TY - JOUR AU - Gerber, G. K. PY - 2014 DA - 2014// TI - The dynamic microbiome JO - FEBS Lett VL - 588 UR - https://doi.org/10.1016/j.febslet.2014.02.037 DO - 10.1016/j.febslet.2014.02.037 ID - Gerber2014 ER - TY - JOUR AU - Bokulich, N. A. AU - Chung, J. AU - Battaglia, T. AU - Henderson, N. AU - Jay, M. AU - Li, H. AU - DL, A. AU - Wu, F. AU - Perez-Perez, G. I. AU - Chen, Y. PY - 2016 DA - 2016// TI - Antibiotics, birth mode, and diet shape microbiome maturation during early life JO - Sci Transl Med VL - 8 UR - https://doi.org/10.1126/scitranslmed.aad7121 DO - 10.1126/scitranslmed.aad7121 ID - Bokulich2016 ER - TY - JOUR AU - David, L. A. AU - Maurice, C. F. AU - Carmody, R. N. AU - Gootenberg, D. B. AU - Button, J. E. AU - Wolfe, B. E. AU - Ling, A. V. AU - Devlin, A. S. AU - Varma, Y. AU - Fischbach, M. A. PY - 2014 DA - 2014// TI - Diet rapidly and reproducibly alters the human gut microbiome JO - Nature VL - 505 UR - https://doi.org/10.1038/nature12820 DO - 10.1038/nature12820 ID - David2014 ER - TY - JOUR AU - Yassour, M. AU - Vatanen, T. AU - Siljander, H. AU - Hamalainen, A. M. AU - Harkonen, T. AU - Ryhanen, S. J. AU - Franzosa, E. A. AU - Vlamakis, H. AU - Huttenhower, C. AU - Gevers, D. PY - 2016 DA - 2016// TI - Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability JO - Sci Transl Med VL - 8 UR - https://doi.org/10.1126/scitranslmed.aad0917 DO - 10.1126/scitranslmed.aad0917 ID - Yassour2016 ER - TY - JOUR AU - Kostic, A. D. AU - Gevers, D. AU - Siljander, H. AU - Vatanen, T. AU - Hyotylainen, T. AU - Hamalainen, A. M. AU - Peet, A. AU - Tillmann, V. AU - Poho, P. AU - Mattila, I. PY - 2015 DA - 2015// TI - The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes JO - Cell Host Microbe VL - 17 UR - https://doi.org/10.1016/j.chom.2015.01.001 DO - 10.1016/j.chom.2015.01.001 ID - Kostic2015 ER - TY - JOUR AU - Vatanen, T. AU - Kostic, A. D. AU - d’Hennezel, E. AU - Siljander, H. AU - Franzosa, E. A. AU - Yassour, M. AU - Kolde, R. AU - Vlamakis, H. AU - Arthur, T. D. AU - Hamalainen, A. M. PY - 2016 DA - 2016// TI - Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans JO - Cell VL - 165 UR - https://doi.org/10.1016/j.cell.2016.04.007 DO - 10.1016/j.cell.2016.04.007 ID - Vatanen2016 ER - TY - JOUR AU - DiGiulio, D. B. AU - Callahan, B. J. AU - McMurdie, P. J. AU - Costello, E. K. AU - Lyell, D. J. AU - Robaczewska, A. AU - Sun, C. L. AU - Goltsman, D. S. AU - Wong, R. J. AU - Shaw, G. PY - 2015 DA - 2015// TI - Temporal and spatial variation of the human microbiota during pregnancy JO - Proc Natl Acad Sci U S A VL - 112 UR - https://doi.org/10.1073/pnas.1502875112 DO - 10.1073/pnas.1502875112 ID - DiGiulio2015 ER - TY - JOUR AU - Romero, R. AU - Hassan, S. S. AU - Gajer, P. AU - Tarca, A. L. AU - Fadrosh, D. W. AU - Bieda, J. AU - Chaemsaithong, P. AU - Miranda, J. AU - Chaiworapongsa, T. AU - Ravel, J. PY - 2014 DA - 2014// TI - The vaginal microbiota of pregnant women who subsequently have spontaneous preterm labor and delivery and those with a normal delivery at term JO - Microbiome VL - 2 UR - https://doi.org/10.1186/2049-2618-2-18 DO - 10.1186/2049-2618-2-18 ID - Romero2014 ER - TY - STD TI - Raveh-Sadka T, Thomas BC, Singh A, Firek B, Brooks B, Castelle CJ, Sharon I, Baker R, Good M, Morowitz MJ, Banfield JF. Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development. Elife. 