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*Underlined denoted group member.

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Submitted

1. Stewart, T.G., Wu, M.C., Zeng, D. "The augmented and weighted support vector machine and for classification with missing covariates". Submitted.
   [*** An earlier version won the ENAR Poster Competition Award AND the ENAR Distinguished Student Paper Award***]
2. Ma, N., Plantinga, A., Wu, M.C. ``Identifying genomic features related to microbiome community composition using a sparse kernel RV coefficient''.
   



2023 and In Press


3. Liu, H., Ling, W., Hua, X., Moon, J., Williams-Nguyen, J., Zhan, X., Plantinga, A.M., Zhao, N., Zhang, A., Knight, R., Qi, Q., Burk, R.D., Kaplan, R.C., Wu, M.C. (2023). ``Kernel-based genetic association analysis for microbiome phenotypes identifies host genetic drivers of beta-diversity''. Microbiome, In Press. Preprint.
4. Song, H., Ling, W., Zhao, N., Plantinga, A.M., Broedlow, C.A., Klatt, N.R., Hensley-McBain, T., Wu, M.C. (2023). ``Accommodating multiple potential normalizations in microbiome associations studies''. BMC Bioinformatics, 24(1):22. PMC9850542 Open Access
5. Bauer, A.E., Avery, C.L., Shi, M., Weinberg, C.R., Olshan, A.F., Harmon, Q.E., Luo, J., Yang, J., Manuck, T., Wu, M.C., Klungsoyr, K., Trogstad, L., Magnus, P., Engel, S.M. (2023). ``Do genetic variants modify the effect of smoking on risk of preeclampsia in pregnancy?''. American Journal of Perinatology, In Press.
6. Carter, K.A., Fodor, A.A., Balkus, J.E., Zhang, A., Serrano, M.G., Buck, G.A., Engel, S.M., Wu, M.C., Sun, S. (2023). ``Vaginal microbiome metagenome inference accuracy: differential measurement error according to community composition.''  mSystems, In Press.



2022


7. Ling, W., Lu, J., Zhao, N., Lulla, A., Plantinga, A.M., Fu, W., Zhang, A., Liu, H., Song, H., Li, Z., Chen, J., Randolph, T., Koay, W.L.A., White, J.R., Launer, L.J., Fodor, A.A., Meyer, K.A., Wu, M.C. (2022). ``Batch effect removal for microbiome data via conditional quantile regression (ConQuR)''. Nature Communications, 13(1):5418. PMC9477887 Open Access
8. Song, H., Liu, H., Wu, M.C. (2022). ``A fast kernel independence test for cluster-correlated data''. Scientific Reports, 12(1): 21659. PMC9755291 Open Access
   
9. Wang, T., Ling, W., Plantinga, A.M., Wu, M.C., Zhan, X. (2022). ``Testing microbiome association using integrated quantile regression models''. Bioinformatics, 38(2): 419-425.  PMID:34554223
   
10. Huang, C., Callahan, B., Wu, M.C., McLaren, M., Brochu, H., Lu, W., Peng, X., Tzeng, J.Y. (2022). ``Phylogeny-guided microbiome OTU-specific association test (POST)''. Microbiome, 10(1):86. PMC9171974 Open Access
11. Sun, S., Serrano, M., Fetweiss, J., Basta, P., Rosen, E., Ludwig, K., Sorgen, A., Blakley, I., Wu, M.C., Dole, N., Thorp, J., Siega-Riz, A., Buck, G.A., Fodor, A.A., Engel, S.M. ``Race, the vaginal microbiome, and spontaneous preterm birth''. mSystems, e00017-22. PMC9238383 Open Access
12. Goo, J., Liu, Y., Sun, W., Hsu, L., Wu, M.C., He, Q. (2022). ``TCR-L: an analysis tool for evaluating the link between the T-cell receptor repertoire and clinical phenotypes''. BMC Bioinformatics, 23(1):152. PMC9052542 Open Access
    
13. Fredricks, D.N., Plantinga, A., Srinivasan, S., Oot, A., Wiser, A., Fiedler, T.L., Proll, S., Wu, M.C., Marrazzo, J.M. (2022). ``Extra-vaginal bacterial colonization and risk for incident bacterial vaginosis in a population of women who have sex with men''. Journal of Infectious Diseases, 225(7): 1261-1265. PMC8974833
    
14. Rosen, E.M., Martin, C.L., Siega-Riz, A.M., Dole, N., Ludwig, K., Basta, P.V., Serrano, M., Fettweis, J., Wu, M., Sun, S., Thorp, J.M., Buck, G., Fodor, A.A., Engel, S.M. (2022). ``Is prenatal diet associated with the composition of the vaginal microbiome?''. Paediatric and Perinatal Epidemiology, 36(2): 243-253. PMC8881389
    
15. Kimmel, M., Jin, W., Xia, K., Lun, K., Azcarate-Peril, M.A., Plantinga, A.,  Wu, M., Ataei, S., Rackers, H., Carroll, I., Meltzer-Brody, S., Fransson, E., Knickmeyer, R. (2022).``Metabolite trajectories across the perinatal period and mental health: A preliminary study of tryptophan-related metabolites, bile acids and microbial composition''.  Behavioural Brain Research, 418:113635.  PMID:34755640
    
