메뉴 건너뛰기




Volumn 24, Issue 12, 2008, Pages 1433-1441

Fast grid layout algorithm for biological networks with sweep calculation

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CALCULATION; CELLULAR DISTRIBUTION; CHEMICAL REACTION; CONTROLLED STUDY; DATA BASE; GENE CONTROL; GENE REGULATORY NETWORK; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

EID: 45449113970     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn196     Document Type: Article
Times cited : (16)

References (33)
  • 1
    • 0024736066 scopus 로고
    • Geometric computing and uniform grid technique
    • Akman,V. et al. (1989) Geometric computing and uniform grid technique. Comput. Aided Des., 21, 410-420.
    • (1989) Comput. Aided Des , vol.21 , pp. 410-420
    • Akman, V.1
  • 2
    • 34249751614 scopus 로고    scopus 로고
    • Cerebral: A Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation
    • Barsky,A. et al. (2007) Cerebral: A Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation. Bioinformatics, 23, 1040-1042.
    • (2007) Bioinformatics , vol.23 , pp. 1040-1042
    • Barsky, A.1
  • 3
    • 43949160006 scopus 로고
    • Annotated bibliography on graph drawing algorithms
    • Battista,D.G. et al. (1994) Annotated bibliography on graph drawing algorithms. Comput. Geom. Theor. Appl., 4, 235-282.
    • (1994) Comput. Geom. Theor. Appl , vol.4 , pp. 235-282
    • Battista, D.G.1
  • 5
    • 85142147787 scopus 로고    scopus 로고
    • Becker.M.Y. and Rojas,I. (2001) A graph layout algorithm for drawing metabolic pathways. Bioinformatics, 17, 461-467.
    • Becker.M.Y. and Rojas,I. (2001) A graph layout algorithm for drawing metabolic pathways. Bioinformatics, 17, 461-467.
  • 6
    • 0343203195 scopus 로고    scopus 로고
    • Algorithmenzum automatischen Zeichnen von Graphen.
    • Brandenburg,F.-J. et al. (1997) Algorithmenzum automatischen Zeichnen von Graphen. Inform. Spektrum, 20, 199-207.
    • (1997) Inform. Spektrum , vol.20 , pp. 199-207
    • Brandenburg, F.-J.1
  • 7
    • 0022701012 scopus 로고
    • Reporting and counting segment intersections
    • Chazelle,B. (1986) Reporting and counting segment intersections. J. Comput. Syst. Sci., 32, 156-182.
    • (1986) J. Comput. Syst. Sci , vol.32 , pp. 156-182
    • Chazelle, B.1
  • 8
    • 85032014893 scopus 로고
    • Space-efficient ray-shooting and intersection searching: Algorithms, dynamization, and applications
    • Society for Industrial & Applied, San Francisco, USA, pp
    • Cheng,S.W. and Janardan,R. (1991) Space-efficient ray-shooting and intersection searching: Algorithms, dynamization, and applications. In Proceedings of the second annual ACM-SIAM symposium on Discrete algorithms. Society for Industrial & Applied, San Francisco, USA, pp. 7-16.
    • (1991) Proceedings of the second annual ACM-SIAM symposium on Discrete algorithms , pp. 7-16
    • Cheng, S.W.1    Janardan, R.2
  • 9
    • 33751376743 scopus 로고    scopus 로고
    • Supporting the SBML layout extension
    • Deckard,A. et al. (2006) Supporting the SBML layout extension. Bioinformatics, 22, 2966-2967.
    • (2006) Bioinformatics , vol.22 , pp. 2966-2967
    • Deckard, A.1
  • 10
    • 0036326896 scopus 로고    scopus 로고
    • PATIKA: An integrated visual environment for collaborative construction and analysis of cellular pathways
    • Demir,E. et al. (2002) PATIKA: An integrated visual environment for collaborative construction and analysis of cellular pathways. Bioinformatics, 18, 996-1003.
    • (2002) Bioinformatics , vol.18 , pp. 996-1003
    • Demir, E.1
  • 11
