications in the biosciences : CABIOS.  27:662-669. 2011
2011 Bayesian analysis of rare variants in genetic association studiesGenetic Epidemiology.  35:57-69. 2011
2011 Evaluation of association tests for rare variants using simulated data sets in the Genetic Analysis Workshop 17 data.BMC Proceedings.  5 Suppl 9:S86. 2011
2010 Recombination-associated sequence homogenization of neighboring Alu elements: Signature of nonallelic gene conversionMolecular Biology and Evolution.  27:2300-2311. 2010
2007 Sequence correlation between neighboring Alu instances suggests post-retrotransposition sequence exchange due to Alu gene conversionGene.  390:117-121. 2007
2007 Correcting base-assignment errors in repeat regions of shotgun assemblyIEEE/ACM Transactions on Computational Biology and Bioinformatics.  4:54-64. 2007
2006 Representing and comparing protein structures as paths in three-dimensional spaceBMC Bioinformatics.  7. 2006
2006 AliWABA: Alignment on the web through an A-Bruijn approachNucleic Acids Research.  34. 2006
2006 Identifying repeat domains in large genomesGenome Biology.  7. 2006
2006 Identification of highly specific localized sequence motifs in human ribosomal protein gene promotersGene.  365:48-56. 2006
2004 A novel method for multiple alignment of sequences with repeated and shuffled elementsPCR methods and applications.  14:2336-2346. 2004
2002 CLiBE: a database of computed ligand binding energy for ligand–receptor complexesComputers and Chemistry.  26:661-666. 2002
2001 Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small moleculeProteins.  43:217-226. 2001

Education And Training

  • Doctor of Philosophy in Bioinformatics, University of California System : San Diego 2006
  • Full Name

  • Degui Zhi