Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples
Author
Abstract
Suggested Citation
DOI: 10.1371/journal.pcbi.1000352
Download full text from publisher
References listed on IDEAS
- Peter J. Turnbaugh & Ruth E. Ley & Michael A. Mahowald & Vincent Magrini & Elaine R. Mardis & Jeffrey I. Gordon, 2006. "An obesity-associated gut microbiome with increased capacity for energy harvest," Nature, Nature, vol. 444(7122), pages 1027-1031, December.
Citations
Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
Cited by:
- Hongjian Wei & Yongqi Wang & Juming Zhang & Liangfa Ge & Tianzeng Liu, 2022. "Changes in Soil Bacterial Community Structure in Bermudagrass Turf under Short-Term Traffic Stress," Agriculture, MDPI, vol. 12(5), pages 1-18, May.
- Zhenqiu Liu & Dechang Chen & Li Sheng & Amy Y Liu, 2013. "Class Prediction and Feature Selection with Linear Optimization for Metagenomic Count Data," PLOS ONE, Public Library of Science, vol. 8(3), pages 1-7, March.
- Yuan Ge & Joshua P Schimel & Patricia A Holden, 2014. "Analysis of Run-to-Run Variation of Bar-Coded Pyrosequencing for Evaluating Bacterial Community Shifts and Individual Taxa Dynamics," PLOS ONE, Public Library of Science, vol. 9(6), pages 1-6, June.
- Zheng Sun & Jiang Liu & Meng Zhang & Tong Wang & Shi Huang & Scott T. Weiss & Yang-Yu Liu, 2023. "Removal of false positives in metagenomics-based taxonomy profiling via targeting Type IIB restriction sites," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
- Pengfei Song & Wen Qin & YanGan Huang & Lei Wang & Zhenyuan Cai & Tongzuo Zhang, 2020. "Grazing Management Influences Gut Microbial Diversity of Livestock in the Same Area," Sustainability, MDPI, vol. 12(10), pages 1-12, May.
- Patricio S La Rosa & Berkley Shands & Elena Deych & Yanjiao Zhou & Erica Sodergren & George Weinstock & William D Shannon, 2012. "Statistical Object Data Analysis of Taxonomic Trees from Human Microbiome Data," PLOS ONE, Public Library of Science, vol. 7(11), pages 1-12, November.
- Edoardo Pasolli & Duy Tin Truong & Faizan Malik & Levi Waldron & Nicola Segata, 2016. "Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights," PLOS Computational Biology, Public Library of Science, vol. 12(7), pages 1-26, July.
- Gregor Gorkiewicz & Gerhard G Thallinger & Slave Trajanoski & Stefan Lackner & Gernot Stocker & Thomas Hinterleitner & Christian Gülly & Christoph Högenauer, 2013. "Alterations in the Colonic Microbiota in Response to Osmotic Diarrhea," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-17, February.
- 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.
- Kai Qiu & Huiyi Cai & Xin Wang & Guohua Liu, 2023. "Effects of Peroral Microbiota Transplantation on the Establishment of Intestinal Microorganisms in a Newly-Hatched Chick Model," Agriculture, MDPI, vol. 13(5), pages 1-13, April.
- Gabriele Bellotti & Eren Taskin & Simone Sello & Cristina Sudiro & Rossella Bortolaso & Francesca Bandini & Maria Chiara Guerrieri & Pier Sandro Cocconcelli & Francesco Vuolo & Edoardo Puglisi, 2022. "LABs Fermentation Side-Product Positively Influences Rhizosphere and Plant Growth in Greenhouse Lettuce and Tomatoes," Land, MDPI, vol. 11(9), pages 1-15, September.
- Amirhossein Shamsaddini & Kimia Dadkhah & Patrick M Gillevet, 2020. "BiomMiner: An advanced exploratory microbiome analysis and visualization pipeline," PLOS ONE, Public Library of Science, vol. 15(6), pages 1-13, June.
- Tsapekos, Panagiotis & Khoshnevisan, Benyamin & Zhu, Xinyu & Treu, Laura & Alfaro, Natalia & Kougias, Panagiotis G. & Angelidaki, Irini, 2022. "Lab- and pilot-scale anaerobic digestion of municipal bio-waste and potential of digestate for biogas upgrading sustained by microbial analysis," Renewable Energy, Elsevier, vol. 201(P1), pages 344-353.
- Yong Li & Jiejie Zhang & Jianqiang Zhang & Wenlai Xu & Zishen Mou, 2019. "Microbial Community Structure in the Sediments and Its Relation to Environmental Factors in Eutrophicated Sancha Lake," IJERPH, MDPI, vol. 16(11), pages 1-15, May.
