TY - CHAP AU - Karp, P. D. AU - Paley, S. M. PY - 1994 DA - 1994// TI - Automated Drawing of Metabolic Pathways BT - Third International Conference on Bioinformatics and Genome Research ID - Karp1994 ER - TY - JOUR AU - Salamonsen AU - Yee AU - Mok AU - Kolatkar PY - 1999 DA - 1999// TI - BioJAKE: a tool for the creation, visualization and manipulation of metabolic pathways JO - Pacific Symposium on Biocomputing VL - 4 ID - Salamonsen1999 ER - TY - BOOK AU - Kanehisa, M. PY - 2000 DA - 2000// TI - Post-genome Informatics PB - Oxford University Press CY - USA ID - Kanehisa2000 ER - TY - JOUR AU - Becker, M. AU - Rojas, I. PY - 2001 DA - 2001// TI - A Graph Layout Algorithm for Drawing Metabolic Pathways JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.5.461 DO - 10.1093/bioinformatics/17.5.461 ID - Becker2001 ER - TY - JOUR AU - Seo, J. AU - Shneiderman, B. PY - 2002 DA - 2002// TI - Interactively Exploring Hierarchical Clustering Results JO - IEEE Computer VL - 35 UR - https://doi.org/10.1109/MC.2002.1016905 DO - 10.1109/MC.2002.1016905 ID - Seo2002 ER - TY - CHAP AU - Schreiber, F. PY - 2003 DA - 2003// TI - Comparison of metabolic pathways using constraint graph drawing BT - APBC 03: Proceedings of the First Asia-Pacific bioinformatics conference on Bioinformatics PB - Australian Computer Society CY - Inc ID - Schreiber2003 ER - TY - CHAP AU - Jourdan, F. AU - Melançon, G. PY - 2003 DA - 2003// TI - A Tool for Metabolic and Regulatory Pathways Visual Analysis BT - Visualization and Data Analysis, VDA PB - SPIE CY - Santa Clara Convention Center ID - Jourdan2003 ER - TY - JOUR AU - Dogrusoz AU - Giral AU - Cetintas AU - Civril AU - Demir PY - 2004 DA - 2004// TI - A Compound Graph Layout Algorithm for Biological Pathways JO - GD 2004 VL - 3383 ID - Dogrusoz2004 ER - TY - JOUR AU - Brandes, U. AU - Dwyer, T. AU - Schreiber, F. PY - 2004 DA - 2004// TI - Visualizing Related Metabolic Pathways in Two and Half Dimensions JO - LNCS VL - 2912 ID - Brandes2004 ER - TY - JOUR AU - Wegner AU - Kummer PY - 2005 DA - 2005// TI - A new dynamical layout algoritmh for complex biochemical reaction networks JO - BMC Bioinformatics VL - 6 UR - https://doi.org/10.1186/1471-2105-6-212 DO - 10.1186/1471-2105-6-212 ID - Wegner2005 ER - TY - STD TI - Gabouje SD, Zimányi : A New Compound Graph Layout Algorithm for Visualizing Biochemical Networks. Poster Proceedings Volume of the 4th International Workshop on Efficient and Experimental Algorithms, WEA 05. ID - ref11 ER - TY - JOUR AU - Dogrusoz AU - Erson AU - Giral AU - Demir AU - Babur AU - Cetintas AU - Colak PY - 2005 DA - 2005// TI - PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/bti776 DO - 10.1093/bioinformatics/bti776 ID - Dogrusoz2005 ER - TY - JOUR AU - Tope, J. AU - Gillespie AU - Vastrik AU - DEustachio AU - Schmidt AU - de Bono AU - Jassal AU - Gopinath AU - Wu AU - Matthews AU - Lewis AU - Birney AU - Stein PY - 2005 DA - 2005// TI - Reactome: a knowledgebase of biological pathways JO - Nucleic Acids Research VL - 33 UR - https://doi.org/10.1093/nar/gki072 DO - 10.1093/nar/gki072 ID - Tope2005 ER - TY - JOUR AU - Paley, S. AU - Karp, P. PY - 2006 DA - 2006// TI - The Pathway Tools cellular overview diagram and Omics Viewer JO - Nucleic Acids Research VL - 34 UR - https://doi.org/10.1093/nar/gkl334 DO - 10.1093/nar/gkl334 ID - Paley2006 ER - TY - JOUR AU - Junker, B. H. AU - Klukas, C. AU - Schreiber, F. PY - 2006 DA - 2006// TI - VANTED: A System for Advanced Data Analysis and Visualization in the Context of Biological Networks JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-109 DO - 10.1186/1471-2105-7-109 ID - Junker2006 ER - TY - JOUR AU - Nikiforova, V. AU - Kopka, J. AU - Tolstikov, V. AU - Fiehn, O. AU - Hopkins, L. AU - Hawkesford, M. AU - Hesse, H. AU - Hoefgen, R. PY - 2005 DA - 2005// TI - Systems Rebalancing of Metabolism in Response to Sulfur Deprivation, as Revealed by Metabolome Analysis of Arabidopsis Plants JO - Plant Physiology VL - 138 UR - https://doi.org/10.1104/pp.104.053793 DO - 10.1104/pp.104.053793 ID - Nikiforova2005 ER - TY - JOUR AU - Lacroix, V. AU - Fernandes, C. G. AU - Sagot, M. F. PY - 2006 DA - 2006// TI - Motif search in graphs: application to metabolic networks JO - IEEE/ACM Trans Comput Biol Bioinform VL - 3 UR - https://doi.org/10.1109/TCBB.2006.55 DO - 10.1109/TCBB.2006.55 ID - Lacroix2006 ER - TY - JOUR AU - Saraiya, P. AU - North, C. AU - Duca, K. PY - 2005 DA - 2005// TI - Visualizing biological pathways: requirements analysis, systems evaluation and research agenda JO - Information Visualization VL - 4 UR - https://doi.org/10.1057/palgrave.ivs.9500102 DO - 10.1057/palgrave.ivs.9500102 ID - Saraiya2005 ER - TY - JOUR AU - Jeong, H. AU - Tombor, B. AU - Albert, R. AU - Oltvai, Z. AU - Barabasi, A. PY - 2000 DA - 2000// TI - The Large-Scale Organization of Metabolic Networks JO - Nature VL - 407 UR - https://doi.org/10.1038/35036627 DO - 10.1038/35036627 ID - Jeong2000 ER - TY - JOUR AU - Pfeiffer, T. AU - Dandekar, T. AU - Moldenhauer, F. AU - Schuster, S. PY - 2000 DA - 2000// TI - Topological analysis of metabolic networks. Application to the metabolism of Mycoplasma pneumoniae JO - BTK2000: Animating the Cellular Map VL - 6 ID - Pfeiffer2000 ER - TY - BOOK AU - Salway, J. G. PY - 2003 DA - 2003// TI - Metabolism at a Glance PB - Blackwell Science Ltd CY - USA ID - Salway2003 ER - TY - JOUR AU - Michal, G. PY - 1998 DA - 1998// TI - On representation of metabolic pathways JO - BioSystems VL - 47 UR - https://doi.org/10.1016/S0303-2647(98)00019-7 DO - 10.1016/S0303-2647(98)00019-7 ID - Michal1998 ER - TY - BOOK AU - Michal, G. PY - 1993 DA - 1993// TI - Biochemical Pathways (Poster) PB - Boehringer Mannheim CY - USA ID - Michal1993 ER - TY - STD TI - BIOCARTA: Charting pathways of life. http://www.biocarta.com UR - http://www.biocarta.com ID - ref24 ER - TY - CHAP AU - Romero, P. AU - Wagg, J. AU - Green, M. AU - Kaiser, D. AU - Krummenacker, M. AU - Karp, P. PY - 2004 DA - 2004// TI - Computational prediction of human metabolic pathways from the complete human genome BT - Genome Biology ID - Romero2004 ER - TY - JOUR AU - Purchase, H. AU - Cohen, R. F. AU - James, M. PY - 1997 DA - 1997// TI - An Experimental Study of the Basis for Graph Drawing Algorithms JO - ACM Journal of Experimental Algorithmics VL - 2 ID - Purchase1997 ER - TY - BOOK AU - Battista, G. D. AU - Eades, P. AU - Tamassia, R. AU - Tollis, I. G. PY - 1999 DA - 1999// TI - Graph Drawing: Algorithms for the Visualization of Graphs PB - Prentice Hall CY - USA ID - Battista1999 ER - TY - BOOK AU - Kaufmann, M. AU - Wagner, D. PY - 2001 DA - 2001// TI - Drawing Graphs Springer UR - https://doi.org/10.1007/3-540-44969-8 DO - 10.1007/3-540-44969-8 ID - Kaufmann2001 ER - TY - JOUR AU - Sugiyama AU - Misue PY - 1991 DA - 1991// TI - Visualisation of structural information : Automatic drawing of compound digraphs JO - IEEE Transactions on Systems, Man, and Cybernetics VL - 21 UR - https://doi.org/10.1109/21.108304 DO - 10.1109/21.108304 ID - Sugiyama1991 ER - TY - CHAP AU - Brandenburg, F. AU - Forster, M. AU - Pick, A. AU - Raitner, M. AU - Schreiber, F. ED - Verlag, S. PY - 2002 DA - 2002// TI - Biopath BT - GD'01 ID - Brandenburg2002 ER - TY - JOUR AU - Eades PY - 1984 DA - 1984// TI - A heuristic for graph drawing JO - Congressus Numerantium VL - 42 ID - Eades1984 ER - TY - JOUR AU - Frick AU - Ludwig AU - Mehldau PY - 1994 DA - 1994// TI - A fast adaptive layout algorithm for undirected graphs JO - Lecture Notes in Computer