Nonlinear machine learning pattern recognition and bacteria-metabolite multilayer network analysis of perturbed gastric microbiome
Published 2021 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Nonlinear machine learning pattern recognition and bacteria-metabolite multilayer network analysis of perturbed gastric microbiome
Authors
Keywords
-
Journal
Nature Communications
Volume 12, Issue 1, Pages -
Publisher
Springer Science and Business Media LLC
Online
2021-03-26
DOI
10.1038/s41467-021-22135-x
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Alterations in Gut Microbiota of Gestational Diabetes Patients During the First Trimester of Pregnancy
- (2020) Shujuan Ma et al. Frontiers in Cellular and Infection Microbiology
- Biological Functions and Analytical Strategies of Sialic Acids in Tumor
- (2020) Xiaoman Zhou et al. Cells
- MetaboAnalystR 3.0: Toward an Optimized Workflow for Global Metabolomics
- (2020) Zhiqiang Pang et al. Metabolites
- Large-scale metabolic interaction network of the mouse and human gut microbiota
- (2020) Roktaek Lim et al. Scientific Data
- Relationship between gut microbiota and circulating metabolites in population-based cohorts
- (2019) Dina Vojinovic et al. Nature Communications
- Effect of diet and gut environment on the gastrointestinal formation of N -nitroso compounds: A review
- (2018) Jun Kobayashi NITRIC OXIDE-BIOLOGY AND CHEMISTRY
- Association between metabolic profile and microbiomic changes in rats with functional dyspepsia
- (2018) Liang Luo et al. RSC Advances
- Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns
- (2018) Federica Del Chierico et al. Frontiers in Microbiology
- Effects of Metabolites Derived From Gut Microbiota and Hosts on Pathogens
- (2018) Zhendong Li et al. Frontiers in Cellular and Infection Microbiology
- 25 Years of Proton Pump Inhibitors: A Comprehensive Review
- (2017) Daniel S. Strand et al. Gut and Liver
- Proton-pump inhibitors: understanding the complications and risks
- (2017) Peter Malfertheiner et al. Nature Reviews Gastroenterology & Hepatology
- Gut microbiome as a clinical tool in gastrointestinal disease management: are we there yet?
- (2017) Eamonn M. M. Quigley Nature Reviews Gastroenterology & Hepatology
- Characterization of the Gastric Microbiota in a Pediatric Population According to Helicobacter pylori Status
- (2017) Laura Llorca et al. PEDIATRIC INFECTIOUS DISEASE JOURNAL
- Machine learning meets complex networks via coalescent embedding in the hyperbolic space
- (2017) Alessandro Muscoloni et al. Nature Communications
- Enlightening discriminative network functional modules behind Principal Component Analysis separation in differential-omic science studies
- (2017) Sara Ciucci et al. Scientific Reports
- Comparison of the human gastric microbiota in hypochlorhydric states arising as a result of Helicobacter pylori-induced atrophic gastritis, autoimmune atrophic gastritis and proton pump inhibitor use
- (2017) Bryony N. Parsons et al. PLoS Pathogens
- The gastric microbiome, its interaction with Helicobacter pylori, and its potential role in the progression to stomach cancer
- (2017) Jennifer M. Noto et al. PLoS Pathogens
- The Human Gastric Microbiome Is Predicated upon Infection with Helicobacter pylori
- (2017) Ingeborg Klymiuk et al. Frontiers in Microbiology
- Leptotrichia species in human infections II
- (2017) Emenike R. K. Eribe et al. Journal of Oral Microbiology
- We Are Using Too Many PPIs and We Need to Stop: A European Perspective
- (2016) Angel Lanas AMERICAN JOURNAL OF GASTROENTEROLOGY
- Effects of Proton Pump Inhibitors on the Gastric Mucosa-Associated Microbiota in Dyspeptic Patients
- (2016) Francesco Paroni Sterbini et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Effective and safe proton pump inhibitor therapy in acid-related diseases – A position paper addressing benefits and potential harms of acid suppression
- (2016) Carmelo Scarpignato et al. BMC Medicine
- Use of Proton Pump Inhibitors and Risks of Fundic Gland Polyps and Gastric Cancer: Systematic Review and Meta-analysis
- (2016) An Tran-Duy et al. Clinical Gastroenterology and Hepatology
- Does Long-Term Proton Pump Inhibitor Therapy Affect the Health of Gut Microbiota?
