Papers

¶ denotes co-first authorship; † denotes corresponding authorship; * denotes mentee 

Journal Papers

1. Koh†, H., Kim*, J., Jang*, H. (2025) MiCML: A causal machine learning cloud platform for the analysis of treatment effects using microbiome profiles. BioData Mining, 18(10), 1-18. 

2. Koh, H. (2024) A general kernel machine regression framework using principal component analysis for jointly testing main and interaction effects: Applications to human microbiome studies. NAR Genomics & Bioinformatics, 6(4), lqae148. 

3. Jang*, H., Koh¶†, H. (2024) A unified web cloud computing platform MiMedSurv for microbiome causal mediation analysis with survival responses. Scientific Reports, 14(20650).

4. Yanai, H., Park, B., Koh, H., Jang*, H., Vaughan, K.L., Tanaka-Yano, M., Aon, M., Blanton, M., Messaoudi, I., Diaz-Ruiz, A., Mattison, J.A., Beerman, I. (2024) Short-term periodic restricted feeding elicits metabolome-microbiome signatures with sex dimorphic persistence in primate intervention. Nature Communications, 15(1088), 1-11. 

5. Kim*, D., Jang*, H., Koh†, H. (2024) MiMultiCat: A unified cloud platform for the analysis of microbiome data with multi-categorical responses. Bioengineering, 11(1), 60. 

6. Koh, H. (2023) Subgroup identification using virtual twins for human microbiome studies. IEEE/ACM Transactions on Computational Biology & Bioinformatics, 20(6), 3800-3808. 

7. Kim*, J., Koh¶†, H. (2023) MiTree: A unified web cloud analytic platform for user-friendly and interpretable microbiome data mining using tree-based methods. Microorganisms, 11(11), 2816. 

8. Jang*, H., Park*, S., Koh¶†, H. (2023) Comprehensive microbiome causal mediation analysis using MiMed on user-friendly web interfaces. Biology Methods & Protocols, 8(1), bpad023. 

9. Park, B., Koh¶, H., Patatanian, M., Reyes-Caballero, H., Zhao, N., Meinert, J., Holbrook, J.T., Leinbach, L.I., Biswal, S. (2023) The mediating roles of the oral microbiome in saliva and subgingival sites between e-cigarette smoking and gingival inflammation. BMC Microbiology, 23(35), 1-18. 

10. Gu*, W., Koh¶†, H., Jang*, H., Lee*, B., Kang, B. (2023) MiSurv: An integrative web cloud platform for user-friendly microbiome data analysis with survival responses. Microbiology Spectrum, 11(3), e05059-22. 

11. Jang*, H., Koh¶†, H., Gu*, W., Kang, B. (2022) Integrative web cloud computing and analytics using MiPair for design-based comparative analysis with paired microbiome data. Scientific Reports, 12(20465), 1-14. 

12. Gu*, W., Moon, J., Chisina*, C., Kang, B., Park, T., Koh†, H. (2022) MiCloud: A unified web platform for comprehensive microbiome data analysis. PLoS One, 17(8), e0272354.

13. Koh†, H., Tuddenham, S., Sears, C.L., Zhao, N. (2021) Meta-analysis methods for multiple related markers: Applications to microbiome studies with the results on multiple α-diversity indices. Statistics in Medicine, 40(12), 2859-76.

14. Nazzal, L., Francois, F., Henderson, N., Liu, M., Li, H., Koh, H., Wang, C., Gao, Z., Perez, G.P., Asplin, J.R., Goldfarb, D.S., Blaser, M.J. (2021) Effect of antibiotic treatment on Oxalobacter formigenes colonization of the gut microbiome and urinary oxalate excretion. Scientific Reports, 11(16428), 1-11.

15. Wilson, N., Zhao, N., Zhan, X., Koh, H., Fu, W., Chen, J., Li, H., Wu, M.C., Plantinga, A.M. (2021) MiRKAT: Kernel machine regression-based global association tests for the microbiome. Bioinformatics, 37(11), 1595-97. 

16. Zhao, N., Khamash, D., Koh, H., Voskertchian, A., Egbert, E., Mongodin, E.F., White, J., Hittle, L., Colantouni, E., Milstone, A.M. (2021) Low diversity in nasal microbiome associated with Staphylococcus aureus colonization and bloodstream infections in hospitalized neonates. Open Forum Infectious Diseases, 8(10), 1-9.

17. Koh, H., Zhao, N. (2020) A powerful microbial group association test based on the higher criticism analysis for sparse microbial association signals. Microbiome, 8(63), 1-16.

