58. Kasela S,..., NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium,..., Christenson SA. Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epithelium. Genome Med. 2021. 13(1):66.

57. Chung RH*, Chiu YF, Wang WC, Hwu CM, Hung YJ, Lee IT, Chuang LM, Quertermous T, Rotter JI, Chen YI, Chang IS, Hsiung CA. Multi-omics analysis identifies CpGs near G6PC2 mediating the effects of genetic variants on fasting glucose. Diabetologia. 2021. Apr 12.

55. Taliun D,..., NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium,...,Abecasis GR. Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. Nature. 2021. 590(7845):290-299.

54. Nielsen JB,..., Chung RH,...,Hveem K. Loss-of-function genomic variants highlight potential therapeutic targets for cardiovascular disease. Nat Commun. 2020. 11(1):6417.

53. Reiner AP, Raffield LM, Franceschini N, Auer PL, Lange EM, Nickerson DA, Zakai NA, Correa A, Olson N; National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine Consortium; Natinal Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine Consortium. Effect of Sickle Cell Trait and APOL1 Genotype on the Association of Soluble uPAR with Kidney Function Measures in Black Americans. Clin J Am Soc Nephrol. 2021. 16(2):287-289.

52. Chen IC, Kuo PH, Yang AC, Tsai SJ, Liu TH, Liu HJ, Lan TH, Chen HM, Huang HN, Chung R-H, Liu YL. CUX2, BRAP and ALDH2 are associated with metabolic traits in people with excessive alcohol consumption. Sci Rep. 2020. 10(1):18118.

51. Bick AG, Weinstock JS,..., NHLBI Trans-Omics for Precision Medicine Consortium,..., Natarajan P. Inherited causes of clonal haematopoiesis in 97,691 whole genomes. Nature. 2020. 586(7831):763-768.

50. Li X, Li Z,..., NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium,..., Lin X. Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale. Nature Genetics. 2020. 52(9):969-983.

49. Fang CP, Liu TH, Chung R-H, Tsou HH, Kuo HW, Wang SC, Liu CC, Liu SC, Chen ACH, Liu YL. Genetic variants in NECTIN4 encoding an adhesion molecule are associated with continued opioid use. PLOS ONE. 2020. 15(6):e0234549.

48. Kessler MD,..., National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine (TOPMed) Consortium,..., O'Connor TD. De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population. Proc Natl Acad Sci U S A. 2020. 117(5):2560-2569.

46. Fang CP, Wang SC, Tsou HH, Chung R-H, Hsu YT, Liu SC, Kuo HW, Liu TH, Chen ACH, Liu YL. Genetic polymorphisms in the opioid receptor delta 1 (OPRD1) gene are associated with methadone dose in methadone maintenance treatment for heroin dependence. J Hum Genet. 2020. 65(4):381-386.

45. Chien LH,...,Chung R-H,..., Hsiung CA. Predicting Lung Cancer Occurrence in Never-Smoking Females in Asia: TNSF-SQ, a Prediction Model. Cancer Epidemiol Biomarkers Prev. 2020. 29(2):452-459.

44. Chung R-H*, Kang CY. pWGBSSimla: a profile-based whole-genome bisulfite sequencing data simulator incorporating methylation QTLs, allele-specific methylations and differentially methylated regions. Bioinformatics. 2020. 36(3):660-665.

43. Chung R-H*, Kang CY. A multi-omics data simulator for complex disease studies and its application to evaluate multi-omics data analysis methods for disease classification. Gigascience. 2019. 8(5).

42. Yao TC, Chung RH, Lin CY, Tsai PC, Chang WC, Yeh KW, Tsai MH, Liao SL, Hua MC, Lai SH, Chen LC, Chang SW, Yu YW, Hsu JY, Chang SC, Cheng WC, Hu D, Hong X, Burchard EG, Wang X, Tzeng JY, Tsai HJ, Huang JL. Genetic loci determining total immunoglobulin E levels from birth through adulthood. Allergy. 2019. 74(3):621-625.

41. Wang SC, Chung RH, Kuo HW, Liu TH, Fang CP, Liu SC, Liu CC, Tsou HH, Chen ACH, Liu YL. GRK5 Is Associated with the Regulation of Methadone Dosage in Heroin Dependence. Int J Neuropsychopharmacol. 2018. 21(10):910-917.

40. Wang WC, Chiu YF, Chung R-H, Hwu CM, Lee IT, Lee CH, Chang YC, Hung KY, Quertermous T, Chen YI, Hsiung CA. IGF1 Gene Is Associated With Triglyceride Levels In Subjects With Family History Of Hypertension From The SAPPHIRe And TWB Projects. Int J Med Sci. 2018. 15(10):1035-1042.

39. Chung R-H*, Kang CY. A Powerful Gene-Based Test Accommodating Common and Low-Frequency Variants to Detect Both Main Effects and Gene-Gene Interaction Effects in Case-Control Studies. Frontiers in Genetics. 2018. 8:228.

