Statistical Methodology: Microbiome

1. Liu H, Ling W, Hua X, Moon JY, Williams-Nguyen JS, Zhan X, Plantinga AM, Zhao N, Zhang A, Knight R, Qi Q, Burk RD, Kaplan RC, Wu MC (2023). Kernel-based genetic association analysis for microbiome phenotypes identifies host genetic drivers of beta-diversity. Microbiome 11: 80. DOI: 10.1186/s40168-023-01530-0

2. Song H, Ling W, Zhao N, Plantinga AM, Broedlow CA, Klatt NR, Hensley-McBain C, Wu MC (2023). Accommodating multiple potential normalizations in microbiome associations studies. BMC Bioinformatics 24: 22. DOI: 10.1186/s12859-023-05147-w

3. Park DJ, Plantinga AM (2023). Impact of data and study characteristics on microbiome volatility estimates. Genes 14(1): 218. doi.org/10.3390/genes14010218

4. Ling W, Lulla A, He M, Zhao N, Plantinga AM, Chen J, Randolph T, Fodor A, Meyer K, Wu MC (2022). Batch effects removal for microbiome data via conditional quantile regression (ConQuR). Nature Communications 13:5418.

5. Wang T, Ling W, Plantinga AM, Wu MC, Zhan X (2022). Testing microbiome association using integrated quantile regression models. Bioinformatics 38(2): 419-425. 

6.  Liu H, Plantinga AM, Xiang Y, Wu MC (2021). A kernel-based test of independence for cluster-correlated data. Advances in Neural Information Processing Systems 34.  

7. Ling W, Zhao N, Plantinga AM, Launer L, Fodor AA, Meyer KA, Wu MC (2021). Powerful and robust non-parametric association testing for microbiome data via a zero-inflated quantile approach (ZINQ). Microbiome 9(1): 1-19. 

8. Wilson N, Zhao N, Zhan X, Koh H, Fu W, Chen J, Li H, Wu MC, Plantinga AM (2021). MiRKAT: Kernel machine regression-based global association tests for the microbiome. Bioinformatics 37(11): 1595-1597. 

9. Plantinga A, Chen J, Jenq RR, Wu MC (2019). pldist: Ecological Dissimilarities for Paired and Longitudinal Microbiome Association Analysis. Bioinformatics 35(19):  3567-3575.

10. Zhan X, Xue L, Zheng H, Plantinga A, Wu MC, Schaid DJ, Zhao N, Chen J (2018). A small-sample kernel association test for correlated data with application to microbiome association studies. Genetic Epidemiology 42.8 (2018): 772-782.

11. Plantinga A, Zhan X, Zhao N, Jenq RR, Wu MC (2017). MiRKAT-S: A community-level test of association between the microbiota and survival times. Microbiome 5(17). 

12. Zhan X, Zhao N, Plantinga A, Thornton TA, Conneely KN, Epstein MP, Wu MC (2017). Powerful Genetic Association Analysis for Common or Rare Variants with High Dimensional Structured Traits. Genetics 206.4: 1779-1790. 

13. Zhan X, Plantinga A, Zhao N, Wu MC (2017). A fast small-sample kernel independence test for microbiome community-level association analysis. Biometrics 73.4 (2017): 1453-1463. 

Underline indicates a student under my supervision. 

Book Chapters 

1. Plantinga AM, Wu MC (2021). Beta Diversity and Distance-Based Analysis of Microbiome Data. In: Guha S, Datta S (Ed.) Statistical Analysis of Microbiome Data. Frontiers in Probability and the Statistical Sciences, Springer Nature, Switzerland.

Collaborative Research: Microbiome 

1. Plantinga AM, Kamp KJ, Wu Q, Raftery D, Chen L, Yoo L, Burr RL, Cain KC, Badu S, So SY, Savidge T, Shulman RJ, Heitkemper MM (2023). Exploration of associations among dietary tryptophan, microbiome composition and function, and symptom severity in IBS. Neurogastroenterology & Motility e14545. doi: 10.1111/nmo.14545

2. Matthews SW, Plantinga AM, Kamp K, Binick S, Tolentino E, Savidge T, Wu Q, Cain K, Burr R, Heitkemper MM (2023). Modulation of Gut Microbiota in Irritable Bowel Syndrome: Is Vitamin D Plasma Concentration a Factor? Biological Research for Nursing 0(0). doi:10.1177/10998004221150395

3. Kimmel M, Jin W, Xia K, Lun K, Azcarate-Peril A, Plantinga AM, Wu MC, 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. 

