RRmix: A method for simultaneous batch effect correction and analysis of metabolomics data in the absence of internal standards

Metabolomics: A Primer

(2017) Xiaojing Liu et al.   TRENDS IN BIOCHEMICAL SCIENCES

A Novel Strategy for Large-Scale Metabolomics Study by Calibrating Gross and Systematic Errors in Gas Chromatography–Mass Spectrometry

(2016) Yanni Zhao et al.   ANALYTICAL CHEMISTRY

Improved batch correction in untargeted MS-based metabolomics

(2016) Ron Wehrens 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

A novel strategy for protein production using non-classical secretion pathway in Bacillus subtilis

(2016) Jingqi Chen et al.   Microbial Cell Factories

Metabolomics: beyond biomarkers and towards mechanisms

(2016) Caroline H. Johnson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Statistical Methods for Handling Unwanted Variation in Metabolomics Data

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

Defining the Metabolome: Size, Flux, and Regulation

(2015) Nicola Zamboni et al.   MOLECULAR CELL

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

MetaboAnalyst 3.0—making metabolomics more meaningful

(2015) Jianguo Xia et al.   NUCLEIC ACIDS RESEARCH

Factor Analysis for Multiple Testing (FAMT): AnRPackage for Large-Scale Significance Testing under Dependence

(2015) David Causeur et al.   Journal of Statistical Software

Development and Quantitative Evaluation of a High-Resolution Metabolomics Technology

(2014) Xiaojing Liu et al.   ANALYTICAL CHEMISTRY

Intensity drift removal in LC/MS metabolomics by common variance compensation

(2014) Francesc Fernández-Albert et al.   BIOINFORMATICS

Metabolomics Data Normalization with EigenMS

(2014) Yuliya V. Karpievitch et al.   PLoS One

Characterization of the Usage of the Serine Metabolic Network in Human Cancer

(2014) Mahya Mehrmohamadi et al.   Cell Reports

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

HEFT: eQTL analysis of many thousands of expressed genes while simultaneously controlling for hidden factors

(2013) Chuan Gao et al.   BIOINFORMATICS

Batch Normalizer: A Fast Total Abundance Regression Calibration Method to Simultaneously Adjust Batch and Injection Order Effects in Liquid Chromatography/Time-of-Flight Mass Spectrometry-Based Metabolomics Data and Comparison with Current Calibration Methods

(2012) San-Yuan Wang et al.   ANALYTICAL CHEMISTRY

Batch effect removal methods for microarray gene expression data integration: a survey

(2012) C. Lazar et al.   BRIEFINGS IN BIOINFORMATICS

Metabolomics: the apogee of the omics trilogy

(2012) Gary J. Patti et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

Laplace Approximated EM Microarray Analysis: An Empirical Bayes Approach for Comparative Microarray Experiments

(2011) Haim Bar et al.   STATISTICAL SCIENCE

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS