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Articles in Scholarly Journals [Incomplete List]

1. The GC and window-averaged DNA curvature profile of secondary metabolite gene cluster in Aspergillus fumigatus genome
   Applied Microbiology and Biotechnology, vol. 80, no. 5, pp. 841–847, 2008
2. Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models
   Bioinformatics, vol. 24, no. 7, pp. 932–942, 2008
3. Fast grid layout algorithm for biological networks with sweep calculation
   Bioinformatics, vol. 24, no. 12, pp. 1433–1441, 2008
4. Systematic reconstruction of TRANSPATH data into Cell System Markup Language
   BMC Systems Biology, vol. 2, no. 1, p. 53, 2008
5. BMC Bioinformatics, vol. 8, no. 1, p. 15, 2007
6. An efficient grid layout algorithm for biological networks utilizing various biological attributes
   BMC Bioinformatics, vol. 8, no. 1, p. 76, 2007
7. Modeling gene expression regulatory networks with the sparse vector autoregressive model
   BMC Systems Biology, vol. 1, no. 1, p. 39, 2007
8. Understanding endothelial cell apoptosis: what can the transcriptome, glycome and proteome reveal?
   Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 362, no. 1484, pp. 1469–1487, 2007
9. Modelling and simulation of signal transductions in an apoptosis pathway by using timed Petri nets
   Journal of Biosciences, vol. 32, no. 1, pp. 113–127, 2007
10. On the complexity of deriving position specific score matrices from positive and negative sequences?
    Discrete Applied Mathematics, vol. 155, no. 6-7, pp. 676–685, 2007
11. Error tolerant model for incorporating biological knowledge with expression data in estimating gene networks
    Statistical Methodology, vol. 3, no. 1, pp. 1–16, 2006
12. Contribution of comparative fish studies to general endocrinology: structure and function of some osmoregulatory hormones
    Journal of Experimental Zoology Part A: Comparative Experimental Biology, vol. 305A, no. 9, pp. 787–798, 2006
13. International Journal on Artificial Intelligence Tools, vol. 15, no. 5, p. 711, 2006
14. Journal of Bioinformatics and Computational Biology, vol. 4, no. 1, p. 139, 2006
15. Journal of Bioinformatics and Computational Biology, vol. 4, no. 5, p. 1119, 2006
16. Petri Net Based Descriptions for Systematic Understanding of Biological Pathways
    IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, vol. E89-A, no. 11, pp. 3166–3174, 2006
17. ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles
    Bioinformatics, vol. 22, no. 12, pp. 1538–1539, 2006
18. Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data
    Bioinformatics, vol. 21, no. suppl_2, pp. ii206–ii212, 2005
19. Journal of Bioinformatics and Computational Biology, vol. 3, no. 6, p. 1295, 2005
20. Journal of Bioinformatics and Computational Biology, vol. 2, no. 1, p. 77, 2004
21. Journal of Bioinformatics and Computational Biology, vol. 2, no. 2, p. 273, 2004
22. Open source clustering software
    Bioinformatics, vol. 20, no. 9, pp. 1453–1454, 2004
23. Superiority of network motifs over optimal networks and an application to the revelation of gene network evolution
    Bioinformatics, vol. 21, no. 2, pp. 227–238, 2004
24. Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data
    Bioinformatics, vol. 20, no. suppl_1, pp. i101–i108, 2004
25. An O(N/sup 2/) algorithm for discovering optimal Boolean pattern pairs
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 1, no. 4, pp. 159–170, 2004
26. Association of a single-nucleotide polymorphism in the immunoglobulin??-binding protein 2 gene with immunoglobulin A nephropathy
    Journal of Human Genetics, vol. 50, no. 1, pp. 30–35, 2004
27. Identification of novel adrenomedullin in mammals: a potent cardiovascular and renal regulator
    FEBS Letters, vol. 556, no. 1-3, pp. 53–58, 2004
28. Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data
