Tanja Laske
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View article: Systematic Comparison of Bone Proteome Extraction Methods to Allow for Integrated Proteomics–Metabolomics Correlation
Systematic Comparison of Bone Proteome Extraction Methods to Allow for Integrated Proteomics–Metabolomics Correlation Open
Bone tissue poses significant challenges for proteomic analysis due to its dense, mineral-rich matrix and predominance of collagen, overshadowing low-abundance proteins critical for understanding bone physiology during LC-MS/MS-based prote…
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: DRaCOon: a novel algorithm for pathway-level differential co-expression analysis in transcriptomics
DRaCOon: a novel algorithm for pathway-level differential co-expression analysis in transcriptomics Open
Understanding the molecular mechanisms underlying diseases is crucial for more precise, personalized medicine. Pathway-level differential co-expression analysis, a powerful approach for transcriptomics, identifies condition-specific change…
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: Meta-analysis of genomic characteristics for antiviral influenza defective interfering particle prioritization
Meta-analysis of genomic characteristics for antiviral influenza defective interfering particle prioritization Open
Defective interfering particles (DIPs) are viral deletion mutants that hamper virus replication and are, thus, potent novel antiviral agents. To evaluate possible antiviral treatments, we first need to get a deeper understanding of DIP cha…
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: UnPaSt: unsupervised patient stratification by differentially expressed biclusters in omics data
UnPaSt: unsupervised patient stratification by differentially expressed biclusters in omics data Open
Most complex diseases, including cancer and non-malignant diseases like asthma, have distinct molecular subtypes that require distinct clinical approaches. However, existing computational patient stratification methods have been benchmarke…
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: <i>De-novo</i>reconstruction and identification of transcriptional gene regulatory network modules differentiating single-cell clusters
<i>De-novo</i>reconstruction and identification of transcriptional gene regulatory network modules differentiating single-cell clusters Open
Single-cell RNA sequencing (scRNA-seq) technology provides an unprecedented opportunity to understand gene functions and interactions at single-cell resolution. While computational tools for scRNA-seq data analysis to decipher differential…
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: 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: Cell Bank Origin of MDCK Parental Cells Shapes Adaptation to Serum-Free Suspension Culture and Canine Adenoviral Vector Production
Cell Bank Origin of MDCK Parental Cells Shapes Adaptation to Serum-Free Suspension Culture and Canine Adenoviral Vector Production Open
Phenotypic variation in cultured mammalian cell lines is known to be induced by passaging and culture conditions. Yet, the effect these variations have on the production of viral vectors has been overlooked. In this work we evaluated the i…
View article: Model-based approach for predicting the impact of genetic modifications on product yield in biopharmaceutical manufacturing—Application to influenza vaccine production
Model-based approach for predicting the impact of genetic modifications on product yield in biopharmaceutical manufacturing—Application to influenza vaccine production Open
A large group of biopharmaceuticals is produced in cell lines. The yield of such products can be increased by genetic engineering of the corresponding cell lines. The prediction of promising genetic modifications by mathematical modeling i…
View article: Production of Defective Interfering Particles of Influenza A Virus in Parallel Continuous Cultures at Two Residence Times—Insights From qPCR Measurements and Viral Dynamics Modeling
Production of Defective Interfering Particles of Influenza A Virus in Parallel Continuous Cultures at Two Residence Times—Insights From qPCR Measurements and Viral Dynamics Modeling Open
Defective interfering particles (DIPs) are a natural byproduct of influenza A virus (IAV) replication. DIPs interfere with the propagation and spread of infectious standard virus (STV), reduce virus yields by competing for viral and cellul…
View article: Model-based analysis of influenza A virus replication in genetically engineered cell lines elucidates the impact of host cell factors on key kinetic parameters of virus growth
Model-based analysis of influenza A virus replication in genetically engineered cell lines elucidates the impact of host cell factors on key kinetic parameters of virus growth Open
The best measure to limit spread of contagious diseases caused by influenza A viruses (IAVs) is annual vaccination. The growing global demand for low-cost vaccines requires the establishment of high-yield production processes. One possible…
View article: Multiscale modeling of influenza A virus replication in cell cultures predicts infection dynamics for highly different infection conditions
Multiscale modeling of influenza A virus replication in cell cultures predicts infection dynamics for highly different infection conditions Open
Influenza A viruses (IAV) are commonly used to infect animal cell cultures for research purposes and vaccine production. Their replication is influenced strongly by the multiplicity of infection (MOI), which ranges over several orders of m…
View article: Mathematical modeling as a tool to improve influenza vaccine production processes
Mathematical modeling as a tool to improve influenza vaccine production processes Open
Cell culture-based production of influenza vaccines is emerging as a promising alternative to conventional production in embryonated chicken eggs. Development and establishment of high-yield producer cell lines represents a major challenge…
View article: Analyzing the Impact of Heterogeneity in Genetically Engineered Cell Lines for Influenza Vaccine Production Using Population Balance Modeling
Analyzing the Impact of Heterogeneity in Genetically Engineered Cell Lines for Influenza Vaccine Production Using Population Balance Modeling Open
Engineering of novel cell lines for biotechnological processes, e.g. influenza virus vaccine production, can be achieved by the genetic modification of host cell gene expression. Therefore, versatile genome editing methods such as lentivir…