Publications 2009 to 2019

2300 Words | Approximately 11 Minutes Read | Last Modified on January 30, 2020

Here are my publications during my PhD and postdoc trainings from 2009 to 2019. Publications from my lab can be found here.

Journal Articles

1. Wang G$^\dagger$, Yang Y and Ott J, Genome-Wide Conditional Search for Epistatic Disease-Predisposing Variants in Human Association Studies. Human Heredity 70:34–41 (2010)

2. Li B, Wang G and Leal SM, SimRare: a program to generate and analyze sequence-based data for association studies of quantitative and qualitative traits. Bioinformatics 28:2703–2704 (2012)

3. Cheung YH, Wang G, Leal SM and Wang S, A fast and noise-resilient approach to detect rare-variant associations with deep sequencing data for complex disorders. Genetic Epidemiology 36:675–685 (2012)

4. San Lucas FA, Wang G, Scheet P and Peng B, Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools. Bioinformatics 28:421–422 (2012)

5. Wiszniewski W, Hunter JV, Hanchard NA, Willer JR, Shaw C, Tian Q, Illner A, Wang X, Cheung SW, Patel A, Campbell IM, Gelowani V, Hixson P, Ester AR, Azamian MS, Potocki L, Zapata G, Hernandez PP, Ramocki MB, Santos-Cortez RLP, Wang G, York MK, Justice MJ, Chu ZD, Bader PI, Omo-Griffith L, Madduri NS, Scharer G, Crawford HP, Yanatatsaneejit P, Eifert A, Kerr J, Bacino CA, Franklin AIA, Goin-Kochel RP, Simpson G, Immken L, Haque ME, Stosic M, Williams MD, Morgan TM, Pruthi S, Omary R, Boyadjiev SA, Win KK, Thida A, Hurles M, Hibberd ML, Khor CC, Van Vinh Chau N et al., TM4SF20 ancestral deletion and susceptibility to a pediatric disorder of early language delay and cerebral white matter hyperintensities. American Journal Of Human Genetics 93:197–210 (2013)

6. Auer PL, Wang G and Leal SM, Testing for rare variant associations in the presence of missing data. Genetic Epidemiology 37:529–538 (2013)

7. He Z, O’Roak BJ, Smith JD, Wang G, Hooker S, Santos-Cortez RLP, Li B, Kan M, Krumm N, Nickerson DA, Shendure J, Eichler EE and Leal SM, Rare-variant extensions of the transmission disequilibrium test: application to autism exome sequence data. American Journal Of Human Genetics 94:33–46 (2014)

8. Wang G$^\dagger$, Li B, Santos-Cortez RLP, Peng B and Leal SM, Power analysis and sample size estimation for sequence-based association studies. Bioinformatics 30:2377–2378 (2014)

9. Cecchi AC, Guo D, Ren Z, Flynn K, Santos-Cortez RLP, Leal SM, Wang G, Regalado ES, Steinberg GK, Shendure J, Bamshad MJ, Genomics oWCfM, Grotta JC, Nickerson DA, Pannu H and Milewicz DM, RNF213 Rare Variants in an Ethnically Diverse Population With Moyamoya Disease. Stroke 45:3200–3207 (2014)

10. Wang G$^\dagger$, Peng B and Leal SM, Variant association tools for quality control and analysis of large-scale sequence and genotyping array data. American Journal Of Human Genetics 94:770–783 (2014)

11. Li B, Wang G and Leal SM, PhenoMan: phenotypic data exploration, selection, management and quality control for association studies of rare and common variants. Bioinformatics 30:442–444 (2014)

12. Li B, Wang G and Leal SM, Generation of sequence-based data for pedigree-segregating Mendelian or Complex traits.. Bioinformatics 31:3706–8 (2015)

13. Santos-Cortez RLP, Chiong CM, Reyes-Quintos MRT, Tantoco MLC, Wang X, Acharya A, Abbe I, Giese AP, Smith JD, Allen EK, Li B, Cutiongco-de la Paz EM, Garcia MC, Llanes EGDV, Labra PJ, Gloria-Cruz TLI, Chan AL, Wang G, Daly KA, Shendure J, Bamshad MJ, Nickerson DA, Patel JA, Riazuddin S, Sale MM, Chonmaitree T, Ahmed ZM, Abes GT and Leal SM, Rare A2ML1 variants confer susceptibility to otitis media.. Nature Genetics 47:917–20 (2015)

14. Rehman AU, Santos-Cortez RLP, Drummond MC, Shahzad M, Lee K, Morell RJ, Ansar M, Jan A, Wang X, Aziz A, Riazuddin S, Smith JD, Wang G, Ahmed ZM, Gul K, Shearer AE, Smith RJH, Shendure J, Bamshad MJ, Nickerson DA, Hinnant J, Khan SN, Fisher RA, Ahmad W, Friderici KH, Riazuddin S, Friedman TB, Wilch ES and Leal SM, Challenges and solutions for gene identification in the presence of familial locus heterogeneity.. European Journal Of Human Genetics 23:1207–15 (2015)

15. Wang G$^\dagger$, Zhang D, Li B, Dai H and Leal SM, Collapsed haplotype pattern method for linkage analysis of next-generation sequence data.. European Journal Of Human Genetics 23:1739–43 (2015)

16. Kan M, Auer PL, Wang G$^\dagger$, Bucasas KL, Hooker S, Rodriguez A, Li B, Ellis J, Adrienne Cupples L, Ida Chen Y, Dupuis J, Fox CS, Gross MD, Smith JD, Heard-Costa N, Meigs JB, Pankow JS, Rotter JI, Siscovick D, Wilson JG, Shendure J, Jackson R, Peters U, Zhong H, Lin D, Hsu L, Franceschini N, Carlson C, Abecasis G, Gabriel S, Bamshad MJ, Altshuler D, Nickerson DA, North KE, Lange LA, Reiner AP and Leal SM, Rare variant associations with waist-to-hip ratio in European-American and African-American women from the NHLBI-Exome Sequencing Project.. European Journal Of Human Genetics 10.1038/ejhg.2015.272 (2016)

17. Auer PL, Reiner AP, Wang G, Kang HM, Abecasis GR, Altshuler D, Bamshad MJ, Nickerson DA, Tracy RP, Rich SS and others, Guidelines for Large-Scale Sequence-Based Complex Trait Association Studies: Lessons Learned from the NHLBI Exome Sequencing Project. The American Journal Of Human Genetics 99:791–801 (2016)

18. vant Hof FN, Ruigrok YM, Lee CH, Ripke S, Anderson G, de Andrade M, Baas AF, Blankensteijn JD, Böttinger EP, Bown MJ and others, Shared Genetic Risk Factors of Intracranial, Abdominal, and Thoracic Aneurysms. Journal Of The American Heart Association 5:e002603 (2016)

19. He Z, Zhang D, Renton AE, Li B, Zhao L, Wang G, Goate AM, Mayeux R and Leal SM, The Rare-Variant Generalized Disequilibrium Test for Association Analysis of Nuclear and Extended Pedigrees with Application to Alzheimer Disease WGS Data. The American Journal Of Human Genetics 100:193–204 (2017)

20. Zhang D, Zhao L, Li B, He Z, Wang G, Liu DJ and Leal SM, SEQSpark: A Complete Analysis Tool for Large-scale Rare Variant Association Studies Using Whole-Genome and Exome Sequence Data. Am J Hum Genet 101:115–122 (2017)

21. Peng B, Wang G, Ma J, Leong MC, Wakefield C, Melott J, Chiu Y, Du D and Weinstein JN, SoS Notebook: an interactive multi-language data analysis environment. Bioinformatics 34:3768–3770 (2018)

22. Urbut SM, Wang G, Carbonetto P and Stephens M, Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions. Nature Genetics 51:187–195 (2018)

23. Wang G$^\dagger$ and Peng B, Script of Scripts: A pragmatic workflow system for daily computational research. PLOS Computational Biology 15:e1006843 (2019)

24. Zhao L, He Z, Zhang D, Wang G, Renton AE, Vardarajan BN, Nothnagel M, Goate AM, Mayeux R and Leal SM, A Rare Variant Nonparametric Linkage Method for Nuclear and Extended Pedigrees with Application to Late-Onset Alzheimer Disease via WGS Data. The American Journal Of Human Genetics 105:822–835 (2019)

25. Wang Y, Wu T, Wang Y and Wang G. Enhancing Model Interpretability and Accuracy for Disease Progression Prediction via Phenotype-Based Patient Similarity Learning. Pacific Symposium On Biocomputing 25:511–522 (2020)


