English

Content

Papers

all_articles.bib

2011

  • Jeong E, Nagasaki M, Ikeda E, Sekiya Y, Saito A, Miyano S, CSO validator: Improving manual curation workflow for biological pathways, Bioinformatics, 2011 Jul 8. Go to article
  • Li C, Kuroyanagi K, Nagasaki M, Miyano S, Parameter estimation of biological pathways using data assimilation and model checking, Proceedings of the 2nd International Workshop on Biological Processes & Petri Nets (BioPPN2011), pp.53-70, Newcastle upon Tyne, UK, June 2011. Go to article
  • Li C, Nagasaki M, Hock Koh C, Miyano S,Online model checking approach based parameter estimation to a neuronal fate decision simulation model in C. elegans with hybrid functional Petri net with extension, Mol. Biosyst., DOI:10.1039/C0MB00253D, 2011. Go to article
  • Hock Koh C, Nagasaki M, Saito A, Li C, Wong L, Miyano S, MIRACH: Efficient Model Checker for Quantitative Biological Pathway Models, Bioinformatics. 2011 Mar 1;27(5):734-5. Epub 2011 Jan 5. Go to article

2010

  • Jeong E, Nagasaki M, Ueno K, Satoru M, Ontology-based instance data validation for high-quality curated biological pathways, APBC2010 To Appear
  • Tasaki S, Nagasaki M, Kozuka-Hata H, Semba K, Gotoh N, Hattori S, Inoue J, Yamamoto T, Miyano S, Sugano S, Oyama M, Phosphoproteomics-based modeling defines the regulatory mechanism underlying aberrant EGFR signaling, PLoS One. 2010 Nov 10;5(11):e13926. Go to article
  • Chalkidis G, Nagasaki M, Miyano S, High Performance Hybrid Functional Petri Net Simulations of Biological Pathway Models on CUDA, IEEE/ACM Trans Comput Biol Bioinform. 2010 Nov 24. Go to article
  • Miwa Y, Murakami Y, Ge QW, Li C, Matsuno H, Miyano S, Delay time determination for the timed Petri net model of a signaling pathway based on its structural information, IEICE Trans. Fundamentals of Electronics, Communications and Computer Sciences, E93-A(12), 2717-2729, 2010. Go to article
  • Do JH, Nagasaki M, Miyano S, The systems approach to the prespore-specific activation of sigma factor SigF in Bacillus subtilis, Biosystems. 2010 Jun;100(3):178-84. Go to article
  • Kojima K, Nagasaki M, Miyano S, An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information. BMC Bioinformatics. 2010, 18;11:335. Go to article
  • Koh CH, Nagasaki M, Saito A, Wong L, Miyano S, DA 1.0: Parameter Estimation of Biological Pathways using Data Assimilation approach, Bioinformatics. 26(14):1794-6. Go to article
  • Li C, Nagasaki M, Saito A and Miyano S, Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram, BMC Syst Biol., 4:39, 2010 Apr. Go to article
  • Nagasaki M, Saito A, Jeong E, Li C, Kojima K, Ikeda E, Miyano S, Cell Illustrator 4.0: A computational platform for systems biology, In Silico Biol., 10, 0002, 2010. Go to article
  • Miwa Y*, Li C*, Ge QW, Matsuno H and Miyano S, On Determining Delay Time of Transitions for Petri Net Based Signaling Pathways by Introducing Stochastic Decision Rules, In Silico Biol., 10, 0004, 2010. (*Equal contributor) Go to article

2009

  • Li C*, Nagasaki M*, Ueno K, Miyano S. Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension. BMC Systems Biology 2009; 3:42. *Equal contributor Go to article
  • Sato Y, Hashiguchi Y, Nishida M. Evolution of multiple phosphodiesterase isoforms in stickleback involved in cAMP signal transduction pathway. BMC Systems Biology 2009; 3:23 Go to article

2008

  • Jeong E, Nagasaki M, Miyano S. Rule-based reasoning for system dynamics in cell systems. Genome Informatics 20: 25-36 (2008).Go to article
  • Nagasaki M, Saito A, Li C, Jeong E, Miyano S. Systematic reconstruction of TRANSPATH data into Cell System Markup Language. BMC Systems Biology. 2008; 2:53.
  • Kojima K, Nagasaki M, Miyano S. Fast grid layout algorithm for biological networks with sweep calculation. Bioinformatics. 2008; 24(12):1433-41.

