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Article
Open AccessResults and lessons learned from the sbv IMPROVER metagenomics diagnostics for inflammatory bowel disease challenge
A growing body of evidence links gut microbiota changes with inflammatory bowel disease (IBD), raising the potential benefit of exploiting metagenomics data for non-invasive IBD diagnostics. The sbv IMPROVER m...
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Article
Open AccessCrowdsourced benchmarking of taxonomic metagenome profilers: lessons learned from the sbv IMPROVER Microbiomics challenge
Selection of optimal computational strategies for analyzing metagenomics data is a decisive step in determining the microbial composition of a sample, and this procedure is complex because of the numerous tool...
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Article
Open AccessThe Apoe−/− mouse model: a suitable model to study cardiovascular and respiratory diseases in the context of cigarette smoke exposure and harm reduction
Atherosclerosis-prone apolipoprotein E-deficient (Apoe−/−) mice display poor lipoprotein clearance with subsequent accumulation of cholesterol ester-enriched particles in the blood, which promote the development ...
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Article
Open AccessComprehensive systems biology analysis of a 7-month cigarette smoke inhalation study in C57BL/6 mice
Smoking of combustible cigarettes has a major impact on human health. Using a systems toxicology approach in a model of chronic obstructive pulmonary disease (C57BL/6 mice), we assessed the health consequences...
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Article
Open AccessTranscriptional profiling and targeted proteomics reveals common molecular changes associated with cigarette smoke-induced lung emphysema development in five susceptible mouse strains
Mouse models are useful for studying cigarette smoke (CS)-induced chronic pulmonary pathologies such as lung emphysema. To enhance translation of large-scale omics data from mechanistic studies into pathophysi...
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Article
Open AccessA vascular biology network model focused on inflammatory processes to investigate atherogenesis and plaque instability
Numerous inflammation-related pathways have been shown to play important roles in atherogenesis. Rapid and efficient assessment of the relative influence of each of those pathways is a challenge in the era of ...
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Article
Open AccessThe species translation challenge—A systems biology perspective on human and rat bronchial epithelial cells
The biological responses to external cues such as drugs, chemicals, viruses and hormones, is an essential question in biomedicine and in the field of toxicology, and cannot be easily studied in humans. Thus, b...
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Article
Open AccessGlobal analysis of alternative splicing regulation by insulin and wingless signaling in Drosophilacells
Despite the prevalence and biological relevance of both signaling pathways and alternative pre-mRNA splicing, our knowledge of how intracellular signaling impacts on alternative splicing regulation remains fra...