26. Wang G$^\dagger$, Sarkar A, Carbonetto P, Stephens M. A simple new approach to variable selection in regression, with application to genetic fine-mapping. In revision at Journal of the Royal Statistical Society: Series B doi:10.1101501114

27. Zhang Z, Luo K, Qiu M, Wang G, Zou Y, Zhu A, Shi H, Qiao M, Li Z, Stephens M, He X, He C. Understanding the genetic basis of mRNA $N^6$-methyladenosine (m6A) modification and its contribution in human common diseases. In revision at Nature Genetics

28. Li L, Huang KL, Gao Y, Elrod N, Wang G, Ji P, Peng F, Russell W, Wanger E, Li W. Genetic Basis of Alternative Polyadenylation as an Emerging Molecular Phenotype for Human Traits and Diseases. Under review at Nature Genetics

29. Zhang S, Zhang H, Zhou Y, Qiao M, Zhao S, ZKozlova A, Shi J, Wang G, Sengupta S, Strait M, Li Z, Sanders A, Cowan C, Chen M, Greenleaf W, Pang Z, Gejman P, He X, Duan J. Allele-specific open chromatin in human iPSC neurons elucidates functional non-coding disease variants. In revision at Science

30. Han S, Knoblauch N, Wang G, Zhao S, Liu Y, Xie Y, Sheng W, Nguyen H, He X. A Bayesian method for rare variant analysis using functional annotations and its application to Autism. biorxiv doi:10.1101828061

In Progress

31. Wang G$^\dagger$, Zou Y, Gerard D, Stephens M. Multi-condition fine-mapping refines the genetic architecture of molecular phenotypes across human tissues.

32. Wang Y, Wu T, Wang Y, Zhao E, Zhou L, Wang G$^\dagger$. Integration of longitudinal health records and clinical features for disease progression prediction using wide and deep neural network.

33. Wang G$^\dagger$, Carbonetto P, Blischak J, Stephens M. Dynamic Statistical Comparisons.

Authorship in Selected Consortia Papers

Genotype Tissue Expression (GTEx) Consortium

34-1. The GTEx Consortium, Genetic effects on gene expression across human tissues. Nature 550:204–213 (2017)

34-2. The GTEx Consortium, The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science 369(6509):1318-1330 (2020)

The NHLBI Exome Sequencing Project

35. Emond MJ, Louie T, Emerson J, Zhao W, Mathias RA, Knowles MR, Wright FA, Rieder MJ, Tabor HK, Nickerson DA, Barnes KC, NHLBI Exome Sequencing Project, Gibson RL and Bamshad MJ, Exome sequencing of extreme phenotypes identifies DCTN4 as a modifier of chronic Pseudomonas aeruginosa infection in cystic fibrosis. Nature Genetics 44:886–889 (2012)

36. Boileau C, Guo D, Hanna N, Regalado ES, Detaint D, Gong L, Varret M, Prakash SK, Li AH, d’Indy H, Braverman AC, Grandchamp B, Kwartler CS, Gouya L, Santos-Cortez RLP, Abifadel M, Leal SM, Muti C, Shendure J, Gross M et al., TGFB2 mutations cause familial thoracic aortic aneurysms and dissections associated with mild systemic features of Marfan syndrome. Nature Genetics 44:916–921 (2012)

37. O’Connor TD, Kiezun A, Bamshad M, Rich SS, Smith JD, Turner E, Project ES, ESP Population Genetics SAWG, Leal SM and Akey JM, Fine-scale patterns of population stratification confound rare variant association tests. plos One 8:e65834 (2013)

38. Fu W, OConnor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Rieder J, Altshuler D, Shendure J, Nickerson DA, Bamshad MJ, NHLBI Exome Sequencing Project and Akey JM, Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature 493:216–220 (2013)

39. Norton N, Li D, Rampersaud E, Morales A, Martin ER, Zuchner S, Guo S, Gonzalez M, Hedges DJ, Robertson PD, Krumm N, Nickerson DA, Hershberger RE and NHLBI Exome Sequencing Project, Exome sequencing and genome-wide linkage analysis in 17 families illustrate the complex contribution of TTN truncating variants to dilated cardiomyopathy. Circulation Cardiovascular Genetics 6:144–153 (2013)