16. Srinivasan, S., Hua, X., Wu, M.C., Proll, S., Valint, D.J., Reed, S.D., Guthrie, K.A., Lacroix, A.Z., Larson, J.C., Pepin, R., Raftery, D., Fredricks, D.N., Mitchell, C.M. (2022). ``Impact of topical interventions on the vaginal microbiota and metabolome in postmenopausal women: A secondary analysis of a randomized clinical trial''. JAMA Network Open, 5(3): e225032. PMC8968546
    



2021


17. Ling, W., Zhao, N., Plantinga, A., Launer, L., Fodor, A., Meyer, K., Wu, M.C. (2021). ``Powerful and robust non-parametric association testing for microbiome data via a zero-inflated quantile approach (ZINQ)''. Microbiome, 9(1):181. PMC8414689  Open Access
18. Liu, H., Plantinga, A.M., Xiang, Y., Wu, M.C. (2021). ``A kernel-based test of independence for cluster-correlated data''. Neural Information Processing Systems (NeurIPS), 34: 9869-9881. Proceedings
    
19. Ling, W., Qi, Y., Hua, X.,  Wu, M.C. (2021). ``Deep ensemble learning over the microbial phylogenetic tree (DeepEn-Phy)''. IEEE Bioinformatics and Biomedicine (BIBM) 2021, 470-477.
    
20. Plantinga, A.M., Wu, M.C. (2021). ``Beta Diversity and Distance-based Analysis of Microbiome Data''. In: Datta, S., Guha, S. (eds): Statistical Analysis of Microbiome Data. Springer Frontiers in Probability and Statistical Sciences, Springer Nature, Switzerland.
21. Wilson, N., Zhao, N., Zhan, X., Fu, W., Chen, J., Li, H., Wu, M.C., Plantinga, A. (2021). ``MiRKAT: Kernel machine regression-based global association tests for the microbiome''. Bioinformatics, 37(11):1595-1597. PMC8495888
    
22. Liu, M., Liu, Y., Wu, M.C., Hsu, L., He, Q. (2021). ``A method for subtype analysis with somatic mutations''. Bioinformatics, 37(1):50-56. PMID: 33416828
    
23. He, Q., Liu, Y., Liu, M., Wu, M.C., Hsu, L. (2021). ``Random-effect based test for multinomial logistic regression''. Genetic Epidemiology, 45 (7), 736-740.
24. Mitchell, C.M., Ma, N., Mitchell, A., Wu, M.C., Valint, D.J., Proll, S., Reed, S.D., Guthrie, K.A., Larson, J., Raftery, D., Fredricks, D.N., Srinivasan, S. (2021). ``Association between postmenopausal vulvovaginal discomfort, vaginal microbiota and mucosal inflammation: Vaginal microbiome and treatment response in postmenopausal women''. American Journal of Obstetrics & Gynecology, 225(2):159.e1-159.e15. PMC8328873
25. Mitchell, C.M., Srinivasan, S., Ma, N., Reed, S.D., Wu, M.C., Hoffman, N.G., Valint, D., Proll, S., Fiedler, T., Agnew, K., Guthrie, K.A., Fredricks, D.N. (2021). ``Bacterial communities associated with abnormal Nugent score are different in pre- vs. post-menopausal women''. Journal of Infectious Diseases, 223(12):2048-2052. PMC8350750
    
26. Hudson, P.L., Ling, W., Wu, M.C., Hayward, M.R., Mitchell, A.J., Larson, J., Guthrie, K.A., Reed, S., Kwon, D.S., Mitchell, C. (2021). ``Comparison of the vaginal microbiota in postmenopausal Black and White women''. Journal of Infectious Diseases, 224(11):1945-1949. PMC8825215
    



2019


27. Plantinga, A., Chen, J., Jenq, R.R., Wu, M.C. (2019). ``pldist: Ecological dissimilarities for paired and longitudinal microbiome association analysis''. Bioinformatics, 35(19):3567-3575. PMC6761933 Open Access
    