2007

  • Jeong E*, Nagasaki M*, Saito A, Miyano S. Cell System Ontology: Representation for modeling, visualizing, and simulating biological pathways. In Silico Biology. 2007; 7(6):623-638. *Equal contributor
  • Jeong E, Nagasaki M, Miyano S. Conversion from BioPAX to CSO for System Dynamics and Visualization of Biological Pathway. Genome Informatics. 2007; 18: 225-236.Go to article
  • Kojima K*, Nagasaki M*, Jeong E, Kato M, Miyano S. An efficient grid layout algorithm for biological networks utilizing various biological attributes. BMC Bioinformatics. 2007; 8:76. *Equal contributor(PubMed_17338825)(.pdf)

2006

  • Doi A. Modeling and simulation of biological pathways with Hybrid Functional Petri Net. Ph.D Thesis, The University of Tokyo. 2006
  • Tasaki S*, Nagasaki M*, Oyama M, Hata H, Ueno K, Yoshida R, Higuchi T, Sugano S, Miyano S. Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic data. Genome Informatics. 2006; 17(2): 226-238. *Equal contributor(Go to article)
  • Matsuno H, Li C, Miyano S. Petri Net based description for systematic understanding of biological pathways. IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences. 2006; 89-A: 3166-3174.
  • Nagasaki M, Yamaguchi R, Yoshida R, Imoto S, Doi A, Tamada Y, Matsuno H, Miyano S, Higuchi T. Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data. Genome Informatics. 2006; 17(1): 46-61.(Go to article)
  • Doi A, Nagasaki M, Ueno K, Matsuno H, Miyano S. A combined pathway to simulate CDK-dependent phosphorylation and ARF-dependent stabilization for p53 transcriptional activity. Genome Informatics. 2006; 17(1): 112-23.(Go to article)
  • Saito A*, Nagasaki M*, Doi A, Ueno K, Miyano S. Cell fate simulation model of gustatory neurons with microRNAs double-negative feedback loop by hybrid function Petri net with extension. Genome Informatics. 2006; 17(1): 100-11. *Equal contributor(Go to article)
  • Matsuno H, Inouye ST, Okitsu Y, Fujii Y, Miyano S. A new regulatory interaction suggested by simulations for circadian genetic control mechanism in mammals. Journal of bioinformatics and computational biology. 2006; 4(1): 139-53.(PubMed_16568547)(.pdf)
  • Doi A, Nagasaki M, Matsuno H, Miyano S. Simulation-based validation of the p53 transcriptional activity with hybrid functional Petri net. In Silico Biology. 2006; 6(1-2): 0001.(PubMed_16789909)(.html)

2005

  • Nagasaki M, Doi A, Matsuno H, Miyano S. Petri Net Based Description and Modeling of Biologinal Pathways. Algebraic Biology 2005 - Computer Algebra in Biology, H. Anai and K. Horimoto, eds., Universal Academy Press, Inc., Tokyo. 2005; 19-31.
  • Kato M*, Nagasaki M*, Doi A , Miyano S. Automatic Drawing of Biological Networks Using Cross Cost and Subcomponent Data. Genome Informatics. 2005; 16(2): 22-31. *Equal contributor(PubMed_16901086)(Go to article)
  • Kitakaze H, Matsuno H, Ikeda N. Prediction of debacle points for robustness of biological pathways by using recurrent neural networks. Genome Informatics. 2005; 16(1): 192-202.(PubMed_16362922)(Go to article)
  • Li C, Suzuki S, Ge Qi-Wei, Nakata M, Matsuno H, Miyano S. On modeling and analyzing signaling pathways with inhibitory interactions based on Petri net, Proc. The 2005 Internatinal Joint Conference of InCoB, AASBi and KSBI (BIOINFO2005). 2005; 348-53.(.pdf)

