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Sparse and Compositionally Robust Inference of Microbial Ecological Networks

Citations

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Cited by:

  1. Runtan Cheng & Lu Wang & Shenglong Le & Yifan Yang & Can Zhao & Xiangqi Zhang & Xin Yang & Ting Xu & Leiting Xu & Petri Wiklund & Jun Ge & Dajiang Lu & Chenhong Zhang & Luonan Chen & Sulin Cheng, 2022. "A randomized controlled trial for response of microbiome network to exercise and diet intervention in patients with nonalcoholic fatty liver disease," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  2. Yu Shang & Johannes Sikorski & Michael Bonkowski & Anna-Maria Fiore-Donno & Ellen Kandeler & Sven Marhan & Runa S Boeddinghaus & Emily F Solly & Marion Schrumpf & Ingo Schöning & Tesfaye Wubet & Franc, 2017. "Inferring interactions in complex microbial communities from nucleotide sequence data and environmental parameters," PLOS ONE, Public Library of Science, vol. 12(3), pages 1-24, March.
  3. Huang Lin & Merete Eggesbø & Shyamal Das Peddada, 2022. "Linear and nonlinear correlation estimators unveil undescribed taxa interactions in microbiome data," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  4. 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.
  5. Lishi Deng & Steff Taelman & Matthew R. Olm & Laeticia Celine Toe & Eva Balini & Lionel Olivier Ouédraogo & Yuri Bastos-Moreira & Alemayehu Argaw & Kokeb Tesfamariam & Erica D. Sonnenburg & Giles T. H, 2025. "Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
  6. Maria Rita Perrone & Salvatore Romano & Giuseppe De Maria & Paolo Tundo & Anna Rita Bruno & Luigi Tagliaferro & Michele Maffia & Mattia Fragola, 2022. "Compositional Data Analysis of 16S rRNA Gene Sequencing Results from Hospital Airborne Microbiome Samples," IJERPH, MDPI, vol. 19(16), pages 1-21, August.
  7. Oliver Aasmets & Kertu Liis Krigul & Kreete Lüll & Andres Metspalu & Elin Org, 2022. "Gut metagenome associations with extensive digital health data in a volunteer-based Estonian microbiome cohort," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
  8. Lingjing Jiang & Niina Haiminen & Anna‐Paola Carrieri & Shi Huang & Yoshiki Vázquez‐Baeza & Laxmi Parida & Ho‐Cheol Kim & Austin D. Swafford & Rob Knight & Loki Natarajan, 2022. "Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data," Biometrics, The International Biometric Society, vol. 78(3), pages 1155-1167, September.
  9. Qin Liu & Qi Su & Fen Zhang & Hein M. Tun & Joyce Wing Yan Mak & Grace Chung-Yan Lui & Susanna So Shan Ng & Jessica Y. L. Ching & Amy Li & Wenqi Lu & Chenyu Liu & Chun Pan Cheung & David S. C. Hui & P, 2022. "Multi-kingdom gut microbiota analyses define COVID-19 severity and post-acute COVID-19 syndrome," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
  10. Kim, Kipoong & Park, Jaesung & Jung, Sungkyu, 2024. "Principal component analysis for zero-inflated compositional data," Computational Statistics & Data Analysis, Elsevier, vol. 198(C).
  11. Courtney M. Thomas & Elie Desmond-Le Quéméner & Simonetta Gribaldo & Guillaume Borrel, 2022. "Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  12. Juan José Egozcue & Vera Pawlowsky-Glahn, 2019. "Compositional data: the sample space and its structure," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 28(3), pages 599-638, September.
  13. Ines Wilms & Jacob Bien, 2021. "Tree-based Node Aggregation in Sparse Graphical Models," Papers 2101.12503, arXiv.org.
  14. Susheel Bhanu Busi & Massimo Bourquin & Stilianos Fodelianakis & Grégoire Michoud & Tyler J. Kohler & Hannes Peter & Paraskevi Pramateftaki & Michail Styllas & Matteo Tolosano & Vincent Staercke & Mar, 2022. "Genomic and metabolic adaptations of biofilms to ecological windows of opportunity in glacier-fed streams," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  15. Jing Ma, 2021. "Joint Microbial and Metabolomic Network Estimation with the Censored Gaussian Graphical Model," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 13(2), pages 351-372, July.
  16. McGillivray, Annaliza & Khalili, Abbas & Stephens, David A., 2020. "Estimating sparse networks with hubs," Journal of Multivariate Analysis, Elsevier, vol. 179(C).
  17. Brandon Kieft & Niko Finke & Ryan J. McLaughlin & Aditi N. Nallan & Martin Krzywinski & Sean A. Crowe & Steven J. Hallam, 2023. "Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  18. Emma Schwager & Himel Mallick & Steffen Ventz & Curtis Huttenhower, 2017. "A Bayesian method for detecting pairwise associations in compositional data," PLOS Computational Biology, Public Library of Science, vol. 13(11), pages 1-21, November.
  19. 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.
  20. 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.
  21. Sara Del Duca & Stefano Mocali & Francesco Vitali & Arturo Fabiani & Maria Alexandra Cucu & Giuseppe Valboa & Giada d’Errico & Francesco Binazzi & Paolo Storchi & Rita Perria & Silvia Landi, 2024. "Impacts of Soil Management and Sustainable Plant Protection Strategies on Soil Biodiversity in a Sangiovese Vineyard," Land, MDPI, vol. 13(5), pages 1-20, April.
  22. Ana Popovic & Celine Bourdon & Pauline W. Wang & David S. Guttman & Sajid Soofi & Zulfiqar A. Bhutta & Robert H. J. Bandsma & John Parkinson & Lisa G. Pell, 2021. "Micronutrient supplements can promote disruptive protozoan and fungal communities in the developing infant gut," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
  23. Tyler A Joseph & Liat Shenhav & Joao B Xavier & Eran Halperin & Itsik Pe’er, 2020. "Compositional Lotka-Volterra describes microbial dynamics in the simplex," PLOS Computational Biology, Public Library of Science, vol. 16(5), pages 1-22, May.
  24. Mendler, Isabella-Hilda & Drossel, Barbara & Hütt, Marc-Thorsten, 2024. "Microbiome abundance patterns as attractors and the implications for the inference of microbial interaction networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 639(C).
  25. Rieser, Christopher & Filzmoser, Peter, 2023. "Extending compositional data analysis from a graph signal processing perspective," Journal of Multivariate Analysis, Elsevier, vol. 198(C).
  26. Jiarui Lu & Pixu Shi & Hongzhe Li, 2019. "Generalized linear models with linear constraints for microbiome compositional data," Biometrics, The International Biometric Society, vol. 75(1), pages 235-244, March.
  27. Dina in ‘t Zandt & Zuzana Kolaříková & Tomáš Cajthaml & Zuzana Münzbergová, 2023. "Plant community stability is associated with a decoupling of prokaryote and fungal soil networks," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  28. Li, Huimin & Wang, Jinru, 2024. "Sparse basis covariance matrix estimation for high dimensional compositional data via hard thresholding," Statistics & Probability Letters, Elsevier, vol. 209(C).
  29. John Matta & Virender Singh & Trevor Auten & Prashant Sanjel, 2023. "Inferred networks, machine learning, and health data," PLOS ONE, Public Library of Science, vol. 18(1), pages 1-20, January.
  30. Xi Peng & Shang Wang & Miaoxiao Wang & Kai Feng & Qing He & Xingsheng Yang & Weiguo Hou & Fangru Li & Yuxiang Zhao & Baolan Hu & Xiao Zou & Ye Deng, 2024. "Metabolic interdependencies in thermophilic communities are revealed using co-occurrence and complementarity networks," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  31. Liang, Wanfeng & Wu, Yue & Ma, Xiaoyan, 2022. "Robust sparse precision matrix estimation for high-dimensional compositional data," Statistics & Probability Letters, Elsevier, vol. 184(C).
  32. Li, Lianwei & Li, Wendy & Zou, Quan & Ma, Zhanshan (Sam), 2020. "Network analysis of the hot spring microbiome sketches out possible niche differentiations among ecological guilds," Ecological Modelling, Elsevier, vol. 431(C).
  33. Mia Riddley & Shannon Hepp & FNU Hardeep & Aruj Nayak & Meimei Liu & Xin Xing & Hailong Zhang & Jingqiu Liao, 2025. "Differential roles of deterministic and stochastic processes in structuring soil bacterial ecotypes across terrestrial ecosystems," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
  34. Koplin, Eric & Forzani, Liliana & Tomassi, Diego & Pfeiffer, Ruth M., 2024. "Sufficient dimension reduction for a novel class of zero-inflated graphical models," Computational Statistics & Data Analysis, Elsevier, vol. 196(C).
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