- (2016) Chansu Lee et al. Gut and Liver
- Application of multivariate statistical techniques in microbial ecology
- (2016) O. Paliy et al. MOLECULAR ECOLOGY
- Gastric Helicobacter pylori Infection Affects Local and Distant Microbial Populations and Host Responses
- (2016) Sabine Kienesberger et al. Cell Reports
- Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort
- (2016) Antonio Gonzalez et al. mSystems
- Preliminary analysis of salivary microbiome and their potential roles in oral lichen planus
- (2016) Kun Wang et al. Scientific Reports
- Gender, Contraceptives and Individual Metabolic Predisposition Shape a Healthy Plasma Lipidome
- (2016) Susanne Sales et al. Scientific Reports
- Proton pump inhibitors affect the gut microbiome
- (2015) Floris Imhann et al. GUT
- Proton pump inhibitors alter the composition of the gut microbiota
- (2015) Matthew A Jackson et al. GUT
- Network Mapping by Replaying Hyperbolic Growth
- (2015) Fragkiskos Papadopoulos et al. IEEE-ACM TRANSACTIONS ON NETWORKING
- 16S Community Profiling Identifies Proton Pump Inhibitor Related Differences in Gastric, Lung, and Oropharyngeal Microflora
- (2015) Rachel Rosen et al. JOURNAL OF PEDIATRICS
- Highlighting nonlinear patterns in population genetics datasets
- (2015) Gregorio Alanis-Lobato et al. Scientific Reports
- Sparse and Compositionally Robust Inference of Microbial Ecological Networks
- (2015) Zachary D. Kurtz et al. PLoS Computational Biology
- The human gastric microbiota: Is it time to rethink the pathogenesis of stomach diseases?
- (2015) Gerardo Nardone et al. United European Gastroenterology Journal
- Influence of Proton-Pump Inhibitors on the Luminal Microbiota in the Gastrointestinal Tract
- (2015) Ayumi Tsuda et al. Clinical and Translational Gastroenterology
- Gastric Microbiome and Gastric Cancer
- (2014) Kyle M. Brawner et al. CANCER JOURNAL
- The Impact of Proton Pump Inhibitors on the Human Gastrointestinal Microbiome
- (2014) Daniel E. Freedberg et al. CLINICS IN LABORATORY MEDICINE
- Potential association between the recent increase in campylobacteriosis incidence in the Netherlands and proton-pump inhibitor use – an ecological study
- (2014) M Bouwknegt et al. Eurosurveillance
- GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater
- (2014) Kristina Bayer et al. FEMS MICROBIOLOGY ECOLOGY
- Differences in Gastric Mucosal Microbiota Profiling in Patients with Chronic Gastritis, Intestinal Metaplasia, and Gastric Cancer Using Pyrosequencing Methods
- (2014) Chang Soo Eun et al. HELICOBACTER
- Methylobacterium and Its Role in Health Care-Associated Infection
- (2014) J. Kovaleva et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Stomach microbiota composition varies between patients with non-atrophic gastritis and patients with intestinal type of gastric cancer
- (2014) Francisco Aviles-Jimenez et al. Scientific Reports
- The role of metabolism in bacterial persistence
- (2014) Stephanie M. Amato et al. Frontiers in Microbiology
- Prolonged use of a proton pump inhibitor reduces microbial diversity: implications for Clostridium difficile susceptibility
- (2014) Charlie T Seto et al. Microbiome
- Multivariate analysis of functional metagenomes
- (2014) Elizabeth Dinsdale Frontiers in Genetics
- Incidence of Campylobacter and Salmonella Infections Following First Prescription for PPI: A Cohort Study Using Routine Data
- (2013) Sinead Brophy et al. AMERICAN JOURNAL OF GASTROENTEROLOGY
- Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding
- (2013) Carlo Vittorio Cannistraci et al. BIOINFORMATICS
- Beta diversity as the variance of community data: dissimilarity coefficients and partitioning
- (2013) Pierre Legendre et al. ECOLOGY LETTERS
- Gastric microbiota is altered in oesophagitis and Barrett's oesophagus and further modified by proton pump inhibitors
- (2013) Itay Amir et al. ENVIRONMENTAL MICROBIOLOGY
- Capnocytophaga spp. involvement in bone infections: a review
- (2013) Caroline Piau et al. INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
- Immune status, antibiotic medication and pH are associated with changes in the stomach fluid microbiota
- (2013) Erik C von Rosenvinge et al. ISME Journal
- Intestinal Dysbiosis and Depletion of Butyrogenic Bacteria in Clostridium difficile Infection and Nosocomial Diarrhea
