Research Summary

Zongli Xu, Ph.D., is a Staff Scientist, His research involves both application and methodology studies in genetic epidemiology. Xu's overall goal is to study the interaction between genetic factors and environmental exposures in human health and therefore deciphering the mechanisms underlying complex human diseases. Along with colleagues in the Laboratory of Molecular Carcinogenesis and Biostatistics Branch of NIEHS, his applied work is mainly focused on human carcinogenesis, while much of his methodological work is to develop bioinformatics methods and software tools to facilitate genetic epidemiology study. The applied work helps to motivate methodological research, which involves issues surrounding the design and data analysis in genetic epidemiological studies.

Studies

• Genetic and Epigenetic studies with Sister Study samples
• Epigenetic study with samples from Norway Facial Clefts Study
• Genetic studies in NC-LA Prostate Cancer Consortium
• LIFE and VALID Lung Study
• Developing bioinformatics methods & software tools

Software

• SNPinfo
  A web server for SNP selection and functional information. It can comprehensively utilize computational, experimental and epidemiological information together with genome wide association study (GWAS) results and linkage disequilibrium (LD) information to prioritize SNPs for further genetic mapping studies
• TAGster
  A software package to select, evaluate and visualize LD tag SNPs for single or multiple populations.
• mPopTag
  A software tool to select or evaluate linkage disequilibrium (LD) tag SNPs for multiple populations.