4. Kamp KJ, Plantinga AM, Cain K, Burr R, Barney P, Jarrett M, Luna RA, Savidge T, Shulman RJ, Heitkemper MM (2021). A comprehensive self-management program with diet education does not alter microbiome characteristics in women with irritable bowel syndrome. Biological Research for Nursing 23(3): 471-480. 

5. Fredricks  DN, Plantinga A, Srinivasan  S,  Oot  A,  Wiser  A,  Fiedler  TL,  Proll  S,  Wu  MC, Marrazzo JM (2020).  Vaginal and Extra-vaginal Bacterial Colonization and Risk for Incident Bacterial  Vaginosis  in  a  Population  of  Women  who  Have  Sex  with  Men. The Journal of Infectious Diseases, jiaa233.  

6. Becker S, Chiang E, Plantinga A, Carey H, Suen G, Swoap S (2020).  Effect of stevia on the gut microbiota and glucose tolerance in a murine model of diet-induced obesity. FEMS Microbiology Ecology 96(6):  fiaa079. 

7. Mitchell CM, Srinivasan S, Plantinga A, Wu MC, Reed SD, Guthrie KA, LaCroix AZ, Fiedler T, Munch M, Liu C, Hoffman NG, Blair IA, Newton K, Freeman EW, Joffe H, Cohen L, Fredricks DN (2018).  Associations between improvement in genitourinary symptoms of menopause and the vaginal ecosystem. Menopause 25(5): 500-507. 

8. Golob JL, Pergam SA, Srinivasan S, Liu C, Garcia K, Ko D, Aker S, Marquis S, Loeffelholz T, Plantinga A, Wu MC, Celustka K, Morrison A, Woodfield M, Fredricks DN (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. 

Collaborative Research: Other Application Areas

1. De Veaux R, Plantinga A, Upton E (2022). Are the Handicaps Fair? Age and Participation Effects in the Dipsea Race. Chance 35(4): 40-49.

2. Drineas P, Tsetsos F, Plantinga A, Lazaridis I, Yannaki E, Razou A, Kanaki K, Michalodimitrakis M, Perez-Jimenez F, De Silvestro G, Renda MC, Stamatoyannopoulos JA, Kidd K, Browning B, Paschou P, Stamatoyannopoulos G (2019). Annals of Human Genetics 83(6):  373-388. 

3. Stamatoyannopoulos G, Bose A, Teodosiadis A, Tsetsos F, Plantinga A, Psatha N, Zogas N, Yannaki E, Zalloua P, Kidd KK, Brian BL, Stamatoyannopoulos JA, Paschou P, Drineas P (2017). Genetics of the Peloponnesean Populations and the Theory of Extinction of the Medieval Peloponnesean Greeks. European Journal of Human Genetics 25(5): 637-645. 

4. Browning SR, Grinde K, Plantinga A, Gogarten SM, Stilp AM, Kaplan RC, Avilés-Santa ML, Browning BL, Laurie CC (2016). Local Ancestry Inference in a Large US-Based Hispanic/Latino Study: Hispanic Community Health Study/Study of Latinos (HCHS/SOL). G3: Genes | Genomes | Genetics 6(6): 1525-1534.

5. Schick UM, Jain D, Hodonsky CJ, Morrison JV, Davis JP, Brown L, Sofer T, Conomos MP, Schurmann C, Nelson S, Vadlamudi S, Stilp A, Plantinga A, Baier L, Bien SA, Gogarten S, Laurie C, Taylor KD, Liu Y, Auer PL, Franceschini N, Szpiro A, Rice K, Kerr KF, Rotter JI, Hanson R, Papanicolaou G, Rich SS, Loos RJF, Browning B, Browning S, Weir B, Laurie C, Mohlke K, North KE, Thornton TA, Reiner AP (2016). Genome-wide association study of platelet count identifies ancestry-specific loci in Hispanic/Latino Americans. The American Journal of Human Genetics 98(2): 229-242.