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A comparison of mechanistic signaling pathway activity analysis methods
Understanding the aspects of cell functionality that account for disease mechanisms or drug
modes of action is a main challenge for precision medicine. Classical gene-based …
modes of action is a main challenge for precision medicine. Classical gene-based …
Babelomics 5.0: functional interpretation for new generations of genomic data
Babelomics has been running for more than one decade offering a user-friendly interface for
the functional analysis of gene expression and genomic data. Here we present its fifth …
the functional analysis of gene expression and genomic data. Here we present its fifth …
High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes
Understanding the aspects of the cell functionality that account for disease or drug action
mechanisms is a main challenge for precision medicine. Here we propose a new method …
mechanisms is a main challenge for precision medicine. Here we propose a new method …
[HTML][HTML] Subpathway analysis of transcriptome profiles reveals new molecular mechanisms of acquired chemotherapy resistance in breast cancer
Simple Summary The use of diverse omics platforms and small sample sizes in current
studies of cancer chemoresistance limits consensus regarding the molecular mechanisms …
studies of cancer chemoresistance limits consensus regarding the molecular mechanisms …
Understanding disease mechanisms with models of signaling pathway activities
Background Understanding the aspects of the cell functionality that account for disease or
drug action mechanisms is one of the main challenges in the analysis of genomic data and …
drug action mechanisms is one of the main challenges in the analysis of genomic data and …
Gene expression integration into pathway modules reveals a pan-cancer metabolic landscape
Metabolic reprogramming plays an important role in cancer development and progression
and is a well-established hallmark of cancer. Despite its inherent complexity, cellular …
and is a well-established hallmark of cancer. Despite its inherent complexity, cellular …
Using activation status of signaling pathways as mechanism-based biomarkers to predict drug sensitivity
Many complex traits, as drug response, are associated with changes in biological pathways
rather than being caused by single gene alterations. Here, a predictive framework is …
rather than being caused by single gene alterations. Here, a predictive framework is …
Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models
In spite of the increasing availability of genomic and transcriptomic data, there is still a gap
between the detection of perturbations in gene expression and the understanding of their …
between the detection of perturbations in gene expression and the understanding of their …
Using mechanistic models for the clinical interpretation of complex genomic variation
The sustained generation of genomic data in the last decade has increased the knowledge
on the causal mutations of a large number of diseases, especially for highly penetrant …
on the causal mutations of a large number of diseases, especially for highly penetrant …
Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models
The discovery of actionable targets is crucial for targeted therapies and is also a constituent
part of the drug discovery process. The success of an intervention over a target depends …
part of the drug discovery process. The success of an intervention over a target depends …