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The Human Microbiome Project

Citations

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Cited by:

  1. Li, Jie & Shen, Xuzhu & Li, YaoTang, 2021. "Modeling the temporal dynamics of gut microbiota from a local community perspective," Ecological Modelling, Elsevier, vol. 460(C).
  2. 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.
  3. Charles K Fisher & Thierry Mora & Aleksandra M Walczak, 2017. "Variable habitat conditions drive species covariation in the human microbiota," PLOS Computational Biology, Public Library of Science, vol. 13(4), pages 1-18, April.
  4. Kyle Ellrott & Lukasz Jaroszewski & Weizhong Li & John C Wooley & Adam Godzik, 2010. "Expansion of the Protein Repertoire in Newly Explored Environments: Human Gut Microbiome Specific Protein Families," PLOS Computational Biology, Public Library of Science, vol. 6(6), pages 1-11, June.
  5. 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.
  6. Yee Sang Wong & Nicholas John Osborne, 2022. "Biodiversity Effects on Human Mental Health via Microbiota Alterations," IJERPH, MDPI, vol. 19(19), pages 1-13, September.
  7. Xinhui Wang & Marinus J C Eijkemans & Jacco Wallinga & Giske Biesbroek & Krzysztof Trzciński & Elisabeth A M Sanders & Debby Bogaert, 2012. "Multivariate Approach for Studying Interactions between Environmental Variables and Microbial Communities," PLOS ONE, Public Library of Science, vol. 7(11), pages 1-7, November.
  8. Weiyue Ji & Handuo Shi & Haoqian Zhang & Rui Sun & Jingyi Xi & Dingqiao Wen & Jingchen Feng & Yiwei Chen & Xiao Qin & Yanrong Ma & Wenhan Luo & Linna Deng & Hanchi Lin & Ruofan Yu & Qi Ouyang, 2013. "A Formalized Design Process for Bacterial Consortia That Perform Logic Computing," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-9, February.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. Margaret Coleman & Christopher Elkins & Bradford Gutting & Emmanuel Mongodin & Gloria Solano‐Aguilar & Isabel Walls, 2018. "Microbiota and Dose Response: Evolving Paradigm of Health Triangle," Risk Analysis, John Wiley & Sons, vol. 38(10), pages 2013-2028, October.
  14. Eman M Fouda, 2017. "Airway Microbiota and Allergic Diseases: Clinical Implications," International Journal of Pulmonary & Respiratory Sciences, Juniper Publishers Inc., vol. 1(5), pages 1-5, May.
  15. Lena Takayasu & Wataru Suda & Eiichiro Watanabe & Shinji Fukuda & Kageyasu Takanashi & Hiroshi Ohno & Misako Takayasu & Hideki Takayasu & Masahira Hattori, 2017. "A 3-dimensional mathematical model of microbial proliferation that generates the characteristic cumulative relative abundance distributions in gut microbiomes," PLOS ONE, Public Library of Science, vol. 12(8), pages 1-20, August.
  16. Disha Tandon & Mohammed Monzoorul Haque & Sharmila S Mande, 2016. "Inferring Intra-Community Microbial Interaction Patterns from Metagenomic Datasets Using Associative Rule Mining Techniques," PLOS ONE, Public Library of Science, vol. 11(4), pages 1-16, April.
  17. 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.
  18. Matthew D. Koslovsky, 2023. "A Bayesian zero‐inflated Dirichlet‐multinomial regression model for multivariate compositional count data," Biometrics, The International Biometric Society, vol. 79(4), pages 3239-3251, December.
  19. Daphna Rothschild & Erez Dekel & Jean Hausser & Anat Bren & Guy Aidelberg & Pablo Szekely & Uri Alon, 2014. "Linear Superposition and Prediction of Bacterial Promoter Activity Dynamics in Complex Conditions," PLOS Computational Biology, Public Library of Science, vol. 10(5), pages 1-9, May.
  20. Victor P Andreev & Gang Liu & Jarcy Zee & Lisa Henn & Gilberto E Flores & Robert M Merion, 2019. "Clustering of the structures by using “snakes-&-dragons” approach, or correlation matrix as a signal," PLOS ONE, Public Library of Science, vol. 14(10), pages 1-27, October.
  21. Pasquale Comberiati & Maria Di Cicco & Francesco Paravati & Umberto Pelosi & Alessandro Di Gangi & Stefania Arasi & Simona Barni & Davide Caimmi & Carla Mastrorilli & Amelia Licari & Fernanda Chiera, 2021. "The Role of Gut and Lung Microbiota in Susceptibility to Tuberculosis," IJERPH, MDPI, vol. 18(22), pages 1-20, November.
  22. Jake M. Robinson & Jacob G. Mills & Martin F. Breed, 2018. "Walking Ecosystems in Microbiome-Inspired Green Infrastructure: An Ecological Perspective on Enhancing Personal and Planetary Health," Challenges, MDPI, vol. 9(2), pages 1-15, November.