2015;4:e05477. ID - ref9 ER - TY - JOUR AU - Zhou, Y. AU - Shan, G. AU - Sodergren, E. AU - Weinstock, G. AU - Walker, W. A. AU - Gregory, K. E. PY - 2015 DA - 2015// TI - Longitudinal analysis of the premature infant intestinal microbiome prior to necrotizing enterocolitis: a case-control study JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0118632 DO - 10.1371/journal.pone.0118632 ID - Zhou2015 ER - TY - JOUR AU - Pop, M. AU - Paulson, J. N. AU - Chakraborty, S. AU - Astrovskaya, I. AU - Lindsay, B. R. AU - Li, S. AU - Bravo, H. C. AU - Harro, C. AU - Parkhill, J. AU - Walker, A. W. PY - 2016 DA - 2016// TI - Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment JO - BMC Genomics VL - 17 UR - https://doi.org/10.1186/s12864-016-2777-0 DO - 10.1186/s12864-016-2777-0 ID - Pop2016 ER - TY - JOUR AU - Rensburg, J. J. AU - Lin, H. AU - Gao, X. AU - Toh, E. AU - Fortney, K. R. AU - Ellinger, S. AU - Zwickl, B. AU - Janowicz, D. M. AU - Katz, B. P. AU - Nelson, D. E. PY - 2015 DA - 2015// TI - The human skin microbiome associates with the outcome of and is influenced by bacterial infection JO - MBio VL - 6 ID - Rensburg2015 ER - TY - STD TI - Bogart E, Creswell R, Gerber G. The microbiome interpretable temporal rule engine. Github. 2019. https://doi.org/10.5281/zenodo.2634301. ID - ref13 ER - TY - JOUR AU - Tandon, D. AU - Haque, M. M. AU - Mande, S. S. PY - 2016 DA - 2016// TI - Inferring intra-community microbial interaction patterns from metagenomic datasets using associative rule mining techniques JO - PLoS One VL - 11 UR - https://doi.org/10.1371/journal.pone.0154493 DO - 10.1371/journal.pone.0154493 ID - Tandon2016 ER - TY - JOUR AU - Bucci, V. AU - Tzen, B. AU - Li, N. AU - Simmons, M. AU - Tanoue, T. AU - Bogart, E. AU - Deng, L. AU - Yeliseyev, V. AU - Delaney, M. L. AU - Liu, Q. PY - 2016 DA - 2016// TI - MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses JO - Genome Biol VL - 17 UR - https://doi.org/10.1186/s13059-016-0980-6 DO - 10.1186/s13059-016-0980-6 ID - Bucci2016 ER - TY - JOUR AU - Subramanian, S. AU - Huq, S. AU - Yatsunenko, T. AU - Haque, R. AU - Mahfuz, M. AU - Alam, M. A. AU - Benezra, A. AU - DeStefano, J. AU - Meier, M. F. AU - Muegge, B. D. PY - 2014 DA - 2014// TI - Persistent gut microbiota immaturity in malnourished Bangladeshi children JO - Nature VL - 510 UR - https://doi.org/10.1038/nature13421 DO - 10.1038/nature13421 ID - Subramanian2014 ER - TY - STD TI - Sze MA, Schloss PD. Looking for a signal in the noise: revisiting obesity and the microbiome. MBio. 2016;7(4):e01018–16. ID - ref17 ER - TY - JOUR AU - Teng, F. AU - Yang, F. AU - Huang, S. AU - Bo, C. AU - Xu, Z. Z. AU - Amir, A. AU - Knight, R. AU - Ling, J. AU - Xu, J. PY - 2015 DA - 2015// TI - Prediction of early childhood caries via spatial-temporal variations of oral microbiota JO - Cell Host Microbe VL - 18 UR - https://doi.org/10.1016/j.chom.2015.08.005 DO - 10.1016/j.chom.2015.08.005 ID - Teng2015 ER - TY - JOUR AU - Matsen, F. A. AU - Kodner, R. B. AU - Armbrust, E. V. PY - 2010 DA - 2010// TI - pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree JO - BMC Bioinformatics VL - 11 UR - https://doi.org/10.1186/1471-2105-11-538 DO - 10.1186/1471-2105-11-538 ID - Matsen2010 ER - TY - JOUR AU - Carmody, R. N. AU - Gerber, G. K. AU - Luevano, J. M. AU - Gatti, D. M. AU - Somes, L. AU - Svenson, K. L. AU - Turnbaugh, P. J. PY - 2015 DA - 2015// TI - Diet dominates host genotype in shaping the murine gut microbiota JO - Cell Host Microbe VL - 17 UR - https://doi.org/10.1016/j.chom.2014.11.010 DO - 10.1016/j.chom.2014.11.010 ID - Carmody2015 ER - TY - JOUR AU - Gerber, G. K. AU - Onderdonk, A. B. AU - Bry, L. PY - 2012 DA - 2012// TI - Inferring dynamic signatures of microbes in complex