Literature DB >> 21551142

TVNViewer: an interactive visualization tool for exploring networks that change over time or space.

Ross E Curtis1, Amos Yuen, Le Song, Anuj Goyal, Eric P Xing.   

Abstract

UNLABELLED: The relationship between genes and proteins is a dynamic relationship that changes across time and differs in different cells. The study of these differences can reveal various insights into biological processes and disease progression, especially with the aid of proper tools for network visualization. Toward this purpose, we have developed TVNViewer, a novel visualization tool, which is specifically designed to aid in the exploration and analysis of dynamic networks. AVAILABILITY: TVNViewer is freely available with documentation and tutorials on the web at http://sailing.cs.cmu.edu/tvnviewer. CONTACT: epxing@cs.cmu.edu.

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Year:  2011        PMID： 21551142      PMCID： PMC3117350          DOI： 10.1093/bioinformatics/btr273

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


  12 in total

1.  Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Authors:  Paul Shannon; Andrew Markiel; Owen Ozier; Nitin S Baliga; Jonathan T Wang; Daniel Ramage; Nada Amin; Benno Schwikowski; Trey Ideker
Journal:  Genome Res       Date:  2003-11       Impact factor: 9.043

2.  Genomic analysis of regulatory network dynamics reveals large topological changes.

Authors:  Nicholas M Luscombe; M Madan Babu; Haiyuan Yu; Michael Snyder; Sarah A Teichmann; Mark Gerstein
Journal:  Nature       Date:  2004-09-16       Impact factor: 49.962

3.  Medusa: a simple tool for interaction graph analysis.

Authors:  Sean D Hooper; Peer Bork
Journal:  Bioinformatics       Date:  2005-09-27       Impact factor: 6.937

Review 4.  Tools for visually exploring biological networks.

Authors:  Matthew Suderman; Michael Hallett
Journal:  Bioinformatics       Date:  2007-08-25       Impact factor: 6.937

5.  A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility.

Authors:  Mark P Keller; YounJeong Choi; Ping Wang; Dawn Belt Davis; Mary E Rabaglia; Angie T Oler; Donald S Stapleton; Carmen Argmann; Kathy L Schueler; Steve Edwards; H Adam Steinberg; Elias Chaibub Neto; Robert Kleinhanz; Scott Turner; Marc K Hellerstein; Eric E Schadt; Brian S Yandell; Christina Kendziorski; Alan D Attie
Journal:  Genome Res       Date:  2008-03-17       Impact factor: 9.043

6.  Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans.

Authors:  Denis Dupuy; Nicolas Bertin; César A Hidalgo; Kavitha Venkatesan; Domena Tu; David Lee; Jennifer Rosenberg; Nenad Svrzikapa; Aurélie Blanc; Alain Carnec; Anne-Ruxandra Carvunis; Rock Pulak; Jane Shingles; John Reece-Hoyes; Rebecca Hunt-Newbury; Ryan Viveiros; William A Mohler; Murat Tasan; Frederick P Roth; Christian Le Peuch; Ian A Hope; Robert Johnsen; Donald G Moerman; Albert-László Barabási; David Baillie; Marc Vidal
Journal:  Nat Biotechnol       Date:  2007-05-07       Impact factor: 54.908

7.  A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies.

Authors:  Yuling Jiao; S Lori Tausta; Neeru Gandotra; Ning Sun; Tie Liu; Nicole K Clay; Teresa Ceserani; Meiqin Chen; Ligeng Ma; Matthew Holford; Hui-yong Zhang; Hongyu Zhao; Xing-Wang Deng; Timothy Nelson
Journal:  Nat Genet       Date:  2009-01-04       Impact factor: 38.330

8.  Osprey: a network visualization system.

Authors:  Bobby-Joe Breitkreutz; Chris Stark; Mike Tyers
Journal:  Genome Biol       Date:  2003-02-27       Impact factor: 13.583

9.  VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology.

Authors:  Zhenjun Hu; Jui-Hung Hung; Yan Wang; Yi-Chien Chang; Chia-Ling Huang; Matt Huyck; Charles DeLisi
Journal:  Nucleic Acids Res       Date:  2009-05-21       Impact factor: 16.971

10.  A survey of visualization tools for biological network analysis.

Authors:  Georgios A Pavlopoulos; Anna-Lynn Wegener; Reinhard Schneider
Journal:  BioData Min       Date:  2008-11-28       Impact factor: 2.522
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  7 in total

1.  Enabling dynamic network analysis through visualization in TVNViewer.

Authors:  Ross E Curtis; Jing Xiang; Ankur Parikh; Peter Kinnaird; Eric P Xing
Journal:  BMC Bioinformatics       Date:  2012-08-16       Impact factor: 3.169

2.  TREEGL: reverse engineering tree-evolving gene networks underlying developing biological lineages.

Authors:  Ankur P Parikh; Wei Wu; Ross E Curtis; Eric P Xing
Journal:  Bioinformatics       Date:  2011-07-01       Impact factor: 6.937

3.  NetworkPainter: dynamic intracellular pathway animation in Cytobank.

Authors:  Jonathan R Karr; Harendra Guturu; Edward Y Chen; Stuart L Blair; Jonathan M Irish; Nikesh Kotecha; Markus W Covert
Journal:  BMC Bioinformatics       Date:  2015-05-25       Impact factor: 3.169

4.  PhenoTimer: software for the visual mapping of time-resolved phenotypic landscapes.

Authors:  Maria Secrier; Reinhard Schneider
Journal:  PLoS One       Date:  2013-08-12       Impact factor: 3.240

Review 5.  Overview of methods for characterization and visualization of a protein-protein interaction network in a multi-omics integration context.

Authors:  Vivian Robin; Antoine Bodein; Marie-Pier Scott-Boyer; Mickaël Leclercq; Olivier Périn; Arnaud Droit
Journal:  Front Mol Biosci       Date:  2022-09-08

Review 6.  Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.

Authors:  Georgios A Pavlopoulos; Dimitris Malliarakis; Nikolas Papanikolaou; Theodosis Theodosiou; Anton J Enright; Ioannis Iliopoulos
Journal:  Gigascience       Date:  2015-08-25       Impact factor: 6.524

Review 7.  Visualizing time-related data in biology, a review.

Authors:  Maria Secrier; Reinhard Schneider
Journal:  Brief Bioinform       Date:  2013-04-12       Impact factor: 11.622
  7 in total

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