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DBnorm as an R package for the comparison and selection of appropriate statistical methods for batch effect correction in metabolomic studies

Related publications (32)

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Innovative Biomarkers for Obesity and Type 1 Diabetes Based on Bifidobacterium and Metabolomic Profiling

Stephan Morgenthaler, Paul Refinetti, Mariya Yuryevna Skvortsova

The role of Bifidobacterium species and microbial metabolites such as short-chain fatty acids (SCFAs) and human milk oligosaccharides in controlling intestinal inflammation and the pathogenesis of obesity and type 1 diabetes (T1D) has been largely studied ...

MDPI2024

New Approach for the Identification of Isobaric and Isomeric Metabolites

Thomas Rizzo, Ahmed Ben Faleh, Stephan Warnke, Ali H Abikhodr, Teun Van Wieringen

The structural elucidation of metabolite molecules is important in many branches of the life sciences. However, the isomeric and isobaric complexity of metabolites makes their identification extremely challenging, and analytical standards are often require ...

AMER CHEMICAL SOC2023

We Need Subject Matter Expertise to Choose and Identify Causal Estimands: Comment on "Estimands for Recurrent Event Endpoints in the Presence of a Terminal Event"

Mats Julius Stensrud, Matias Janvin

We summarize what we consider to be the two main limitations of the "Estimands for Recurrent Event Endpoints in the Presence of a Terminal Event" (Schmidli et al. 2022). First, the authors did not give detailed guidance on how to choose an appropriate esti ...

TAYLOR & FRANCIS INC2023

Glycans play a pivotal role in both physiological processes; however, the field of glycobiology remains relatively understudied within biochemistry. The intricate complexity of glycans, coupled with their abundance of isomeric forms, presents formidable ch ...

EPFL2023

Assessing normalization methods in mass spectrometry-based proteome profiling of clinical samples

Loïc Dayon

Background: Large-scale proteomic studies have to deal with unwanted variability, especially when samples originate from different centers and multiple analytical batches are needed. Such variability is typically added throughout all the steps of a clinica ...

ELSEVIER SCI LTD2022

Accelerating photofragmentation UV Spectroscopy–Mass spectrometry fingerprinting for quantification of isomeric peptides

Oleg Boyarkine, Elizaveta Solovyeva, Erik Saparbayev

Identification of isomeric biomolecules remains a challenging analytical problem. A recently developed spectroscopic method that combines UV photofragmentation and mass spectrometry for fingerprinting of cold ions (2D UV-MS), has already demonstrated its h ...

2021

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Insects are frequently infected with heritable bacterial endosymbionts. Endosymbionts have a dramatic impact on their host physiology and evolution. Their tissue distribution is variable with some species being housed intracellularly, some extracellularly ...

2021

Cell-to-cell variability plays a key role in tissue patterning by setting initial asymmetry that primes cell fate decisions. Fluctuations in the activity of regulatory molecules can commit individual cells to divergent differentiation pathways, and cell-to ...

EPFL2021

Exploration of human cerebrospinal fluid: A large proteome dataset revealed by trapped ion mobility time-of-flight mass spectrometry

Loïc Dayon

Cerebrospinal fluid (CSF) is a biofluid in direct contact with the brain and as such constitutes a sample of choice in neu-rological disorder research, including neurodegenerative dis-eases such as Alzheimer or Parkinson. Human CSF has still been less stud ...

ELSEVIER2020

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The ever-increasing availability of transcriptomic and metabolomic data can be used to deeply analyze and make ever-expanding predictions about biological processes, as changes in the reaction fluxes through genome-wide pathways can now be tracked. Current ...

2019