Ruzong Fan's Publications

Methodological Manuscripts:

  1. Lin N, Zhu Y, Fan RZ, and Xiong MM (2017) A quadratically regularized functional canonical correlation analysis for identifying the global structure of pleiotropy with NGS data. Plos Computational Biology 13(10):e1005788. PubMed PMID: 29040274.

  2. Chiu CY, Jung JS, Chen W, Weeks DE, Ren H, Boehnke M, Amos CI, Liu AY, Mills JL, Lee MLT, Xiong MM and Fan RZ3 (2017) Meta-analysis of quantitative pleiotropic traits for next-generation sequencing with multivariate functional linear models. European Journal of Human Genetics 25:350-359. PMID: 28000696 DOI: 10.1038/ejhg.2016.170.

  3. Chiu CY, Jung JS, Wang YF, Weeks DE, Wilson AF, Bailey-Wilson JE, Amos CI, Mills JL, Boehnke M, Xiong MM, and Fan RZ4 (2017) A comparison study of multivariate fixed models and gene association with multiple traits (GAMuT) for next-generation sequencing. Genetic Epidemiology 41 (1):18-34. PubMed Central PMCID: PMC5154843; NIHMSID 821410

  4. Fan RZ, Chiu CY, Jung JS, Weeks DE, Wilson AF, Bailey-Wilson JE, Amos CI, Chen Z, Mills JL, and Xiong MM (2016) A comparison study of fixed and mixed effect models for gene level association studies of complex traits. Genetic Epidemiology 40 (8):702-721. PubMed PMID: 27374056; NIHMSID, 817749.

  5. Fan RZ, Wang YF, Chiu CY, Chen W, Ren HB, Li Y, Boehnke M, Amos CI, Moore J, and Xiong MM (2016) Meta-analysis of complex diseases at gene level with generalized functional linear models. Genetics 202 (2):457-470. PubMed PMID: 26715663; PubMed Central PMCID: PMC4788228; NIHMSID 753319.

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  1. Fan RZ, Wang YF, Q Yan, Ding Y, Weeks DE, Lu ZH, Ren HB, Cook RJ, Xiong MM, and Chen W (2016) Gene-based association analysis for censored traits via functional regressions. Genetic Epidemiology 40 (2):133-143. PubMed PMID: 26782979; PubMed Central PMCID: PMC4724326; NIHMSID 741245.

  2. Fan RZ, Wang YF, Boehnke M, Chen W, Li Y, Ren HB, Lobach I, and Xiong MM (2015) Gene level meta-analysis of quantitative traits by functional linear models. Genetics 200 (4):1089-1104. PubMed PMID: 26058849; PubMed Central PMCID: PMC4574252; NIHMSID 715713.

  3. Wang YF, Liu AY, Mills JL, Boehnke M, Wilson AF, Bailey-Wilson JE, Xiong MM, Wu CO, and Fan RZ5 (2015) Pleiotropy analysis of quantitative traits at gene level by multivariate functional linear models. Genetic Epidemiology 39 (4):259-275. PubMed PMID: 25809955; PubMed Central PMCID: PMC4443751; NIHMSID 690743.

  4. Fan RZ, Chen V, Xie YL, Yin LL, Kim SD, Albert P, and Simons-Morton B (2015) A functional data analysis approach to analyze circadian rhythm patterns in activity counts for teenage girls. Journal of Circadian Rhythms 13(3):1-13. doi: http://dx.doi.org/10.5334/jcr.ac. NIHMSID 690963.

  5. Fan RZ, Zhu B, and Wang Y (2014) Stochastic dynamic models and Chebyshev splines. The Canadian Journal of Statistics 42 (4):610-634. PubMed PMID: 26045632; PubMed Central PMCID: PMC4451187; NIHMSID 690965.

  6. Fan RZ, Wang YF, Mills JL, Carter TC, Lobach I, Wilson AF, Bailey-Wilson JE, Weeks DE, and Xiong MM (2014) Generalized functional linear models for case-control association studies. Genetic Epidemiology 38 (7):622-637. PubMed PMID: 25203683; PubMed Central PMCID: PMC4189986; NIHMSID 617886.