Science VL - 894 UR - https://doi.org/10.1007/3-540-58950-3_393 DO - 10.1007/3-540-58950-3_393 ID - Frick1994 ER - TY - JOUR AU - Shannon, P. AU - Markiel, A. AU - Ozierand, O. AU - Baliga, N. AU - Wang, J. AU - Ramage, D. AU - Amin, N. AU - Schwikowski, B. AU - Ideker, T. PY - 2003 DA - 2003// TI - Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks JO - Genome Research VL - 13 UR - https://doi.org/10.1101/gr.1239303 DO - 10.1101/gr.1239303 ID - Shannon2003 ER - TY - STD TI - SBML viewer. http://sbw.kgi.edu/layout/ UR - http://sbw.kgi.edu/layout/ ID - ref34 ER - TY - JOUR AU - van Helden, J. AU - Wernisch, L. AU - Gilbert, D. AU - Wodak, S. PY - 2002 DA - 2002// TI - Graph-based analysis of metabolic networks JO - Ernst Schering Research Foundation Workshop VL - 38 ID - van Helden2002 ER - TY - BOOK AU - Garey, M. R. AU - Johnson, D. S. PY - 1979 DA - 1979// TI - Computers and Intractability: A Guide to the Theory of NP-Completeness PB - Co CY - New York, NY, USA ID - Garey1979 ER - TY - JOUR AU - Welsh AU - Powell PY - 1967 DA - 1967// TI - An upper Bound to the chromatic number of a graph and its application to timetabling problems JO - The Computer journal VL - 10 UR - https://doi.org/10.1093/comjnl/10.1.85 DO - 10.1093/comjnl/10.1.85 ID - Welsh1967 ER - TY - STD TI - Auber D: Graph Drawing Software. Springer-Verlag 2003 chap. Tulip- A Huge Graph Visualization Framework ID - ref38 ER - TY - CHAP AU - Gutwenger, C. AU - Mutzel, P. PY - 1998 DA - 1998// TI - Planar Polyline Drawings with Good Angular Resolution BT - Graph Drawing '98 (Proc.) PB - Springer-Verlag CY - Lecture Notes in Computer Science UR - https://doi.org/10.1007/3-540-37623-2_13 DO - 10.1007/3-540-37623-2_13 ID - Gutwenger1998 ER - TY - CHAP AU - Lui, P. AU - Geldmacher, R. PY - 1977 DA - 1977// TI - On the deletion of nonplanar edges of a graph BT - Proceeding on the 10th conf. on Comb., Graph Theory, and Comp ID - Lui1977 ER - TY - JOUR AU - Liebers, A. PY - 2001 DA - 2001// TI - Planarizing Graphs – A Survey and Annotated Bibliography JO - Journal of Graph Algorithms and Applications VL - 5 UR - https://doi.org/10.7155/jgaa.00032 DO - 10.7155/jgaa.00032 ID - Liebers2001 ER - TY - JOUR AU - Karp, P. AU - Riley, M. AU - Saier, M. AU - Paulsen, I. PY - 2000 DA - 2000// TI - The EcoCyc and MetaCyc databases JO - Nucleic Acids Research VL - 28 UR - https://doi.org/10.1093/nar/28.1.56 DO - 10.1093/nar/28.1.56 ID - Karp2000 ER - TY - JOUR AU - Karp, P. D. AU - Paley, S. AU - Romero, P. PY - 2002 DA - 2002// TI - The Pathway Tools software JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.suppl_1.S225 DO - 10.1093/bioinformatics/18.suppl_1.S225 ID - Karp2002 ER - TY - JOUR AU - Krummenacker, M. AU - Paley, S. AU - Mueller, L. AU - Yan, T. AU - Karp, P. D. PY - 2005 DA - 2005// TI - Querying and computing with BioCyc databases JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti546 DO - 10.1093/bioinformatics/bti546 ID - Krummenacker2005 ER - TY - JOUR AU - Schuster, S. AU - Hilgetag, C. AU - Woods, J. H. AU - Fell, D. A. PY - 2002 DA - 2002// TI - Reaction routes in biochemical reaction systems: algebraic properties, validated calculation procedure and example from nucleotide metabolism JO - J Math Biol VL - 45 UR - https://doi.org/10.1007/s002850200143 DO - 10.1007/s002850200143 ID - Schuster2002 ER - TY - JOUR AU - Schilling, C. H. AU - Letscher, D. AU - Palsson, B. O. PY - 2000 DA - 2000// TI - Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective JO - J Theor Biol VL - 203 UR - https://doi.org/10.1006/jtbi.2000.1073 DO - 10.1006/jtbi.2000.1073 ID - Schilling2000 ER - TY - CHAP AU - Finney, A. H. M. PY - 2003 DA - 2003// TI - Systems biology markup language: Level 2 and beyond BT - Biochem Soc Trans ID - Finney2003 ER -