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

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

NMR and MS reveal characteristic metabolome atlas and optimize esophageal squamous cell carcinoma early detection

Lijing Xin, Yan Lin, Wei Ye, Yubo Zhao

Metabolic changes precede malignant histology. However, it remains unclear whether detectable characteristic metabolome exists in esophageal squamous cell carcinoma (ESCC) tissues and biofluids for early diagnosis. Here, we conduct NMR- and MS-based metabo ...

Nature Portfolio2024

Spectral Estimators for High-Dimensional Matrix Inference

Farzad Pourkamali

A key challenge across many disciplines is to extract meaningful information from data which is often obscured by noise. These datasets are typically represented as large matrices. Given the current trend of ever-increasing data volumes, with datasets grow ...

EPFL2024

Random matrix methods for high-dimensional machine learning models

Antoine Philippe Michel Bodin

In the rapidly evolving landscape of machine learning research, neural networks stand out with their ever-expanding number of parameters and reliance on increasingly large datasets. The financial cost and computational resources required for the training p ...

EPFL2024

Deciphering the nature of cell state transitions in single cells using quantitative modeling of temporal dynamics

Alex Russell Lederer

Cells are the smallest operational units of living systems. Through synthesis of various biomolecules and exchange of signals with the environment, cells tightly regulate their composition to realize a specific functional state. The transformation of a cel ...

EPFL2024

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 ...

2023

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"

Matias Janvin, Mats Julius Stensrud

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

Advancing Glycan Analysis: Cryogenic Ion Spectroscopy for Database-Driven Identification

Ali H Abikhodr

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

An Unbiased Method of Measuring the Ratio of Two Data Sets

Jean-Paul Richard Kneib, Huanyuan Shan

In certain cases of astronomical data analysis, the meaningful physical quantity to extract is the ratio R between two data sets. Examples include the lensing ratio, the interloper rate in spectroscopic redshift samples, and the decay rate of gravitational ...

IOP Publishing Ltd2023

Higher Order Asymptotics: Applications to Satellite Conjunction and Boundary Problems

Soumaya Elkantassi

Higher-order asymptotics provide accurate approximations for use in parametric statistical modelling. In this thesis, we investigate using higher-order approximations in two-specific settings, with a particular emphasis on the tangent exponential model. ...

EPFL2023

Machine Learning Security in Industry: A Quantitative Survey

Kathrin Grosse

Despite the large body of academic work on machine learning security, little is known about the occurrence of attacks on machine learning systems in the wild. In this paper, we report on a quantitative study with 139 industrial practitioners. We analyze at ...

IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2023

Identification of human milk oligosaccharide positional isomers by combining IMS-CID-IMS and cryogenic IR spectroscopy

Thomas Rizzo, Ahmed Ben Faleh, Stephan Warnke, Ali H Abikhodr, Vasyl Yatsyna

High-resolution ion mobility spectrometry (IMS) coupled with cryogenic infrared spectroscopy has proven to be a powerful technique for the identification of oligosaccharides. However, the need for an extensive database, combined with the scarcity of pure s ...

2023

Modelling of metal alloys in realistic conditions with machine learning

Nataliya Lopanitsyna

Computer simulations based on statistical methods have emerged as a powerful tool for studying structure-property relationships at the atomistic level. However, to provide reliable insights into materials in realistic conditions, it is essential to accurat ...

EPFL2023

Investigating the bioaccumulation potential of anionic organic compounds using a permanent rainbow trout liver cell line

Kristin Schirmer, Fabian Gerhard Peter Balk, Juliane Hollender

Permanent rainbow trout (Oncorhynchus mykiss) cell lines represent potential in vitro alternatives to experiments with fish. We here developed a method to assess the bioaccumulation potential of anionic organic compounds in fish, using the rainbow trout li ...

PERGAMON-ELSEVIER SCIENCE LTD2023

Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics

Hamed Khakzad

Author summaryIn recent years, the application of deep learning represented a breakthrough in the mass spectrometry (MS) field by improving the assignment of the correct sequence of amino acids from observable MS spectra without prior knowledge, also known ...

PUBLIC LIBRARY SCIENCE2023

Combining ion mobility spectrometry and cryogenic ion spectroscopy with enzymatic digestion/synthesis for the study of N-linked glycans

Irina Märki

Glycans play an essential role in numerous physiological and pathological processes of living organisms. Despite their significant biological relevance, glycobiology remains one of the least explored fields of biochemistry. The intrinsic isomeric complexit ...

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

A New Strategy Coupling Ion-Mobility-Selective CID and Cryogenic IR Spectroscopy to Identify Glycan Anomers

Thomas Rizzo, Ahmed Ben Faleh, Robert Paul Pellegrinelli, Stephan Warnke, Priyanka Bansal, Eduardo Carrascosa Casado, Lei Yue

Determining the primary structure of glycans remains challenging due to their isomeric complexity. While high-resolution ion mobility spectrometry (IMS) has recently allowed distinguishing between many glycan isomers, the arrival-time distributions (ATDs) ...

2022

Standard-Free Quantification of Dicarboxylic Acids: Case Studies with Salt-Rich Effluents and Serum

Christian Ludwig, Daniil Salionov, Sasa Bjelic

The present study evaluates the ionization efficiency (IE) of linear and branched C2–C14 dicarboxylic acids (DCAs) by electrospray ionization (ESI) under different conditions. The influence of the concentration of organic modifier (MeOH); mobile phase addi ...

2022

Identification of Mobility-Resolved N-Glycan Isomers

Thomas Rizzo, Ahmed Ben Faleh, Robert Paul Pellegrinelli, Stephan Warnke, Priyanka Bansal

Glycan analysis has evolved considerably during the last decade. The advent of high-resolution ion-mobility spectrometry has enabled the separation of isomers with only the slightest of structural differences. However, the ability to separate such species ...

AMER CHEMICAL SOC2022