  7. Lobach I, Fan RZ, and Manga P (2014) Genotype-Based association models of complex diseases to detect gene-gene and gene-environment interactions. Statistics and Its Interface 7:51-60. PubMed PMID: 26191336; PubMed Central PMCID: PMC4504431; NIHMSID 690969.

  8. Fan RZ, Wang YF, Mills JL, Wilson AF, Bailey-Wilson JE, and Xiong MM (2013) Functional linear models for association analysis of quantitative traits. Genetic Epidemiology 37 (7):726-742. PubMed PMID: 24130119; PubMed Central PMCID: PMC4163942; NIHMSID 623409.

  9. Fan RZ, Lee A, Liu AY, Troendle J, and Mills JL (2013) Association analysis of complex diseases using triads, parent-child dyads and singleton monads. BMC Genetics 14:78. doi: 10.1186/10.1186/1471-2156-14-78. PubMed PMID: 24007308; PubMed Central PMCID: PMC3844511.  URL: http://www.biomedcentral.com/1471-2156/14/78.

  10. Fan RZ, Zhang YW, Albert PS, Liu AY, Wang YJ, and Xiong MM (2012) Longitudinal association analysis of quantitative traits. Genetic Epidemiology 36:856-869. PubMed PMID: 2296581; PubMed Central PMCID: PMC4444073; NIHMSID 690972.

  11. Lobach I, Fan RZ (2012) Genotype-based Bayesian analysis of gene-environment interactions with multiple genetic markers and misclassification in environmental factors. Journal of Probability and Statistics, Volume 2012, Article ID 151259, 15 pages. doi:10.1155/2012/151259. PubMed PMID: 26180529; PubMed Central PMCID: PMC4500528; NIHMSID 690975.

  12. Mechanic LE, Chen HS, Amos CI, Chatterjee N, Cox NJ, Divi RL, Fan RZ, Harris EL, et al. (2012) Next generation analytic tools for large scale genetic epidemiology studies of complex diseases. Genetic Epidemiology 36:22-35. doi: 10.1002/gepi.20652. PubMed PMID: 22147673; PubMed Central PMCID: PMC3368075.

  13. Fan RZ, Zhong M, Wang SF, Zhang YW, Andrew A, Karagas M, Chen H, Amos CI, Xiong M, and Moore J (2011) Entropy-based information gain approaches to detect and to characterize gene-gene and gene-environment interactions/correlations of complex diseases. Genetic Epidemiology 35:706-721. doi: 10.1002/gepi.20621. PubMed PMID: 22009792; PubMed Central PMCID: PMC3384547.

  14. Zhong M, Zhang YW, Lange K, and Fan RZ6 (2011) A cross-population extended haplotype-based homozygosity score test to detect positive selection in genome-wide scans. Statistics and Its Interface 4:51-63. PubMed PMID: 26097641; PubMed Central PMCID: PMC4470573; NIHMSID 696723.

  15. Lobach I, Fan RZ7, and Carroll RJ (2010) Genotype-based association mapping of complex diseases: gene-environment interactions with multiple genetic markers and measurement error in environmental exposures. Genetic Epidemiology 34:792-802. doi: 10.1002/gepi.20523. PubMed PMID: 21031455; PubMed Central PMCID: PMC3021130.

  16. Zhong M, Lange K, Papp JC, and Fan RZ8 (2010) A powerful score test to detect positive selection in genome-wide scans. European Journal of Human Genetics 18:1148-1159. doi: 10.1038/ejhg.2010.60. PubMed PMID: 20461112; PubMed Central PMCID: PMC2987455.

  17. Chen LF, Zhong M, Chen WV, Amos C, and Fan RZ9 (2009) A genome-wide association scan for rheumatoid arthritis data by Hotelling's T2 tests. BMC Proceedings 3 (Suppl 7):S6. PubMed PMID: 20018053; PubMed Central PMCID: PMC2795960.

  18. Jung JS, Zhong M, Liu L, and Fan RZ10 (2008) Bi-variate combined linkage and association mapping of quantitative trait loci. Genetic Epidemiology 32:396-412. doi: 10.1002/gepi.20313. PubMed PMID: 18278817.

