VRL

Resources

Diagrammatic Maps for Rule-Based Models

Author: Yao Sun, Adam Smith, Jim Faeder, Liz Marai

[Blinov-2006-ANM]
M.L. Blinov, J.R. Faeder, B. Goldstein, W.S. Hlavacek, "A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity", Bio Systems, Vol. 83(2), pp. 136--151, Feb 2006. (pdf) (bibtex: Blinov-2006-ANM).
[Blinov-2006-DSC]
M.L. Blinov, J. Yang, J.R. Faeder, W.S. Hlavacek., "Depicting Signaling Cascades", NATURE BIOTECHNOLOGY, Vol. 24(2), pp. 137--138, Feb 2006. (pdf) (bibtex: Blinov-2006-DSC).
[Blinov-2007-RBM]

M.L. Blinov, J.R. Faeder, W.S. Hlavacek, "Rule-Based Modeling of Biological Systems using BioNetGen modeling language (Tutorial)", 2007 International Conference on Systems Biology, pp. 0--0, 2007. (pdf) (bibtex: Blinov-2007-RBM).
[Blinov-2008-CAM]
Michael L. Blinov, Oliver Ruebenacker and Ion I. Moraru, "Complexity and Modularity of Intracellular Networks - A Systematic Approach for Modeling and Simulation.", IET Systems Biology, Vol. 0(0), pp. 0--0, 2008. (pdf) (bibtex: Blinov-2008-CAM).
[Bonneau-2006-TIA]
Richard Bonneau, David J Reiss, Paul Shannon, Marc Facciotti, Leroy Hood, Nitin S Baliga and Vesteinn Thorsson, "The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo", Genome Biology, Vol. 7(0), pp. 0--0, 2006. (pdf) (bibtex: Bonneau-2006-TIA).
[Danos-2007-RBM]
V. Danos, J. Feret, W. Fontana, R. Harmer, J. Krivine, "Rule-Based Modelling of Cellular Signalling", , Vol. 0(0), pp. 0--0, 2007. (pdf) (bibtex: Danos-2007-RBM).
[Danos-2007-SSO]
V. Danos, J. Feret, W. Fontana, J. Krivine, "Scalable simulation of cellular signaling networks", , Vol. 0(0), pp. 0--0, 2007. (pdf) (bibtex: Danos-2007-SSO).
[Delest-2001-GVA]

M. Delest, B. Leblanc, M. S. Marshall, and G. Melanon, "Graph visualization and navigation as an interface to data exploration", , pp. 0--0, 2001. (pdf) (bibtex: Delest-2001-GVA).
[Edelman-2009-ISM]
Lucas B. Edelman, James A. Eddy, and Nathan D. Price, "In Silico Models of Cancer", Wiley Interdisciplinary Reviews: Systems Biology and Medicine, Vol. 2(7), pp. 438--459, Jul 2009. (pdf) (bibtex: Edelman-2009-ISM).
[Faeder-2005-GRB]

