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  • 1
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    The BioPAX Validator (2013)
    Oxford University Press
    Details
    Publication Date: 2013-10-04
    Description: : BioPAX is a community-developed standard language for biological pathway data. A key functionality required for efficient BioPAX data exchange is validation— detecting errors and inconsistencies in BioPAX documents. The BioPAX Validator is a command-line tool, Java library and online web service for BioPAX that performs 〉100 classes of consistency checks. Availability and implementation: The validator recognizes common syntactic errors and semantic inconsistencies and reports them in a customizable human readable format. It can also automatically fix some errors and normalize BioPAX data. Since its release, the validator has become a critical tool for the pathway informatics community, detecting thousands of errors and helping substantially increase the conformity and uniformity of BioPAX-formatted data. The BioPAX Validator is open source and released under LGPL v3 license. All sources, binaries and documentation can be found at sf.net/p/biopax, and the latest stable version of the web application is available at biopax.org/validator. Contact: igor.rodchenkov@utoronto.ca or gary.bader@utoronto.ca
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast (2016)
    Oxford University Press
    Details
    Publication Date: 2016-06-16
    Description: Motivation: Many intracellular signaling processes are mediated by interactions involving peptide recognition modules such as SH3 domains. These domains bind to small, linear protein sequence motifs which can be identified using high-throughput experimental screens such as phage display. Binding motif patterns can then be used to computationally predict protein interactions mediated by these domains. While many protein–protein interaction prediction methods exist, most do not work with peptide recognition module mediated interactions or do not consider many of the known constraints governing physiologically relevant interactions between two proteins. Results: A novel method for predicting physiologically relevant SH3 domain-peptide mediated protein–protein interactions in S. cerevisae using phage display data is presented. Like some previous similar methods, this method uses position weight matrix models of protein linear motif preference for individual SH3 domains to scan the proteome for potential hits and then filters these hits using a range of evidence sources related to sequence-based and cellular constraints on protein interactions. The novelty of this approach is the large number of evidence sources used and the method of combination of sequence based and protein pair based evidence sources. By combining different peptide and protein features using multiple Bayesian models we are able to predict high confidence interactions with an overall accuracy of 0.97. Availability and implementation: Do main- Mo tif Mediated Interaction Pred iction (DoMo-Pred) command line tool and all relevant datasets are available under GNU LGPL license for download from http://www.baderlab.org/Software/DoMo-Pred . The DoMo-Pred command line tool is implemented using Python 2.7 and C ++. Contact: gary.bader@utoronto.ca Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 3
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    GESTODIFFERENT: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process (2013)
    Oxford University Press
    Details
    Publication Date: 2013-02-13
    Description: : The characterization of the complex phenomenon of cell differentiation is a key goal of both systems and computational biology. G e S to D ifferent is a Cytoscape plugin aimed at the generation and the identification of gene regulatory networks (GRNs) describing an arbitrary stochastic cell differentiation process. The (dynamical) model adopted to describe general GRNs is that of noisy random Boolean networks (NRBNs), with a specific focus on their emergent dynamical behavior. G e S to D ifferent explores the space of GRNs by filtering the NRBN instances inconsistent with a stochastic lineage differentiation tree representing the cell lineages that can be obtained by following the fate of a stem cell descendant. Matched networks can then be analyzed by Cytoscape network analysis algorithms or, for instance, used to define (multiscale) models of cellular dynamics. Availability: Freely available at http://bimib.disco.unimib.it/index.php/Retronet#GESTODifferent or at the Cytoscape App Store http://apps.cytoscape.org/ . Contact: marco.antoniotti@unimib.it
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 4
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    MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets (2012)
    Oxford University Press
    Details
    Publication Date: 2012-03-29
    Description: Peptide recognition domains and transcription factors play crucial roles in cellular signaling. They bind linear stretches of amino acids or nucleotides, respectively, with high specificity. Experimental techniques that assess the binding specificity of these domains, such as microarrays or phage display, can retrieve thousands of distinct ligands, providing detailed insight into binding specificity. In particular, the advent of next-generation sequencing has recently increased the throughput of such methods by several orders of magnitude. These advances have helped reveal the presence of distinct binding specificity classes that co-exist within a set of ligands interacting with the same target. Here, we introduce a software system called MUSI that can rapidly analyze very large data sets of binding sequences to determine the relevant binding specificity patterns. Our pipeline provides two major advances. First, it can detect previously unrecognized multiple specificity patterns in any data set. Second, it offers integrated processing of very large data sets from next-generation sequencing machines. The results are visualized as multiple sequence logos describing the different binding preferences of the protein under investigation. We demonstrate the performance of MUSI by analyzing recent phage display data for human SH3 domains as well as microarray data for mouse transcription factors.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery (2014)
    Oxford University Press
    Details
    Publication Date: 2014-07-19
    Description: : Correlating disease mutations with clinical and phenotypic information such as drug response or patient survival is an important goal of personalized cancer genomics and a first step in biomarker discovery. HyperModules is a network search algorithm that finds frequently mutated gene modules with significant clinical or phenotypic signatures from biomolecular interaction networks. Availability and implementation: HyperModules is available in Cytoscape App Store and as a command line tool at www.baderlab.org/Sofware/HyperModules . Contact: Juri.Reimand@utoronto.ca or Gary.Bader@utoronto.ca Supplementary information: Supplementary data are available at Bioinformatics online
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 6
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    Cytoscape App Store (2013)
    Oxford University Press
    Details
    Publication Date: 2013-05-16
    Description: : Cytoscape is an open source software tool for biological network visualization and analysis, which can be extended with independently developed apps. We launched the Cytoscape App Store to highlight the important features that apps add to Cytoscape, enable researchers to find and install apps they need and help developers promote their apps. Availability: The App Store is available at http://apps.cytoscape.org . Contact: apico@gladstone.ucsf.edu
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    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 7
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    GeneMANIA Prediction Server 2013 Update (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-23
    Description: GeneMANIA ( http://www.genemania.org ) is a flexible user-friendly web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Given a query gene list, GeneMANIA extends the list with functionally similar genes that it identifies using available genomics and proteomics data. GeneMANIA also reports weights that indicate the predictive value of each selected data set for the query. GeneMANIA can also be used in a function prediction setting: given a query gene, GeneMANIA finds a small set of genes that are most likely to share function with that gene based on their interactions with it. Enriched Gene Ontology categories among this set can sometimes point to the function of the gene. Seven organisms are currently supported ( Arabidopsis thaliana , Caenorhabditis elegans , Drosophila melanogaster , Mus musculus , Homo sapiens , Rattus norvegicus and Saccharomyces cerevisiae ), and hundreds of data sets have been collected from GEO, BioGRID, IRefIndex and I2D, as well as organism-specific functional genomics data sets. Users can customize their search by selecting specific data sets to query and by uploading their own data sets to analyze.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Cytoscape.js: a graph theory library for visualisation and analysis (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-10
    Description: : Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser. It also can be used in a headless manner, useful for graph operations on a server, such as Node.js. Availability and implementation: Cytoscape.js is implemented in JavaScript. Documentation, downloads and source code are available at http://js.cytoscape.org . Contact: gary.bader@utoronto.ca
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    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 9
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    Cytoscape App Store (2013)
    Oxford University Press
    Details
    Publication Date: 2013-04-16
    Print ISSN: 1367-4803
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    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 10
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    GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop (2010)
    Oxford University Press
    Details
    Publication Date: 2010-10-05
    Print ISSN: 1367-4803
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    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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