38. Liu TH, Chung R-H, Wang SC, Fang CP, Tsou HH, Shih CL, Kuo HW, Wang Y, Liu YL. Missense mutation at CLDN8 associated with a high plasma interferon gamma-inducible protein 10 level in methadone-maintained patients with urine test positive for morphine. PLOS ONE. 2017. 12(11):e0187639.

37. Zhao W, Rasheed A,..., Chung R-H,...,Voight BF, Saleheen D. Identification of new susceptibility loci for type 2 diabetes and shared etiological pathways with coronary heart disease. Nature Genetics. 2017. 49(10):1450-1457.

36. Chung R-H, Chiu YF, Hung YJ, Lee WJ, Wu KD, Chen HL, Lin MW, Chen YDI, Quertermous T, Hsiung CA. Genome-wide copy number variation analysis identified deletions in SFMBT1 associated with fasting plasma glucose in a Han Chinese population. BMC Genomics. 2017. 18:591.

35. Howson JMM, Zhao W,..., Chung R-H,...,Butterworth AS, Munroe PB. Fifteen new risk loci for coronary artery disease highlight arterial-wall-specific mechanisms. Nature Genetics. 2017. 49(7):1113-1119.

34. Yao TC, Tsai HJ, Chang SW, Chung R-H, Hsu JY, Tsai MH, et al. Obesity disproportionately impacts lung volumes, airflow and exhaled nitric oxide in children. PLOS ONE. 2017. 12(4):e0174691.

33. Zubair N, Mariaelisa G,..., Chung R-H,..., Kooperberg C, Carty CL. Fine-mapping of lipid regions in global populations discovers ethnic-specific signals and refines previously identified lipid loci. Human Molecular Genetics. 2016. 25(24):5500-5512.

32. Ehret GB, Ferreira T,..., Chung R-H,...,Newton-Cheh CN, Munroe PB. The genetics of blood pressure regulation and its target organs from association studies in 342,415 individuals. Nature Genetics. 2016. 48(10):1171-84.

31. Lin PL, Yu YW, Chung R-H*. Pathway Analysis Incorporating Protein-Protein Interaction Networks Identified Candidate Pathways for the Seven Common Diseases. PLOS ONE. 2016. Sep 13;11(9):e0162910.

30. Chen YE, Kao SS, Chung R-H. Cost-Effectiveness Analysis of Different Genetic Testing Strategies for Lynch Syndrome in Taiwan. PLOS ONE. 2016. 11(8): e0160599.

29. Sung PY, Wang YT, Hsiung C.A., Chung R-H*. GCORE-sib: An efficient gene-gene interaction tool for genome-wide association studies based on discordant sib pairs. BMC Bioinformatics. 2016. Jul 8;17(1):273.

28. Chung R-H*, Tsai WY, Kang CY, Yao PJ, Tsai HJ, Chen CH. FamPipe: An automatic analysis pipeline for analyzing sequencing data in families for disease studies. PLOS Computational Biology. 2016. 12(6):e1004980.

27. Yao PJ, Chung R-H*. GESDB: A Platform of Simulation Resources for Genetic Epidemiology Studies. Database (Oxford). 2016. May 30.

26. Sung PY, Wang YT, Yu YW, Chung R-H*. An efficient gene-gene interaction test for genome-wide association studies in trio families. Bioinformatics. 2016. 32(12):1848-1855.

25. Yao P-J, Chung R-H*. SeqSIMLA2_exact: Simulate multiple disease sites in large pedigrees with given disease status for diseases with low prevalence. Bioinformatics. 2016. 32(4): 557-562.

24. Hsieh C-H, Chung R-H, Lee W-J, Lin M-W, Chuang L-M, Quertermous T, Assimes T, Hung Y-J, Yu Y-W. Effect of Common Genetic Variants of Growth Arrest-Specific 6 Gene on Insulin Resistance, Obesity and Type 2 Diabetes in an Asian Population. PLOS One. 2015. Aug 18;10(8):e0135681

23. Wang YT, Sung PY, Lin PL, Yu YW, Chung R-H*. A multi-SNP association test for complex diseases incorporating an optimal p-value threshold algorithm in nuclear families. BMC Genomics. 2015. 16:381.

22. Lin PL, Tsai WY, Chung R-H*. A combined association test for rare variants using family and case-control data. BMC Proceedings. 2016. Volume 10. Suppl 7.

21. Chung RH*, Tsai WY, Hsieh CH, Hung KY, Hsiung CA, Hauser ER. SeqSIMLA2: Simulating Correlated Quantitative Traits Accounting for Shared Environmental Effects in User-Specified Pedigree Structure. Genetic Epidemiology. 2015. 39(1):20-24

20. Chiu YF, Chung R-H, Lee CY, Kao HY, Hou L, Hsu FC. Identification of rare variants for hypertension with incorporation of linkage information. BMC Proceedings. 2014. 8(Suppl 1):S109

19. Chung RH*, Tsai WY, Martin ER. Family-based association test using both common and rare variants and accounting for directions of effects for sequencing data. PLOS ONE. 2014. 9(9):e107800.

