A generic algorithm for layout of biological networks
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Kim Marriott | Tim Dwyer | Falk Schreiber | Michael Wybrow | K. Marriott | F. Schreiber | Michael Wybrow | Tim Dwyer
[1] Peter Eades,et al. A Heuristic for Graph Drawing , 1984 .
[2] Edgar Wingender,et al. TRANSPATH: An integrated database on signal transduction and a tool for array analysis , 2003, Nucleic Acids Res..
[3] Falk Schreiber,et al. Wiley Series on Bioinformatics: Computational Techniques and Engineering , 2008 .
[4] Dimitri P. Bertsekas,et al. Nonlinear Programming , 1997 .
[5] Ugur Dogrusöz,et al. A layout algorithm for signaling pathways , 2006, Inf. Sci..
[6] Kim Marriott,et al. Constrained Stress Majorization Using Diagonally Scaled Gradient Projection , 2007, Graph Drawing.
[7] Masao Nagasaki,et al. An efficient grid layout algorithm for biological networks utilizing various biological attributes , 2007, BMC Bioinformatics.
[8] Peter D. Karp,et al. The Pathway Tools software , 2002, ISMB.
[9] Ursula Kummer,et al. A new dynamical layout algorithm for complex biochemical reaction networks , 2005, BMC Bioinformatics.
[10] Satoru Kawai,et al. An Algorithm for Drawing General Undirected Graphs , 1989, Inf. Process. Lett..
[11] Dorothea Emig,et al. Integrative Visual Analysis of the Effects of Alternative Splicing on Protein Domain Interaction Networks , 2008, J. Integr. Bioinform..
[12] S. Shen-Orr,et al. Network motifs: simple building blocks of complex networks. , 2002, Science.
[13] Falk Schreiber,et al. Frequency Concepts and Pattern Detection for the Analysis of Motifs in Networks , 2005, Trans. Comp. Sys. Biology.
[14] B. Palsson,et al. Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use , 1994, Bio/Technology.
[15] Falk Schreiber,et al. Analysis of Biological Networks (Wiley Series in Bioinformatics) , 2008 .
[16] H. Kitano. Systems Biology: A Brief Overview , 2002, Science.
[17] Kim Marriott,et al. IPSep-CoLa: An Incremental Procedure for Separation Constraint Layout of Graphs , 2006, IEEE Transactions on Visualization and Computer Graphics.
[18] Xuemin Lin,et al. How to draw a directed graph , 1989, [Proceedings] 1989 IEEE Workshop on Visual Languages.
[19] Nikolay A. Kolchanov,et al. GeneNet: a gene network database and its automated visualization , 1998, Bioinform..
[20] Peter D. Karp,et al. Automated Drawing of Metabolic Pathways , 2000 .
[21] Kyungsook Han,et al. A fast layout algorithm for protein interaction networks , 2003, Bioinform..
[22] Ioannis G. Tollis,et al. A Framework for Circular Drawings of Networks , 1999, GD.
[23] Peter J. Stuckey,et al. Fast Node Overlap Removal , 2005, GD.
[24] Jesper Tegnér,et al. Systems biology is taking off. , 2003, Genome research.
[25] Xuemin Lin,et al. A Fast and Effective Heuristic for the Feedback Arc Set Problem , 1993, Inf. Process. Lett..
[26] Hiroyuki Kurata,et al. A grid layout algorithm for automatic drawing of biochemical networks , 2005, Bioinform..
[27] Jens Gerken,et al. IPSep-CoLa: An Incremental Procedure for Separation Constraint Layout of Graphs , 2006 .
[28] Isabel Rojas,et al. A graph layout algorithm for drawing metabolic pathways , 2001, Bioinform..
[29] Sergiy Butenko,et al. Network Clustering , 2014, Encyclopedia of Social Network Analysis and Mining.
[30] Falk Schreiber,et al. High quality visualization of biochemical pathways in BioPath , 2002, Silico Biol..
[31] Ugur Dogrusöz,et al. A Constrained, Force-Directed Layout Algorithm for Biological Pathways , 2003, Graph Drawing.
[32] Edward M. Reingold,et al. Graph drawing by force‐directed placement , 1991, Softw. Pract. Exp..
[33] David P. Dobkin,et al. Implementing a General-Purpose Edge Router , 1997, Graph Drawing.
[34] Karen Eilbeck,et al. Straight-Line Drawings of Protein Interactions , 1999, Graph Drawing.
[35] Peter J. Stuckey,et al. Incremental Connector Routing , 2005, GD.
[36] Susumu Goto,et al. The KEGG databases at GenomeNet , 2002, Nucleic Acids Res..
[37] Uwe Scholz,et al. MetaCrop: a detailed database of crop plant metabolism , 2007, Nucleic Acids Res..
[38] Mitsuhiko Toda,et al. Methods for Visual Understanding of Hierarchical System Structures , 1981, IEEE Transactions on Systems, Man, and Cybernetics.
[39] Erich Bornberg-Bauer,et al. BioMiner - modeling, analyzing, and visualizing biochemical pathways and networks , 2002, ECCB.
[40] Peter Eades,et al. A Heuristics for Graph Drawing , 1984 .
[41] Falk Schreiber,et al. The system architecture of the BioPath system , 2002, Silico Biol..