28. Zhao, N., Zhang, H., Clark, J.J., Maity, A., Wu, M.C. (2019) ``Composite kernel machine regression based on likelihood ratio test for joint testing of genetic and gene-environment interaction effect''. Biometrics, 75(2): 363-717. PMID:30430548.
29. Marceau-West, R., Lu, W., Rotroff, D.M., Kuenemann, M., Chang, S., Wu, M.C., Wagner, M.J., Buse, J.B., Motsinger-Reif, A., Fourches, D., Tzeng, J. (2019). ``Identifying individual risk rare variants using protein structure-guided local tests (POINT)''. PLoS Computational Biology, 15(2):e1006722. PMC6396946
30. Hishida, A., Ugai, T., Fujii, R., Nakatochi, M., Wu, M.C., Ito, H., Oze, I., Masahiro, T., Yasumasa, N., Nishiyama, T., Nakagawa-Senda, H., Suzuki, S., Koyama, T., Matsui, D., Watanabe, Y., Kawaguchi, T., Matsuda, F., Momozawa, Y., Kubo, M., Naito, M., Matsuo, K., Wakai, K. (2019). ``GWAS and genome-wide SNP-set analysis for the risk of H. pylori-induced gastric atrophy revealed the significant contribution of PSCA to its risk''. Carcinogenesis, 40(5):661-668. PMID: 30753327
31. Sun, S., Lulla, A., Sioda, M., Winglee, K., Wu, M.C., Jacobs, D.R., Shikany, J.M., Lloyd-Jones, D.M., Launer, L.J., Fodor, A.A.. Meyer, K.A. (2019). ``Gut microbiota composition and blood pressure: The CARDIA Study''. Hypertension, 73(5):998-1006. PMC6458072.
32. Hensley-McBain, T., Wu, M.C., Manuzak, J., Cheu, R., Gustin, A., Driscoll, C., Zevin, A.S., Miller, C., Coronado, E., Smith, E., Law, L., Gale Jr., M., Somsouk, M., Burgener, A.D., Hunt, P.W., Hope, T., Collier, A., Klatt, N.R. (2019). ``Increased mucosal neutrophil survival is associated with altered microbiota in HIV infection''. PLoS Pathogens, 15(4):e1007672. PMC6459500.
33. Golob, J.L., DeMeules, M.M., Loeffelholz, T., Quinn, Z.Z., Dame, M., Wu, M.C., Schmidt, T., Fiedler, T.L., Pergam, S.A., Fredricks, D.N. (2019). ``Butyrogenic bacteria after severe acute graft versus host disease associate with the development of chronic gut GVHD and steroid refractory GVHD.'' Blood Advances, 3(19): 2866-2869. PMC6784520
    
34. Kaplan, R.C., Wang, Z., Usyk, M., Sotres-Alvarez, D., Daviglus, M., Schneiderman, N., Talavera, G.A., Gellman, M.D., Thyagarajan, B., Moon, J., Vazquez-Baeza, Y., McDonald, D., Williams-Nguyen, J.S., Wu, M.C., North, K., Sollecito, C.C., Qi, Q., Isasi, C.R., Wang, T., Knight, R., Burk, R.D. (2019). ``Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity''. Genome Biology, 20(1):219. PMC6824043.



2018

35. Zhao, N., Zhan, X., Huang, Y-T., Almli, L.M., Smith, A., Epstein, M.P., Conneely, K.N., Wu, M.C. (2018). "Kernel machine methods for integrative analysis of genome-wide methylation and genotyping studies". Genetic Epidemiology, 42(2):156-167. PMC5592124 PDF
    [***Selected as the IGES Highlight/Paper of the Month ***]
36. Teran Hidalgo, S.J., Wu, M.C., Engel, S.M., Kosorok, M.R. (2018). "Goodness-of-fit test for smoothing spline ANOVA models: missing covariates and interaction terms". Computational Statistics and Data Analysis, 122: 135-155. PMC5983390 PDF
37. Wu, M.C., Kuan, P.F. (2018). "A guide to illumina beadchip data analysis". In Tost, J. (ed): DNA Methylation Protocols, 3rd Edition. Springer Methods in Molecular Biology. 303-330. Humana Press, New York, NY. PMID: 29224151
    
38. Zhan, X., Wu, M.C. (2018). "Note on testing and estimation in marker-set association study using semiparametric quantile regression kernel machine". Biometrics, 74(2): 764-766. PMC5932287
    
39. Stewart, T.G., Zeng, D., Wu, M.C. (2018). ``Constructing support vector machines with missing data''. WIREs Computational Statistics. 10(4): e1430. PDF
40. Zhan, X., Xue, L., Zheng, H., Plantinga, A., Wu, M.C., Schaid, D.J., Zhao, N., Chen, J. (2018). ``Small sample kernel association tests for correlated data with application to microbiome data analysis''. Genetic Epidemiology, 42(8):772-782.
41. Luo, Y., Maity, A., Wu, M.C., Smith, C., Duan, Q., Li, Y., Tzeng, J-Y. (2018). ``On the substructure controls in rare variant analysis --- principal components or variance components?''. Genetic Epidemiology, 42(3):276-287. PMC5851819
    
42. Bauer, A.E., Avery, C.L., Shi, M., Weinberg, C.R., Olshan, A.F., Harmon, Q.E., Luo, J., Yang, J., Manuck, T., Wu, M.C., Williams, N., McGinnis, R., Morgan, L., K'ungsoyr, K., Trogstad, L., Magnus, P., Engel, S.M. (2018). ``A family-based study of carbon monoxide and nitric oxide signaling genes and preeclampsia''. Paediatric and Perinatal Epidemiology, 32:1-12. PMC5771849
43. Fujii, R., Hishida, A., Wu, M.C., Kondo, T., Hattori, Y., Naito, M., Endoh, K., Nakatochi, M., Hamajima, N., Kubo, M., Kuriki, K., Wakai, K. (2018). ``Genome-wide association study for pollinosis identified two novel loci in interleukin (IL)-1B in a Japanese population''. Nagoya Journal of Medical Science, 80: 109-120. PMC5857507
    
