Michael Wu's Group

Michael Wu's Group

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Publications

2025 |2024 |2023 |2022 |2021 | 2019 | 2018 | 2017 | 2016 | 2015 and earlier | Technical Reports

*Underlined denoted group member.

Link to Google Scholar Profile or PubMed Profile

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. Song, H.#, Ma, N.#, Plantinga, A., Wu, M.C. ``Identifying genomic features related to microbiome community composition using a sparse kernel RV coefficient''.
  3. Samorodnitsky, S., Campbell, K., Little, A., Ling, W., Zhao, N., Chen, Y.-C., Wu, M.C. ``Detecting clinically relevant topological structures in multiplexed spatial proteomics imaging using TopKAT.'' Preprint

     

    2025 and In Press

  4. Little, A., Zhao, N., Mikhaylova, A., Zhang, A., Ling, W., Thibord, F., Johnson, A. D., Raffield, L.M., Curran, J.E., Blangero, J., O’Connell, J.R., Xu, H., Rotter, J.I., Rich, S.S., Rice, K. M., Chen, M., Reiner, A., Kooperberg, C., Vu, T., Hou, L., Fornage, M., Loos, R.J.F., Kenny, E., Mathias, R., Becker, L., Smith, A.V., Boerwinkle, E., Yu, B., Thornton, T., Wu, M.C. (2025). ``General kernel machine methods for multi-omics integration and genome-wide association testing with related individuals''. Genetic Epidemiology, 49 (1), e22610.
  5. Othus, M., Sharon, E., Wu, M.C., Sondak, V.K., Ribas, A., Patel, S.P. ``Design considerations for randomized comparisons of neoadjuvant-adjuvant versus adjuvant-only cancer immunotherapy when tumor measurement schedules do not align (SWOG S1801)''. Clinical Trials, In Press.

    2024

  6. Samorodnitsky, S., Campbell, K., Ribas, A., Wu, M.C. (2024). ``A spatial omnibus test (SPOT) for spatial proteomic data''. Bioinformatics, 40(7): btae425. PMC11257711 Open Access
  7. Little, A., Deek, R.A., Zhang, A., Zhao, N., Ling, W., Wu, M.C. (2024). ``Enhanced visualization of microbiome data in repeated measures designs''. Frontiers in Genetics, 15:1480972. PMC11604720 Open Access
  8. Samorodnitsky, S., Othus, M., LeBlanc, M., Wu, M.C. (2024). ``Reverse selection designs for accommodating multiple control arms.'' Clinical Cancer Research, 30 (24), 5535-5539.  PMC11649439
  9. Li, M., Hua, X., Wu, M.C.#, Zhao, N.# (2024). ``A multi-bin rarefaction method for evaluating alpha diversities in TCR sequencing data''. Bioinformatics, 40(7):btae431.  PMC11246167 Open Access
    [#Joint Corresponding Author]
  10. Samorodnitsky, S., Wu, M.C. (2024). ``Statistical analysis of multiple regions-of-interest in multiplexed spatial proteomics data''. Briefings in Bioinformatics, 25(6):bbae522.  PMC11491162
  11. Song, H., Wu, M.C. (2024). ``Multivariate differential association analysis''. Stat, 13:e704. PMC11661859 Preprint
  12. Casto A.M., Song H., Xie H., Selke S., Roychoudhury P., Wu M.C., Wald A., Greninger A.L., Johnston C. (2024). ``Viral genomic variation and the severity of genital HSV-2 infection as quantified by shedding rate: a viral genome-wide association study''. Journal of Infectious Diseases, 230(6): 1357-1366.  PMC11646587
  13. Byrne, E.H., Song, H., Srinivasan, S., Fredricks, D.N., Reed, S.D., Guthrie, K., Wu, M., Mitchell, C.M. (2024). ``Association between vaginal microbiota and vaginal inflammatory immune markers in postmenopause''. Menopause, 31(7):575-581. PMC11213660
  14. 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. (2024). ``Do genetic variants modify the effect of smoking on risk of preeclampsia in pregnancy?''. American Journal of Perinatology, 41(1):44-52. PMC10127527
  15. Pete, D., Lampe, J.W., Wu, M.C., Salama, N.R., Phipps, A.I. (2024). ``The prevalence and risk factors of Helicobacter pylori infection and cagA virulence gene carriage in adults in the Navajo Nation''. Microbiota in Health and Disease,  6: e1007. PMC11282893
  16. Kozono, D., Hua, X., Wu, M.C., Tolba, K.A., Waqar, S.N., Dragnev, K.H., Cheng, H., Hirsch, F.R., Mack, P.C.,Gray, J.,  Kelly, K., Borghaei, H., Herbst, R.S., Gandara, D.R., Redman, M.W. (2024). ``Lung-MAP next generation sequencing analysis of advanced squamous cell lung cancers (SWOG S1400)''.  Journal of Thoracic Oncology, 19(12):1618-1629.  PMC11625613