2004

  • Nagasaki M, Doi A, Matsuno H, Miyano S. A versatile Petri net based architecture for modeling and simulation of complex biological processes. Genome Informatics. 2004; 15(1): 180-97.(PubMed_15712121)(Go to article)
  • Nagasaki M. A Platform for Biopathway Modeling/Simulation and Recreating biopathway databases towards simulation. Ph.D Thesis, The University of Tokyo. 2004.(.pdf)
  • Nagasaki M, Doi A, Matsuno H, Miyano S. Integrating biopathway databases for large-scale modeling and simulation. The Second Asia-Pacific Bioinformatics Conferences, Volume 29 of Conferences in Research and Practice in Information Technology, Australian Computer Society. 2004; 43-52.(.pdf)
  • Doi A, Fujita S, Matsuno H, Nagasaki M, Miyano S. Constructing biological pathway models with hybrid functional Petri nets. In Silico Biology. 2004; 4(3): 271-91.(PubMed_15724280)(.html)
  • Matsui M, Fujita S, Suzuki S, Matsuno H, Miyano S. Simulated Cell Division Processes of the Xenopus Cell Cycle Pathway by Genomic Object Net. Journal of Integrative Bioinformatics. 2004; 0001.(.pdf)
  • Fujita S, Matsui M, Matsuno H, Miyano S. Modeling and simulation of fission yeast cell cycle on hybrid functional Petri net. IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences. 2004; E87-A(11): 2919-28.(.pdf)

2003

  • Matsuno H, Murakami R, Yamane R, Yamasaki N, Fujita S, Yoshimori H, Miyano S. Boundary formation by notch signaling in Drosophila multicellular systems: experimental observations and a gene network modeling by Genomic Object Net. Pacific Symposium on Biocomputing. 2003: 152-63.(PubMed_12603025)(.pdf)
  • Nagasaki M, Doi A, Matsuno H, Miyano S. Recreating biopathway databases towards simulation. In: Computational Methods in Systems Biology. Lecture Notes in Computer Science. 2003; 2602: 191-2.(.pdf)
  • Matsuno H, Tanaka Y, Aoshima H, Doi A, Matsui M, Miyano S. Biopathways Representation and Simulation on Hybrid Functional Petri Net. In Silico Biology. 2003; 3(3): 389-404.(PubMed_12954096)(.html)
  • Nagasaki M, Doi A, Matsuno H, Miyano S. Genomic Object Net: I. A platform for modeling and simulating biopathways. Applied Bioinformatics. 2003; 2: 181-4.(PubMed_15130806)(.pdf)
  • Doi A, Nagasaki M, Fujita S, Matsuno H, Miyano S. Genomic Object Net: II. Modeling biopathways by hybrid functional Petri net with extension. Applied Bioinformatics. 2003; 2: 185-8.(PubMed_15130807)(.pdf)
  • Matsuno H, Fujita S, Doi A, Nagasaki M, Miyano S. Towards biopathway modeling and simulation. Lecture Notes in Computer Science. 2003; 2679; 3-22.

2002

  • Doi A, Matsuno H, Matsui M, Hirata Y, Miyano S. Simulation of biological systems by hybrid Petri net with an enhancement. Proc. The International Conference on Fundamentals of Electronics, Communications and Computer Science 2002. 2002; S5: 13-8.(.pdf)

2001

  • Matsuno H, Doi A, Hirata Y, Miyano S. XML Documentation of Biopathways and Their Simulations in Genomic Object Net. Genome Informatics. 2001; 12: 54-62.(PubMed_11791224)(Go to article)

