NOREVA: enhanced normalization and evaluation of time-course and multi-class metabolomic data

AlpsNMR: an R package for signal processing of fully untargeted NMR-based metabolomics

(2020) Francisco Madrid-Gambin et al.   BIOINFORMATICS

SSizer: Determining the Sample Sufficiency for Comparative Biological Study

(2020) Fengcheng Li et al.   JOURNAL OF MOLECULAR BIOLOGY

Lactobacillus and Pediococcus ameliorate progression of non-alcoholic fatty liver disease through modulation of the gut microbiome

(2020) Na Young Lee et al.   Gut Microbes

Tumor metastasis to lymph nodes requires YAP-dependent metabolic adaptation

(2019) Choong-kun Lee et al.   SCIENCE

Revelation of the metabolic pathway of hederacoside C using an innovative data analysis strategy for dynamic multiclass biotransformation experiments

(2019) Laura Peeters et al.   JOURNAL OF CHROMATOGRAPHY A

Simultaneous Improvement in the Precision, Accuracy and Robustness of Label-free Proteome Quantification by Optimizing Data Manipulation Chains

(2019) Jing Tang et al.   MOLECULAR & CELLULAR PROTEOMICS

Large-scale plasma metabolome analysis reveals alterations in HDL metabolism in migraine

(2019) Gerrit L.J. Onderwater et al.   NEUROLOGY

Untargeted metabolomics analysis of Mucor racemosus Douchi fermentation process by gas chromatography with time‐of‐flight mass spectrometry

(2019) Pao Li et al.   Food Science & Nutrition

The effect of sampling procedures and day-to-day variations in metabolomics studies of biofluids

(2019) Guro F. Giskeødegård et al.   ANALYTICA CHIMICA ACTA

Highly geographical specificity of metabolomic traits among Korean domestic soybeans (Glycine max)

(2019) Eun Mi Lee et al.   FOOD RESEARCH INTERNATIONAL

Role of Gut Microbiota in Hepatocarcinogenesis

(2019) Haripriya Gupta et al.   Microorganisms

Metandem: An online software tool for mass spectrometry-based isobaric labeling metabolomics

(2019) Ling Hao et al.   ANALYTICA CHIMICA ACTA

VARIDT 1.0: variability of drug transporter database

(2019) Jiayi Yin et al.   NUCLEIC ACIDS RESEARCH

pseudoQC: A Regression‐Based Simulation Software for Correction and Normalization of Complex Metabolomics and Proteomics Datasets

(2019) Shisheng Wang et al.   PROTEOMICS

A novel bioinformatics approach to identify the consistently well-performing normalization strategy for current metabolomic studies

(2019) Qingxia Yang et al.   BRIEFINGS IN BIOINFORMATICS

Convolutional neural network-based annotation of bacterial type IV secretion system effectors with enhanced accuracy and reduced false discovery

(2019) Jiajun Hong et al.   BRIEFINGS IN BIOINFORMATICS

WebSpecmine: A Website for Metabolomics Data Analysis and Mining

(2019) Sara Cardoso et al.   Metabolites

What Contributes to Serotonin–Norepinephrine Reuptake Inhibitors’ Dual-Targeting Mechanism? The Key Role of Transmembrane Domain 6 in Human Serotonin and Norepinephrine Transporters Revealed by Molecular Dynamics Simulation

(2018) Weiwei Xue et al.   ACS Chemical Neuroscience

Best-Matched Internal Standard Normalization in Liquid Chromatography–Mass Spectrometry Metabolomics Applied to Environmental Samples

(2018) Angela K. Boysen et al.   ANALYTICAL CHEMISTRY

NormalizeMets: assessing, selecting and implementing statistical methods for normalizing metabolomics data

(2018) Alysha M. De Livera et al.   Metabolomics

Cancer-cell-secreted exosomal miR-105 promotes tumour growth through the MYC-dependent metabolic reprogramming of stromal cells

(2018) Wei Yan et al.   NATURE CELL BIOLOGY

Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online

(2018) Erica M Forsberg et al.   Nature Protocols

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis

(2018) Jasmine Chong et al.   NUCLEIC ACIDS RESEARCH

Simultaneous detection of multiple inherited metabolic diseases using GC-MS urinary metabolomics by chemometrics multi-class classification strategies

(2018) Qin Yang et al.   TALANTA

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

(2018) Tami L. Swenson et al.   Nature Communications

Discovery of the Consistently Well-Performed Analysis Chain for SWATH-MS Based Pharmacoproteomic Quantification

(2018) Jianbo Fu et al.   Frontiers in Pharmacology

Integrative metabolomics and transcriptomics signatures of clinical tolerance to Plasmodium vivax reveal activation of innate cell immunity and T cell signaling

(2018) Luiz G. Gardinassi et al.   Redox Biology

statTarget: A streamlined tool for signal drift correction and interpretations of quantitative mass spectrometry-based omics data

(2018) Hemi Luan et al.   ANALYTICA CHIMICA ACTA

MetaboGroupS: A Group Entropy-Based Web Platform for Evaluating Normalization Methods in Blood Metabolomics Data from Maintenance Hemodialysis Patients

(2018) Shisheng Wang et al.   ANALYTICAL CHEMISTRY

Oxylipin profiling of human plasma reflects the renal dysfunction in uremic patients

(2018) Da-Yong Hu et al.   Metabolomics

Characterization of Cultivar Differences of Blueberry Wines Using GC-QTOF-MS and Metabolic Profiling Methods

