Comparative study of classifiers for human microbiome data

Medicine in Microecology - Tập 4 - Trang 100013 - 2020
Xu-Wen Wang1, Yang-Yu Liu1,2
1Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
2Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA

Tài liệu tham khảo

Kinross, 2011, Gut microbiome-host interactions in health and disease, Genome Med, 3, 14, 10.1186/gm228 MetaHIT Consortium, 2010, A human gut microbial gene catalogue established by metagenomic sequencing, Nature, 464, 59, 10.1038/nature08821 Franzosa, 2018, Species-level functional profiling of metagenomes and metatranscriptomes, Nat Methods, 15, 962, 10.1038/s41592-018-0176-y Gill, 2006, Metagenomic analysis of the human distal gut microbiome, Science, 312, 1355, 10.1126/science.1124234 Goodrich, 2014, Conducting a microbiome study, Cell, 158, 250, 10.1016/j.cell.2014.06.037 Lynch, 2016, The human intestinal microbiome in health and disease, N Engl J Med, 375, 2369, 10.1056/NEJMra1600266 Cryan, 2019, The microbiota-gut-brain Axis, Physiol Rev, 99, 1877, 10.1152/physrev.00018.2018 Schubert, 2014, Microbiome data distinguish patients with Clostridium difficile infection and non-C. difficile-associated diarrhea from healthy controls, mBio, 5, 10.1128/mBio.01021-14 Morgan, 2012, Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment, Genome Biol, 13, R79, 10.1186/gb-2012-13-9-r79 Enck, 2016, Irritable bowel syndrome, Nat Rev Dis Prim, 2, 16014, 10.1038/nrdp.2016.14 Kang, 2013, Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children, PloS One, 8 Liu, 2015, Treatment of obesity with celastrol, Cell, 161, 999, 10.1016/j.cell.2015.05.011 Jangi, 2016, Alterations of the human gut microbiome in multiple sclerosis, Nat Commun, 7, 12015, 10.1038/ncomms12015 Kindt, 2018, The gut microbiota promotes hepatic fatty acid desaturation and elongation in mice, Nat Commun, 9, 3760, 10.1038/s41467-018-05767-4 Scheperjans, 2015, Gut microbiota are related to Parkinson's disease and clinical phenotype, Mov Disord, 30, 350, 10.1002/mds.26069 Lloyd-Price, 2016, The healthy human microbiome, Genome Med, 8, 10.1186/s13073-016-0307-y LeCun, 2015, Deep learning, Nature, 521, 436, 10.1038/nature14539 Wang, 2018, Link prediction through deep learning, bioRxiv, 247577 Angermueller, 2016, Deep learning for computational biology, Mol Syst Biol, 12, 878, 10.15252/msb.20156651 Li, 2016, A review on machine learning principles for multi-view biological data integration, Briefings Bioinf, bbw113, 10.1093/bib/bbw113 Jordan, 2015, Machine learning: trends, perspectives, and prospects, Science, 349, 255, 10.1126/science.aaa8415 Knights, 2011, Supervised classification of human microbiota, FEMS (Fed Eur Microbiol Soc) Microbiol Rev, 35, 343 Bleakley, 2009, Supervised prediction of drug–target interactions using bipartite local models, Bioinformatics, 25, 2397, 10.1093/bioinformatics/btp433 Esteva, 2017, Dermatologist-level classification of skin cancer with deep neural networks, Nature, 542, 115, 10.1038/nature21056 Caruana, 2008, An empirical evaluation of supervised learning in high dimensions Caruana, 2006, An empirical comparison of supervised learning algorithms Chen, 2016, A scalable tree boosting system Tomita, 2015, Random projection forests Liaw, 2002, Classification and regression by randomForest, 2, 6 Sundaram, 2018 Zou, 2005, Regularization and variable selection via the elastic net, J Roy Stat Soc B, 67, 301, 10.1111/j.1467-9868.2005.00503.x Suykens, J. A. K. & Vandewalle, J. Least squares support vector machine classifiers. vol. 8. Duvallet, 2017, Meta-analysis of gut microbiome studies identifies disease-specific and shared responses, Nat Commun, 8, 10.1038/s41467-017-01973-8 Ponomareva, 2017 Scher, 2013, Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis, elife, 2, 10.7554/eLife.01202 Son, 2015, Comparison of fecal microbiota in children with autism spectrum disorders and neurotypical siblings in the simons simplex collection, PloS One, 10, 10.1371/journal.pone.0137725 Gopalakrishnan, 2018, Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients, Science, 359, 97, 10.1126/science.aan4236 Baxter, 2016, Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions, Genome Med, 8, 37, 10.1186/s13073-016-0290-3 Chen, 2012, Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer, PloS One, 7 Wang, 2012, Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers, ISME J, 6, 320, 10.1038/ismej.2011.109 Singh, 2015, Intestinal microbial communities associated with acute enteric infections and disease recovery, Microbiome, 3, 45, 10.1186/s40168-015-0109-2 Dinh, 2014, Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection, J Infect Dis, 211, 19, 10.1093/infdis/jiu409 Lozupone, 2013, Alterations in the gut microbiota associated with HIV-1 infection, Cell Host Microbe, 14, 329, 10.1016/j.chom.2013.08.006 Noguera-Julian, 2016, Gut microbiota linked to sexual preference and HIV infection, EBioMedicine, 5, 135, 10.1016/j.ebiom.2016.01.032 Gevers, 2014, The treatment-naive microbiome in new-onset Crohn's disease, Cell Host Microbe, 15, 382, 10.1016/j.chom.2014.02.005 Papa, 2012, Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease, PloS One, 7, 10.1371/journal.pone.0039242 Willing, 2010, A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes, Gastroenterology, 139, 1844, 10.1053/j.gastro.2010.08.049 Zhang, 2013 Zhu, 2013, Characterization of gut microbiomes in nonalcoholic steatohepatitis (NASH) patients: a connection between endogenous alcohol and NASH, Hepatology, 57, 601, 10.1002/hep.26093 Ross, 2015, 16S gut community of the cameron county hispanic cohort, Microbiome, 3, 7, 10.1186/s40168-015-0072-y Turnbaugh, 2009, A core gut microbiome in obese and lean twins, nature, 457, 480, 10.1038/nature07540 Zupancic, 2012, Analysis of the gut microbiota in the old order Amish and its relation to the metabolic syndrome, PloS One, 7, 10.1371/journal.pone.0043052 Tang, 2017, Endothelial TLR4 and the microbiome drive cerebral cavernous malformations, Nature, 545, 305, 10.1038/nature22075 Costello, 2009, Bacterial community variation in human body habitats across space and time, Science, 326, 1694, 10.1126/science.1177486 Fierer, 2010, Forensic identification using skin bacterial communities, Proc Natl Acad Sci Unit States Am, 107, 6477, 10.1073/pnas.1000162107