18. Wang SC, Tsou HH, Chung RH, Chang YS, Fang CP, Chen CH, Ho IK, Kuo HW, Liu SC, Shih YH, Wu HY, Huang BH, Lin KM, Chen AC, Hsiao CF, Liu YL. The association of genetic polymorphisms in the κ-opioid receptor 1 gene with body weight, alcohol use, and withdrawal symptoms in patients with methadone maintenance. J Clin Psychopharmacol. 2014. 34(2):205-211.

Chung R-H, Martin ER. Chapter 12: Linkage disequilibrium and association analysis. Genetic analysis of complex diseases, 3rd edition. Wiley-Liss, USA.

17. Park YS, Schmidt MA, Martin ER, Pericak-Vance MA, Chung R-H*. Pathway-PDT: a flexible pathway analysis tool for nuclear families. BMC Bioinformatics. 2013. 14:267.

16. Chung R-H* and Shih CC. SeqSIMLA: a sequence and phenotype simulation tool for complex disease studies. BMC Bioinformatics. 2013. 14:199.

15. Griswold AJ, Ma DQ, Cukier HN, Nations LD, Schmidt MA, Chung R-H, Jaworski JM, Salyakina D, Konidari I, Whitehead PL, Wright HH, Abramson RK, Williams SM, Menon R, Martin ER, Haines JL, Gilbert JR, Cuccaro ML, Pericak- Vance MA. Evaluation of Copy Number Variations Reveals Novel Candidate Genes in Autism Spectrum Disorder Associated Pathways. Human Molecular Genetics. 2012. 21(15):3513-23.

14. Chung R-H, Martin ER. Single marker family-based association analysis conditional on parental information. Methods in molecular biology. 2012. 850:359-370.

13. Chung R-H*, Chen Y-E. A two-stage random forest-based pathway analysis method. PLoS One. 2012. 7(5):e36662.

12. Chung RH, Ma D, Wang K, Hedges DJ, Jaworski JM, Gilbert JR, Cuccaro ML, Wright HH, Abrahamson RK, Konidari I, Whitehead PL, Schellenberg GD, Hakonarson H, Haines JL, Pericak-Vance MA, Martin ER. An X-chromosome- wide association study in autism families identifies a novel autism gene TBL1X. Molecular Autism. 2011. 2(1):18.

11. Chung R-H*, Schmidt MA, Martin ER. CAPL: an efficient association software package using family and case-control data and accounting for population stratification. BMC Bioinformatics. 2011. Published Online: May 25: 12-201.

10. Hussman JP, Chung R-H, Griswold AJ, Jaworkski JM, Salyakina D, Ma D, Konidari I, Whitehead P, Vance JM, Martin ER, Cuccaro ML, Gilbert JR, Haines JL, Pericak-Vance MA. A Noise-Reduction GWAS Analysis Implicates Altered Regulation of Neurite Outgrowth and Guidance in Autism. Molecular Autism. 2011. Jan 19;2(1):1.

9. Chung R-H*, Schmidt MA, Morris RW, Martin ER. CAPL: A Novel Association Test Using Case-Control and Family Data and Accounting for Population Stratification. Genetic Epidemiology. 2010. 34(7):747-55.

8. Chung R-H, Schmidt S, Martin ER, Hauser ER. Ordered subset analysis (OSA) for family-based association mapping of complex traits. Genetic Epidemiology. 2008. 32 (7):627-37.

7. Zhang L, Martin ER, Chung R-H, Li Y-J, Morris RW. X-LRT: A likelihood approach to estimate genetic risks and test association with X-linked markers using a case-parents design. Genetic Epidemiology. 2008 32(4):370-380.

6. Chung R-H, Morris RW, Martin ER. Response to “XMCPDT does have correct type I error rates” by Jie Ding and Shili Lin. The American Journal of Human Genetics. 2008 82(2):530-531.

5. Chung R-H, Morris RW, Zhang L, Li Y-J, Martin ER. X-APL: An improved family- based test of association for the X chromosome. The American Journal of Human Genetics 2007 80(1): 59-68.

4. Chung R-H, Hauser ER, Martin ER. Interpretation of simultaneous linkage and family-based association tests in genome screens. Genetic Epidemiology 2007. 31:134-142.

3. Chung R-H, Hauser ER, Martin ER. The APL test: Extension to general nuclear families and haplotypes and examination of Its robustness. Human Heredity 2006 61(4):189-199.

2. Martin ER, Bronson PG, Li YJ, Wall N, Chung R-H, Schmechel DE, Small G, Xu PT, Bartlett J, Schnetz-Boutaud N, Haines JL, Gilbert JR, Pericak-Vance MA. Interaction between the alpha-T catenin gene (VR22) and APOE in Alzheimer's disease. Journal of Medical Genetics 2005 42(10):787-792.

1. Chung R-H, Gusfield D. Perfect phylogeny haplotyper: haplotype inferral using a tree model. Bioinformatics. 2003 19(6): 780-781.