Literature DB >> 17138585

BioNetBuilder: automatic integration of biological networks.

Iliana Avila-Campillo1, Kevin Drew, John Lin, David J Reiss, Richard Bonneau.   

Abstract

UNLABELLED: BioNetBuilder is an open-source client-server Cytoscape plugin that offers a user-friendly interface to create biological networks integrated from several databases. Users can create networks for approximately 1500 organisms, including common model organisms and human. Currently supported databases include: DIP, BIND, Prolinks, KEGG, HPRD, The BioGrid and GO, among others. The BioNetBuilder plugin client is available as a Java Webstart, providing a platform-independent network interface to these public databases. AVAILABILITY: http://err.bio.nyu.edu/cytoscape/bionetbuilder/

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Year:  2006        PMID： 17138585     DOI： 10.1093/bioinformatics/btl604

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  32 in total

1.  Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology.

Authors:  Renu Goel; Babylakshmi Muthusamy; Akhilesh Pandey; T S Keshava Prasad
Journal:  Mol Biotechnol       Date:  2011-05       Impact factor: 2.695

2.  New take on comparative immunology: relevance to immunotherapy.

Authors:  Ena Wang; Adriana Albini; David F Stroncek; Francesco M Marincola
Journal:  Immunotherapy       Date:  2009-05       Impact factor: 4.196

3.  Flexible network reconstruction from relational databases with Cytoscape and CytoSQL.

Authors:  Kris Laukens; Jens Hollunder; Thanh Hai Dang; Geert De Jaeger; Martin Kuiper; Erwin Witters; Alain Verschoren; Koenraad Van Leemput
Journal:  BMC Bioinformatics       Date:  2010-07-01       Impact factor: 3.169

4.  Integration of biological networks and gene expression data using Cytoscape.

Authors:  Melissa S Cline; Michael Smoot; Ethan Cerami; Allan Kuchinsky; Nerius Landys; Chris Workman; Rowan Christmas; Iliana Avila-Campilo; Michael Creech; Benjamin Gross; Kristina Hanspers; Ruth Isserlin; Ryan Kelley; Sarah Killcoyne; Samad Lotia; Steven Maere; John Morris; Keiichiro Ono; Vuk Pavlovic; Alexander R Pico; Aditya Vailaya; Peng-Liang Wang; Annette Adler; Bruce R Conklin; Leroy Hood; Martin Kuiper; Chris Sander; Ilya Schmulevich; Benno Schwikowski; Guy J Warner; Trey Ideker; Gary D Bader
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

Review 5.  Network integration and graph analysis in mammalian molecular systems biology.

Authors:  A Ma'ayan
Journal:  IET Syst Biol       Date:  2008-09       Impact factor: 1.615

6.  Construction of gene regulatory networks using biclustering and Bayesian networks.

Authors:  Fadhl M Alakwaa; Nahed H Solouma; Yasser M Kadah
Journal:  Theor Biol Med Model       Date:  2011-10-22       Impact factor: 2.432

7.  Integrating and annotating the interactome using the MiMI plugin for cytoscape.

Authors:  Jing Gao; Alex S Ade; V Glenn Tarcea; Terry E Weymouth; Barbara R Mirel; H V Jagadish; David J States
Journal:  Bioinformatics       Date:  2008-09-23       Impact factor: 6.937

8.  Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks.

Authors:  Mathieu Clément-Ziza; Christophe Malabat; Christian Weber; Ivan Moszer; Tero Aittokallio; Catherine Letondal; Sandrine Rousseau
Journal:  Bioinformatics       Date:  2009-08-03       Impact factor: 6.937

9.  Human Protein Reference Database--2009 update.

Authors:  T S Keshava Prasad; Renu Goel; Kumaran Kandasamy; Shivakumar Keerthikumar; Sameer Kumar; Suresh Mathivanan; Deepthi Telikicherla; Rajesh Raju; Beema Shafreen; Abhilash Venugopal; Lavanya Balakrishnan; Arivusudar Marimuthu; Sutopa Banerjee; Devi S Somanathan; Aimy Sebastian; Sandhya Rani; Somak Ray; C J Harrys Kishore; Sashi Kanth; Mukhtar Ahmed; Manoj K Kashyap; Riaz Mohmood; Y L Ramachandra; V Krishna; B Abdul Rahiman; Sujatha Mohan; Prathibha Ranganathan; Subhashri Ramabadran; Raghothama Chaerkady; Akhilesh Pandey
Journal:  Nucleic Acids Res       Date:  2008-11-06       Impact factor: 16.971

10.  myGRN: a database and visualisation system for the storage and analysis of developmental genetic regulatory networks.

Authors:  Jamil Bacha; James S Brodie; Matthew W Loose
Journal:  BMC Dev Biol       Date:  2009-06-06       Impact factor: 1.978
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