44. Mitchell, C.M., Srinivasan, S., Plantinga, A., Wu, M.C., Reed, S.D., Guthrie, K.A., LaCroix, A.Z., Fiedler, T., Munch, M., Liu, C., Homan, N.G., Blair, I.A., Newton, K., Freedman, E.W., Joffe, H., Cohen, L., Fredricks, D.N. (2018). "Associations between improvement in genitourinary symptoms of menopause and changes in the vaginal ecosystem". Menopause, 25(5): 500-507. PMC5898977
    
45. Manuzak, J.A., Gott, T.M., Kirkwood, J.S., Coronado, E., Hensley-McBain, T., Miller, C., Cheu, R.K., Collier, A.C., Funderburg, N.T., Martin, J.N., Wu, M.C., Isoherranen, N., Hunt, P.W., Klatt, N.R. (2018). ``Heavy cannabis use associated with reduction in activated and inflammatory immune cell frequencies in antiretroviral therapy–treated Human Immunodeficiency Virus–infected individuals.'' Clinical Infectious Diseases, 66(12): 1872-1882. PMC6248381



2017

46. Plantinga, A., Zhan, X., Zhao, N., Chen, J., Jenq, R.R., Wu, M.C. (2017). "MiRKAT-S: A community-level test of association between the microbiota and survival times". Microbiome, 5(1): 17. PMC5299808 Open Access
47. Zhan, X., Plantinga, A., Zhao, N., Wu, M.C. (2017). "A fast small-sample kernel independence test with application to microbiome association studies". Biometrics, 73(4):1453–1463. PMC5592124 PDF
    [*** An earlier version won an ASA Biometrics Section JSM Paper Award ***]
48. Zhan, X., Tong, X., Zhao, N., Maity, A., Wu, M.C.#, Chen, J.# (2017). "A small-sample multivariate kernel machine test for microbiome association studies". Genetic Epidemiology, 41(3):210-220. PDF
    [#Joint Corresponding Author]
49. Zhan, X., Zhao, N., Plantinga, A., Thornton, T.A., Conneely, K.N., Epstein, M.P., Wu, M.C. (2017). ``Dual kernel-based association test for genome-wide association studies with high-dimensional structured traits''. Genetics, 206(4): 1779-1790. PMC5560787 PDF
    
50. Reese, S.E., Zhao, S., Wu, M.C., Joubert, B.R., Parr, C.L., Håberg, S.E., Ueland, P.M., Nilsen, R.M., Midttun, O., Vellset, S.E., Peddada, S., Nystad, W., London, S.J. (2017). "DNA methylation score as a biomarker in newborns for sustained maternal smoking during pregnancy". Environmental Health Perspectives, 125(4):760-766. PMC5381987
    
51. Mitchell, C.M., Srinivasan, S., Zhan, X., Wu, M.C., Reed, S.D., Guthrie, K.A., LaCroix, A.Z., Fiedler, T., Munch, M., Liu, C., Hoffman, N., Blair, I.A., Newton, K., Freeman, E.W., Joffe, H., Cohen, L., Fredricks, D.N. (2017). ``Vaginal microbiota and genitourinary menopausal symptoms: a cross sectional analysis''. Menopause, 24(10):1160-1166. PMC5607086
52. Golob, J.L., Pergam, S.A., Srinivasan, S., Fiedler, T.L., Liu, C., Garcia, K., Mielcarak, M., Ko, D., Aker, S., Marquis, S., Loeffelholz, T., Plantinga, A., Wu, M.C., Celustka, K., Morrison, A., Woodfield, M., Fredricks, D.N. (2017). ``The stool microbiota at neutrophil recovery is predictive for severe acute graft versus host disease after hematopoietic cell transplantation.'' Clinical Infectious Diseases, 65(12):1984-1991. PMC5850019



2016

53. He, Q.#, Cai, T., Liu, Y., Zhao, N., Harmon, Q.E., Almli, L.M., Binder, E.B., Engel, S.M., Ressler, K.J., Conneely, K.N., Lin, X., Wu, M.C.# (2016). "Prioritizing individual variants after kernel machine testing using variable selection". Genetic Epidemiology, 40(8):722-731. PMC5118060 PDF
    [#Joint Corresponding Author]
54. Chen, J., Chen, W., Zhao, N., Wu, M.C., Schaid, D.J. (2016). "Small-sample kernel association tests for human genetic and microbiome association studies". Genetic Epidemiology, 40:5-19. PMC4679685
    
55. Lin, Xinyi, Lee, S., Wu, M.C., Wang, C., Chen, H., Li, Z., Lin, X. (2016). "Test for rare variants by environment interactions in sequencing association studies". Biometrics, 72: 156-164. PMC4733434
56. Zhan, X., Girirajan, S., Zhao, N., Wu, M.C., Ghosh, D. (2016). "A novel copy number variants kernel association test with application to autism spectrum disorders studies". Bioinformatics, 32 (23): 3603-3610. PMC5181531
    