  19. Fan RZ, Liu L, Jung J, and Zhong M (2008) Combined linkage and association mapping of quantitative trait loci with missing completely at random genotype data. Behavior Genetics 38:316-336. doi: 10.1007/s10519-008-9194-3. PubMed PMID: 1830603

NOTE:
3Corresponding author as mentor of post-doctoral fellow, Dr. Chiu CY
4Corresponding author as mentor of post-doctoral fellow, Dr. Chiu CY
5Corresponding author as mentor of post-doctoral fellow, Dr. Wang YF
6Corresponding author as mentor of Ph.D student, Dr. Zhong M.
7Corresponding author. Fan RZ contributed the main idea and did most of the theoretical justication and was responsible to write the paper.
8Corresponding author as mentor of Ph.D student, Dr. Zhong M.
9Corresponding author as mentor of master student, Mr. Chen LF.
10Corresponding author as mentor of Ph.D student, Dr. Jung JS.

 

Collaborative Manuscripts:

  1. Yan Q, Ding Y, Liu Y, Sun T, Fritsche LG, Clemons T, Ratnapriya R, Klein ML, Cook RJ, Liu Y,  Fan RZ, Wei L, Abecasis GR, Swaroop A, Chew EY, AREDS2 research group, Weeks DE, and Chen W (2018) Genome-wide analysis of disease progression in age-related macular degeneration. Human Molecular Genetics 27 (5):929-940. PMID: 29346644.

  2. Brosnan JT, Mills JL, Ueland PM, Shane B, Fan RZ, Chiu CY, Pangilinan F, Brody LC, Brosnan ME, Pongnopparat T, and Molloy AM (2018) Lifestyle, metabolite and genetic determinants of formate concentrations in a cross-sectional study of young, healthy adults. American Journal of Clinical Nutrition 107 (3):345–354. PubMed Central PMCID: PMC4520942

  3. Boghossian NS, Sicko RJ, Giannakou A, Dimopoulos A, Caggana M, Tsai MY, Yeung EH, Druschel CM, Romitti PA, Browne ML, Fan RZ, Liu AY, Brody LC, Kay DM, and Mills JL (2017) Rare copy number variants identified in Prune Belly syndrome. European Journal of Medical Genetics, in press.

  4. Carter TC, Sicko RJ, Kay DM, Browne ML, Romitti PA, Edmunds Z, Liu AY, Fan RZDruschel CM, Caggana M, Brody LC, and Mills JL (2017) Copy-number variants and candidate gene mutations in non-syndromic split hand/foot malformation. Journal of Human Genetics 62, 877-884. NIHMSID: NIHMS871047; PubMed PMID: 28539665. PubMed Central PMCID: PMC5612852.

  5. Dimopoulos A, Sicko RJ, Kay DM, Rigler SL, Druschel CM, Caggana M, Browne ML, Fan RZ, Romitti PA, Brody LC, and Mills JL (2017) Rare copy number variants in a population based investigation of hypoplastic right heart syndrome. Defects Research Part A: Clinical and Molecular Teratology 109:8-15. NIHMSID: NIHMS821488. PubMed PMID: 28009100. PubMed Central PMCID: PMC5388571.

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  1. Dimopoulos A, Sicko RJ, Kay DM, Rigler SL, Fan RZ, Romitti PA, Browne ML, Druschel CM, Caganna M, Brody LC, and Mills JL (2016) Copy number variants in a population-based investigation of Klippel Trenaunay syndrome. American Journal of Medical Genetics Part A 173A:352-359. PubMed PMID: 27901321.

  2. Sicko RJ, Browne ML, Rigler SL, Druschel CM, Liu G, Fan RZ, Romitti PA, Caggana M, Kay DM, Brody LC, and Mills JL (2016) Genetic variants in isolated Ebstein anomaly implicated in myocardial development pathways. PloS one 11(10):e0165174. PubMed PMID: 27788187. PubMed Central PMCID: PMC5082909.

  3. Hagen EM, Sicko RJ, Kay DM, Rigler SL, Dimopoulos A, Ahmad S, Doleman MH, Fan RZ, Romitti PA, Browne ML, Caggana M, Brody LC, Shaw GM, Jelliffe-Pawlowski LL, and Mills JL (2016) Copy-number variant analysis of classic heterotaxy highlights the importance of body patterning pathways. Human Genetics 135(12):1355-1364. doi: 10.1007/s00439-016-1727-x. PubMed PMID: 27637763. PubMed Central PMCID: PMC5065782.