- (2013) V. C. Antharam et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Microbiota in the stomach: New insights
- (2013) Wen Ming Wu et al. Journal of Digestive Diseases
- Specificity and transcriptional activity of microbiota associated with low and high microbial abundance sponges from the Red Sea
- (2013) Lucas Moitinho-Silva et al. MOLECULAR ECOLOGY
- Helicobacter pylori infection in functional dyspepsia
- (2013) Hidekazu Suzuki et al. Nature Reviews Gastroenterology & Hepatology
- Veillonella, Firmicutes: Microbes disguised as Gram negatives
- (2013) Tammi Vesth et al. Standards in Genomic Sciences
- Associating microbiome composition with environmental covariates using generalized UniFrac distances
- (2012) Jun Chen et al. BIOINFORMATICS
- graphite - a Bioconductor package to convert pathway topology to gene network
- (2012) Gabriele Sales et al. BMC BIOINFORMATICS
- The evolution of ultraconserved elements with different phylogenetic origins
- (2012) Taewoo Ryu et al. BMC EVOLUTIONARY BIOLOGY
- Identification and Predictive Value of Interleukin-6 + Interleukin-10 + and Interleukin-6 − Interleukin-10 + Cytokine Patterns in ST-Elevation Acute Myocardial Infarction
- (2012) Enrico Ammirati et al. CIRCULATION RESEARCH
- Prescribing Proton Pump Inhibitors
- (2012) Nimish Vakil DRUGS
- Management ofHelicobacter pyloriinfection—the Maastricht IV/ Florence Consensus Report
- (2012) Peter Malfertheiner et al. GUT
- Catonella morbi as a cause of native valve endocarditis in Chennai, India
- (2012) T. Menon et al. INFECTION
- Granulicatella infection: diagnosis and management
- (2012) J. S. Cargill et al. JOURNAL OF MEDICAL MICROBIOLOGY
- Techniques used to characterize the gut microbiota: a guide for the clinician
- (2012) Marianne H. Fraher et al. Nature Reviews Gastroenterology & Hepatology
- Stochastic neighbor embedding (SNE) for dimension reduction and visualization using arbitrary divergences
- (2012) Kerstin Bunte et al. NEUROCOMPUTING
- Symptomatic atherosclerosis is associated with an altered gut metagenome
- (2012) Fredrik H. Karlsson et al. Nature Communications
- Inferring Correlation Networks from Genomic Survey Data
- (2012) Jonathan Friedman et al. PLoS Computational Biology
- Systematic review: the use of proton pump inhibitors and increased susceptibility to enteric infection
- (2011) C. Bavishi et al. ALIMENTARY PHARMACOLOGY & THERAPEUTICS
- Stage prediction of embryonic stem cell differentiation from genome-wide expression data
- (2011) Lan Zagar et al. BIOINFORMATICS
- FLASH: fast length adjustment of short reads to improve genome assemblies
- (2011) T. Magoc et al. BIOINFORMATICS
- Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
- (2011) B. J. Haas et al. GENOME RESEARCH
- Defining the Pseudomonas Genus: Where Do We Draw the Line with Azotobacter?
- (2011) Asli I. Özen et al. MICROBIAL ECOLOGY
- Gut microbiome-host interactions in health and disease
- (2011) James M Kinross et al. Genome Medicine
- UniFrac: an effective distance metric for microbial community comparison
- (2010) Catherine Lozupone et al. ISME Journal
- Structure of the human gastric bacterial community in relation to Helicobacter pylori status
- (2010) Ana Maldonado-Contreras et al. ISME Journal
- QIIME allows analysis of high-throughput community sequencing data
- (2010) J Gregory Caporaso et al. NATURE METHODS
- Review: Evaluation and management of dyspepsia
- (2010) R. Christopher Harmon et al. Therapeutic Advances in Gastroenterology
- Pitfalls of supervised feature selection
- (2009) Pawel Smialowski et al. BIOINFORMATICS
- PyNAST: a flexible tool for aligning sequences to a template alignment
- (2009) J. G. Caporaso et al. BIOINFORMATICS
- The Effect of Proton Pump Inhibitors on the Human Microbiota
- (2009) B. Vesper et al. CURRENT DRUG METABOLISM
- Helicobacter pylori in Health and Disease
- (2009) Timothy L. Cover et al. GASTROENTEROLOGY
- Host-Bacterial Interactions in Helicobacter pylori Infection
- (2008) Manuel R. Amieva et al. GASTROENTEROLOGY
- What is principal component analysis?
- (2008) Markus Ringnér NATURE BIOTECHNOLOGY
- Navigability of complex networks
- (2008) Marián Boguñá et al. Nature Physics
- Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing
- (2008) Anders F. Andersson et al. PLoS One
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now