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Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

Citations

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Cited by:

  1. Aaron C Ericsson & J Wade Davis & William Spollen & Nathan Bivens & Scott Givan & Catherine E Hagan & Mark McIntosh & Craig L Franklin, 2015. "Effects of Vendor and Genetic Background on the Composition of the Fecal Microbiota of Inbred Mice," PLOS ONE, Public Library of Science, vol. 10(2), pages 1-19, February.
  2. Kurtis Shuler & Samuel Verbanic & Irene A. Chen & Juhee Lee, 2021. "A Bayesian nonparametric analysis for zero‐inflated multivariate count data with application to microbiome study," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 70(4), pages 961-979, August.
  3. Dawid Nosek & Tomasz Mikołajczyk & Agnieszka Cydzik-Kwiatkowska, 2023. "Anode Modification with Fe 2 O 3 Affects the Anode Microbiome and Improves Energy Generation in Microbial Fuel Cells Powered by Wastewater," IJERPH, MDPI, vol. 20(3), pages 1-21, January.
  4. Amanda H Pendegraft & Boyi Guo & Nengjun Yi, 2019. "Bayesian hierarchical negative binomial models for multivariable analyses with applications to human microbiome count data," PLOS ONE, Public Library of Science, vol. 14(8), pages 1-23, August.
  5. Pratheepa Jeganathan & Susan P. Holmes, 2021. "A Statistical Perspective on the Challenges in Molecular Microbial Biology," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 26(2), pages 131-160, June.
  6. Ewa Sajnaga & Marcin Skowronek & Agnieszka Kalwasińska & Waldemar Kazimierczak & Magdalena Lis & Monika Elżbieta Jach & Adrian Wiater, 2022. "Comparative Nanopore Sequencing-Based Evaluation of the Midgut Microbiota of the Summer Chafer ( Amphimallon solstitiale L.) Associated with Possible Resistance to Entomopathogenic Nematodes," IJERPH, MDPI, vol. 19(6), pages 1-16, March.
  7. Tianchen Xu & Ryan T. Demmer & Gen Li, 2021. "Zero‐inflated Poisson factor model with application to microbiome read counts," Biometrics, The International Biometric Society, vol. 77(1), pages 91-101, March.
  8. Duo Jiang & Thomas Sharpton & Yuan Jiang, 2021. "Microbial Interaction Network Estimation via Bias-Corrected Graphical Lasso," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 13(2), pages 329-350, July.
  9. Toby Kenney & Hong Gu & Tianshu Huang, 2021. "Poisson PCA: Poisson measurement error corrected PCA, with application to microbiome data," Biometrics, The International Biometric Society, vol. 77(4), pages 1369-1384, December.
  10. Jianshi Jin & Reiko Yamamoto & Tadashi Takeuchi & Guangwei Cui & Eiji Miyauchi & Nozomi Hojo & Koichi Ikuta & Hiroshi Ohno & Katsuyuki Shiroguchi, 2022. "High-throughput identification and quantification of single bacterial cells in the microbiota," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  11. Lucas Czech & Alexandros Stamatakis, 2019. "Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples," PLOS ONE, Public Library of Science, vol. 14(5), pages 1-50, May.
  12. Zhigang Li & Katherine Lee & Margaret R. Karagas & Juliette C. Madan & Anne G. Hoen & A. James O’Malley & Hongzhe Li, 2018. "Conditional Regression Based on a Multivariate Zero-Inflated Logistic-Normal Model for Microbiome Relative Abundance Data," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 10(3), pages 587-608, December.
  13. Shilan Li & Jianxin Shi & Paul Albert & Hong-Bin Fang, 2022. "Dependence Structure Analysis and Its Application in Human Microbiome," Mathematics, MDPI, vol. 11(1), pages 1-14, December.