  4. Deac O, Mills JL, Gardiner CM, Shane B, Quinn L, Midttun O, McCann A, Meyer K, Ueland PM, Fan RZ, Lu ZH, Brody LC, and Molloy AM (2016) Serum immune system biomarkers neopterin and interleukin-10 are strongly related to tryptophan metabolism in healthy young adults. The Journal of Nutrition 146(9):1801-1806. doi: 10.3945/jn.116.230698. PubMed PMID: 27489009. PubMed Central PMCID: PMC4997280.

  5. Boghossian NS, Sicko RJ, Kay DM, Rigler SL, Caggana M, Tsai MY, Yeung EH, Pankratz N, Cole BR, Druschel CM, Romitti PA, Browne ML, Fan RZ, Liu AY, Brody LC, and Mills JL (2016) Rare copy number variants implicated in posterior Uurethral valves. American Journal of Medical Genetics Part A 170(3):622-633. doi: 10.1002/ajmg.a.37493. PubMed PMID: 26663319.

  6. Ozaki M, Molloy AM, Mills JL, Pangilinan F, Fan RZ,Wang Y, Gibney E, Shane B, Brody LC, and Parle-McDermott A (2015) The dihydrofolate reductase 19bp polymorphism is not associated with biomarkers of folate status in healthy young adults, irrespective of folic acid intake. The Journal of Nutrition 145 (10):2207-2211. PubMed PMID: 26269242. PubMed Central PMCID: PMC4580961.

  7. Bailey RL, Looker AC, Lu ZH, Fan RZ, Eicher-Miller HA, Fakhouri TH, Gahche JJ, Weaver CM, and Mills JL (2015) B-vitamins and bone mineral density and risk of lumbar osteoporosis in older females in the U.S. The American Journal of Clinical Nutrition 102 (3):687-694. doi: 10.3945/ajcn.115.108787. PubMed PMID: 26224297; PubMed Central PMCID: PMC4548174.

  8. Carter TC, Pangilinan F, Molloy AM, Fan RZ, Wang YF, Shane B, Gibney ER, Midttun O, Ueland PM, Cropp CD, Kim Y, Wilson AF, Bailey-Wilson JE, Brody LC, and Mills JL (2015) Common variants at putative regulatory sites nonspecific alkaline phosphatase gene influence circulating pyridoxal 5-phosphate concentration in healthy adults. The Journal of Nutrition 145:1386-1393. doi: 10.3945/jn.114.208769. PubMed PMID: 25972531; PubMed Central PMCID: PMC4478949.

  9. Rigler SL, Kay DM, Sicko RJ, Fan RZ, Liu AY, Caggana M, Browne ML, Druschel CM, Romitti PA, Brody LC, and Mills JL (2015) Novel copy-number variants in a population-based investigation of classic heterotaxy. Genetics in Medicine 17(5):348-357. doi: 10.1038/gim.2014.112PubMed PMID: 25232849.

  10. Deac O, Mills JL, Shane B, Midttun O, Ueland PM, Brosnan JT, Brosnan ME, Laird E, Gibney ER, Fan RZ, Wang YF, Brody LC, and Molloy AM (2015) Tryptophan catabolism and vitamin B6 status are affected by gender and lifestyle factors in healthy young adults. The Journal of Nutrition 145 (4):701-707. doi: 10.3945/jn.114.203091. PubMed PMID: 25833774; PubMed Central PMCID: PMC4381767.

  11. Zhang CL, Hu FB, Olsen SF, Vaag A, Gore-Langton R, Chavarro J, Bao W, Edwina Y, Bowers K, Grunnet LG, Sherman S, Kiely M, Strom M, Hansen S, Liu A, Mills JL, and Fan RZ (2014) Rationale, design, and method of the diabetes &Womens Health Study -a study of long-term health implications of glucose intolerance in pregnancy and their determinants. Acta Obstetricia et Gynecologica Scandinavica (www.aogs-online.com) 93:1123-1130. doi: 10.1111/aogs.12425. PubMed PMID: 24828694; PubMed Central PMCID: PMC4205761.

  12. Mills JL, Fan RZ, Brody LC, Aiyi Liu A, Ueland P, Wang YF, Kirke PN, Shane B, and AM Molloy (2014) Maternal choline concentrations during pregnancy and choline-related genetic variants as risk factors for neural tube defects. The American Journal of Clinical Nutrition 100(4):1069-1074. doi: 10.3945/ajcn.113.0793. PubMed PMID: 25240073; PubMed Central PMCID: PMC4163794.

