4.8 Article

Predicting metabolomic profiles from microbial composition through neural ordinary differential equations

Related references

Note: Only part of the references are listed.
Review Immunology

The Emerging Role of Bile Acids in the Pathogenesis of Inflammatory Bowel Disease

John P. Thomas et al.

Summary: This review examines the interaction between bile acid metabolites and intestinal inflammation in inflammatory bowel disease (IBD), highlighting their role in regulation of the inflammatory milieu through pathways such as autophagy, apoptosis, and the inflammasome pathway. The study also discusses the potential of novel experimental and bioinformatics approaches to further advance our understanding of the role of bile acids in IBD and inform therapeutic strategies.

FRONTIERS IN IMMUNOLOGY (2022)

Review Biochemical Research Methods

Metabolomics for personalized medicine: the input of analytical chemistry from biomarker discovery to point-of-care tests

Florence Anne Castelli et al.

Summary: Metabolomics involves detecting, quantifying, and analyzing small molecules in biological samples on a large scale. While it has shown relevance for patient stratification in research projects and clinical studies, challenges related to standardization, metabolite identification, and data processing hinder its implementation in clinical practice, especially in personalized medicine. Streamlining complex molecular signatures and improving interoperability of data are crucial for the future integration of metabolomics into healthcare.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2022)

Article Allergy

Association of the Gut Microbiome and Metabolome with Wheeze Frequency in Childhood Asthma

Kathleen Lee-Sarwar et al.

JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY (2021)

Article Multidisciplinary Sciences

Ecology-guided prediction of cross-feeding interactions in the human gut microbiome

Akshit Goyal et al.

Summary: Combining ecology-based computational methods and optimization techniques, GutCP predicts a large number of experimentally untested cross-feeding interactions in the human gut microbiome. It has the potential to improve microbial community models and predict the metabolic profile of the gut.

NATURE COMMUNICATIONS (2021)

Article Biochemical Research Methods

MiMeNet: Exploring microbiome-metabolome relationships using neural networks

Derek Reiman et al.

Summary: MiMeNet is a neural network framework that accurately predicts metabolite abundances and identifies well-predicted metabolites. It can group microbes and metabolites with similar interaction patterns and functions, shedding light on the underlying structure of the microbe-metabolite interaction network. MiMeNet is a powerful tool for generating insights into metabolic dysregulation in disease and facilitating future hypothesis generation at the microbiome and metabolomics interface.

PLOS COMPUTATIONAL BIOLOGY (2021)

Review Biochemical Research Methods

New approaches for metagenome assembly with short reads

Martin Ayling et al.

BRIEFINGS IN BIOINFORMATICS (2020)

Article Medicine, General & Internal

Six-Year Follow-up of a Trial of Antenatal Vitamin D for Asthma Reduction

Augusto A. Litonjua et al.

NEW ENGLAND JOURNAL OF MEDICINE (2020)

Article Biotechnology & Applied Microbiology

Combining Machine Learning and Metabolomics to Identify Weight Gain Biomarkers

Flavia Luisa Dias-Audibert et al.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2020)

Article Allergy

Integrative analysis of the intestinal metabolome of childhood asthma

Kathleen A. Lee-Sarwar et al.

JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY (2019)

Article Biochemical Research Methods

Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities

Robert Marsland et al.

PLOS COMPUTATIONAL BIOLOGY (2019)

Article Multidisciplinary Sciences

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

Jason Lloyd-Price et al.

NATURE (2019)

Letter Biotechnology & Applied Microbiology

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Evan Bolyen et al.

NATURE BIOTECHNOLOGY (2019)

Article Multidisciplinary Sciences

Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences

Himel Mallick et al.

NATURE COMMUNICATIONS (2019)

Article Biochemical Research Methods

Learning representations of microbe-metabolite interactions

James T. Morton et al.

NATURE METHODS (2019)

Article Microbiology

Gut microbiome structure and metabolic activity in inflammatory bowel disease

Eric A. Franzosa et al.

NATURE MICROBIOLOGY (2019)

Article Biochemical Research Methods

Evidence for a multi-level trophic organization of the human gut microbiome

Tong Wang et al.

PLOS COMPUTATIONAL BIOLOGY (2019)

Review Chemistry, Multidisciplinary

Metabolomics biotechnology, applications, and future trends: a systematic review

Qiang Yang et al.

RSC ADVANCES (2019)

Review Gastroenterology & Hepatology

Bile acid-microbiota crosstalk in gastrointestinal inflammation and carcinogenesis

Wei Jia et al.

NATURE REVIEWS GASTROENTEROLOGY & HEPATOLOGY (2018)

Article Multidisciplinary Sciences

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics

Tami L. Swenson et al.

NATURE COMMUNICATIONS (2018)

Article Multidisciplinary Sciences

Niche partitioning of a pathogenic microbiome driven by chemical gradients

Robert A. Quinn et al.

SCIENCE ADVANCES (2018)

Review Multidisciplinary Sciences

Chemical transformation of xenobiotics by the human gut microbiota

Nitzan Koppel et al.

SCIENCE (2017)

Review Biochemistry & Molecular Biology

A review of the relationship between the gut microbiota and amino acid metabolism

Rui Lin et al.

AMINO ACIDS (2017)

Article Gastroenterology & Hepatology

The Role of the Gut Microbiota in Bile Acid Metabolism

Oscar Ramirez-Perez et al.

ANNALS OF HEPATOLOGY (2017)

Article Medicine, General & Internal

Effect of Prenatal Supplementation With Vitamin D on Asthma or Recurrent Wheezing in Offspring by Age 3 Years The VDAART Randomized Clinical Trial

Augusto A. Litonjua et al.

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2016)

Article Biochemical Research Methods

DADA2: High-resolution sample inference from Illumina amplicon data

Benjamin J. Callahan et al.

NATURE METHODS (2016)

Review Multidisciplinary Sciences

Small molecules from the human microbiota

Mohamed S. Donia et al.

SCIENCE (2015)

Article Infectious Diseases

Bile Salts Modulate the Mucin-Activated Type VI Secretion System of Pandemic Vibrio cholerae

Verena Bachmann et al.

PLOS NEGLECTED TROPICAL DISEASES (2015)

Article Microbiology

Modelling the emergent dynamics and major metabolites of the human colonic microbiota

Helen Kettle et al.

ENVIRONMENTAL MICROBIOLOGY (2015)

Review Nutrition & Dietetics

The food metabolome: a window over dietary exposure

Augustin Scalbert et al.

AMERICAN JOURNAL OF CLINICAL NUTRITION (2014)

Review Cell Biology

Challenges and opportunities of metabolomics

Caroline H. Johnson et al.

JOURNAL OF CELLULAR PHYSIOLOGY (2012)

Review Gastroenterology & Hepatology

The role of the gut microbiota in nutrition and health

Harry J. Flint et al.

NATURE REVIEWS GASTROENTEROLOGY & HEPATOLOGY (2012)

Article Biochemical Research Methods

Identification and quantification of metabolites in 1H NMR spectra by Bayesian model selection

Cheng Zheng et al.

BIOINFORMATICS (2011)

Review Food Science & Technology

Intake of Added Sugars and Selected Nutrients in the United States, National Health and Nutrition Examination Survey (NHANES) 20032006

Bernadette P. Marriott et al.

CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION (2010)

Review Biochemistry & Molecular Biology

Bile salt biotransformations by human intestinal bacteria

JM Ridlon et al.

JOURNAL OF LIPID RESEARCH (2006)

Article Endocrinology & Metabolism

Diet and exercise among adults with type Z diabetes

KM Nelson et al.

DIABETES CARE (2002)