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Application of MATLAB in -Omics and Systems Biology [chapter]

Arsen Arakelyan, Lilit Nersisyan, Anna Hakobyan
2016 Applications from Engineering with MATLAB Concepts  
Additionally, we have created a KEGGParser tool for parsing, editing, and visualizing Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway maps.  ...  We have used these tools to obtain a collection of KEGG pathways and evaluate their activity changes in different clinical forms of pulmonary sarcoidosis (PS).  ...  KEGGParser KEGGParser is a MATLAB graph-based graphical user interface tool for parsing, editing, visualization, and analysis of biological pathway maps from Kyoto Encyclopedia of Genes and Genomes (KEGG  ... 
doi:10.5772/62847 fatcat:iogbyxvxy5fhbi6yvabccu3qyy

KENeV : A web-application for the automated reconstruction and visualization of the enriched metabolic and signaling super-pathways deriving from genomic experiments

Eleftherios Pilalis, Theodoros Koutsandreas, Ioannis Valavanis, Emmanouil Athanasiadis, George Spyrou, Aristotelis Chatziioannou
2015 Computational and Structural Biotechnology Journal  
enriched KEGG metabolic and signaling pathways, merged into two respective, non-redundant super-networks.  ...  Existing tools enable pathway analysis, visualization, or pathway merging but none integrates a fully automated workflow, combining all above-mentioned modules and destined to non-programmer users.  ...  Acknowledgments The presented work in this article has been cofunded by European and Greek National Funds, through the Greek National Strategic Reference  ... 
doi:10.1016/j.csbj.2015.03.009 pmid:26925206 pmcid:PMC4733223 fatcat:x5xaonbwmnhtnet5mtdhaaaoae

Telomere maintenance pathway activity analysis enables tissue- and gene-level inferences [article]

Lilit Nersisyan, Arman Simonyan, Hans Binder, Arsen Arakelyan
2021 bioRxiv   pre-print
Application to healthy human tissues showed high ALT and TEL pathway activities in testis, and identified genes and pathways that may trigger TMM activation.  ...  In this study, we have performed literature based reconstruction of signaling pathways for the ALT and TEL TMMs.  ...  KEGGParser: Parsing and editing KEGG pathway maps in Matlab. Bioinformatics 29, 518-519. Bechter, O. E., Zou, Y., Walker, W., Wright, W. E., and Shay, J. W. (2004).  ... 
doi:10.1101/2021.02.01.429081 fatcat:gotldxuc75garpberecfkhteiu