2000

  • Matsuno H, Doi A, Nagasaki M, Miyano S. Hybrid Petri net representation of gene regulatory network. Pacific Symposium on Biocomputing 5. 2000; 341-52.(PubMed_10902182)(.pdf)

Books

  • Masao Nagasaki, Ayumu Saito, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano. Foundations of Systems Biology: Using Cell Illustrator and Pathway Databases. Springer; 1 edition (May 31, 2009).
  • Nagasaki M, Doi A, Matsuno H, Miyano S. Computational modeling of biological processes with Petri Net-based architecture. Bioinformatics Technologies (Yi-Ping Phoebe Chen (Ed.)). Springer. 2005; 179-242.

Poster abstracts

  1. Li C, Ge Qi-Wei, Matsuno H, Miyano S. On Timed Petri Nets Based Modeling and Simulation of Signaling Pathways. The 2007 Annual Conference of Japanese Society for Bioinformatics. 2007; P032.(.pdf)
  2. Jeong E, Nagasaki M, Miyano S. A Converter from BioPAX to CSO. The 2007 Annual Conference of Japanese Society for Bioinformatics. 2007; P016.(.pdf)
  3. Saito A, Nagasaki M, Miyano S. A Converter from CSML to Scalable Vector Graphics. The 2007 Annual Conference of Japanese Society for Bioinformatics. 2007; P015.(.pdf)
  4. Kojima K, Nagasaki M, Miyano S. A Fast Grid Layout Algorithm for Biological Pathways. The 2007 Annual Conference of Japanese Society for Bioinformatics. 2007; P014.(.pdf)
  5. Li C, Ge Qi-Wei, Nakata M, Matsuno H, Miyano S. Petri Net Based Modeling and Time-Related Simulation of Signaling Pathways Demonstrated for Apoptosis. The Eighteenth International Conference on Genome Informatics. poster abstract. 2007; P030.(.pdf)
  6. Bruand J, Hashimoto T, Nagasaki M, Miyano S. A Converter from SBML2.1 to CSML3.0 and its Implementation. The Eighteenth International Conference on Genome Informatics. poster abstract. 2007; P028.(.pdf)
  7. Kojima K, Nagasaki M, Jeong E, Kato M, Miyano S. A Grid Layout Algorithm for Biological Networks by Utilizing Biological Attributes. The Eighteenth International Conference on Genome Informatics. poster abstract. 2007; P022.(.pdf)
  8. Nagasaki M, Doi A, Saito A, Ikeda E, Ueno K, Jeong E, ChristopherJ. Savoie CJ, Miyano S. Cell Illustrator3.0: A Platform for Biopathway Modeling and Simulation. The Seventeenth International Conference on Genome Informatics. software demonstration. 2006; S07.(.pdf)
  9. Saito A, Nagasaki M, Doi A, Ueno K, Miyano S. Cell Fate Simulation of ASE Cell in Caenorhabditis elegans using Hybrid Functional Petri Net with Extension. The Seventeenth International Conference on Genome Informatics. poster abstract. 2006; P018.(.pdf)
  10. Yoshida R, Numata K, Imoto S, Nagasaki M, Doi A, Ueno K, Miyano S. A Statistical Framework for Genome Wide Discovery of Biomarker Splice Variations with GeneChip Human Exon 1.0 ST Arrays. The Seventeenth International Conference on Genome Informatics. poster abstract. 2006; P122.(.pdf)
  11. Nagasaki M, Yamaguchi R, Yoshida R, Imoto S, Doi A, Tamada Y, Matsuno H, Miyano S, Higuchi T. Genomic Data Assimilation for a Hybrid Functional Petri Net Model of Circadian Rhythm with Time Course Gene Expression Data. The Seventeenth International Conference on Genome Informatics. poster abstract. 2006; P017.(.pdf)
  12. Hirose O, Yoshida R, Imoto S, Miyano S. Identification of Apoptosis-Induced Gene Networks from Time Course Expression Profiles with Replicated Measurements. The Seventeenth International Conference on Genome Informatics. poster abstract. 2006; P005.(.pdf)
