{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,4]],"date-time":"2025-10-04T14:31:53Z","timestamp":1759588313716},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability: SiGN-SSM is distributed under GNU Affero General Public Licence (GNU AGPL) version 3 and can be downloaded at http:\/\/sign.hgc.jp\/signssm\/. The pre-compiled binaries for some architectures are available in addition to the source code. The pre-installed binaries are also available on the Human Genome Center supercomputer system. The online manual and the supplementary information of SiGN-SSM is available on our web site.<\/jats:p>\n               <jats:p>Contact: \u00a0tamada@ims.u-tokyo.ac.jp<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr078","type":"journal-article","created":{"date-parts":[[2011,2,12]],"date-time":"2011-02-12T01:30:50Z","timestamp":1297474250000},"page":"1172-1173","source":"Crossref","is-referenced-by-count":5,"title":["SiGN-SSM: open source parallel software for estimating gene networks with state space models"],"prefix":"10.1093","volume":"27","author":[{"given":"Yoshinori","family":"Tamada","sequence":"first","affiliation":[{"name":"1 Laboratory 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"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rui","family":"Yamaguchi","sequence":"additional","affiliation":[{"name":"1 Laboratory 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"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Seiya","family":"Imoto","sequence":"additional","affiliation":[{"name":"1 Laboratory 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"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Osamu","family":"Hirose","sequence":"additional","affiliation":[{"name":"1 Laboratory 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"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ryo","family":"Yoshida","sequence":"additional","affiliation":[{"name":"1 Laboratory 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"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Masao","family":"Nagasaki","sequence":"additional","affiliation":[{"name":"1 Laboratory 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 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