Learning representations of microbe–metabolite interactions

作者: James T. Morton , Alexander A. Aksenov , Louis Felix Nothias , James R. Foulds , Robert A. Quinn

DOI: 10.1038/S41592-019-0616-3

关键词: BiologyMetaboliteMicrobiomeComputational biologyExtramuralArtificial neural networkConditional probability

摘要: Integrating multiomics datasets is critical for microbiome research; however, inferring interactions across omics datasets has multiple statistical challenges. We solve this problem …

参考文章(56)
Juan J. Egozcue, Vera Pawlowsky-Glahn, Raimon Tolosana-Delgado, Modeling and Analysis of Compositional Data ,(2015)
Alžběta Kalivodová, Karel Hron, Peter Filzmoser, Lukáš Najdekr, Hana Janečková, Tomáš Adam, PLS‐DA for compositional data with application to metabolomics Journal of Chemometrics. ,vol. 29, pp. 21- 28 ,(2015) , 10.1002/CEM.2657
Christopher M. Bishop, Pattern Recognition and Machine Learning ,(2006)
Zachary D. Kurtz, Christian L. Müller, Emily R. Miraldi, Dan R. Littman, Martin J. Blaser, Richard A. Bonneau, Sparse and Compositionally Robust Inference of Microbial Ecological Networks PLOS Computational Biology. ,vol. 11, pp. e1004226- 25 ,(2015) , 10.1371/JOURNAL.PCBI.1004226
David M Blei, Andrew Y Ng, Michael I Jordan, None, Latent dirichlet allocation Journal of Machine Learning Research. ,vol. 3, pp. 993- 1022 ,(2003) , 10.5555/944919.944937
Benoît Foligné, Sandrine Parayre, Redouane Cheddani, Marie-Hélène Famelart, Marie-Noëlle Madec, Coline Plé, Jérôme Breton, Joëlle Dewulf, Gwénaël Jan, Stéphanie-Marie Deutsch, Immunomodulation properties of multi-species fermented milks. Food Microbiology. ,vol. 53, pp. 60- 69 ,(2016) , 10.1016/J.FM.2015.04.002
Bo Wang, Aziz M Mezlini, Feyyaz Demir, Marc Fiume, Zhuowen Tu, Michael Brudno, Benjamin Haibe-Kains, Anna Goldenberg, Similarity network fusion for aggregating data types on a genomic scale Nature Methods. ,vol. 11, pp. 333- 337 ,(2014) , 10.1038/NMETH.2810
Keqi Tang, Jason S. Page, Richard D. Smith, Charge competition and the linear dynamic range of detection in electrospray ionization mass spectrometry Journal of the American Society for Mass Spectrometry. ,vol. 15, pp. 1416- 1423 ,(2004) , 10.1016/J.JASMS.2004.04.034
W. J. Moree, V. V. Phelan, C.-H. Wu, N. Bandeira, D. S. Cornett, B. M. Duggan, P. C. Dorrestein, Interkingdom metabolic transformations captured by microbial imaging mass spectrometry Proceedings of the National Academy of Sciences of the United States of America. ,vol. 109, pp. 13811- 13816 ,(2012) , 10.1073/PNAS.1206855109
Richard King, Ryan Bonfiglio, Carmen Fernandez-Metzler, Cynthia Miller-Stein, Timothy Olah, Mechanistic investigation of ionization suppression in electrospray ionization Journal of the American Society for Mass Spectrometry. ,vol. 11, pp. 942- 950 ,(2000) , 10.1016/S1044-0305(00)00163-X