host ecosystems JO - PLoS Comput Biol VL - 8 UR - https://doi.org/10.1371/journal.pcbi.1002624 DO - 10.1371/journal.pcbi.1002624 ID - Gerber2012 ER - TY - CHAP AU - Lu, J. AU - Shi, P. AU - Li, H. PY - 2018 DA - 2018// TI - Generalized linear models with linear constraints for microbiome compositional data BT - ArXiv e-prints ID - Lu2018 ER - TY - JOUR AU - Crost, E. H. AU - Tailford, L. E. AU - Monestier, M. AU - Swarbreck, D. AU - Henrissat, B. AU - Crossman, L. C. AU - Juge, N. PY - 2016 DA - 2016// TI - The mucin-degradation strategy of Ruminococcus gnavus: the importance of intramolecular trans-sialidases JO - Gut Microbes VL - 7 UR - https://doi.org/10.1080/19490976.2016.1186334 DO - 10.1080/19490976.2016.1186334 ID - Crost2016 ER - TY - JOUR AU - Berry, D. A. PY - 2006 DA - 2006// TI - Bayesian clinical trials JO - Nat Rev Drug Discov VL - 5 UR - https://doi.org/10.1038/nrd1927 DO - 10.1038/nrd1927 ID - Berry2006 ER - TY - JOUR AU - Donald, B. AU - Rubin, D. PY - 2016 DA - 2016// TI - Fisher, Neyman, and Bayes at FDA JO - J Biopharm Stat VL - 26 UR - https://doi.org/10.1080/10543406.2016.1226333 DO - 10.1080/10543406.2016.1226333 ID - Donald2016 ER - TY - JOUR AU - Wasserstein, R. AU - Lazar, N. PY - 2016 DA - 2016// TI - The ASA’s statement on p-values: context, process, and purpose JO - Am Stat VL - 70 UR - https://doi.org/10.1080/00031305.2016.1154108 DO - 10.1080/00031305.2016.1154108 ID - Wasserstein2016 ER - TY - JOUR AU - Kass, R. AU - Raftery, A. PY - 1995 DA - 1995// TI - Bayes factors JO - J Am Stat Assoc VL - 90 UR - https://doi.org/10.1080/01621459.1995.10476572 DO - 10.1080/01621459.1995.10476572 ID - Kass1995 ER - TY - JOUR AU - Friedman, J. AU - Popescu, B. PY - 2008 DA - 2008// TI - Predictive learning via rule ensembles JO - Ann Appl Stat VL - 2 UR - https://doi.org/10.1214/07-AOAS148 DO - 10.1214/07-AOAS148 ID - Friedman2008 ER - TY - JOUR AU - Letham, B. AU - Rudin, C. AU - McCormick, T. AU - Madigan, D. PY - 2015 DA - 2015// TI - Interpretable classifiers using rules and Bayesian analysis: building a better stroke prediction model JO - Ann Appl Stat VL - 9 UR - https://doi.org/10.1214/15-AOAS848 DO - 10.1214/15-AOAS848 ID - Letham2015 ER - TY - JOUR AU - Urbanowicz, R. y. a. n. J. AU - Moore, J. a. s. o. n. H. PY - 2009 DA - 2009// TI - Learning Classifier Systems: A Complete Introduction, Review, and Roadmap JO - Journal of Artificial Evolution and Applications VL - 2009 UR - https://doi.org/10.1155/2009/736398 DO - 10.1155/2009/736398 ID - Urbanowicz2009 ER - TY - JOUR AU - Polson, N. AU - Scott, J. AU - Windle, J. PY - 2013 DA - 2013// TI - Bayesian inference for logistic models using Pólya–Gamma latent variables JO - J Am Stat Assoc VL - 108 UR - https://doi.org/10.1080/01621459.2013.829001 DO - 10.1080/01621459.2013.829001 ID - Polson2013 ER - TY - STD TI - Gibson T, Gerber G. Robust and scalable models of microbiome dynamics. In: Jennifer D, Andreas K, editors. Proceedings of the 35th International Conference on Machine Learning. Stockholm: Proceedings of Machine Learning Research; 2018. ID - ref32 ER - TY - JOUR AU - Callahan, B. J. AU - McMurdie, P. J. AU - Rosen, M. J. AU - Han, A. W. AU - Johnson, A. J. AU - Holmes, S. P. PY - 2016 DA - 2016// TI - DADA2: high-resolution sample inference from Illumina amplicon data JO - Nat Methods VL - 13 UR - https://doi.org/10.1038/nmeth.3869 DO - 10.1038/nmeth.3869 ID - Callahan2016 ER - TY - JOUR AU - Cole, J. R. AU - Wang, Q. AU - Fish, J. A. AU - Chai, B. AU - McGarrell, D. M. AU - Sun, Y. AU - Brown, C. T. AU - Porras-Alfaro, A. AU - Kuske, C. R. AU - Tiedje, J. M. PY - 2014 DA - 2014// TI - Ribosomal Database Project: data and tools for high throughput rRNA analysis JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1244 DO - 10.1093/nar/gkt1244 ID - Cole2014 ER - TY - JOUR AU - Schloss, P. D. AU - Westcott, S. L. AU - Ryabin, T. AU - Hall, J. R. AU - Hartmann, M. AU - Hollister, E. B. AU - Lesniewski, R. A. AU - Oakley, B. B. AU - Parks, D. H. AU - Robinson, C. J. PY - 2009 DA - 2009// TI - Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities JO - Appl Environ Microbiol VL - 75 UR - https://doi.org/10.1128/AEM.01541-09 DO - 10.1128/AEM.01541-09 ID - Schloss2009 ER - TY - JOUR AU - Kozich, J. J. AU - Westcott, S. L. AU - Baxter, N. T. AU - Highlander, S. K. AU - Schloss, P. D. PY - 2013 DA - 2013// TI - Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform JO - Appl Environ Microbiol VL - 79 UR - https://doi.org/10.1128/AEM.01043-13 DO - 10.1128/AEM.01043-13 ID - Kozich2013 ER - TY - JOUR AU - Pedregosa, F. AU - Varoquax, G. AU - Gramfort, A. AU - Michel, V. AU - Thirion, B. AU - Grisel, O. AU - Blondel, M. AU - Prettenhofer, P. AU - Weiss, R. AU - Dubourg, V. PY - 2012 DA - 2012// TI - Scikit-learn: machine learning in Python JO - J Mach Learn Res VL - 12 ID - Pedregosa2012 ER - TY - STD TI - Bogart E, Creswell R, Gerber G. Supporting files for the microbiome interpretable temporal rule engine manuscript. Github. 2019. https://doi.org/10.5281/zenodo.3345235. ID - ref38 ER - TY - STD TI - Bokulich NA, Chung J, Battaglia T, Henderson N, Jay M, Li H, DL A, Wu F, Perez-Perez GI, Chen Y, et al. Antibiotics, birth mode, and diet shape microbiome maturation during early life. Datasets. Eur Nucleotide Arch. 2016. https://www.ebi.ac.uk/ena/data/view/PRJEB14529. Accessed 21 July 2019. UR - https://www.ebi.ac.uk/ena/data/view/PRJEB14529 ID - ref39 ER - TY - STD TI - Bokulich NA, Chung J, Battaglia T, Henderson N, Jay M, Li H, A DL, Wu F, Perez-Perez GI, Chen Y, et al: Antibiotics, birth mode, and diet shape microbiome maturation during early life. Datasets. QIITA. 2016. https://qiita.ucsd.edu/study/description/10249;. Accessed 21 July 2019. UR - https://qiita.ucsd.edu/study/description/10249; ID - ref40 ER - TY - STD TI - David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, et al: DietTimeSeries. Datasets. MG-RAST. 2013. https://www.mg-rast.org/linkin.cgi?project=mgp6248;. Accessed 21 July 2019. UR - https://www.mg-rast.org/linkin.cgi?project=mgp6248; ID - ref41 ER - TY - STD TI - Kostic AD, Gevers D, Siljander H, Vatanen T, Hyotylainen T, Hamalainen AM, Peet A, Tillmann V, Poho P, Mattila I, et al: T1D cohort. Datasets. DIABIMMUNE. 2015. https://pubs.broadinstitute.org/diabimmune/t1d-cohort;. Accessed 21 July 2019. UR - https://pubs.broadinstitute.org/diabimmune/t1d-cohort; ID - ref42 ER - TY - STD TI - Vatanen T, Kostic AD, d’Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hamalainen AM, et al: Three country cohort. Datasets. DIABIMMUNE. 2016. https://pubs.broadinstitute.org/diabimmune/three-country-cohort. Accessed 21 July 2019. UR - https://pubs.broadinstitute.org/diabimmune/three-country-cohort ID - ref43 ER - TY - STD TI - DiGiulio DB, Callahan BJ, McMurdie PJ, Costello EK, Lyell DJ, Robaczewska A, Sun CL, Goltsman DS, Wong RJ, Shaw G, et al: Temporal and spatial variation of the human microbiota during pregnancy. Datasets. NCBI. 2018. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA288562;. Accessed 21 July 2019 UR - https://www.ncbi.nlm.nih.gov/bioproject/PRJNA288562; ID - ref44 ER -