    • 24144477533 scopus 로고    scopus 로고
    • A compound graph layout algorithm for biological pathways
    • Springer-Verlag, New York City, USA, pp
    • Dogrusoz,U. et al. (2004) A compound graph layout algorithm for biological pathways. In Proceedings of the 12th International Symposium on Graph Drawing. Springer-Verlag, New York City, USA, pp. 442-47.
    • (2004) Proceedings of the 12th International Symposium on Graph Drawing , pp. 442-447
    • Dogrusoz, U.1
  • 12
    • 32144455205 scopus 로고    scopus 로고
    • PATIKA web: A Web interface for analyzing biological pathways through advanced querying and visualization
    • Dogrusoz,U, et al. (2006) PATIKA web: A Web interface for analyzing biological pathways through advanced querying and visualization. Bioinformatics, 22, 374-375.
    • (2006) Bioinformatics , vol.22 , pp. 374-375
    • Dogrusoz, U.1
  • 13
    • 2642527148 scopus 로고    scopus 로고
    • Genomic Object Net: II. Modelling biopathways by hybrid functional Petri net with extension
    • Doi,A. et al. (2003) Genomic Object Net: II. Modelling biopathways by hybrid functional Petri net with extension. Appl. Bioinformatics 2, 185-188.
    • (2003) Appl. Bioinformatics , vol.2 , pp. 185-188
    • Doi, A.1
  • 14
    • 84905389375 scopus 로고    scopus 로고
    • A constrained, force-directed layout algorithm for biological pathways
    • Springer-Verlag, Rerugia, Italy, pp
    • Genc,B. and Dogrusoz,U. (2003) A constrained, force-directed layout algorithm for biological pathways. In Proceedings of the 11th International Symposium on Graph Drawing. Springer-Verlag, Rerugia, Italy, pp. 314-319.
    • (2003) Proceedings of the 11th International Symposium on Graph Drawing , pp. 314-319
    • Genc, B.1    Dogrusoz, U.2
  • 15
    • 33847274309 scopus 로고    scopus 로고
    • GOlorize: A cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring
    • Garcia,O. et al. (2007) GOlorize: A cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. Bioinformatics, 23, 394-396.
    • (2007) Bioinformatics , vol.23 , pp. 394-396
    • Garcia, O.1
  • 17
    • 33747825750 scopus 로고    scopus 로고
    • A model diagram layout extension for SBML
    • Gauges,R. et al. (2006) A model diagram layout extension for SBML. Bioinformatics, 22, 1879-1885.
    • (2006) Bioinformatics , vol.22 , pp. 1879-1885
    • Gauges, R.1
  • 18
    • 0037805576 scopus 로고    scopus 로고
    • The KEGG database
    • Kanehisa,M. (2002) The KEGG database. Novartis Found Symp., 247 91-101.
    • (2002) Novartis Found Symp , vol.247 , pp. 91-101
    • Kanehisa, M.1
  • 20
    • 33748545276 scopus 로고    scopus 로고
    • Automatic drawing of biological networks using cross cost and subcomponent data
    • Kato,M. et al. (2005) Automatic drawing of biological networks using cross cost and subcomponent data. Genome Inform., 16, 22-31.
    • (2005) Genome Inform , vol.16 , pp. 22-31
    • Kato, M.1
  • 21
    • 33947388382 scopus 로고    scopus 로고
    • An efficient grid layout algorithm for biological networks utilizing various biological attributes
    • Kojima,K. et al. (2007) An efficient grid layout algorithm for biological networks utilizing various biological attributes. BMC Bioinformatics, 8, 1-16.
    • (2007) BMC Bioinformatics , vol.8 , pp. 1-16
    • Kojima, K.1
  • 22
    • 0242380634 scopus 로고    scopus 로고
    • CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle
    • Kurata,H. et al. (2003) CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle. Nucleic Acids Res., 31, 4071-4084.
    • (2003) Nucleic Acids Res , vol.31 , pp. 4071-4084
