Scholarly Publications - BCBI

Permanent URI for this collectionhttps://hdl.handle.net/11693/115591

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Browsing Scholarly Publications - BCBI by Subject "Biological model"

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    ChiBE: interactive visualization and manipulation of BioPAX pathway models
    (Oxford University Press, 2010-02-01) Babur, Özgün; Doğrusöz, Uğur; Demir, Emek; Sander, C.
    SUMMARY: Representing models of cellular processes or pathways in a graphically rich form facilitates interpretation of biological observations and generation of new hypotheses. Solving biological problems using large pathway datasets requires software that can combine data mapping, querying and visualization as well as providing access to diverse data resources on the Internet. ChiBE is an open source software application that features user-friendly multi-view display, navigation and manipulation of pathway models in BioPAX format. Pathway views are rendered in a feature-rich format, and may be laid out and edited with state-of-the-art visualization methods, including compound or nested structures for visualizing cellular compartments and molecular complexes. Users can easily query and visualize pathways through an integrated Pathway Commons query tool and analyze molecular profiles in pathway context. AVAILABILITY: http://www.bilkent.edu.tr/%7Ebcbi/chibe.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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    Discovering modulators of gene expression
    (Oxford University Press, 2010-09-01) Babur, Özgün; Demir, Emek; Gönen, M.; Sander, C.; Doğrusöz, Uğur
    Proteins that modulate the activity of transcription factors, often called modulators, play a critical role in creating tissue- and context-specific gene expression responses to the signals cells receive. GEM (Gene Expression Modulation) is a probabilistic framework that predicts modulators, their affected targets and mode of action by combining gene expression profiles, protein-protein interactions and transcription factor-target relationships. Using GEM, we correctly predicted a significant number of androgen receptor modulators and observed that most modulators can both act as co-activators and co-repressors for different target genes. © The Author(s) 2010. Published by Oxford University Press.
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    VISIBIOweb: visualization and layout services for BioPAX pathway models
    (Oxford University Press, 2010-06-01) Dilek, Alptuğ; Belviranlı, Mehmet E.; Doğrusöz, Uğur
    With recent advancements in techniques for cellular data acquisition, information on cellular processes has been increasing at a dramatic rate. Visualization is critical to analyzing and interpreting complex information; representing cellular processes or pathways is no exception. VISIBIOweb is a free, open-source, web-based pathway visualization and layout service for pathway models in BioPAX format. With VISIBIOweb, one can obtain well-laid-out views of pathway models using the standard notation of the Systems Biology Graphical Notation (SBGN), and can embed such views within onés web pages as desired. Pathway views may be navigated using zoom and scroll tools; pathway object properties, including any external database references available in the data, may be inspected interactively. The automatic layout component of VISIBIOweb may also be accessed programmatically from other tools using Hypertext Transfer Protocol (HTTP). The web site is free and open to all users and there is no login requirement. It is available at: http://visibioweb.patika.org. © The Author(s) 2010. Published by Oxford University Press.