Most-cited papers on Microbiome Analysis Methods

Ranked by citation count via OpenAlex. Citations update on a rolling basis; list regenerates every 24h.

1. Analysis of composition of microbiomes: a novel method for studying microbial composition

   2015 · Microbial Ecology in Health and Disease · Mandal, Siddhartha, Treuren, Will Van, White, Richard et al.

   2,114 cited

2. Microbiome differential abundance methods produce different results across 38 datasets

   2022 · Nature Communications · Nearing, Jacob T., Douglas, Gavin M., Hayes, Molly G. et al.

   901 cited

3. Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies

   2016 · Nature Biotechnology · Gohl, Daryl M., Vangay, Pajau, Garbe, John et al.

   853 cited

4. Optimizing methods and dodging pitfalls in microbiome research

   2017 · Microbiome · Kim, Dorothy, Hofstaedter, Casey E., Zhao, Chunyu et al.

   562 cited

5. Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome

   2012 · PLoS ONE · Yuan, Sanqing, Cohen, Dora Boyd, Ravel, Jacques et al.

   534 cited

6. Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution

   2018 · Frontiers in Microbiology · Ingala, Melissa R., Simmons, Nancy B., Wultsch, Claudia et al.

   511 cited

7. Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies

   2016 · mSystems · Song, Se Jin, Amir, Amnon, Metcalf, Jessica L. et al.

   503 cited

8. Methods for normalizing microbiome data: An ecological perspective

   2018 · Methods in Ecology and Evolution · McKnight, Donald T., Huerlimann, Roger, Bower, Deborah S. et al.

   391 cited

9. High throughput sequencing methods and analysis for microbiome research

   2013 · Journal of Microbiological Methods · Bella, Julia M. Di, Bao, Yige, Gloor, Gregory B. et al.

   321 cited

10. Methods for Improving Human Gut Microbiome Data by Reducing Variability through Sample Processing and Storage of Stool

    2015 · PLoS ONE · Gorzelak, Monika A., Gill, SK, Tasnim, Nishat et al.

    313 cited

11. GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data

    2018 · PeerJ · Chen, Li, Reeve, James, Zhang, L. et al.

    240 cited

12. A broken promise: microbiome differential abundance methods do not control the false discovery rate

    2017 · Briefings in Bioinformatics · Hawinkel, Stijn, Mattiello, Federico, Bijnens, Luc et al.

    234 cited

13. Performing Skin Microbiome Research: A Method to the Madness

    2017 · Journal of Investigative Dermatology · Kong, Heidi H., Andersson, Björn, Clavel, Thomas et al.

    226 cited

14. High-throughput Methods Redefine the Rumen Microbiome and Its Relationship with Nutrition and Metabolism

    2014 · Bioinformatics and Biology Insights · McCann, Joshua C, Wickersham, Tryon A, Loor, Juan J.

    222 cited

15. Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

    2016 · Microbiome · Thorsen, Jonathan, Brejnrod, Asker, Mortensen, Martin Steen et al.

    221 cited

16. A Review and Tutorial of Machine Learning Methods for Microbiome Host Trait Prediction

    2019 · Frontiers in Genetics · Zhou, Yi‐Hui, Gallins, Paul J.

    210 cited

17. Methods in Lung Microbiome Research

    2019 · American Journal of Respiratory Cell and Molecular Biology · Carney, Sharon M., Clemente, José C., Cox, Michael J. et al.

    208 cited

18. Comparison of methods for fecal microbiome biospecimen collection

    2014 · BMC Microbiology · Dominianni, Christine, Wu, Jing, Hayes, Richard B. et al.

    177 cited

19. Multi-Method Characterization of the Human Circulating Microbiome

    2019 · Frontiers in Microbiology · Whittle, E., Leonard, Martin O., Harrison, Rebecca D et al.

    175 cited

20. Comparison of Fecal Collection Methods for Microbiome and Metabolomics Studies

    2018 · Frontiers in Cellular and Infection Microbiology · Wang, Zheng, Zolnik, Christine P., Qiu, Yunping et al.

    169 cited

21. Has the use of molecular methods for the characterization of the human oral microbiome changed our understanding of the role of bacteria in the pathogenesis of periodontal disease?

    2011 · Journal Of Clinical Periodontology · Wade, William G.

    165 cited

22. Comparison of Collection Methods for Fecal Samples in Microbiome Studies

    2016 · American Journal of Epidemiology · Vogtmann, Emily, Chen, Jun, Amir, Amnon et al.

    161 cited

23. Performance of Microbiome Sequence Inference Methods in Environments with Varying Biomass

    2019 · mSystems · Caruso, Vincent, Song, Xubo, Asquith, Mark et al.

    154 cited

24. Optimisation of methods for bacterial skin microbiome investigation: primer selection and comparison of the 454 versus MiSeq platform

    2017 · BMC Microbiology · Castelino, Madhura, Eyre, Stephen, Moat, John et al.

    151 cited

25. Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data

    2020 · Genome biology · Calgaro, Matteo, Romualdi, Chiara, Waldron, Levi et al.

    139 cited

26. The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols

    2017 · Scientific Reports · Lim, Yenkai, Totsika, Makrina, Morrison, Mark et al.

    138 cited

27. Surveying the Microbiome of Ants: Comparing 454 Pyrosequencing with Traditional Methods To Uncover Bacterial Diversity

    2012 · Applied and Environmental Microbiology · Kautz, Stefanie, Rubin, Benjamin E. R., Russell, Jacob A. et al.

    136 cited

28. Machine learning methods for microbiome studies

    2020 · The Journal of Microbiology · Namkung, Junghyun

    122 cited

29. The Urine Microbiome of Healthy Men and Women Differs by Urine Collection Method

    2020 · International Neurourology Journal · Pohl, Hans G., Groah, Suzanne L., Pérez‐Losada, Marcos et al.

    121 cited

30. Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements

    2021 · Microbiome · Tourlousse, Dieter M., Narita, Koji, Miura, Takamasa et al.

    118 cited