ArticleBioinformatics and biology insights2013
Construction of a computable network model for DNA damage, autophagy, cell death, and senescence.
Article in Bioinformatics and biology insights, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
26 citing papers in PubMed.
- The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling.Briefings in bioinformatics · 2021Article
- Article
- NPA: an R package for computing network perturbation amplitudes using gene expression data and two-layer networks.BMC bioinformatics · 2019Article
- Combining relation extraction with function detection for BEL statement extraction.Database : the journal of biological databases and curation · 2019Article
- The extraction of complex relationships and their conversion to biological expression language (BEL) overview of the BioCreative VI (2017) BEL track.Database : the journal of biological databases and curation · 2019Article
- Construction of a Suite of Computable Biological Network Models Focused on Mucociliary Clearance in the Respiratory Tract.Frontiers in genetics · 2019Article
- Systems toxicology meta-analysis ofToxicology research · 2017Article
- Mechanistic Evaluation of the Impact of Smoking and Chronic Obstructive Pulmonary Disease on the Nasal Epithelium.Clinical medicine insights. Circulatory, respiratory and pulmonary medicine · 2017Article
- Ageing in relation to skeletal muscle dysfunction: redox homoeostasis to regulation of gene expression.Mammalian genome : official journal of the International Mammalian Genome Society · 2016Review
- BELTracker: evidence sentence retrieval for BEL statements.Database : the journal of biological databases and curation · 2016Article
- Community-Reviewed Biological Network Models for Toxicology and Drug Discovery Applications.Gene regulation and systems biology · 2016Article
- Semi-Automated Curation Allows Causal Network Model Building for the Quantification of Age-Dependent Plaque Progression in ApoEGene regulation and systems biology · 2016Article
- BioCreative V track 4: a shared task for the extraction of causal network information using the Biological Expression Language.Database : the journal of biological databases and curation · 2016Article
- Impact Assessment of Cigarette Smoke Exposure on Organotypic Bronchial Epithelial Tissue Cultures: A Comparison of Mono-Culture and Coculture Model Containing Fibroblasts.Toxicological sciences : an official journal of the Society of Toxicology · 2015Article
- Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems.Database : the journal of biological databases and curation · 2015Article
- Enhancement of COPD biological networks using a web-based collaboration interface.F1000Research · 2015Article
- In vitro systems toxicology approach to investigate the effects of repeated cigarette smoke exposure on human buccal and gingival organotypic epithelial tissue cultures.Toxicology mechanisms and methods · 2014Article
- An algorithm for score aggregation over causal biological networks based on random walk sampling.BMC research notes · 2014Article
- Proteomics for systems toxicology.Computational and structural biotechnology journal · 2014Review
- Quantification of biological network perturbations for mechanistic insight and diagnostics using two-layer causal models.BMC bioinformatics · 2014Article
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Towards the development of a systems biology-based risk assessment approach for environmental toxicants, including tobacco products in a systems toxicology setting such as the "21st Century Toxicology", we are building a series of computable biological network models specific to non-diseased pulmonary and cardiovascular cells/tissues which capture the molecular events that can be activated following exposure to environmental toxicants. Here we extend on previous work and report on the construction and evaluation of a mechanistic network model focused on DNA damage response and the four main cellular fates induced by stress: autophagy, apoptosis, necroptosis, and senescence. In total, the network consists of 34 sub-models containing 1052 unique nodes and 1538 unique edges which are supported by 1231 PubMed-referenced literature citations. Causal node-edge relationships are described using the Biological Expression Language (BEL), which allows for the semantic representation of life science relationships in a computable format. The Network is provided in .XGMML format and can be viewed using freely available network visualization software, such as Cytoscape.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.