Literature DB >> 15247099

SARGE: a tool for creation of putative genetic networks.

O J Shaw1, C Harwood, L J Steggles, A Wipat.   

Abstract

SUMMARY: SARGE is a tool for creating, visualizing and manipulating a putative genetic network from time series microarray data. The tool assigns potential edges through time-lagged correlation, incorporates a clustering mechanism, an interactive visual graph representation and employs simulated annealing for network optimization. AVAILABILITY: The application is available as a .jar file from http://www.bioinformatics.cs.ncl.ac.uk/sarge/index.html.

Mesh:

Year:  2004        PMID: 15247099     DOI: 10.1093/bioinformatics/bth395

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


  6 in total

Review 1.  Advantages and limitations of current network inference methods.

Authors:  Riet De Smet; Kathleen Marchal
Journal:  Nat Rev Microbiol       Date:  2010-08-31       Impact factor: 60.633

2.  A parallel algorithm for reverse engineering of biological networks.

Authors:  Jason N Bazil; Feng Qi; Daniel A Beard
Journal:  Integr Biol (Camb)       Date:  2011-11-14       Impact factor: 2.192

3.  Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics.

Authors:  Stephen A Ramsey; Sandy L Klemm; Daniel E Zak; Kathleen A Kennedy; Vesteinn Thorsson; Bin Li; Mark Gilchrist; Elizabeth S Gold; Carrie D Johnson; Vladimir Litvak; Garnet Navarro; Jared C Roach; Carrie M Rosenberger; Alistair G Rust; Natalya Yudkovsky; Alan Aderem; Ilya Shmulevich
Journal:  PLoS Comput Biol       Date:  2008-03-21       Impact factor: 4.475

4.  Passing messages between biological networks to refine predicted interactions.

Authors:  Kimberly Glass; Curtis Huttenhower; John Quackenbush; Guo-Cheng Yuan
Journal:  PLoS One       Date:  2013-05-31       Impact factor: 3.240

5.  The feasibility of genome-scale biological network inference using Graphics Processing Units.

Authors:  Raghuram Thiagarajan; Amir Alavi; Jagdeep T Podichetty; Jason N Bazil; Daniel A Beard
Journal:  Algorithms Mol Biol       Date:  2017-03-20       Impact factor: 1.405

6.  The inferred cardiogenic gene regulatory network in the mammalian heart.

Authors:  Jason N Bazil; Karl D Stamm; Xing Li; Raghuram Thiagarajan; Timothy J Nelson; Aoy Tomita-Mitchell; Daniel A Beard
Journal:  PLoS One       Date:  2014-06-27       Impact factor: 3.240

  6 in total

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