18. Koh, H., Li, Y., Zhan, X., Chen, J., Zhao, N. (2019) A distance-based kernel association test based on the generalized linear mixed model for correlated microbiome studies. Frontiers in Genetics, 458(10), 1-14. 

19. Koh, H. (2018) An adaptive microbiome α-diversity-based association analysis method. Scientific Reports, 8(18026), 1-12.

20. Hu, J., Koh, H., He, L., Liu, M., Blaser, M.J., Li, H. (2018) A two-stage microbial association mapping framework with advanced FDR control. Microbiome, 6(131), 1-15.

21. Koh, H., Livanos, A.E., Blaser, M.J., Li, H. (2018) A highly adaptive microbiome-based association test for survival traits. BMC Genomics, 19(210), 1-14.

22. Zhang, X., Li, J., Krautkramer, K., Badri, M., Battaglia, T., Borbet, T.C., Koh, H., Ng, S., Sibley, R.A., Li, Y., Pathmasiri, W., Jindal, S., Shields-Cutler, R.R., Hillmann, B., Al-Ghalith, G.A., Ruiz, V.E., Livanos, A., Wout, A., Nagalingam, N., Rogers, A.B., Sumner, S.J., Knights, D., Denu, J.M., Li, H., Ruggles, K.V., Bonneau, R., Williams, A.R., Rauch, M., Blaser, M.J. (2018) Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity. eLife, 7(e37816), 1-37.

23. Derk, J., Hernandez, K.B., Rodriguez, M., He, M., Koh, H., Abedini, A., Li, H., Fenyö, D., Schmidt, A.M. (2018) Diaphanous 1 (DIAPH1) is highly expressed in the aged human medial temporal cortex and upregulated in myeloid cells during alzheimer’s disease. Journal of Alzheimer’s Disease, 64 (3), 995-1007. 

24. Abedini, A., Cao, P., Plesner, A., Zhang, J., He, M., Derk, J., Patil, S.A., Rosario, R., Lonier, J., Song, F., Koh, H., Li, H., Raleigh, D.P., Schmidt, A.M. (2018) RAGE binds preamyloid IAPP intermediates and mediates pancreatic β cell proteotoxicity. Journal of Clinical Investigation, 128(2), 682-98.

25. Koh, H., Blaser, M.J., Li, H. (2017) A powerful microbiome-based association test and a microbial taxa discovery framework for comprehensive association mapping. Microbiome, 5(45), 1-15. 

26. Inman, C.K., Junaibi, A.A., Koh, H., Abdulle, A., Ali, R., Alnaeemi, A., Zaabi, E.A., Oumeziane, N., Bastaki, M.A., Al-Houqani, M., Al-Maskari, F., Dhaheri, A.A., Shah, S.M., Wareth, L.A., Mahmeed, W.A., Alsafar, H., Anouti, F.A., Hosani, A.A., Haji, M., Galani, D., O’Connor, M.J., Ahn, J., Kirchhoff, T., Sherman, S., Hayes, R.B., Li, H., Ramasamy, R., Schmidt, A.M. (2017) The AGE-RAGE axis in an Arab population: Results from the United Arab Emirates Healthy Futures (UAEHFS) pilot study. Journal of Clinical & Translational Endocrinology, 10, 1-8. 

27. Liu, M., Koh, H., Kurtz, Z., Battaglia, T., PeBenito, A., Li, H., Nazzal, L., Blaser, M.J. (2017) Oxalobacter formigenes-associated host features and microbial community structures examined using the American Gut Project. Microbiome, 5(108), 1-17. 

28. Yassine, H.N., Jackson, A.M., Borges, C.R., Billheimer, D., Koh, H., Smith, D., Reaven, P., Lau, S.S., Borchers, C.H. (2014) The application of multiple reaction monitoring and multi-analyte profiling to HDL proteins. Lipids in Health & Disease, 13(8), 1-11. 

Proceedings/Newsletters

1. Wang, X., Verma, S., Qin, Y., Sterling, J., Zhou, A., Zhang, J., Martinez, C., Casebeer, N., Koh, H., Winstein, C., Liu, B. (2013) Imaging informatics-based multimedia ePR system for data management and decision support in rehabilitation research. Proceedings of SPIE, 8674, Medical Imaging  2013: Advanced PACS-based Imaging Informatics and Therapeutic Applications; https://doi.org/10.1117/12.2008585 (Paper)

2. Koh, H., Sadigov, S. (2010) Analyzing repeated measures data. Cornell Statistical Consulting Unit (CSCU) StatNews, 77. (Newsletter)