Wanwan Hou
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View article: A ratio-based framework using Quartet reference materials for integrating long- and short-read RNA-seq
A ratio-based framework using Quartet reference materials for integrating long- and short-read RNA-seq Open
Long-read RNA sequencing (lrRNA-seq) enables full-length transcript profiling but is confounded by technical batch effects that compromise quantification and prevent data integration across platforms, protocols, and laboratories. The lack …
View article: Metabolic Master Switch: Pyruvate Carboxylase Fuels Antimicrobial Resistance and Virulence in Foodborne Staphylococcus aureus
Metabolic Master Switch: Pyruvate Carboxylase Fuels Antimicrobial Resistance and Virulence in Foodborne Staphylococcus aureus Open
Staphylococcus aureus, a major cause of foodborne illness globally, presents significant challenges due to its multidrug resistance and biofilm-forming capabilities. Pyruvate carboxylase (PycA), a metabolic master switch linking glycolysis…
View article: Quantitative methylation reference datasets of Quartet DNA reference materials for benchmarking genome-wide epigenome sequencing
Quantitative methylation reference datasets of Quartet DNA reference materials for benchmarking genome-wide epigenome sequencing Open
The absence of cross-lab and cross-replicate reproducibility assessments and the lack of quantitative methylation reference datasets (ground truth) impedes benchmarking genome-wide epigenome sequencing for its intended use in clinical sett…
View article: Ultrasonic Hemodynamics of Middle Meningeal Artery in Chronic Subdural Hematoma
Ultrasonic Hemodynamics of Middle Meningeal Artery in Chronic Subdural Hematoma Open
Utilizing CDUS in a half-open mouth position is a feasible method for evaluating extracranial MMA. Monitoring hemodynamic changes in the MMA of patients with CSDH postsurgery holds significant value in indicating the potential for postoper…
View article: Inhibitory Effects of Lactobionic Acid on Biofilm Formation and Virulence of Staphylococcus aureus
Inhibitory Effects of Lactobionic Acid on Biofilm Formation and Virulence of Staphylococcus aureus Open
Staphylococcus aureus biofilm is a common bio-contaminant source that leads to food cross-contamination and foodborne disease outbreaks. Hence, there is a need for searching novel antibiofilm agents with potential anti-virulence properties…
View article: A real-world multi-center RNA-seq benchmarking study using the Quartet and MAQC reference materials
A real-world multi-center RNA-seq benchmarking study using the Quartet and MAQC reference materials Open
Translating RNA-seq into clinical diagnostics requires ensuring the reliability and cross-laboratory consistency of detecting clinically relevant subtle differential expressions, such as those between different disease subtypes or stages. …
View article: Integrated molecular portraits of breast cancer
Integrated molecular portraits of breast cancer Open
The associated article reports multiomic analysis of breast cancers, where we provided a unique public resource that contributes novel insights into the breast cancer, holding promise for further precision treatment approaches. This protoc…
View article: Quartet metabolite reference materials for inter-laboratory proficiency test and data integration of metabolomics profiling
Quartet metabolite reference materials for inter-laboratory proficiency test and data integration of metabolomics profiling Open
Background Various laboratory-developed metabolomic methods lead to big challenges in inter-laboratory comparability and effective integration of diverse datasets. Results As part of the Quartet Project, we establish a publicly available s…
View article: Toward Best Practice in Identifying Subtle Differential Expression with RNA-seq: A Real-World Multi-Center Benchmarking Study Using Quartet and MAQC Reference Materials
Toward Best Practice in Identifying Subtle Differential Expression with RNA-seq: A Real-World Multi-Center Benchmarking Study Using Quartet and MAQC Reference Materials Open
Translating RNA-seq into clinical diagnostics requires ensuring the reliability of detecting clinically relevant subtle differential expressions, such as those between different disease subtypes or stages. Moreover, cross-laboratory reprod…
View article: Toward Best Practice in Identifying Subtle Differential Expression with RNA-seq: A Real-World Multi-Center Benchmarking Study Using Quartet and MAQC Reference Materials
Toward Best Practice in Identifying Subtle Differential Expression with RNA-seq: A Real-World Multi-Center Benchmarking Study Using Quartet and MAQC Reference Materials Open
Translating RNA-seq into clinical diagnostics requires ensuring the reliability of detecting clinically relevant subtle differential expressions, such as those between different disease subtypes or stages. Moreover, cross-laboratory reprod…
View article: Integrated molecular portraits of breast cancer
Integrated molecular portraits of breast cancer Open
