発表論文（原著）

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.

Saito A, Nagasaki M, Oyama M, Kozuka-Hata H, Sugano S, Yamamoto T, Miyano S, AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction.　BMC Bioinformatics. 2007; 8:15.

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.

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.

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.

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.

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.

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. Genome Informatics, 2006; 17(1), 88-99.

Nagasaki M, Doi A, Matsuno H, Miyano S. Petri Net Based Description and Modeling of Biologinal Pathways. Algebraic Biology - 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.

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.

Nagasaki M. A Platform for Biopathway Modeling/Simulation and Recreating biopathway databases towards simulation. Ph.D Thesis, The University of Tokyo. 2004.

Nagasaki M, Doi A, Matsuno H, Miyano S. Integrating biopathway databases for large-scale modeling and simulation. The Second Asia-Pacific Bioinformatics Conferences　(peer-reviewed), Volume 29 of Conferences in Research and Practice in Information Technology, Australian Computer Society. 2004; 43-52.

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.

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.

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.

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.

Matsuno H, Fujita S, Doi A, Nagasaki M, Miyano S. Towards biopathway modeling and simulation. Lecture Notes in Computer Science 2679:3-22, 2003.

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

Nagasaki M, Onami S, Miyano S, Kitano H. Bio-calculus: its concept and molecular interaction. Genome Informatics 10: 133-143.