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 …

Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling

Y Yu, W Hou, Y Liu, H Wang, L Dong, Y Mai… - Nature …, 2024 - nature.com
Certified RNA reference materials are indispensable for assessing the reliability of RNA
sequencing to detect intrinsically small biological differences in clinical settings, such as …

Intercellular pathways of cancer treatment-related cardiotoxicity and their therapeutic implications: the paradigm of radiotherapy

S Logotheti, A Pavlopoulou, HK Rudsari… - Pharmacology & …, 2024 - Elsevier
Advances in cancer therapeutics have improved patient survival rates. However, cancer
survivors may suffer from adverse events either at the time of therapy or later in life …

Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method

Y Yu, N Zhang, Y Mai, L Ren, Q Chen, Z Cao, Q Chen… - Genome biology, 2023 - Springer
Background Batch effects are notoriously common technical variations in multiomics data
and may result in misleading outcomes if uncorrected or over-corrected. A plethora of batch …

A real-world multi-center RNA-seq benchmarking study using the Quartet and MAQC reference materials

D Wang, Y Liu, Y Zhang, Q Chen, Y Han, W Hou… - Nature …, 2024 - nature.com
Translating RNA-seq into clinical diagnostics requires ensuring the reliability and cross-
laboratory consistency of detecting clinically relevant subtle differential expressions, such as …

Multi-OMICS approaches in cancer biology: New era in cancer therapy

S Chakraborty, G Sharma, S Karmakar… - Biochimica et Biophysica …, 2024 - Elsevier
Innovative multi-omics frameworks integrate diverse datasets from the same patients to
enhance our understanding of the molecular and clinical aspects of cancers. Advanced …

Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance

L Ren, X Duan, L Dong, R Zhang, J Yang, Y Gao… - Genome Biology, 2023 - Springer
Background Genomic DNA reference materials are widely recognized as essential for
ensuring data quality in omics research. However, relying solely on reference datasets to …

The Quartet Data Portal: integration of community-wide resources for multiomics quality control

J Yang, Y Liu, J Shang, Q Chen, Q Chen, L Ren… - Genome Biology, 2023 - Springer
Abstract The Quartet Data Portal facilitates community access to well-characterized
reference materials, reference datasets, and related resources established based on a …

Exposome-wide ranking to uncover environmental chemicals associated with dyslipidemia: a panel study in healthy older Chinese adults from the BAPE study

E Ding, F Deng, J Fang, J Liu, W Yan… - Environmental …, 2024 - ehp.niehs.nih.gov
Background: Environmental contaminants (ECs) are increasingly recognized as crucial
drivers of dyslipidemia and cardiovascular disease (CVD), but the comprehensive impact …

A review of artificial intelligence based biological-tree construction: priorities, methods, applications and trends

Z Zang, Y Xu, C Duan, J Wu, SZ Li, Z Lei - arxiv preprint arxiv:2410.04815, 2024 - arxiv.org
Biological tree analysis serves as a pivotal tool in uncovering the evolutionary and
differentiation relationships among organisms, genes, and cells. Its applications span …