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Open AccessDeviating HER2 test results in gastric cancer: analysis from the prospective multicenter VARIANZ study
The prospective multicenter VARIANZ study aimed to identify resistance biomarkers for HER2-targeted treatment in advanced gastric and esophago-gastric junction cancer (GC, EGJC). HER2 test deviations were foun...
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Article
Open AccessCombining gene expression analysis of gastric cancer cell lines and tumor specimens to identify biomarkers for anti-HER therapies—the role of HAS2, SHB and HBEGF
The standard treatment for patients with advanced HER2-positive gastric cancer is a combination of the antibody trastuzumab and platin-fluoropyrimidine chemotherapy. As some patients do not respond to trastuzu...
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Article
Open AccessNucleo-cytoplasmic shuttling of murine RBPJ by Hairless protein matches that of Su(H) protein in the model system Drosophila melanogaster
CSL transcription factors are central to signal transduction in the highly conserved Notch signaling pathway. CSL acts as a molecular switch: depending on the cofactors recruited, CSL induces either activation...
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Article
Open AccessGenetic interactions between Protein Kinase D and Lobe mutants during eye development of Drosophila melanogaster
In Drosophila, the development of the fly eye involves the activity of several, interconnected pathways that first define the presumptive eye field within the eye anlagen, followed by establishment of the dorso-v...
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Article
Open AccessSTATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse
Multi-omics approaches use a diversity of high-throughput technologies to profile the different molecular layers of living cells. Ideally, the integration of this information should result in comprehensive sys...
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Article
Open AccessThe evolution of transcriptional repressors in the Notch signaling pathway: a computational analysis
The Notch signaling pathway governs the specification of different cell types in flies, nematodes and vertebrates alike. Principal components of the pathway that activate Notch target genes are highly conserve...
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Article
Open AccessWhither systems medicine?
New technologies to generate, store and retrieve medical and research data are inducing a rapid change in clinical and translational research and health care. Systems medicine is the interdisciplinary approach...
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Open AccessEvaluation of epidermal growth factor receptor signaling effects in gastric cancer cell lines by detailed motility-focused phenotypic characterization linked with molecular analysis
Gastric cancers frequently overexpress the epidermal growth factor receptor (EGFR), which has been implicated in pathological processes including tumor cell motility, invasion and metastasis. Targeting EGFR wi...
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Article
Open AccessFrom comorbidities of chronic obstructive pulmonary disease to identification of shared molecular mechanisms by data integration
Deep mining of healthcare data has provided maps of comorbidity relationships between diseases. In parallel, integrative multi-omics investigations have generated high-resolution molecular maps of putative rel...
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Article
Open AccessIn vivo analysis of internal ribosome entry at the Hairless locus by genome engineering in Drosophila
Cell communication in metazoans requires the highly conserved Notch signaling pathway, which is subjected to strict regulation of both activation and silencing. In Drosophila melanogaster, silencing involves the ...
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Article
Open AccessChainRank, a chain prioritisation method for contextualisation of biological networks
Advances in high throughput technologies and growth of biomedical knowledge have contributed to an exponential increase in associative data. These data can be represented in the form of complex networks of bio...
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Article
Open AccessImplementing systems medicine within healthcare
The cause of a complex disease cannot be pinpointed to a single origin; rather, a highly complex network of many factors that interact on different levels over time and space is disturbed. This complexity requ...
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Open AccessSimulation environment and graphical visualization environment: a COPD use-case
Today, many different tools are developed to execute and visualize physiological models that represent the human physiology. Most of these tools run models written in very specific programming languages which ...
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Open AccessBiomedical research in a Digital Health Framework
This article describes a Digital Health Framework (DHF), benefitting from the lessons learnt during the three-year life span of the FP7 Synergy-COPD project. The DHF aims to embrace the emerging requirements -...
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Article
Open AccessSystems Medicine: from molecular features and models to the clinic in COPD
Chronic Obstructive Pulmonary Disease (COPD) patients are characterized by heterogeneous clinical manifestations and patterns of disease progression. Two major factors that can be used to identify COPD subtypes a...
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Open AccessThe COPD Knowledge Base: enabling data analysis and computational simulation in translational COPD research
Previously we generated a chronic obstructive pulmonary disease (COPD) specific knowledge base (http://www.copdknowledgebase.eu) from clinical and experiment...
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Open AccessWorkforce preparation: the Biohealth computing model for Master and PhD students
The article addresses the strategic role of workforce preparation in the process of adoption of Systems Medicine as a driver of biomedical research in the new health paradigm. It reports on relevant initiative...
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Article
Open AccessChronic Obstructive Pulmonary Disease heterogeneity: challenges for health risk assessment, stratification and management
Heterogeneity in clinical manifestations and disease progression in Chronic Obstructive Pulmonary Disease (COPD) lead to consequences for patient health risk assessment, stratification and management. Implicit...
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Article
Open AccessData integration in the era of omics: current and future challenges
To integrate heterogeneous and large omics data constitutes not only a conceptual challenge but a practical hurdle in the daily analysis of omics data. With the rise of novel omics technologies and through lar...
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Open AccessKnowledge management for systems biology a general and visually driven framework applied to translational medicine
To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypothe...