40. Johnsen JM, Auer PL, Morrison AC, Jiao S, Wei P, Haessler J, Fox K, McGee SR, Smith JD, Carlson CS, Smith N, Boerwinkle E, Kooperberg C, Nickerson DA, Rich SS, Green D, Peters U, Cushman M, Reiner AP and NHLBI Exome Sequencing Project, Common and rare von Willebrand factor (VWF) coding variants, VWF levels, and factor VIII levels in African Americans: the NHLBI Exome Sequencing Project. Blood 122:590–597 (2013)

41. Guo D, Regalado E, Casteel DE, Santos-Cortez RL, Gong L, Kim JJ, Dyack S, Horne SG, Chang G, Jondeau G, Boileau C, Coselli JS, Li Z, Leal SM, Shendure J, Rieder MJ, Bamshad MJ, Nickerson DA, Consortium R, NHLBI Exome Sequencing Project et al., Recurrent gain-of-function mutation in PRKG1 causes thoracic aortic aneurysms and acute aortic dissections. American Journal Of Human Genetics 93:398–404 (2013)

42. Rosenthal EA, Ranchalis J, Crosslin DR, Burt A, Brunzell JD, Motulsky AG, Nickerson DA, Project GES, Wijsman EM and Jarvik GP, Joint linkage and association analysis with exome sequence data implicates SLC25A40 in hypertriglyceridemia. American Journal Of Human Genetics 93:1035–1045 (2013)

43. Lange LA, Hu Y, Zhang H, Xue C, Schmidt EM, Tang Z, Bizon C, Lange EM, Smith JD, Turner EH, Jun G, Kang HM, Peloso G, Auer P, Li K, Flannick J, Zhang J, Fuchsberger C, Gaulton K, Lindgren C et al., Whole-exome sequencing identifies rare and low-frequency coding variants associated with LDL cholesterol. American Journal Of Human Genetics 94:233–245 (2014)

44. Gordon AS, Tabor HK, Johnson AD, Snively BM, Assimes TL, Auer PL, Ioannidis JPA, Peters U, Robinson JG, Sucheston LE, Wang D, Sotoodehnia N, Rotter JI, Psaty BM, Jackson RD, Herrington DM, O’Donnell CJ, Reiner AP, Rich SS, Rieder MJ et al., Quantifying rare, deleterious variation in 12 human cytochrome P450 drug-metabolism genes in a large-scale exome dataset. Human Molecular Genetics 23:1957–1963 (2014)

45. Tabor HK, Auer PL, Jamal SM, Chong JX, Yu J, Gordon AS, Graubert TA, O’Donnell CJ, Rich SS, Nickerson DA, NHLBI Exome Sequencing Project and Bamshad MJ, Pathogenic variants for Mendelian and complex traits in exomes of 6,517 European and African Americans: implications for the return of incidental results. American Journal Of Human Genetics 95:183–193 (2014)

46. Auer PL, Nalls M, Meschia JF, Worrall BB, Longstreth WT, Seshadri S, Kooperberg C, Burger KM, Carlson CS, Carty CL, Chen W, Cupples LA, DeStefano AL, Fornage M, Hardy J, Hsu L, Jackson RD, Jarvik GP, Kim DS, Lakshminarayan K et al., Rare and Coding Region Genetic Variants Associated With Risk of Ischemic Stroke. Jama Neurology 72:781 (2015)

University of Washington Center for Mendelian Genomics

47. Chong J, McMillin M, Shively K, Beck A, Marvin C, Armenteros J, Buckingham K, Nkinsi N, Boyle E, Berry M, Bocian M, Foulds N, Uzielli M, Haldeman-Englert C, Hennekam R, Kaplan P, Kline A, Mercer C, Nowaczyk M, Klein Wassink-Ruiter J et al., De Novo Mutations in NALCN Cause a Syndrome Characterized by Congenital Contractures of the Limbs and Face, Hypotonia, and Developmental Delay. The American Journal Of Human Genetics 96:462–473 (2015)

48. Heimer G, Kerätär J, Riley L, Balasubramaniam S, Eyal E, Pietikäinen L, Hiltunen JK, Marek-Yagel D, Hamada J, Gregory A, Rogers C, Hogarth P, Nance MA, Shalva N, Veber A, Tzadok M, Nissenkorn A, Tonduti D, Renaldo F, Bamshad M et al., MECR Mutations Cause Childhood-Onset Dystonia and Optic Atrophy, a Mitochondrial Fatty Acid Synthesis Disorder. The American Journal Of Human Genetics 99:1229–1244 (2016)