Workflow for Evaluating Normalization Tools for Omics Data Using Supervised and Unsupervised Machine Learning

Integrative analysis of multimodal mass spectrometry data in MZmine 3

(2023) Robin Schmid et al.   NATURE BIOTECHNOLOGY

Lipidomic Comparison of 2D and 3D Colon Cancer Cell Culture Models

(2022) Fernando Tobias et al.   JOURNAL OF MASS SPECTROMETRY

How (Not) to Generate a Highly Predictive Biomarker Panel Using Machine Learning

(2022) Heather Desaire   JOURNAL OF PROTEOME RESEARCH

Improved Discrimination of Disease States Using Proteomics Data with the Updated Aristotle Classifier

(2021) David Hua et al.   JOURNAL OF PROTEOME RESEARCH

How to Apply Supervised Machine Learning Tools to MS Imaging Files: Case Study with Cancer Spheroids Undergoing Treatment with the Monoclonal Antibody, Cetuximab

(2020) David Hua et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

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

(2020) Qingxia Yang et al.   NUCLEIC ACIDS RESEARCH

Systematic Evaluation of Normalization Methods for Glycomics Data Based on Performance of Network Inference

(2020) Elisa Benedetti et al.   Metabolites

WaveICA: A novel algorithm to remove batch effects for large-scale untargeted metabolomics data based on wavelet analysis

(2019) Kui Deng et al.   ANALYTICA CHIMICA ACTA

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

NOREVA: normalization and evaluation of MS-based metabolomics data

(2017) Bo Li et al.   NUCLEIC ACIDS RESEARCH

A systematic evaluation of normalization methods in quantitative label-free proteomics

(2016) Tommi Välikangas et al.   BRIEFINGS IN BIOINFORMATICS

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

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

Metabolomics Data Normalization with EigenMS

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

Sample Preparation Strategies for Mass Spectrometry Imaging of 3D Cell Culture Models

(2014) Dorothy R. Ahlf Wheatcraft et al.   Jove-Journal of Visualized Experiments

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

Imaging Mass Spectrometry of Three-Dimensional Cell Culture Systems

(2011) Haohang Li et al.   ANALYTICAL CHEMISTRY

Algorithms and tools for the preprocessing of LC–MS metabolomics data

(2011) Sandra Castillo et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Spheroid-based drug screen: considerations and practical approach

(2009) Juergen Friedrich et al.   Nature Protocols

MetaboAnalyst: a web server for metabolomic data analysis and interpretation

(2009) J. Xia et al.   NUCLEIC ACIDS RESEARCH