- Paul J McMurdie & Susan Holmes, 2014. "Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible," PLOS Computational Biology, Public Library of Science, vol. 10(4), pages 1-12, April.
- Bin Wang, 2020. "A Zipf-plot based normalization method for high-throughput RNA-seq data," PLOS ONE, Public Library of Science, vol. 15(4), pages 1-15, April.
- Allison G. White & George S. Watts & Zhenqiang Lu & Maria M. Meza-Montenegro & Eric A. Lutz & Philip Harber & Jefferey L. Burgess, 2014. "Environmental Arsenic Exposure and Microbiota in Induced Sputum," IJERPH, MDPI, vol. 11(2), pages 1-15, February.
- Wu, Peijie & Chen, Tianyi & Diew Wong, Yiik & Meng, Xianghai & Wang, Xueqin & Liu, Wei, 2023. "Exploring key spatio-temporal features of crash risk hot spots on urban road network: A machine learning approach," Transportation Research Part A: Policy and Practice, Elsevier, vol. 173(C).
- Monica Vera-Lise Tulstrup & Ellen Gerd Christensen & Vera Carvalho & Caroline Linninge & Siv Ahrné & Ole Højberg & Tine Rask Licht & Martin Iain Bahl, 2015. "Antibiotic Treatment Affects Intestinal Permeability and Gut Microbial Composition in Wistar Rats Dependent on Antibiotic Class," PLOS ONE, Public Library of Science, vol. 10(12), pages 1-17, December.
- Qi Xu & Xiaoya Yuan & Tiantian Gu & Yang Li & Wangcheng Dai & Xiaokun Shen & Yadong Song & Yang Zhang & Wenming Zhao & Guobin Chang & Guohong Chen, 2017. "Comparative characterization of bacterial communities in geese fed all-grass or high-grain diets," PLOS ONE, Public Library of Science, vol. 12(10), pages 1-14, October.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Kiran Konain & Sadia & Turfa Nadeem & Adeed Khan & Warda Iqbal & Arsalan & Amir Javed & Ruby Khan & Kainat Jamil & Kainat Jamil, 2018. "Importance of Probiotics in Gastrointestinal Tract," Journal of Asian Scientific Research, Asian Economic and Social Society, vol. 8(3), pages 128-143, March.
- Marjolein Heddes & Baraa Altaha & Yunhui Niu & Sandra Reitmeier & Karin Kleigrewe & Dirk Haller & Silke Kiessling, 2022. "The intestinal clock drives the microbiome to maintain gastrointestinal homeostasis," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
- Cristiane R. S. Câmara & Carlos A. Urrea & Vicki Schlegel, 2013. "Pinto Beans ( Phaseolus vulgaris L.) as a Functional Food: Implications on Human Health," Agriculture, MDPI, vol. 3(1), pages 1-22, February.
- Vinod Nikhra, 2019. "The Novel Dimensions of Cardio-Metabolic Health Gut Microbiota, Dysbiosis and its Fallouts," Current Research in Diabetes & Obesity Journal, Juniper Publishers Inc., vol. 11(1), pages 28-37, June.
- Shinji Fukuda & Yumiko Nakanishi & Eisuke Chikayama & Hiroshi Ohno & Tsuneo Hino & Jun Kikuchi, 2009. "Evaluation and Characterization of Bacterial Metabolic Dynamics with a Novel Profiling Technique, Real-Time Metabolotyping," PLOS ONE, Public Library of Science, vol. 4(3), pages 1-10, March.
- Michael DiMarzio & Brigida Rusconi & Neela H Yennawar & Mark Eppinger & Andrew D Patterson & Edward G Dudley, 2017. "Identification of a mouse Lactobacillus johnsonii strain with deconjugase activity against the FXR antagonist T-β-MCA," PLOS ONE, Public Library of Science, vol. 12(9), pages 1-15, September.
- Tamar Ringel-Kulka & Jing Cheng & Yehuda Ringel & Jarkko Salojärvi & Ian Carroll & Airi Palva & Willem M de Vos & Reetta Satokari, 2013. "Intestinal Microbiota in Healthy U.S. Young Children and Adults—A High Throughput Microarray Analysis," PLOS ONE, Public Library of Science, vol. 8(5), pages 1-10, May.