Selected Publications

1. Xu Z, Niu L, Taylor JA. 2021. The ENmix DNA methylation analysis pipeline for Illumina BeadChip and comparisons with seven other preprocessing pipelines. Clin Epigenetics 13(1):216. [Abstract Xu Z, Niu L, Taylor JA. 2021. The ENmix DNA methylation analysis pipeline for Illumina BeadChip and comparisons with seven other preprocessing pipelines. Clin Epigenetics 13(1):216.]
2. Denault WRP, Romanowska J, Haaland ØA, Lyle R, Taylor JA, Xu Z, Lie RT, Gjessing HK, Jugessur A. 2021. Wavelet screening identifies regions highly enriched for differentially methylated loci for orofacial clefts. NAR Genom Bioinform 3(2):lqab035. [Abstract Denault WRP, Romanowska J, Haaland ØA, Lyle R, Taylor JA, Xu Z, Lie RT, Gjessing HK, Jugessur A. 2021. Wavelet screening identifies regions highly enriched for differentially methylated loci for orofacial clefts. NAR Genom Bioinform 3(2):lqab035.]
3. Lawrence KG, Kresovich JK, O'Brien KM, Hoang TT, Xu Z, Taylor JA, Sandler DP. Association of Neighborhood Deprivation With Epigenetic Aging Using 4 Clock Metrics. JAMA Netw Open. 2020 Nov 2;3(11):e2024329. doi: 10.1001/jamanetworkopen.2020.24329. PMID: 33146735; PMCID: PMC7643028. [Abstract Lawrence KG, Kresovich JK, O'Brien KM, Hoang TT, Xu Z, Taylor JA, Sandler DP. Association of Neighborhood Deprivation With Epigenetic Aging Using 4 Clock Metrics. JAMA Netw Open. 2020 Nov 2;3(11):e2024329. doi: 10.1001/jamanetworkopen.2020.24329. PMID: 33146735; PMCID: PMC7643028.]
4. Xu Z, Xie C, Taylor JA, Niu L. 2020. ipDMR: Identification of differentially methylated regions with interval p-values. Bioinformatics; doi: 10.1093/bioinformatics/btaa732 [Online 17 August 2020]. [Abstract Xu Z, Xie C, Taylor JA, Niu L. 2020. ipDMR: Identification of differentially methylated regions with interval p-values. Bioinformatics; doi: 10.1093/bioinformatics/btaa732 [Online 17 August 2020].] 
5. Xu Z, Taylor JA. 2020. Reliability of DNA methylation measures using Illumina methylation BeadChip. Epigenetics; doi: 10.1080/15592294.2020.1805692 [Online 4 August 2020]. [Abstract Xu Z, Taylor JA. 2020. Reliability of DNA methylation measures using Illumina methylation BeadChip. Epigenetics; doi: 10.1080/15592294.2020.1805692 [Online 4 August 2020].]
6. Xu Z, Sandler DP, Taylor JA. 2020. Blood DNA methylation and breast cancer: A prospective case-cohort analysis in the Sister Study. J Natl Cancer Inst 112(1):87-94. [Abstract Xu Z, Sandler DP, Taylor JA. 2020. Blood DNA methylation and breast cancer: A prospective case-cohort analysis in the Sister Study. J Natl Cancer Inst 112(1):87-94.]
7. Romanowska J, Haaland OA, Jugessur A, Gjerdevik M, Xu Z, Taylor J, Wilcox AJ, Jonassen I, Lie RT, Gjessing HK. 2020. Gene-methylation interactions: discovering region-wise DNA methylation levels that modify SNP-associated disease risk. Clin Epigenetics; doi: 10.1186/s13148-020-00881-x [Online 16 July 2020]. [Abstract Romanowska J, Haaland OA, Jugessur A, Gjerdevik M, Xu Z, Taylor J, Wilcox AJ, Jonassen I, Lie RT, Gjessing HK. 2020. Gene-methylation interactions: discovering region-wise DNA methylation levels that modify SNP-associated disease risk. Clin Epigenetics; doi: 10.1186/s13148-020-00881-x [Online 16 July 2020].] 
8. Niu L, Xu Z, Taylor JA. RCP: a novel probe design bias correction method for Illumina Methylation BeadChip. Bioinformatics (Oxford, England) 2016 32(17):2659-2663. [Abstract Niu L, Xu Z, Taylor JA. RCP: a novel probe design bias correction method for Illumina Methylation BeadChip. Bioinformatics (Oxford, England) 2016 32(17):2659-2663.]
9. Xu, Zongli, Taylor, Jack A., Leung, Yuet-Kin, Ho, Shuk-Mei, Niu, Liang. oxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA. Bioinformatics (Oxford, England) 2016; ():-. [Abstract Xu, Zongli, Taylor, Jack A., Leung, Yuet-Kin, Ho, Shuk-Mei, Niu, Liang. oxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA. Bioinformatics (Oxford, England) 2016; ():-.]
10. Harlid SS, Xu Z, Panduri V, Sandler DP, Taylor JA. CpG sites associated with cigarette smoking: analysis of epigenome-wide data from the Sister Study. Environmental health perspectives 2014 122(7):673-678. [Abstract Harlid SS, Xu Z, Panduri V, Sandler DP, Taylor JA. CpG sites associated with cigarette smoking: analysis of epigenome-wide data from the Sister Study. Environmental health perspectives 2014 122(7):673-678.]
11. Markunas CA, Xu Z, Harlid S, Wade PA, Lie RT, Taylor JA, Wilcox AJ. Identification of DNA methylation changes in newborns related to maternal smoking during pregnancy. Environ Health Perspect 2014 122(10):1147-1153. [Abstract Markunas CA, Xu Z, Harlid S, Wade PA, Lie RT, Taylor JA, Wilcox AJ. Identification of DNA methylation changes in newborns related to maternal smoking during pregnancy. Environ Health Perspect 2014 122(10):1147-1153.]
