Paper Info
Title
SiGN-SSM: open source parallel software for estimating gene networks with state space models.
Abstract
SiGN-SSM is an open-source gene network estimation software able to run in parallel on PCs and massively parallel supercomputers. The software estimates a state space model (SSM), that is a statistical dynamic model suitable for analyzing short time and/or replicated time series gene expression profiles. SiGN-SSM implements a novel parameter constraint effective to stabilize the estimated models. Also, by using a supercomputer, it is able to determine the gene network structure by a statistical permutation test in a practical time. SiGN-SSM is applicable not only to analyzing temporal regulatory dependencies between genes, but also to extracting the differentially regulated genes from time series expression profiles.
Year
DOI
Venue
2011
10.1093/bioinformatics/btr078
BIOINFORMATICS
Keywords
Field
DocType
state space model,gene network
General public licence,Data mining,Supercomputer,Massively parallel,Source code,Computer science,State-space representation,Software,Bioinformatics,Gene regulatory network,Resampling
Journal
Volume
Issue
ISSN
27
8
1367-4803
Citations 
PageRank 
References 
0
0.34
3
Authors
7
Name
Order
Citations
PageRank
Yoshinori Tamada120319.46
Rui Yamaguchi218026.49
Seiya Imoto397584.16
Osamu Hirose4698.27
Ryo Yoshida511911.64
Masao Nagasaki636826.22
Satoru Miyano72406250.71