     

    2023

  17. 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, 8(2):e0100322. PMC10134888 Open Access
  18. 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
  19. Song, H., Wu, M.C.  (2023).``Limitation of permutation-based differential correlation analysis''. Genetic Epidemiology, 47(8):637-641. PMC10833089
  20. 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, 8(2):e0100322. PMC10134888
  21. Byrd, D.A., Fan, W., Greathouse, L., Wu, M.C., Xie, H., Wang, X. (2023). ``The intratumor microbiome is associated with microsatellite instability.''  Journal of the National Cancer Institute, 115(8):989-993. PMC10407713
  22. VanderWalde, A., Bellasea, S., Kendra, K., Khushalani, N.I., Campbell, K.M., Scumpia, P.O., Kuklinski, L.F., Collichio, F., Sosman, J.A., Ikeguchi, A., Victor, A.I., Truong, T., Chmielowski, B., Portnoy, D.C., Chen, Y., Margolin, K., Bane, C., Dasanu, C.A., Johnson, D.B., Eroglu, Z., Chandra, S., Medina, E., Gonzalez, C.R., Baselga Carretero, I., Vega-Crespo, A., Perez Garcilazo, I., Sharon, E., Hu-Lieskovan, S., Patel, S.P., Grossmann, K.F., Moon, J., Wu, M.C., Ribas, A. (2023). “Ipilimumab with or without nivolumab in PD1/PDL1 blockade refractory metastatic melanoma: a randomized phase 2 trial”. Nature Medicine, 29(9):2278-2285. PMC10708907

     

    2022

  23. 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
    [*** Received the ASA's 2023 W.J. Youden Award in Interlaboratory Testing***]
  24. 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
  25. 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
  26. 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
  27. 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. (2022). ``Race, the vaginal microbiome, and spontaneous preterm birth''. mSystems, e00017-22. PMC9238383 Open Access
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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

  33. 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
  34. 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. PMC9801702 Proceedings
  35. 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. PMC9875567
  36. 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.
  37. 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
  38. 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
  39. 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.
  40. 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
  41. 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
  42. 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

  43. 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
  44. 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.
  45. 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
  46. 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
  47. 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.
  48. 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.
  49. 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
  50. 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

  51. 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 ***]
  52. 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
  53. 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
  54. 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
  55. Stewart, T.G., Zeng, D., Wu, M.C. (2018). ``Constructing support vector machines with missing data''. WIREs Computational Statistics. 10(4): e1430. PDF
  56. 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.
  57. 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
  58. 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
  59. 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
  60. 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
  61. 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

  62. 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
  63. 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 ***]
  64. 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]
  65. 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
  66. 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
  67. 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
  68. 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

  69. 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]
  70. 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
  71. 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
  72. 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
  73. 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
  74. 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
  75. 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
  76. 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 ***]
  77. 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

  78. 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
  79. 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
  80. 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***]
  81. 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
  82. 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
  83. 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
  84. 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
  85. 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 profiling of DNA methylation in paired prostate cancer versus adjacent benign tissue". The Prostate, 75(16):1941-50. PMID:26383847

    2014

  86. 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
  87. 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"***]
  88. 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
  89. 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
  90. 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
  91. 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
  92. 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

  93. 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
  94. 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
  95. 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
  96. 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
  97. 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
  98. 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
  99. 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
  100. 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

  101. 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
  102. 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 ***]
  103. 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
  104. 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
  105. 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

  106. 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 ***]
  107. 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
  108. 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

  109. 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
  110. 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
  111. 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

  112. 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***]
  113. 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
  114. 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
  115. 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]
  116. 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
  117. 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
  118. 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
  119. 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

  120. Wu, M.C., Dai, J., LeBlanc, M. (2017). ``Design and Analysis Guidelines for Translational Medicine Studies (v. 1.0)''. Technical Report, SWOG SDMC .
  121. 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.
  122. Li, L., Wu, M.C., Lin, X. "Prioritizing phenotype-associated uncommon variants in sequencing association studies". Technical Report.
  123. 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
  124. 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 ***]
  125. Wu, M.C. (2009). "Statistical methods for high-dimensional genomic data". Ph.D. Dissertation, Harvard University.
  126. 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 ***]
  127. Wu, M.C., Lin, X. (2007). "Adaptively penalized logistic regression for testing the significance of gene pathways". Technical Report, Harvard University.
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