@article{43a8d6f2b8c9495b9e2fd1609a8b6324,
title = "SiGN-SSM: Open source parallel software for estimating gene networks with state space models",
abstract = "Summary: 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.",
author = "Yoshinori Tamada and Rui Yamaguchi and Seiya Imoto and Osamu Hirose and Ryo Yoshida and Masao Nagasaki and Satoru Miyano",
note = "Funding Information: 1Laboratory of DNA Information Analysis, 2Laboratory of Sequence Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, 3Bioinformation Engineering Laboratory, Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, 4Department of Statistical Modeling, Institute of Statistical Mathematics, Research Organization of Information and Systems, 10-3 Midori-cho, Tachikawa, Tokyo 190-8562, 5Laboratory of Functional Genomics, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639 and 6Data Analysis Fusion Team, RIKEN Computational Science Research Program, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan Funding Information: Funding: ISLiM (Next-generation integrated simulation of living matter) project in RIKEN Computational Science Research Program.",
year = "2011",
month = apr,
doi = "10.1093/bioinformatics/btr078",
language = "English",
volume = "27",
pages = "1172--1173",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "8",
}