    • Kurata, H.1
  • 23
    • 17844397967 scopus 로고    scopus 로고
    • CADLIVE dynamic simulator: Direct link of biochemical networks to dynamic models
    • Kurata,H. et al. (2005) CADLIVE dynamic simulator: Direct link of biochemical networks to dynamic models. Genome Res., 15, 590-600.
    • (2005) Genome Res , vol.15 , pp. 590-600
    • Kurata, H.1
  • 24
    • 18744387729 scopus 로고    scopus 로고
    • A grid layout algorithm for automatic drawing of biochemical networks
    • Li,W. and Kurata,H. (2005) A grid layout algorithm for automatic drawing of biochemical networks, Bioinformatics, 21, 2036-2042.
    • (2005) Bioinformatics , vol.21 , pp. 2036-2042
    • Li, W.1    Kurata, H.2
  • 25
    • 2642533799 scopus 로고    scopus 로고
    • Genomic Object Net: I. A platform for modelling and simulating biopathways
    • Nagasaki,M. et al. (2003) Genomic Object Net: I. A platform for modelling and simulating biopathways. Appl. Bioinformatics, 2 181-184.
    • (2003) Appl. Bioinformatics , vol.2 , pp. 181-184
    • Nagasaki, M.1
  • 26
    • 0028667911 scopus 로고
    • Counting and reporting red/blue segment intersections
    • Palazzi,L. and Snoeyink,J. (1993) Counting and reporting red/blue segment intersections. CVGIP: Graph. Model. Im., 56, 304-310.
    • (1993) CVGIP: Graph. Model. Im , vol.56 , pp. 304-310
    • Palazzi, L.1    Snoeyink, J.2
  • 27
    • 84877261134 scopus 로고    scopus 로고
    • Endothelial activation: Intercellular signalizing pathways
    • Pober,J.S. (2002) Endothelial activation: Intercellular signalizing pathways. Arthritis Res., 4, S109-S116.
    • (2002) Arthritis Res , vol.4
    • Pober, J.S.1
  • 28
    • 33947371802 scopus 로고    scopus 로고
    • Cell fate simulation model of gustatory neurons with microRNAs double-negative feedback loop by hybrid functional Petri net with extension
    • Saito,A. et al. (2006) Cell fate simulation model of gustatory neurons with microRNAs double-negative feedback loop by hybrid functional Petri net with extension. Genome Inform., 17, 100-111.
    • (2006) Genome Inform , vol.17 , pp. 100-111
    • Saito, A.1
  • 29
    • 0035177003 scopus 로고    scopus 로고
    • The TRANSPATH signal transduction database: A knowledge base on signal transduction networks
    • Schacherer,F. et al. (2001) The TRANSPATH signal transduction database: A knowledge base on signal transduction networks. Bioinformatics, 17, 1053-1057.
    • (2001) Bioinformatics , vol.17 , pp. 1053-1057
    • Schacherer, F.1
  • 30
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: A software environment for integrated models of biomolecular interaction networks
    • Shannon,P. et al. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504.
    • (2003) Genome Res , vol.13 , pp. 2498-2504
    • Shannon, P.1
  • 31
    • 0003751973 scopus 로고
    • A practical approach to drawing undirected graphs
    • Technical Report CMUCS-94-161. Carnegie Mellon University, School of Computer Science
    • Tunkelang,D. (1994) A practical approach to drawing undirected graphs. Technical Report CMUCS-94-161. Carnegie Mellon University, School of Computer Science.
    • (1994)
    • Tunkelang, D.1
  • 32
  • 33
    • 25444504488 scopus 로고    scopus 로고
    • A new dynamical layout algorithm for complex biochemical reaction networks
    • Wegner,K. and Kummer,U. (2005) A new dynamical layout algorithm for complex biochemical reaction networks. BMC Bioinformatics, 6 1-12.
    • (2005) BMC Bioinformatics , vol.6 , pp. 1-12
    • Wegner, K.1    Kummer, U.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.