  14. Yask Gupta & Anna Lara Ernst & Artem Vorobyev & Foteini Beltsiou & Detlef Zillikens & Katja Bieber & Simone Sanna-Cherchi & Angela M. Christiano & Christian D. Sadik & Ralf J. Ludwig & Tanya Sezin, 2023. "Impact of diet and host genetics on the murine intestinal mycobiome," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  15. Andrea Quagliariello & Alessandra Modi & Gabriel Innocenti & Valentina Zaro & Cecilia Conati Barbaro & Annamaria Ronchitelli & Francesco Boschin & Claudio Cavazzuti & Elena Dellù & Francesca Radina & , 2022. "Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  16. William Bernard Perry & Mathew Seymour & Luisa Orsini & Ifan Bryn Jâms & Nigel Milner & François Edwards & Rachel Harvey & Mark Bruyn & Iliana Bista & Kerry Walsh & Bridget Emmett & Rosetta Blackman &, 2024. "An integrated spatio-temporal view of riverine biodiversity using environmental DNA metabarcoding," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  17. Francesco Spennati & Salvatore La China & Giovanna Siracusa & Simona Di Gregorio & Alessandra Bardi & Valeria Tigini & Gualtiero Mori & David Gabriel & Giulio Munz, 2021. "Tannery Wastewater Recalcitrant Compounds Foster the Selection of Fungi in Non-Sterile Conditions: A Pilot Scale Long-Term Test," IJERPH, MDPI, vol. 18(12), pages 1-18, June.
  18. Georgia Charalampous & Efsevia Fragkou & Konstantinos A. Kormas & Alexandre B. De Menezes & Paraskevi N. Polymenakou & Nikos Pasadakis & Nicolas Kalogerakis & Eleftheria Antoniou & Evangelia Gontikaki, 2021. "Comparison of Hydrocarbon-Degrading Consortia from Surface and Deep Waters of the Eastern Mediterranean Sea: Characterization and Degradation Potential," Energies, MDPI, vol. 14(8), pages 1-18, April.
  19. Zachary D Kurtz & Christian L Müller & Emily R Miraldi & Dan R Littman & Martin J Blaser & Richard A Bonneau, 2015. "Sparse and Compositionally Robust Inference of Microbial Ecological Networks," PLOS Computational Biology, Public Library of Science, vol. 11(5), pages 1-25, May.
  20. Stijn Hawinkel & J C W Rayner & Luc Bijnens & Olivier Thas, 2020. "Sequence count data are poorly fit by the negative binomial distribution," PLOS ONE, Public Library of Science, vol. 15(4), pages 1-16, April.
  21. M. McCauley & T. L. Goulet & C. R. Jackson & S. Loesgen, 2023. "Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  22. Robert H. Lampe & Tyler H. Coale & Kiefer O. Forsch & Loay J. Jabre & Samuel Kekuewa & Erin M. Bertrand & Aleš Horák & Miroslav Oborník & Ariel J. Rabines & Elden Rowland & Hong Zheng & Andreas J. And, 2023. "Short-term acidification promotes diverse iron acquisition and conservation mechanisms in upwelling-associated phytoplankton," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
  23. Cameron Wagg & Aafke van Erk & Erica Fava & Louis-Pierre Comeau & T. Fatima Mitterboeck & Claudia Goyer & Sheng Li & Andrew McKenzie-Gopsill & Aaron Mills, 2021. "Full-Season Cover Crops and Their Traits That Promote Agroecosystem Services," Agriculture, MDPI, vol. 11(9), pages 1-26, August.
  24. Chase C. James & Andrew D. Barton & Lisa Zeigler Allen & Robert H. Lampe & Ariel Rabines & Anne Schulberg & Hong Zheng & Ralf Goericke & Kelly D. Goodwin & Andrew E. Allen, 2022. "Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  25. Anna C. Peterson & Himanshu Sharma & Arvind Kumar & Bruno M. Ghersi & Scott J. Emrich & Kurt J. Vandegrift & Amit Kapoor & Michael J. Blum, 2021. "Rodent Virus Diversity and Differentiation across Post-Katrina New Orleans," Sustainability, MDPI, vol. 13(14), pages 1-18, July.
  26. Chieh Lo & Radu Marculescu, 2017. "MPLasso: Inferring microbial association networks using prior microbial knowledge," PLOS Computational Biology, Public Library of Science, vol. 13(12), pages 1-20, December.
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