Literature DB >> 18819079

Browsing multidimensional molecular networks with the generic network browser (N-Browse).

Huey-Ling Kao1, Kristin C Gunsalus.   

Abstract

N-Browse is a graphical network browser for the visualization and navigation of heterogeneous molecular interaction data. N-Browse runs as a Java applet in a Web browser, providing highly dynamic and interactive on-demand access to network data available from a remote server. The N-Browse interface is easy to use and accommodates multiple types of functional linkages with associated information, allowing the exploration of many layers of functional information simultaneously. Although created for applications in biology, N-Browse uses a generic database schema that can be adapted to network representations in any knowledge domain. The N-Browse client-server package is freely available for distribution, providing a convenient way for data producers and providers to distribute and offer interactive visualization of network-based data. (c) 2008 by John Wiley & Sons, Inc.

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Year:  2008        PMID: 18819079      PMCID: PMC3217184          DOI: 10.1002/0471250953.bi0911s23

Source DB:  PubMed          Journal:  Curr Protoc Bioinformatics        ISSN: 1934-3396


  1 in total

1.  A genome-wide map of conserved microRNA targets in C. elegans.

Authors:  Sabbi Lall; Dominic Grün; Azra Krek; Kevin Chen; Yi-Lu Wang; Colin N Dewey; Pranidhi Sood; Teresa Colombo; Nicolas Bray; Philip Macmenamin; Huey-Ling Kao; Kristin C Gunsalus; Lior Pachter; Fabio Piano; Nikolaus Rajewsky
Journal:  Curr Biol       Date:  2006-02-02       Impact factor: 10.834

  1 in total
  21 in total

Review 1.  Gene-centered regulatory networks.

Authors:  H Efsun Arda; Albertha J M Walhout
Journal:  Brief Funct Genomics       Date:  2009-12-13       Impact factor: 4.241

Review 2.  Visualization of omics data for systems biology.

Authors:  Nils Gehlenborg; Seán I O'Donoghue; Nitin S Baliga; Alexander Goesmann; Matthew A Hibbs; Hiroaki Kitano; Oliver Kohlbacher; Heiko Neuweger; Reinhard Schneider; Dan Tenenbaum; Anne-Claude Gavin
Journal:  Nat Methods       Date:  2010-03       Impact factor: 28.547

3.  VirtualPlant: a software platform to support systems biology research.

Authors:  Manpreet S Katari; Steve D Nowicki; Felipe F Aceituno; Damion Nero; Jonathan Kelfer; Lee Parnell Thompson; Juan M Cabello; Rebecca S Davidson; Arthur P Goldberg; Dennis E Shasha; Gloria M Coruzzi; Rodrigo A Gutiérrez
Journal:  Plant Physiol       Date:  2009-12-09       Impact factor: 8.340

4.  The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function.

Authors:  David Warde-Farley; Sylva L Donaldson; Ovi Comes; Khalid Zuberi; Rashad Badrawi; Pauline Chao; Max Franz; Chris Grouios; Farzana Kazi; Christian Tannus Lopes; Anson Maitland; Sara Mostafavi; Jason Montojo; Quentin Shao; George Wright; Gary D Bader; Quaid Morris
Journal:  Nucleic Acids Res       Date:  2010-07       Impact factor: 16.971

5.  Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network.

Authors:  Nicolas Simonis; Jean-François Rual; Anne-Ruxandra Carvunis; Murat Tasan; Irma Lemmens; Tomoko Hirozane-Kishikawa; Tong Hao; Julie M Sahalie; Kavitha Venkatesan; Fana Gebreab; Sebiha Cevik; Niels Klitgord; Changyu Fan; Pascal Braun; Ning Li; Nono Ayivi-Guedehoussou; Elizabeth Dann; Nicolas Bertin; David Szeto; Amélie Dricot; Muhammed A Yildirim; Chenwei Lin; Anne-Sophie de Smet; Huey-Ling Kao; Christophe Simon; Alex Smolyar; Jin Sook Ahn; Muneesh Tewari; Mike Boxem; Stuart Milstein; Haiyuan Yu; Matija Dreze; Jean Vandenhaute; Kristin C Gunsalus; Michael E Cusick; David E Hill; Jan Tavernier; Frederick P Roth; Marc Vidal
Journal:  Nat Methods       Date:  2009-01       Impact factor: 28.547

6.  IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.

Authors:  Aaron K Wong; Christopher Y Park; Casey S Greene; Lars A Bongo; Yuanfang Guan; Olga G Troyanskaya
Journal:  Nucleic Acids Res       Date:  2012-06-07       Impact factor: 16.971

7.  Structure, function and networks of transcription factors involved in abiotic stress responses.

Authors:  Søren Lindemose; Charlotte O'Shea; Michael Krogh Jensen; Karen Skriver
Journal:  Int J Mol Sci       Date:  2013-03-13       Impact factor: 5.923

8.  GeneMANIA prediction server 2013 update.

Authors:  Khalid Zuberi; Max Franz; Harold Rodriguez; Jason Montojo; Christian Tannus Lopes; Gary D Bader; Quaid Morris
Journal:  Nucleic Acids Res       Date:  2013-07       Impact factor: 16.971

9.  WormBase: a comprehensive resource for nematode research.

Authors:  Todd W Harris; Igor Antoshechkin; Tamberlyn Bieri; Darin Blasiar; Juancarlos Chan; Wen J Chen; Norie De La Cruz; Paul Davis; Margaret Duesbury; Ruihua Fang; Jolene Fernandes; Michael Han; Ranjana Kishore; Raymond Lee; Hans-Michael Müller; Cecilia Nakamura; Philip Ozersky; Andrei Petcherski; Arun Rangarajan; Anthony Rogers; Gary Schindelman; Erich M Schwarz; Mary Ann Tuli; Kimberly Van Auken; Daniel Wang; Xiaodong Wang; Gary Williams; Karen Yook; Richard Durbin; Lincoln D Stein; John Spieth; Paul W Sternberg
Journal:  Nucleic Acids Res       Date:  2009-11-12       Impact factor: 16.971

10.  Genes2FANs: connecting genes through functional association networks.

Authors:  Ruth Dannenfelser; Neil R Clark; Avi Ma'ayan
Journal:  BMC Bioinformatics       Date:  2012-07-02       Impact factor: 3.169

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