  13. Doi A, Nagasaki M, Ueno K, Matsuno H, Miyano S. p53 Pathways to Simulate the p53 Transcriptional Activity. The Seventeenth International Conference on Genome Informatics. poster abstract. 2006; P006.(.pdf)
  14. Numata K, Termier A, Yoshida R, Imoto S, Tamada Y, Higuchi T, Miyano S. A Graph Mining Approach to Gene Network Motif Extraction. The Seventeenth International Conference on Genome Informatics. poster abstract. 2006; P131.(.pdf)
  15. Jeong E, Nagasaki M, Saito A, Miyano S. Ontology-Based Representation for Cell Systems Markup Language. The Seventeenth International Conference on Genome Informatics. poster abstract. 2006; P141.(.pdf)
  16. Kojima K, Nagasaki M, Jeong E, Kato M, Miyano S. A New Grid Layout Algorithm with Swap Operation that Extends the Search Space while Keeping the Time Complexity. The Seventeenth International Conference on Genome Informatics. poster abstract. 2006; P142.(.pdf)
  17. Li C, Suzuki S, Takeuchi Y, Ge Qi-Wei, Nakata M, Matsuno H, Miyano S. Petri Net Based Modeling of Signaling Pathways Including Inhibitory Function. The Sixteenth International Conference on Genome Informatics. poster abstract. 2005; P115.(Go to article)
  18. Harada Y, Mito N, Fujii Y, Inouye S, Matsuno H, Miyano S. Simulation of Light-Induced Phase Response in Mammals with Hybrid Function Petri Net. The Sixteenth International Conference on Genome Informatics. poster abstract. 2005; P111.(Go to article)
  19. Okada R, Miyakawa C, Sugii M, Matsuno H, Miyano S. Machine Learning Prediction of Amino Acid Sequence Characterization in Protein N-Myristoylation. The Sixteenth International Conference on Genome Informatics. poster abstract. 2005; P096.(Go to article)
  20. Tanaka T, Harada K, Kitakaze H, Yamanaka J, Matsuno H, Miyano S. Tools for Supporting Computational Experiments on Genomic Object Net. The Sixteenth International Conference on Genome Informatics. poster abstract. 2005; S11.(Go to article)
  21. Li C, Ge Qi-Wei, Nakata M, Matsuno H, Miyano S. A new Petri net modeling method for signaling pathways with a focus on enzyme, The Fifteenth International Conference on Genome Informatics, poster abstract, P004 (2004).(Go to article)
  22. Fujii Y, Okitsu Y, Matsuno H, Miyano S, Inouye ST, A new regulatory interactions suggested by simulations for circadian genetic control mechanism in mammals. The Fifteenth International Conference on Genome Informatics. poster abstract. 2004; P003.(Go to article)
  23. Yamaji M, Iwasaki H, Matsuno H, Miyano S. Modeling and simulation of cyanobacterial circadian clock mechanism by hybrid functional Petri net. The Fifteenth International Conference on Genome Informatics. poster abstract. 2004; P002.(Go to article)
  24. Kitakaze H, Noda R, Matsuno H, Ikeda N, Miyano S. Prediction of debacle parts for robustness in a cell by using recurrent neural networks. The Fifteenth International Conference on Genome Informatics. poster abstract. 2004; P001.(Go to article)
  25. Kono T, Noda R, Kitakaze H, Nagasaki M, Doi A, Matsuno H, Miyano S. Distributed client-server system architecture for high performance simulations on Genomic Object Net. Genome Informatics. 2003; 14: 619-20.(Go to article)
  26. Yamane R, Umezaki J, Matsuno H, Murakami R, Yamasaki N, Miyano S. Simulation of Drosophila boundary cell formation in forced-expression on Notch-deltaE. Genome Informatics. 2003; 14: 617-8.(Go to article)