The associated article reports multiomic analysis of breast cancers, where we provided a unique public resource that contributes novel insights into the breast cancer, holding promise for further precision treatment approaches. This protoc…
View article: Plasma-Free Blood as a Potential Alternative to Whole Blood for Transcriptomic Analysis
Plasma-Free Blood as a Potential Alternative to Whole Blood for Transcriptomic Analysis Open
RNA sequencing (RNAseq) technology has become increasingly important in precision medicine and clinical diagnostics, and emerged as a powerful tool for identifying protein-coding genes, performing differential gene analysis, and inferring …
View article: Plasma-free samples for transcriptomic analysis: a potential alternative to whole blood samples
Plasma-free samples for transcriptomic analysis: a potential alternative to whole blood samples Open
RNA sequencing (RNAseq) technology has become increasingly important in precision medicine and clinical diagnostics and emerged as a powerful tool for identifying protein-coding genes, performing differential gene analysis, and inferring i…
View article: Ratio-based quantitative multiomics profiling using universal reference materials empowers data integration
Ratio-based quantitative multiomics profiling using universal reference materials empowers data integration Open
Multiomics profiling is a powerful tool to characterize the same samples with complementary features orchestrating the genome, epigenome, transcriptome, proteome, and metabolome. However, the lack of ground truth hampers the objective asse…
View article: Quartet RNA reference materials and ratio-based reference datasets for reliable transcriptomic profiling
Quartet RNA reference materials and ratio-based reference datasets for reliable transcriptomic profiling Open
As an indispensable tool for transcriptome-wide analysis of differential gene expression, RNA sequencing (RNAseq) has demonstrated great potential in clinical applications such as companion diagnostics and prognostics. However, there is a …
View article: Quartet metabolite reference materials for assessing inter-laboratory reliability and data integration of metabolomic profiling
Quartet metabolite reference materials for assessing inter-laboratory reliability and data integration of metabolomic profiling Open
Various laboratory-developed metabolomic methods lead to big challenges in inter-laboratory comparability and effective integration of diverse datasets. As part of the Quartet Project, we established a publicly available suite of four meta…
View article: Correlation Analysis between GlpQ-Regulated Degradation of Wall Teichoic Acid and Biofilm Formation Triggered by Lactobionic Acid in Staphylococcus aureus
Correlation Analysis between GlpQ-Regulated Degradation of Wall Teichoic Acid and Biofilm Formation Triggered by Lactobionic Acid in Staphylococcus aureus Open
Staphylococcus aureus biofilms are a serious problem in the food industry. Wall teichoic acid (WTA) is crucial in S. aureus biofilm formation. Overexpression of the WTA-hydrolyzing enzyme glycerophosphoryl diester phosphodiesterase (GlpQ),…
View article: Ratio-based quantitative multiomics profiling using universal reference materials empowers data integration
Ratio-based quantitative multiomics profiling using universal reference materials empowers data integration Open
Multiomics profiling is a powerful tool to characterize the same samples with complementary features orchestrating the genome, epigenome, transcriptome, proteome, and metabolome. However, the lack of ground truth hampers the objective asse…
View article: Correcting batch effects in large-scale multiomic studies using a reference-material-based ratio method
Correcting batch effects in large-scale multiomic studies using a reference-material-based ratio method Open
Batch effects are notorious technical variations that are common in multiomic data and may result in misleading outcomes. With the era of big data, tackling batch effects in multiomic integration is urgently needed. As part of the Quartet …
View article: Quartet DNA reference materials and datasets for comprehensively evaluating germline variants calling performance
Quartet DNA reference materials and datasets for comprehensively evaluating germline variants calling performance Open
Current methods for evaluating the accuracy of germline variant calls are restricted to easy-to-detect high-confidence regions, thus ignoring a substantial portion of difficult variants beyond the benchmark regions. We established four DNA…
View article: Quartet RNA reference materials and ratio-based reference datasets for reliable transcriptomic profiling
Quartet RNA reference materials and ratio-based reference datasets for reliable transcriptomic profiling Open
As an indispensable tool for transcriptome-wide analysis of differential gene expression, RNA sequencing (RNAseq) has demonstrated great potential in clinical applications. However, the lack of multi-group RNA reference materials of biolog…