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View article: Reticulated platelets in coronary artery disease: a multidimensional approach unveils prothrombotic signalling and novel therapeutic targets
Reticulated platelets in coronary artery disease: a multidimensional approach unveils prothrombotic signalling and novel therapeutic targets Open
Background and Aims Reticulated platelets (RPs), hyperreactive and RNA-rich, are associated with increased risk of cardiovascular events and suboptimal response to antiplatelet therapy in coronary artery disease (CAD). However, the underly…
View article: Privacy-preserving multicenter differential protein abundance analysis with FedProt
Privacy-preserving multicenter differential protein abundance analysis with FedProt Open
Quantitative mass spectrometry has revolutionized proteomics by enabling simultaneous quantification of thousands of proteins. Pooling patient-derived data from multiple institutions enhances statistical power but raises serious privacy co…
View article: Privacy-preserving multicenter differential protein abundance analysis with FedProt
Privacy-preserving multicenter differential protein abundance analysis with FedProt Open
Quantitative mass spectrometry has revolutionized proteomics by enabling simultaneous quantification of thousands of proteins. Pooling patient-derived data from multiple institutions enhances statistical power but raises serious privacy co…
View article: Systematic evaluation of normalization approaches in tandem mass tag and label-free protein quantification data using PRONE
Systematic evaluation of normalization approaches in tandem mass tag and label-free protein quantification data using PRONE Open
Despite the significant progress in accuracy and reliability in mass spectrometry technology, as well as the development of strategies based on isotopic labeling or internal standards in recent decades, systematic biases originating from n…
View article: Systematic Evaluation of Normalization Approaches in Tandem Mass Tag and Label-Free Protein Quantification Data Using PRONE
Systematic Evaluation of Normalization Approaches in Tandem Mass Tag and Label-Free Protein Quantification Data Using PRONE Open
Despite the significant progress in accuracy and reliability in mass spectrometry technology, as well as the development of strategies based on isotopic labeling or internal standards in recent decades, systematic biases originating from n…
View article: NApy: efficient statistics in Python for large-scale heterogeneous data with enhanced support for missing data
NApy: efficient statistics in Python for large-scale heterogeneous data with enhanced support for missing data Open
Background Existing Python libraries and tools lack the ability to efficiently compute statistical test results for large datasets in the presence of missing values. This presents an issue as soon as constraints on runtime and memory avail…
View article: Deep proteome profiling of reticulated platelets in patients with chronic coronary syndrome using mass cytometry
Deep proteome profiling of reticulated platelets in patients with chronic coronary syndrome using mass cytometry Open
Funding Acknowledgements Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Else Körner Fresenius Stiftung (EKFS) Background Immature or reticulated platelets (RPs), a subgroup of larger and RNA-rich p…
View article: Meta-analysis of proteomics data from osteoblasts, bone, and blood: Insights into druggable targets, active factors, and potential biomarkers for bone biomaterial design
Meta-analysis of proteomics data from osteoblasts, bone, and blood: Insights into druggable targets, active factors, and potential biomarkers for bone biomaterial design Open
Non-healing bone defects are a pressing public health concern accounting for one main cause for decreased life expectancy and quality. An aging population accompanied with increasing incidence of comorbidities, foreshadows a worsening of t…
View article: Systematic Evaluation of Normalization Approaches in Tandem Mass Tag and Label-Free Protein Quantification Data
Systematic Evaluation of Normalization Approaches in Tandem Mass Tag and Label-Free Protein Quantification Data Open
Systematic biases introduced throughout every step of clinical studies affect high-throughput omics data. Normalization methods (NMs) aim to adjust for these biases to make the biological signal more prominent. Due to the NM’s potential im…
View article: A systematic comparison of novel and existing differential analysis methods for CyTOF data
A systematic comparison of novel and existing differential analysis methods for CyTOF data Open
Cytometry techniques are widely used to discover cellular characteristics at single-cell resolution. Many data analysis methods for cytometry data focus solely on identifying subpopulations via clustering and testing for differential cell …
View article: Proteomic Meta-Study Harmonization, Mechanotyping and Drug Repurposing Candidate Prediction with ProHarMeD
Proteomic Meta-Study Harmonization, Mechanotyping and Drug Repurposing Candidate Prediction with ProHarMeD Open
Mass spectrometry-based proteomics plays a vital role in biomarker identification and understanding disease mechanisms through mechanotyping. However, utilizing publicly available proteomics data for these purposes poses challenges due to …
View article: CYANUS - a web platform for analyzing drug response markers in cytometry data
CYANUS - a web platform for analyzing drug response markers in cytometry data Open
Cytometry techniques are widely used to analyze cellular characteristics at single-cell resolution. This allows forstudying disease-specific mechanisms and potential drug targets, as well as pre-clinical therapy response indiseases such as…
View article: A Systematic Comparison of Differential Analysis Methods for CyTOF Data
A Systematic Comparison of Differential Analysis Methods for CyTOF Data Open
Cytometry techniques are widely used to discover cellular characteristics at single-cell resolution. Many data analysis methods for cytometry data focus solely on identifying subpopulations via clustering and testing for differential cell …