  23. Ruiz-Moreno, Héctor Alejandro & López-Tamayo, Ana María & Caro-Quintero, Alejandro & Husserl, Johana & González Barrios, Andrés Fernando, 2019. "Metagenome level metabolic network reconstruction analysis reveals the microbiome in the Bogotá River is functionally close to the microbiome in produced water," Ecological Modelling, Elsevier, vol. 399(C), pages 1-12.
  24. Eric Z. Chen & Frederic D. Bushman & Hongzhe Li, 2017. "A Model-Based Approach for Species Abundance Quantification Based on Shotgun Metagenomic Data," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 9(1), pages 13-27, June.
  25. Bahareh Mansoorian & Emilie Combet & Areej Alkhaldy & Ada L. Garcia & Christine Ann Edwards, 2019. "Impact of Fermentable Fibres on the Colonic Microbiota Metabolism of Dietary Polyphenols Rutin and Quercetin," IJERPH, MDPI, vol. 16(2), pages 1-12, January.
  26. Filippo Grazioli & Raman Siarheyeu & Israa Alqassem & Andreas Henschel & Giampaolo Pileggi & Andrea Meiser, 2022. "Microbiome-based disease prediction with multimodal variational information bottlenecks," PLOS Computational Biology, Public Library of Science, vol. 18(4), pages 1-27, April.
  27. Liangliang Zhang & Yushu Shi & Robert R. Jenq & Kim‐Anh Do & Christine B. Peterson, 2021. "Bayesian compositional regression with structured priors for microbiome feature selection," Biometrics, The International Biometric Society, vol. 77(3), pages 824-838, September.
  28. 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.
  29. Ran Li & Yongming Wang & Han Hu & Yan Tan & Yingfei Ma, 2022. "Metagenomic analysis reveals unexplored diversity of archaeal virome in the human gut," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  30. Jae-Chang Cho, 2021. "Human microbiome privacy risks associated with summary statistics," PLOS ONE, Public Library of Science, vol. 16(4), pages 1-11, April.
  31. Sean M Gibbons & Sean M Kearney & Chris S Smillie & Eric J Alm, 2017. "Two dynamic regimes in the human gut microbiome," PLOS Computational Biology, Public Library of Science, vol. 13(2), pages 1-20, February.
  32. Lucía Guadamuro & M. Andrea Azcárate-Peril & Rafael Tojo & Baltasar Mayo & Susana Delgado, 2021. "Impact of Dietary Isoflavone Supplementation on the Fecal Microbiota and Its Metabolites in Postmenopausal Women," IJERPH, MDPI, vol. 18(15), pages 1-11, July.
  33. Lilis Yuaningsih & R. Adjeng Mariana Febrianti & Hafiz Waqas Kamran, 2020. "Reducing CO2 Emissions through Biogas, Wind and Solar Energy Production: Evidence from Indonesia," International Journal of Energy Economics and Policy, Econjournals, vol. 10(6), pages 684-689.
  34. McGillivray, Annaliza & Khalili, Abbas & Stephens, David A., 2020. "Estimating sparse networks with hubs," Journal of Multivariate Analysis, Elsevier, vol. 179(C).
  35. Sarah L Hagerty & Kent E Hutchison & Christopher A Lowry & Angela D Bryan, 2020. "An empirically derived method for measuring human gut microbiome alpha diversity: Demonstrated utility in predicting health-related outcomes among a human clinical sample," PLOS ONE, Public Library of Science, vol. 15(3), pages 1-21, March.
  36. Patricio S La Rosa & J Paul Brooks & Elena Deych & Edward L Boone & David J Edwards & Qin Wang & Erica Sodergren & George Weinstock & William D Shannon, 2012. "Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data," PLOS ONE, Public Library of Science, vol. 7(12), pages 1-13, December.
  37. Charles K Fisher & Pankaj Mehta, 2014. "Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression," PLOS ONE, Public Library of Science, vol. 9(7), pages 1-10, July.
  38. Kumar P Mainali & Sharon Bewick & Peter Thielen & Thomas Mehoke & Florian P Breitwieser & Shishir Paudel & Arjun Adhikari & Joshua Wolfe & Eric V Slud & David Karig & William F Fagan, 2017. "Statistical analysis of co-occurrence patterns in microbial presence-absence datasets," PLOS ONE, Public Library of Science, vol. 12(11), pages 1-21, November.
  39. Rajita Menon & Vivek Ramanan & Kirill S Korolev, 2018. "Interactions between species introduce spurious associations in microbiome studies," PLOS Computational Biology, Public Library of Science, vol. 14(1), pages 1-20, January.
  40. Pirjo Wacklin & Harri Mäkivuokko & Noora Alakulppi & Janne Nikkilä & Heli Tenkanen & Jarkko Räbinä & Jukka Partanen & Kari Aranko & Jaana Mättö, 2011. "Secretor Genotype (FUT2 gene) Is Strongly Associated with the Composition of Bifidobacteria in the Human Intestine," PLOS ONE, Public Library of Science, vol. 6(5), pages 1-10, May.
  41. Eman M Fouda, 2017. "Airway Microbiota and Allergic Diseases: Clinical Implications," International Journal of Pulmonary & Respiratory Sciences, Juniper Publishers Inc., vol. 1(5), pages 119-124, May.
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