57. Dai, H., Wu, G., Wu, M., Zhi, D. (2016). "An optimal bahadur-efficient method in detection of sparse signals with applications to pathway analysis in sequencing association studies". PLOS One, 11(7):e0152667. PMC4933358
58. Joubert, B.R., den Dekker, H.T., Felix, J.F., Bohlin, J., Beckett, E., Tiemeier, H., van Meurs, J.B., Uitterlinden, A.G., Hofman, A., Håberg, S.E., Reese, S.E., Andreassen, B.K., Nilsen, R.M., Vollset, S.E., Midttun, O., Ueland, P.M., Wu, M.C., Wang, T., Peddada, S.D., Jaddoe, V.W.V., Nystad, W., Dujits, L., London, S.J. (2016). "Maternal plasma folate during pregnancy impacts differential DNA methylation in an epigenome-wide meta-analysis of newborns". Nature Communications, 7:10577. PMC474995
    
59. Suderman, M., Stene, L.C., Bohlin, J., Page, C.M., Holvik, K., Parr, C.L., Magnus, M.C., Håberg, S.E., Joubert, B.R., Wu, M.C., London, S.J., Relton, C., Nystad, W. (2016). "25-hydroxyvitamin D in pregnancy and genome wide cord blood DNA methylation in two pregnancy cohorts (MoBa and ALSPAC)". The Journal of Steroid Biochemistry and Molecular Biology, 159:102-109. PMC4829940
    
60. Joubert, B.R., Felix, J.F., Yousefi, P., Bakulski, K.M., Just, A.C., Breton, C., Reese, S., Markunas, C., ..., Wu, M.C., ... , London, S.J. (2016). "DNA methylation in newborns and maternal smoking in pregnancy: Genome-wide consortium meta-analysis". The American Journal of Human Genetics, 98(4):680-96. PMC4833289
    [*** This article selected by AJHG as one of the "Best of" 2015-2016 ***]
61. Rotroff, D.M., Joubert, B.R., Marvel, S.W., Håberg, S.E., Wu, M.C., Nilsen, R.M., Ueland, P.M., Nystad, W., London, S.J., Motsinger-Reif, A. (2016). "Maternal smoking impacts key biological pathways in newborns through epigenetic modification in utero". BMC Genomics, 17(1):976. PMC5124223



2015

62. Zhao, N., Chen, J., Carroll, I.M., Ringel-Kulka, T., Epstein, M.P., Zhou, H., Zhou, J.J., Ringel, Y., Li, H., Wu, M.C. (2015). "Testing in microbiome profiling studies with MiRKAT, the Microbiome Regression-based Kernel Association Test". The American Journal of Human Genetics, 96(5): 797 - 807. PMC4570290 PDF
    
63. Zhao, N., Bell, D.A., Maity, A., Staicu, A.-M., Joubert, B.R., London, S.J., Wu, M.C. (2015). "Global analysis of methylation profiles from high resolution CpG data". Genetic Epidemiology, 39:53-64. PMC4314375 PDF
    
64. Urrutia, E., Lee, S., Maity, A., Zhao, N., Shen, J., Li, Y., Wu, M.C. (2015). "Rare variant testing across methods and thresholds using the multi-kernel sequence kernel association test (MK-SKAT)". Statistics and Its Interface, 8:495-505. PMC4698916 PDF
    [*** An earlier version won an ASHG Predoctoral Trainee Research Semifinalist Award***]
65. Family, L., Bensen, J.T., Troester, M.A., Wu, M.C., Anders, C.K., Olshan, A.F. (2015). "Single nucleotide polymorphisms in DNA bypass polymerase genes and association with breast cancer and breast cancer subtypes among African Americans and Whites". Breast Cancer Research and Treatment, 149(1):181-90. PMC4498665
    
66. Hair, B.Y., Troester, M.A., Edmiston, S.N., Parrish, E.A., Robinson, W.R., Wu, M.C., Olshan, A.F., Swift-Scanlan, T., Conway, K. (2015). "Body mass index is associated with gene methylation in estrogen receptor-positive breast tumors". Cancer Epidemiology, Biomarkers & Prevention, 24(3):580-86. PMC4355173
67. Hair, B.Y., Xu, Z., Kirk, E., Harlid, S., Sandhu, R., Robinson, W.R., Wu, M.C., Olshan, A.F., Conway, K., Taylor, J., Troester, M.A. (2015). "Body mass index associated with genome-wide methylation in breast tissue". Breast Cancer Research and Treatment, 151(2):453-63. PMC4474159
68. Bohlin, J., Andreassen, B.K., Joubert, B.R., Magnus, M., Wu, M.C., Parr, C.L., Håberg, S.E., Magnus, P., Reese, S.E., Stoltenberg, C., London, S.J., Nystad, W. (2015). "Effect of maternal gestational weight gain on offspring DNA methylation: a follow-up to the ALSPAC cohort study". BMC Research Notes, 8:321. PMC4518864
    
69. Geybels, M.S., Zhao, S., Wong, C., Bibikova, M., Klotzle, B., Wu, M., Ostrander, E.A., Fan, J., Feng, Z., Stanford, J.L. (2015). "Epigenome-wide profiling of DNA methylation in paired prostate cancer versus adjacent benign tissue". The Prostate, 75(16):1941-50. PMID:26383847