  13. Molloy AM, Einri CN, Jain D, Laird E, Fan RZ, Wang YF, Scott JM, Shane B, Brody LC, Kirke PN, and Mills JL (2014) Is low iron status a risk factor for neural tube defects? Birth Defects Research Part A: Clinical and Molecular Teratology 100 (2):100106. doi: 10.1002/bdra.23223. PubMed PMID: 24535840; PubMed Central PMCID: PMC4018583.

  14. Feenstra B, Geller F, Carstensen L, Romitti PA, Korberg IB, Bedell B, Krogh C, Fan RZ, Svenningsson A, Caggana M, Nordenskjold A, Mills JL, Murray JC, and Melbye M (2013) Plasma lipids, genetic variants near APOA1, and the risk of infantile hypertrophic pyloric stenosis. The Journal of American Medical Association 310(7):714-721. doi: 10.1001/jama.2013.242978. PubMed PMID: 23989729; PubMed Central PMCID: PMC4031654.

  15. Massett MP, Fan RZ, and Berk BC (2009) Quantitative trait loci for exercise training responses in FVB/NJ and C57BL/6J mice. Physiological Genomics 40:15-22. doi: 10.1152/physiolgenomics.00116.2009. PubMed PMID: 19789284; PubMed Central PM-CID: PMC2807210.

  16. Thomas NJ, DiAngelo S, Hess JC, Fan RZ, Ball MW, Geskey JM, Willson DF, and Floros J (2009) Transmission of surfactant protein variants and haplotypes in children hospitalized with respiratory syncytial virus. Pediatric Research 66:70-73. doi: 10.1203/PDR.0b013e3181a1d768. PubMed PMID: 19287351; PubMed Central PMCID: PMC2710771.

  17. Thomas NJ, Fan RZ, DiAngelo S, Hess JC, and Floros Y (2007) Haplotypes of the surfactant protein genes A and D as susceptibility factors for the development of respiratory distress syndrome. Acta Paediatrica 96:985-989. doi: 10.1111/j.1651-2227.2007.00319.x. PubMed PMID: 17524024.

  18. Pavlovic J, Papagaroufalis C, Xanthou M, Liu W, Fan RZ, Thomas NJ, Apostolidou I, Papathoma E, Megaloyianni E, DiAngelo S, and Floros J (2006) Genetic variants of surfactant proteins A, B, C, and D in Bronchopulmonary Dysplasia. Disease Markers 22:277-291. PubMed PMID: 17264398; PubMed Central PMCID: PMC3850613.

  19. Floros J, Thomas N, Liu W, Papagaroufalis C, Xanthou M, Pereira S, Fan RZ, Guo X, DiAngelo S, and Pavlovic J (2006) Family-based association tests suggest linkage between SP-B (and anking region) and RDS; SP-B haplotypes and alleles from SP-B-linked loci are risk factors for RDS. Pediatric Research 59:616-621. doi:  10.1203/01.pdr.0000203145.48585.2c. PubMed PMID: 16549540.

  20. Floros J, Fan RZ, Diangelo S, Guo XX,Wert J, and Luo JM (2001) Surfactant protein (SP) B associations and interactions with SP-A in whites and black subjects with respiratory distress syndrome. Pediatric International 43:567-576. PubMed PMID: 11737731; PubMed Central PMCID: PMC2907917.

  21. Floros J, Fan RZ, Matthews A, DiAngelo S, Luo JM, Nielsen H, Dunn M, Gewolb I, Koppe J, vanSonderen L, Farri-Kostopoulos L, Ramet M, Merrill J, and Robbins (2001) Family based transmission disequilibrium test (TDT) and case-control association studies reveal surfactant protein A (SP-A) susceptibility alleles for respiratory distress syndrome (RDS) and possible race differences. Clinical Genetics 60:178-187. PubMed PMID: 11595019.

  22. Floros Y and Fan RZ (2001) Surfactant protein A and B genetic variants and respiratory distress syndrome: allele interactions. Biology of the Neonate 80 (Suppl 1):22-25. doi: 47173. PubMed PMID: 11359041.