Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial

J Čuklina, CH Lee, EG Williams, T Sajic… - Molecular systems …, 2021 - embopress.org
Advancements in mass spectrometry‐based proteomics have enabled experiments
encompassing hundreds of samples. While these large sample sets deliver much‐needed …

Harmonization strategies for multicenter radiomics investigations

R Da-Ano, D Visvikis, M Hatt - Physics in Medicine & Biology, 2020 - iopscience.iop.org
Carrying out large multicenter studies is one of the key goals to be achieved towards a faster
transfer of the radiomics approach in the clinical setting. This requires large-scale radiomics …

A guide to ComBat harmonization of imaging biomarkers in multicenter studies

F Orlhac, JJ Eertink, AS Cottereau… - Journal of Nuclear …, 2022 - jnm.snmjournals.org
The impact of PET image acquisition and reconstruction parameters on SUV measurements
or radiomic feature values is widely documented. This scanner effect is detrimental to the …

Faecal microbiome-based machine learning for multi-class disease diagnosis

Q Su, Q Liu, RI Lau, J Zhang, Z Xu, YK Yeoh… - Nature …, 2022 - nature.com
Systemic characterisation of the human faecal microbiome provides the opportunity to
develop non-invasive approaches in the diagnosis of a major human disease. However …

[HTML][HTML] Genetic drivers of epigenetic and transcriptional variation in human immune cells

L Chen, B Ge, FP Casale, L Vasquez, T Kwan… - Cell, 2016 - cell.com
Characterizing the multifaceted contribution of genetic and epigenetic factors to disease
phenotypes is a major challenge in human genetics and medicine. We carried out high …

Histone H3F3A and HIST1H3B K27M mutations define two subgroups of diffuse intrinsic pontine gliomas with different prognosis and phenotypes

D Castel, C Philippe, R Calmon, L Le Dret… - Acta …, 2015 - Springer
Diffuse intrinsic pontine glioma (DIPG) is the most severe paediatric solid tumour, with no
significant therapeutic progress made in the past 50 years. Recent studies suggest that …

Assessment of variability in the SOMAscan assay

J Candia, F Cheung, Y Kotliarov, G Fantoni, B Sellers… - Scientific reports, 2017 - nature.com
SOMAscan is an aptamer-based proteomics assay capable of measuring 1,305 human
protein analytes in serum, plasma, and other biological matrices with high sensitivity and …

Transcriptional atlas of intestinal immune cells reveals that neuropeptide α-CGRP modulates group 2 innate lymphoid cell responses

H Xu, J Ding, CBM Porter, A Wallrapp, M Tabaka, S Ma… - Immunity, 2019 - cell.com
Signaling abnormalities in immune responses in the small intestine can trigger chronic type
2 inflammation involving interaction of multiple immune cell types. To systematically …

Performance comparison of modified ComBat for harmonization of radiomic features for multicenter studies

R Da-Ano, I Masson, F Lucia, M Doré, P Robin… - Scientific reports, 2020 - nature.com
Multicenter studies are needed to demonstrate the clinical potential value of radiomics as a
prognostic tool. However, variability in scanner models, acquisition protocols and …

ProteomicsDB: a multi-omics and multi-organism resource for life science research

P Samaras, T Schmidt, M Frejno… - Nucleic acids …, 2020 - academic.oup.com
Abstract ProteomicsDB (https://www. ProteomicsDB. org) started as a protein-centric in-
memory database for the exploration of large collections of quantitative mass spectrometry …