2014

70. Wu, M.C., Joubert, B.R., Kuan, P.F., Håberg, S.E., Nystad, W., Peddada, S.D., London, S.J. (2014). "A systematic assessment of normalization approaches for the Infinium 450k methylation platform". Epigenetics, 9(2): 212-222. PMC3962542 Open Access
71. Engel, S.M.#, Joubert, B.R.#, Wu, M.C.#, Olshan, A.F., Håberg, S.E., Ueland, P.M., Nystad, W., Nilsen, R.M., Vollset, S.E., Peddada, S.D., London, S.J. (2014). "Neonatal genome-wide methylation patterns in relation to birthweight in the Norwegian Mother and Child Birth Cohort". American Journal of Epidemiology, 179(7): 834-42. PMC3969535
    [#Equal Contribution]
    [*** This paper was selected as an AJE "Editor's Choice" Article AND a 2014 AJE and SER "Paper of the Year"***]
72. Sanders, A.P., Smeester, L., Rojas, D., DeBussycher, T., Wu, M.C., Wright, F.A., Zhou, Y., Laine, J.E., Rager, J.L., Swamy, G.K., Ashley-Koch, A., Miranda, M.L., Fry, R.C. (2014). "Cadmium exposure and the epigenome: exposure-associated patterns of DNA methylation in leukocytes from mother-baby pair". Epigenetics, 9(2): 318-329. PMC3962531
    
73. Ebert, C.S., McKinney, K.A., Urrutia, G., Wu, M., Rose, A.S., Fleischman, G.M., Thorp, B., Senior, B.A., Zanation, A.M. (2014). "Expression of protease-activated receptors in allergic fungal rhinosinusitis". International Forum of Allergy & Rhinology, 4(4): 266-71. PMID:24500840
    
74. Harmon, Q.E., Engel, S.M., Wu, M.C., Moran, T., Luo, J., Stuebe, A., Avery, C., Olshan, A. (2014). "Polymorphisms in inflammatory genes associated with term SGA and preeclampsia". American Journal of Reproductive Immunology, 71(5): 472-84. PMC4040534
    
75. Joubert, B.R., Håberg, S.E., Bell, D.A., Nilsen, R.M., Vollset, S.E., Midttun, O., Ueland, P.M., Wu, M.C., Nystad, W., Peddada, S.D., London, S.J. (2014). "Maternal smoking and DNA methylation in newborns: In utero effect or epigenetic inheritance?". Cancer Epidemiology, Biomarkers & Prevention, 23(6): 1007-17. PMC4140220
    
76. Nylander-French, L.A., Wu, M.C., Boyner, J., Smeester, L., Sanders, A.P., French, J.E., Fry, R.C. (2014). "DNA methylation modifies urine biomarker levels in 1,6-hexamethylene diisocyanate (HDI) exposed workers: a pilot study". Toxicology Letters, 231(2): 217-26. PMID:25445006



2013

77. Wu, M.C., Maity, A., Lee, S., Simmons, E.M., Harmon, Q.E., Lin, Xinyi, Engel, S.M., Molldrem, J.J., Armistead, P.M. (2013). "Kernel machine SNP-set testing under multiple candidate kernels". Genetic Epidemiology, 37(3): 267-75. PMC3769109 PDF
78. Byrnes, A.E., Wu, M.C., Wright, F.A., Li, M., Li, Y. (2013). "The value of statistical or bioinformatics annotation for rare variant association with quantitative trait". Genetic Epidemiology, 37(7): 666-74. PMC4083762
    
79. Carroll, I.M., Ringel-Kulka, T., Ferrier, L., Wu, M.C., Siddle, J.P., Bueno, L., Ringel, Y. (2013). "Fecal protease activity is associated with compositional alterations in the intestinal microbiota". PLOS One, 8(10): e78017. PMC3798377
    
80. Harmon, Q.E., Engel, S.M., Olshan, A., Moran, T., Stuebe, A., Luo, J., Wu, M.C., Avery, C. (2013). "Association of polymorphisms in natural killer cell-related genes with preterm birth". American Journal of Epidemiology, 178(8): 1208-18. PMC3792727
    
81. Cleary, S.P., Jeck, W.R., Zhao, X., Chen, K., Selitsky, S.R., Savich, G.L., Tan, T.X, Wu, M.C., Getz, G., Lawrence, M.S., Parker, J.S., Li, J, Powers, S., Kim, H., Fischer, S., Giundi, M., Ghanekar, A., Chiang, D.Y. (2013). "Identification of Driver Genes in Hepatocellular Carcinoma by Exome Sequencing". Hepatology, 58(5): 1693-1702. PMC3830584
    
82. Bencharit, S., Baxter, S.S., Carlson, J., Byrd, W.C., Mayo, M.V., Border, M.B., Kohltfarber, H., Urrutia, E., Saldarriaga, I., Howard-Williams, E.L., Offenbacher, S., Wu, M.C., Buse, J.B. (2013). "Salivary proteins associated with hyperglycemia in diabetes: a proteomic analysis". Molecular Biosystems, 9: 2785-97. PMC3888809
    