(2018) Fang Yuan et al.   MOLECULES

Accumulation of succinate controls activation of adipose tissue thermogenesis

(2018) Evanna L. Mills et al.   NATURE

Arginine-deprivation–induced oxidative damage sterilizes Mycobacterium tuberculosis

(2018) Sangeeta Tiwari et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Seasonal variation of secondary metabolites in nine different bryophytes

(2018) Kristian Peters et al.   Ecology and Evolution

MetFlow: an interactive and integrated workflow for metabolomics data cleaning and differential metabolite discovery

(2018) Xiaotao Shen et al.   BIOINFORMATICS

NormalyzerDE: Online Tool for Improved Normalization of Omics Expression Data and High-Sensitivity Differential Expression Analysis

(2018) Jakob Willforss et al.   JOURNAL OF PROTEOME RESEARCH

PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud

(2018) Kristian Peters et al.   GigaScience

Robust clinical marker identification for diabetic kidney disease with ensemble feature selection

(2018) Xing Song et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

EgoNet identifies differential ego-modules and pathways related to prednisolone resistance in childhood acute lymphoblastic leukemia

(2017) Jian Jiang et al.   Hematology

Create, run, share, publish, and reference your LC–MS, FIA–MS, GC–MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics

(2017) Yann Guitton et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks

(2017) James T. Yurkovich et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The kynurenine pathway and parasitic infections that affect CNS function

(2017) Nicholas H. Hunt et al.   NEUROPHARMACOLOGY

NOREVA: normalization and evaluation of MS-based metabolomics data

(2017) Bo Li et al.   NUCLEIC ACIDS RESEARCH

An efficient data-filtering strategy for easy metabolite detection from the direct analysis of a biological fluid using Fourier transform mass spectrometry

(2017) Estelle Rathahao-Paris et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Controlling the Overfitting of Heritability in Genomic Selection through Cross Validation

(2017) Zhenyu Jia   Scientific Reports

A Pilot Characterization of the Human Chronobiome

(2017) Carsten Skarke et al.   Scientific Reports

Metabolic analysis of the response of Pseudomonas putida DOT-T1E strains to toluene using Fourier transform infrared spectroscopy and gas chromatography mass spectrometry

(2016) Ali Sayqal et al.   Metabolomics

A novel targeted/untargeted GC-Orbitrap metabolomics methodology applied to Candida albicans and Staphylococcus aureus biofilms

(2016) Stefan Weidt et al.   Metabolomics

Large-scale untargeted LC-MS metabolomics data correction using between-batch feature alignment and cluster-based within-batch signal intensity drift correction

(2016) Carl Brunius et al.   Metabolomics

Methodology series module 5: Sampling strategies

(2016) ManinderSingh Setia   INDIAN JOURNAL OF DERMATOLOGY

Performance Evaluation and Online Realization of Data-driven Normalization Methods Used in LC/MS based Untargeted Metabolomics Analysis

(2016) Bo Li et al.   Scientific Reports

Statistical Methods for Handling Unwanted Variation in Metabolomics Data

(2015) Alysha M. De Livera et al.   ANALYTICAL CHEMISTRY

Prioritizing precision medicine for prostate cancer

(2015) G. Attard et al.   ANNALS OF ONCOLOGY

Analysis of the Human Adult Urinary Metabolome Variations with Age, Body Mass Index, and Gender by Implementing a Comprehensive Workflow for Univariate and OPLS Statistical Analyses

(2015) Etienne A. Thévenot et al.   JOURNAL OF PROTEOME RESEARCH

Optimal consistency in microRNA expression analysis using reference-gene-based normalization

(2015) Xi Wang et al.   Molecular BioSystems

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools

(2015) Manish Sud et al.   NUCLEIC ACIDS RESEARCH

Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms

(2015) Young-Mo Kim et al.   Frontiers in Microbiology

Normalyzer: A Tool for Rapid Evaluation of Normalization Methods for Omics Data Sets

(2014) Aakash Chawade et al.   JOURNAL OF PROTEOME RESEARCH

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

A Formal Algorithm for Verifying the Validity of Clustering Results Based on Model Checking

(2014) Shaobin Huang et al.   PLoS One

Normalizing and Integrating Metabolomics Data

(2012) Alysha M. De Livera et al.   ANALYTICAL CHEMISTRY

A benchmark spike-in data set for biomarker identification in metabolomics

(2012) Pietro Franceschi et al.   JOURNAL OF CHEMOMETRICS

The role of indirect connections in gene networks in predicting function

(2011) Jesse Gillis et al.   BIOINFORMATICS

Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst

(2011) Jianguo Xia et al.   Nature Protocols

Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry

(2011) Warwick B Dunn et al.   Nature Protocols

Trend analysis of time-series data: A novel method for untargeted metabolite discovery

(2010) Sonja Peters et al.   ANALYTICA CHIMICA ACTA

Evaluating Stability and Comparing Output of Feature Selectors that Optimize Feature Subset Cardinality

(2010) Petr Somol et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Development of a Robust and Repeatable UPLC−MS Method for the Long-Term Metabolomic Study of Human Serum

(2009) Eva Zelena et al.   ANALYTICAL CHEMISTRY

Normalization strategies for metabonomic analysis of urine samples

(2009) Bethanne M. Warrack et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

Analytical Error Reduction Using Single Point Calibration for Accurate and Precise Metabolomic Phenotyping

(2009) Frans M. van der Kloet et al.   JOURNAL OF PROTEOME RESEARCH

On Gene Ranking Using Replicated Microarray Time Course Data

(2008) Yu Chuan Tai et al.   BIOMETRICS