  27. Matsui M, Fujita S, Suzuki S, Matsuno H, Miyano S. Xenopus cell cycle pathway for simulating cell division processes by Genomic Object Net. Genome Informatics. 2003; 14: 615-6.(Go to article)
  28. Nagasaki M, Doi A, Ueno K, Torikai E, Matsuno H, Miyano S. BPE:Biopathway executer for large-scale modeling and simulation. Genome Informatics. 2003; 14: 296-7.(Go to article)
  29. Nakano M, Kitakaze H, Matsuno H, Miyano S. XML Pathway File Conversion between Genomic Object Net and SBML. Genome Informatics. 2002; 13: 457-8.(Go to article)
  30. Tanaka T, Kitakaze H, Matsuno H, Miyano S. Development of Genomic Object Net Builder for Supporting XML Design for Visualization. Genome Informatics. 2002; 13: 455-6.(Go to article)
  31. Matsuno H, Murakami R, Yamane R, Yamazaki N, Fujita S, Yoshimori H, Miyano S. Experimental Observations and Simulations by Genomic Object Net of Notch Signaling in Drosophila Multicellular Systems. Genome Informatics. 2002; 13: 453-4.(Go to article)
  32. Nagasaki M, Doi A, Sasaki M, Savoie CJ, Matsuno H, Miyano S. Genomic Object Net (ver.1.0): A platform for biopathway modeling and simulation. European Conference on Computational Biology 2002. poster abstract. 2002: P112.
  33. Matsuno H, Yamane R, Fujita S, Yamasaki N, Murakami R, Miyano S. Modeling and visualization of the pattern formation in Drosophila melanogaster by Genomic Object Net. The 10th International Conference on Intelligent Systems for Morecular Biology. poster abstract. 2002: 46A.
  34. Matsuno H, Hirata Y, Doi A, Miyano S. Genomic Object Net: On-going report on biopathway modeling and simulation. Currents in Computational Molecular Biology 2002 (RECOMB2002). 2002: 132-3.
  35. Matsui M, Doi A, Matsuno H, Hirata Y, Miyano S. Converting biopathway models of E-Cell to Genomic Object Net. Pacific Symposium on Biocomputing. poster abstract. 2002: pp.117.
  36. Hirata Y, Matsuno H, Sasaki M, Miyano S. Genomic Object Net: Petri Net Enhancement for Multi-Cellular Processes. Genome Informatics. 2001; 12: 292-3.(Go to article)
  37. Matsui M, Doi A, Matsuno H, Hirata Y, Miyano S. Biopathway Model Conversion from E-CELL to Genomic Object Net. Genome Informatics. 2001; 12: 290-1.(Go to article)
  38. Doi A, Yamane R, Yamasaki N, Yoshimori H, Murakami R, Matsuno H, Miyano S. Simulation of the Pattern Formation in Multicellular Organism by Genomic Object Net. Genome Informatics. 2001; 12: 288-9.(Go to article)
  39. Matsuno H, Doi A, Fujita S, Sasaki M, Hirata Y, Miyano S. Genomic Object Net: XML Visualization of Simulation Results from Biological Modeling on Hybrid Functional Petri Net. Genome Informatics. 2001; 12: 239-40.(Go to article)
  40. Matsuno H, Doi A, Drath R, Miyano S. Genomic Object Net: Hybrid Petri net for describing biological systems. Currents in Computational Molecular Biology 2001 (RECOMB2001). 2001: 233-4.
  41. Matsuno H, Doi A, Drath R, Miyano S. Genomic Object Net: Object oriented representation of biological systems. Genome Informatics. 2000; 11: 229-30.(Go to article)
  42. Doi A, Matsuno H, Miyano S. Induction mechanism description of lambda phage by hybrid Petri net. Currents in Computational Molecular Biology (RECOMB2000). 2000: 26-7.
  43. Doi A, Drath R, Nagasaki M, Miyano S. Protein dynamics observation of lambda phage by hybrid Petri net. Genome Informatics. 1999; 10: 217-8.(Go to article)