83. Bailey, K.M., Wu, M.C., Ward, W.O., Smeester, L., Rager, J.E., Garcia-Varga, G., Del Razo, L., Drobna, Z., Styblo, M., Fry, R.C. (2013). "Arsenic and the epigenome: interindividual differences in arsenic metabolism related to distinc patterns of DNA methylation". Journal of Biochemical and Molecular Toxicology, 27(2):106-115. PMC3892431
    
84. Schuck, R.N., Theken, K.N., Edin, M.L., Caughey, M., Bass, A., Ellis, K., Tran, B., Steele, S., Simmons, B.P., Lih, B.P., Tomer, K.B., Wu, M.C., Hinderliter, A.L., Stouffer, G.A., Zeldin, D.R., Lee, C.R. (2013). "Cytochrome P450 derived eicosanoids and vascular function in coronary artery disease patients". Atherosclerosis, 227:442-48. PMC3638946



2012

85. Lee, S., Wu, M.C., Lin, X. "Optimal tests for rare variant effects in sequencing association studies". (2012). Biostatistics, 13(4): 762-75. PMC3440237 PDF
86. Joubert, B.R., Håberg, S.E., Nilsen, R.M., Wang, X., Vollset, S.E., Murphey, S.K., Huang, Z., Hoyo, C., Midttun, O., Cupul-Uicab, L.A., Ueland, P.M., Wu, M.C., Nystad, W., Bell, D.A., Peddada, S.D., London, S.J. (2012). "450K Epigenome-wide scan identifies differential DNA methylation in newborns related to maternal smoking during pregnancy". Environmental Health Perspectives, 120: 1425-31. PMC3491949
    [*** This article selected by EHP as the 2013 Paper of the Year ***]
87. Wu, H., Wu, M.C., Zhi, D., Santorico, S.A., Cui, X. (2012). "Statistical analysis for next generation sequencing -- meeting report". Frontiers in Genetics, 3:128. PMC3395795
    
88. Glickman, S.W., Shofer, F.S., Wu, M.C., Scholer, M.J., Ndubuizu, A., Cairns, C.B., Glickman, L.T. (2012). "Development and validation of a prioritization rule for obtaining an immediate 12-lead electrocardiogram in the emergency department to identify ST-elevation myocardial infarction". The American Heart Journal, 163(3): 372-382. PMID22424007
    
89. Theken, K.N., Schuck, R.N., Edin, M.L., Tran, B., Ellis, K., Bass, A., Lih, F.B., Tomer, K.B., Poloyac, S.M., Wu, M.C., Hinderliter, A.L., Zeldin, D.C, Stouffer, G.A., Lee, C.R. (2012). "Evaluation of cytochrome P450-derived eicosanoids in humans with stable atherosclerotic cardiovascular disease". Atherosclerosis, 222(2): 530-536. PMC3361525



2011

90. Wu, M.C.#, Lee, S.#, Cai, T., Li, Y., Boehnke, M., Lin, X. (2011). "Rare variant association testing for sequencing data with the sequence kernel association test (SKAT)". The American Journal of Human Genetics, 89, 82-93. PMC3135811 PDF
    [#Equal Contribution]
    [*** This article selected by AJHG as one of the "Best of" 2011-2012 ***]
91. Lin, X., Cai, T., Wu, M.C., Zhou, Q., Liu, G., Christiani, D.C., Lin, X. (2011). "Kernel machine SNP-set analysis for censored survival outcomes in genome-wide association studies". Genetic Epidemiology, 35, 620-31. PMC3373190
    
92. Ter-Minassian, M., Wang, Z., Asomaning, K., Wu, M.C., Paulus, J.K., Liu, G., Bradbury, P.A., Zhai, R., Su, L., Frauenhoffer, C.S., Hooshman, S.M., De Vivo, I., Lin, X., Christiani, D.C., Kulke, M.H. (2011). "Genetic associations with sporadic neuroendocrine tumor risk". Carcinogenesis, 32(8):1216-22. PMC3149206



2010

93. Wu, M.C., Kraft, P., Epstein, M.P., Taylor, D.M., Chanock, S.J., Hunter, D.J., and Lin, X. (2010). "Powerful SNP set analysis for case-control genome wide association studies". The American Journal of Human Genetics, 86, 929-942. PMC3032061 PDF
94. Locke, A.E., Dooley, K.J., Tinker, S.W., Cheong, S.Y., Feingold, E., Allen, E.G., Freeman, S.B., Torfs, C.P., Cua, C., Epstein, M.P., Wu, M.C., Lin, X., Capone, G., Sherman, S.L., Bean, L.J.H. (2010). "Variation in folate pathway genes contributes to risk of congenital heart defects among individuals with Down syndrome". Genetic Epidemiology, 34(6):613-23. PMC3378053
    
95. Liu, C.Y., Wu, M.C., Chen, F., Ter-Minassian, M., Asomaning, K., Zhai, R., Wang, Z., Su, L., Heist, R.S., Kulke, M.H., Lin, X., Liu, G., Christiani, D.C. (2010). "A large-scale genetic association study of esophageal adenocarcinoma risk". Carcinogenesis, 31(7):1259-63. PMC2893800



