[HTML][HTML] Data harmonisation for information fusion in digital healthcare: A state-of-the-art systematic review, meta-analysis and future research directions

Y Nan, J Del Ser, S Walsh, C Schönlieb, M Roberts… - Information …, 2022 - Elsevier
Removing the bias and variance of multicentre data has always been a challenge in large
scale digital healthcare studies, which requires the ability to integrate clinical features …

Assessing and mitigating batch effects in large-scale omics studies

Y Yu, Y Mai, Y Zheng, L Shi - Genome Biology, 2024 - Springer
Batch effects in omics data are notoriously common technical variations unrelated to study
objectives, and may result in misleading outcomes if uncorrected, or hinder biomedical …

[PDF][PDF] ComBat-seq: batch effect adjustment for RNA-seq count data

Y Zhang, G Parmigiani… - NAR genomics and …, 2020 - academic.oup.com
The benefit of integrating batches of genomic data to increase statistical power is often
hindered by batch effects, or unwanted variation in data caused by differences in technical …

Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes

JP Jacobs, V Lagishetty, MC Hauer, JS Labus… - Microbiome, 2023 - Springer
Background Irritable bowel syndrome (IBS) is a common gastrointestinal disorder that is
thought to involve alterations in the gut microbiome, but robust microbial signatures have …

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

JT Leek, WE Johnson, HS Parker, AE Jaffe… - …, 2012 - academic.oup.com
Heterogeneity and latent variables are now widely recognized as major sources of bias and
variability in high-throughput experiments. The most well-known source of latent variation in …

Site effects how-to and when: An overview of retrospective techniques to accommodate site effects in multi-site neuroimaging analyses

JMM Bayer, PM Thompson, CRK Ching, M Liu… - Frontiers in …, 2022 - frontiersin.org
Site differences, or systematic differences in feature distributions across multiple data-
acquisition sites, are a known source of heterogeneity that may adversely affect large-scale …

Machine learning analysis of lung squamous cell carcinoma gene expression datasets reveals novel prognostic signatures

HK Joon, A Thalor, D Gupta - Computers in Biology and Medicine, 2023 - Elsevier
Background Lung squamous cell carcinoma (LUSC) patients are often diagnosed at an
advanced stage and have poor prognoses. Thus, identifying novel biomarkers for the LUSC …

Systematic review of functional MRI applications for psychiatric disease subtyping

L Miranda, R Paul, B Pütz, N Koutsouleris… - Frontiers in …, 2021 - frontiersin.org
Background: Psychiatric disorders have been historically classified using symptom
information alone. Recently, there has been a dramatic increase in research interest not only …

Identification of BRCA1/2 mutation female carriers using circulating microRNA profiles

K Elias, U Smyczynska, K Stawiski, Z Nowicka… - Nature …, 2023 - nature.com
Identifying germline BRCA1/2 mutation carriers is vital for reducing their risk of breast and
ovarian cancer. To derive a serum miRNA-based diagnostic test we used samples from 653 …

[HTML][HTML] Machine learning assisted analysis of breast cancer gene expression profiles reveals novel potential prognostic biomarkers for triple-negative breast cancer

A Thalor, HK Joon, G Singh, S Roy, D Gupta - Computational and structural …, 2022 - Elsevier
Tumor heterogeneity and the unclear metastasis mechanisms are the leading cause for the
unavailability of effective targeted therapy for Triple-negative breast cancer (TNBC), a breast …