- Hannah Lees & Jonathan Swann & Simon M Poucher & Jeremy K Nicholson & Elaine Holmes & Ian D Wilson & Julian R Marchesi, 2014. "Age and Microenvironment Outweigh Genetic Influence on the Zucker Rat Microbiome," PLOS ONE, Public Library of Science, vol. 9(9), pages 1-11, September.
- Barbara Emmenegger & Julien Massoni & Christine M. Pestalozzi & Miriam Bortfeld-Miller & Benjamin A. Maier & Julia A. Vorholt, 2023. "Identifying microbiota community patterns important for plant protection using synthetic communities and machine learning," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
- Liat Shenhav & Ori Furman & Leah Briscoe & Mike Thompson & Justin D Silverman & Itzhak Mizrahi & Eran Halperin, 2019. "Modeling the temporal dynamics of the gut microbial community in adults and infants," PLOS Computational Biology, Public Library of Science, vol. 15(6), pages 1-21, June.
- Yunjia Lai & Chih-Wei Liu & Yifei Yang & Yun-Chung Hsiao & Hongyu Ru & Kun Lu, 2021. "High-coverage metabolomics uncovers microbiota-driven biochemical landscape of interorgan transport and gut-brain communication in mice," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
- Ankita Das & Sandeep Das & Nandita Das & Prisha Pandey & Birson Ingti & Vladimir Panchenko & Vadim Bolshev & Andrey Kovalev & Piyush Pandey, 2023. "Advancements and Innovations in Harnessing Microbial Processes for Enhanced Biogas Production from Waste Materials," Agriculture, MDPI, vol. 13(9), pages 1-34, August.
- Amirhossein Shamsaddini & Kimia Dadkhah & Patrick M Gillevet, 2020. "BiomMiner: An advanced exploratory microbiome analysis and visualization pipeline," PLOS ONE, Public Library of Science, vol. 15(6), pages 1-13, June.
- Lukas Schwingshackl & Georg Hoffmann & Carolina Schwedhelm & Tamara Kalle-Uhlmann & Benjamin Missbach & Sven Knüppel & Heiner Boeing, 2016. "Consumption of Dairy Products in Relation to Changes in Anthropometric Variables in Adult Populations: A Systematic Review and Meta-Analysis of Cohort Studies," PLOS ONE, Public Library of Science, vol. 11(6), pages 1-15, June.
- Kotaro Soeda & Takayoshi Sasako & Kenichiro Enooku & Naoto Kubota & Naoki Kobayashi & Yoshiko Matsumoto Ikushima & Motoharu Awazawa & Ryotaro Bouchi & Gotaro Toda & Tomoharu Yamada & Takuma Nakatsuka , 2023. "Gut insulin action protects from hepatocarcinogenesis in diabetic mice comorbid with nonalcoholic steatohepatitis," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
- Xiuying Zhang & Dongqian Shen & Zhiwei Fang & Zhuye Jie & Xinmin Qiu & Chunfang Zhang & Yingli Chen & Linong Ji, 2013. "Human Gut Microbiota Changes Reveal the Progression of Glucose Intolerance," PLOS ONE, Public Library of Science, vol. 8(8), pages 1-11, August.
- Alessandra N. Bazzano & Kaitlin S. Potts & Lydia A. Bazzano & John B. Mason, 2017. "The Life Course Implications of Ready to Use Therapeutic Food for Children in Low-Income Countries," IJERPH, MDPI, vol. 14(4), pages 1-19, April.
- Eryun Zhang & Lihua Jin & Yangmeng Wang & Jui Tu & Ruirong Zheng & Lili Ding & Zhipeng Fang & Mingjie Fan & Ismail Al-Abdullah & Rama Natarajan & Ke Ma & Zhengtao Wang & Arthur D. Riggs & Sarah C. Shu, 2022. "Intestinal AMPK modulation of microbiota mediates crosstalk with brown fat to control thermogenesis," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
- Mile Volarić & Dunja Šojat & Ljiljana Trtica Majnarić & Domagoj Vučić, 2024. "The Association between Functional Dyspepsia and Metabolic Syndrome—The State of the Art," IJERPH, MDPI, vol. 21(2), pages 1-19, February.
- Jonathan B. Lynch & Erika L. Gonzalez & Kayli Choy & Kym F. Faull & Talia Jewell & Abelardo Arellano & Jennifer Liang & Kristie B. Yu & Jorge Paramo & Elaine Y. Hsiao, 2023. "Gut microbiota Turicibacter strains differentially modify bile acids and host lipids," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pcbi00:1000352. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: ploscompbiol (email available below). General contact details of provider: https://journals.plos.org/ploscompbiol/ .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.