2009 and earlier

96. Wu, M.C., Zhang, L., Wang, Z., Christiani, D.C., Lin, X. (2009). "Sparse linear discriminant analysis for simultaneous gene set/pathway significance test and gene selection". Bioinformatics, 25,1145-1151. PMC2732305 PDF
    [*** An earlier version received the 2008 ICSA Student Paper Award and corresponding technical report received the 2008 ASA Statistical Computing and Graphics Section Student Paper Award***]
    
97. Huang, Y.T., Heist, R.S., Chirieac, L.R., Lin, X., Skaug, V., Haugen, A., Wu, M.C., Wang, Z., Su, L., Asomaning, K., Christiani, D.C. (2009). "Genome-wide analysis of survival in early-stage non-small cell lung cancer". Journal of Clinical Oncology, 27(16):2660-2667. PMC2690391
    
98. Wu, M.C., Lin, X. (2009). "Prior biological knowledge based approaches for the analysis of genome-wide expression profiles using gene sets and pathways". Statistical Methods in Medical Research,18(6):577-93. PMC2827341 PDF
99. Harezlak, J.#, Wu, M.C.#, Wang, M., Schwartzman, A., Christiani D.C., Lin, X. (2008). "Biomarker discovery for arsenic exposure using functional learning of mass-spectrometry proteomic data". Journal of Proteome Research, 7(1):217-24. PMID18173220 PDF
    [#Equal Contribution]
    
100. Engbring, J.A., Hossain, R., VanOsdol, S.J., Kaplan-Singer, B., Wu, M., Hibino, S., Koblinski, J.E. (2008). "The laminin alpha-1 chain derived peptide, AG73, increases fibronectin levels in breast and melanoma cancer cells". Clinical and Experimental Metastasis, 25(3):241-252. PMID18185912
     
101. Ji, H., Ramsey, M.R., Hayes, D.N., Fan, C., McNamara, K., Kozlowski, P., Torrice, C., Wu, M.C., Shimamura, T., Perera, S., Liang, M-C., Cai, D., Naumov, G.N., Bao, L., Contreras, C., Li, D., Chen, L., Krishnamurthy, J., Koivunen, J., Chirieac, L.R., Padera, R., Bronson, R.T., Lindeman, N.I., Christiani, D.C., Lin, X., Shapiro, G.I., Janne, P.A., Johnson, B., Meyerson, M., Kwiatkowski, D.J., Castrillon, D.H., Badeesy, N.,Sharpless, N.E., Wong, K-K. (2007). "LKB1 modulates lung cancer differentiation and metastasis". Nature, 448(7155):807-10. PMID17676035
     
102. Koblinski, J.E., Wu, M., Demeler, B., Kleinman, H.K. (2005). "Matrix cell adhesion activation by non-adhesion proteins". Journal of Cell Science, 118(Pt 13):2965-74. PMID15976454
     
103. Koblinski, J.E., Kaplan-Singer, B.R., VanOsdol, S.J., Wu, M., Engbring, J.A., Goldsmith, C.M., Piper, J.T., Vostal, J.G., Harms, J.F., Welch, D.R., Kleinman, H.K. (2005). "Endogenous osteonectin/SPARC/BM-40 expression inhibits MDA-MB-231 breast cancer cell metastasis". Cancer Research, 65(16):7370-7. PMID16103089



Technical Reports

104. Wu, M.C., Dai, J., LeBlanc, M. (2017). ``Design and Analysis Guidelines for Translational Medicine Studies (v. 1.0)''. Technical Report, SWOG SDMC .
     
105. Family, L., Bensen, J.T., Troester, M.A., Wu, M.C., Anders, C.K., Olshan, A.F. (2015). ``Single nucleotide polymorphisms in base excision repair pathway genes and association with breast cancer and breast cancer subtypes among African Americans and Whites''. Technical Report.
     
106. Li, L., Wu, M.C., Lin, X. "Prioritizing phenotype-associated uncommon variants in sequencing association studies". Technical Report.
     
107. Lee, S., Wu, M.C., Cai, T., Li, Y., Boehnke, M., Lin, X. (2011). "Power and sample size calculations for designing rare variant sequencing association studies". Technical Report, Harvard University. PDF
108. Wu, M.C., Cai, T., Lin, X. "Testing for regression coefficients in LASSO regularized regression". Technical Report.
     [*** An earlier version received an ENAR Student Paper Award ***]
109. Wu, M.C. (2009). "Statistical methods for high-dimensional genomic data". Ph.D. Dissertation, Harvard University.
110. Wu, M.C., Zhang, L., Lin, X. (2008)."Two group classification using sparse linear discriminant analysis". Technical Report, Harvard University.
     [*** An earlier version won the 2008 ASA Statistical Computing and Graphics Section Student Paper Award ***]
     
111. Wu, M.C., Lin, X. (2007). "Adaptively penalized logistic regression for testing the significance of gene pathways". Technical Report, Harvard University.