12. Godfrey AC, Xu Z, Weinberg CR, Getts RC, Wade PA, DeRoo LA, Sandler DP, Taylor JA. Serum microRNA expression as an early marker for breast cancer risk in prospectively collected samples from the Sister Study cohort. Breast cancer research: BCR 2014 15(3):R42-.  [Abstract Godfrey AC, Xu Z, Weinberg CR, Getts RC, Wade PA, DeRoo LA, Sandler DP, Taylor JA. Serum microRNA expression as an early marker for breast cancer risk in prospectively collected samples from the Sister Study cohort. Breast cancer research: BCR 2014 15(3):R42-. ]
13. Xu Z, Taylor JA. Genome-wide age-related DNA methylation changes in blood and other tissues relate to histone modification, expression and cancer. Carcinogenesis 2014 35(2):356-364. [Abstract Xu Z, Taylor JA. Genome-wide age-related DNA methylation changes in blood and other tissues relate to histone modification, expression and cancer. Carcinogenesis 2014 35(2):356-364.]
14. DeRoo LA, Bolick SCE, Xu Z, Umbach DM, Shore D, Weinberg CR, Sandler DP, Taylor JA. Global DNA methylation and one-carbon metabolism gene polymorphisms and the risk of breast cancer in the Sister Study. Carcinogenesis 35(2):333-338, 2014. [Abstract DeRoo LA, Bolick SCE, Xu Z, Umbach DM, Shore D, Weinberg CR, Sandler DP, Taylor JA. Global DNA methylation and one-carbon metabolism gene polymorphisms and the risk of breast cancer in the Sister Study. Carcinogenesis 35(2):333-338, 2014.]
15. Huang L, Bao Y, Xu Z, Lei X, Chen Y, Zhang Y, Zhang J. Neonatal Bilirubin Levels and Childhood Asthma in the US Collaborative Perinatal Project, 1959-1965. American journal of epidemiology. 2013 178(12):1691-1697. [Abstract Huang L, Bao Y, Xu Z, Lei X, Chen Y, Zhang Y, Zhang J. Neonatal Bilirubin Levels and Childhood Asthma in the US Collaborative Perinatal Project, 1959-1965. American journal of epidemiology. 2013 178(12):1691-1697.]
16. Xu Z, Bolick SCE, DeRoo LA, Weinberg CR, Sandler DP, Taylor JA. DNA methylation in blood is associated with breast cancer: A study in prospective samples from the Sister Study. Journal of the National Cancer Institute. 2013 105(10):694-700. [Abstract Xu Z, Bolick SCE, DeRoo LA, Weinberg CR, Sandler DP, Taylor JA. DNA methylation in blood is associated with breast cancer: A study in prospective samples from the Sister Study. Journal of the National Cancer Institute. 2013 105(10):694-700.]
17. White AJ, Sandler DP, Bolick SCE, Xu Z, Baldwin K, Taylor JA, DeRoo LA. Recreational and household physical activity at different time points and DNA global methylation. 2013 European journal of cancer.  49:2199-2206. [Abstract White AJ, Sandler DP, Bolick SCE, Xu Z, Baldwin K, Taylor JA, DeRoo LA. Recreational and household physical activity at different time points and DNA global methylation. 2013 European journal of cancer.  49:2199-2206.]
18. Xu Z, Bensen JT, Smith GJ, Mohler JL, Taylor JA. GWAS SNP Replication among African American and European American men in the North Carolina-Louisiana prostate cancer project (PCaP). Prostate. 2011 Jun 1;71(8):881-891. doi: 10.1002/pros.21304. Epub 2010 Nov 17. [Abstract Xu Z, Bensen JT, Smith GJ, Mohler JL, Taylor JA. GWAS SNP Replication among African American and European American men in the North Carolina-Louisiana prostate cancer project (PCaP). Prostate. 2011 Jun 1;71(8):881-891. doi: 10.1002/pros.21304. Epub 2010 Nov 17.]  
19. Xu Z, Taylor JA. Integrating GWAS and Candidate Gene Information into Functional SNP Selection for Genetic Association Studies. Nucleic Acids Research. 2009. [Abstract Xu Z, Taylor JA. Integrating GWAS and Candidate Gene Information into Functional SNP Selection for Genetic Association Studies. Nucleic Acids Research. 2009.]  
20. Xu Z, Kaplan NL, Taylor JA. Tagster: Efficient selection of LD tag SNPs in single or multiple populations. Bioinformatics (Oxford, England) 2007 23(23):3254-3255. [Abstract Xu Z, Kaplan NL, Taylor JA. Tagster: Efficient selection of LD tag SNPs in single or multiple populations. Bioinformatics (Oxford, England) 2007 23(23):3254-3255.]
21. Xu Z, Kaplan NL, Taylor JA. LD tag SNP selection for candidate gene association studies using HapMap and gene resequencing data. Eur J Hum Genet. 2007 Oct;15(10):1063-1070. [Abstract Xu Z, Kaplan NL, Taylor JA. LD tag SNP selection for candidate gene association studies using HapMap and gene resequencing data. Eur J Hum Genet. 2007 Oct;15(10):1063-1070.]
22. Xu Z, Zou F, Vision TJ. High resolution QTL mapping in genotypically selected samples from experimental crosses. Genetics. 2005. 170(1):401-408. [Abstract Xu Z, Zou F, Vision TJ. High resolution QTL mapping in genotypically selected samples from experimental crosses. Genetics. 2005. 170(1):401-408.]