    Biosystems, vol. 75, no. 1-3, pp. 57–65, 2004
29. A simple greedy algorithm for finding functional relations: efficient implementation and average case analysis
    Theoretical Computer Science, vol. 292, no. 2, pp. 481–495, 2003
30. Identification of genetic networks by strategic gene disruptions and gene overexpressions under a boolean model
    Theoretical Computer Science, vol. 298, no. 1, pp. 235–251, 2003
31. Inferring gene networks from time series microarray data using dynamic Bayesian networks
    Briefings in Bioinformatics, vol. 4, no. 3, pp. 228–235, 2003
32. Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection
    Bioinformatics, vol. 19, no. 90002, pp. 227ii–236, 2003
33. Use of Gene Networks from Full Genome Microarray Libraries to Identify Functionally Relevant Drug-affected Genes and Gene Regulation Cascades
    DNA Research, vol. 10, no. 1, pp. 19–25, 2003
34. Journal of Bioinformatics and Computational Biology, vol. 1, no. 2, p. 231, 2003
35. Journal of Bioinformatics and Computational Biology, vol. 1, no. 3, p. 459, 2003
36. Single-nucleotide polymorphisms in the class II region of the major histocompatibility complex in Japanese patients with immunoglobulin A nephropathy
    Journal of Human Genetics, vol. 47, no. 10, pp. 532–538, 2002
37. Statistical analysis of a small set of time-ordered gene expression data using linear splines
    Bioinformatics, vol. 18, no. 11, pp. 1477–1485, 2002
38. Extensive feature detection of N-terminal protein sorting signals
    Bioinformatics, vol. 18, no. 2, pp. 298–305, 2002
39. Association between Single-Nucleotide Polymorphisms in Selectin Genes and Immunoglobulin A Nephropathy
    The American Journal of Human Genetics, vol. 70, no. 3, pp. 781–786, 2002
40. Fast algorithm for extracting multiple unordered short motifs using bit operations
    Information Sciences, vol. 146, no. 1-4, pp. 115–126, 2002
41. ProDDO: a database of disordered proteins from the Protein Data Bank (PDB)
    Bioinformatics, vol. 17, no. 4, pp. 379–380, 2001
42. Algorithms for Identifying Boolean Networks and Related Biological Networks Based on Matrix Multiplication and Fingerprint Function
    Journal of Computational Biology, vol. 7, no. 3-4, pp. 331–343, 2000
43. Inferring qualitative relations in genetic networks and metabolic pathways
    Bioinformatics, vol. 16, no. 8, pp. 727–734, 2000
44. On the approximation of protein threading
    Theoretical Computer Science, vol. 210, no. 2, pp. 261–275, 1999
45. Inferring a tree from walks
    Theoretical Computer Science, vol. 161, no. 1-2, pp. 289–300, 1996
46. Using maximal independent sets to solve problems in parallel
    Theoretical Computer Science, vol. 148, no. 1, pp. 57–65, 1995
47. ?P2-complete lexicographically first maximal subgraph problems
    Theoretical Computer Science, vol. 88, no. 1, pp. 33–57, 1991
48. The lexicographically first maximal subgraph problems:P-completeness andNC algorithms
    Mathematical Systems Theory, vol. 22, no. 1, pp. 47–73, 1989
49. A parallelizable lexicographically first maximal edge-induced subgraph problem
    Information Processing Letters, vol. 27, no. 2, pp. 75–78, 1988
50. Remarks on two-way automata with weak-counters
    Information Processing Letters, vol. 18, no. 2, pp. 105–107, 1984
51. Alternating finite automata on ?-words
    Theoretical Computer Science, vol. 32, no. 3, pp. 321–330, 1984
52. Remarks on multihead pushdown automata and multihead stack automata
    Journal of Computer and System Sciences, vol. 27, no. 1, pp. 116–124, 1983
53. Two-way deterministic multi-weak-counter machines
    Theoretical Computer Science, vol. 21, no. 1, pp. 27–37, 1982
54. A hierarchy theorem for multihead stack-counter automata
    Acta Informatica, vol. 17, no. 1, 1982
55. One-way weak-stack-counter automata
    Journal of Computer and System Sciences, vol. 20, no. 1, pp. 59–76, 1980