J.R. Faeder, M.L. Blinov, W.S. Hlavacek, "Graphical Rule-Based Representation of Signal-Transduction Networks", Proceedings of the 2005 ACM symposium on Applied computing, pp. 133--140, 2005. (pdf) (bibtex: Faeder-2005-GRB).
[Faeder-2008-ACF]
J.R. Faeder, M.L. Blinov, W.S. Hlavacek, "A Chapter from Methods in Molecular Biology: Systems Biology : Rule-Based Modeling of Biochemical Systems with BioNetGen", Humana Press, pp. 0--0, Jul 2008. In Press. (pdf) (bibtex: Faeder-2008-ACF).
[Faeder-2008-MAM]
J. Faeder, "Mapping and Modeling Biochemical Signal Transduction", , pp. 0--0, Feb 2008. (pdf) (bibtex: Faeder-2008-MAM).
[Faith-2007-LSM]
Jeremiah J. Faith, Boris Hayete, Joshua T. Thaden, Ilaria Mogno, Jamey Wierzbowski, Guillaume Cottarel, Simon Kasif, James J. Collins, Timothy S. Gardner, "Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles", Public Library of Science Biology, Vol. 5(0), pp. 54--66, 2007. (pdf) (bibtex: Faith-2007-LSM).
[Finney-2006-SMI]
Andrew Finney, Michael Hucka, Benjamin J. Bornstein, Sarah M. Keating, Bruce E. Shapiro, Joanne Matthews, Ben L. Kovitz, Maria J. Schilstra, Akira Funahashi, John Doyle, and Hiroaki Kitano, "System Modeling in Cell Biology: From Concepts to Nuts and Bolts. Chapter:Software Infrastructure for Effective Communication and Reuse of Computational Models", , Vol. 0(0), pp. 0--0, 2006. (pdf) (bibtex: Finney-2006-SMI).
[Furnas-1986-GFV]
G. W. Furnas, "Generalized fisheye views", CHI, Vol. 0(0), pp. 0--0, 1986. (pdf) (bibtex: Furnas-1986-GFV).
[Han-2003-CMI]
B.-H. Ju and K. Han, "Complexity management in visualizing protein interaction networks", BioInformatics, Vol. 0(0), pp. 0--0, 2003. (pdf) (bibtex: Han-2003-CMI).
[Hartemink-2001-UGM]
Hartemink, A., Gifford, D., Jaakkola, T., & Young, R., "Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks", , Vol. 0(0), pp. 422--433, 2001. (pdf) (bibtex: Hartemink-2001-UGM).
[Hlavacek-2006-RFM]
W.S. Hlavacek, J.R. Faeder, M.L. Blinov, R.G. Posner, M. Hucka, W. Fontana, "Rules for Modeling Signal-Transduction Systems", Sci. STKE 2006 (344), Vol. 344(7), pp. 1--18, Jul 2006. (pdf) (bibtex: Hlavacek-2006-RFM).
[Hughes-2004-VVL]
T. Hughes, Y. Hyun, and D. A. Liberles, "Visualising very large phylogenetic trees in three dimensional hyperbolic space", BMC BioInformatics, Vol. 0(0), pp. 0--0, 2004. (pdf) (bibtex: Hughes-2004-VVL).
[Jianu-2008-APN]
R. Jianu, K. Yu, L. Cao, V. Nguyen, A.R. Salomon, D.H. Laidlaw, "Accelerated protein network analysis by interactive visual integration of quantitative proteomic data, known signaling pathways, and protein interactions", TVCG, Vol. 0(0), pp. 0--0, 2008. (pdf) (bibtex: Jianu-2008-APN).
[Jr.-2006-GAS]

J. F. R. Jr., H. Tong, A. J. M. Traina, C. Faloutsos, and J. Leskovec, "Gmine: A system for scalable, interactive graph visualization and mining", VLDB, pp. 0--0, 2006. (pdf) (bibtex: Jr.-2006-GAS).
[Jurisica-2009-ITF]
M. J. McGuffin and I. Jurisica, "Interaction techniques for selecting and manipulating subgraphs in network visualizations", IEEE Trans. on Visualization and Computer Graphics, Vol. 0(0), pp. 0--0, 2009. (pdf) (bibtex: Jurisica-2009-ITF).
[Kitano-2005-UPD]
H. Kitano, A. Funahashi, Y. Matsuoka, K. Oda, "Using process diagrams for the graphical representation of biological networks", Nature Biotechnology, Vol. 23(8), pp. 961--966, Aug 2005. (pdf) (bibtex: Kitano-2005-UPD).
[Kohn-2006-DCC]
K.W. Kohn, M.I. Aladjem, S. Kim, J.N. Weinstein, Y. Pommier, "Depicting Combinatorial Complexity with the Molecular Interaction Map Notation", Molecular Systems Biology, Vol. 2(10), pp. 1--12, Oct 2006. (pdf) (bibtex: Kohn-2006-DCC).
[Kono-2009-PPW]
N. Kono, K. Arakawa, R. Ogawa, N. Kido, K. Oshita, K. Ikegami, S. Tamaki, and M. Tomita., "Pathway projector: Web-based zoomable pathway browser using kegg atlas and google maps api", PLoS ONE, Vol. 0(0), pp. 0--0, 2009. (pdf) (bibtex: Kono-2009-PPW).
[Lemons--HGF]
Nathan W Lemons, Bin Hu, and William S Hlavacek, "Hierarchical Graphs for Rule-based Modeling of Biochemical Systems", , Vol. 0(0), pp. 0--0, 0. (pdf) (bibtex: Lemons--HGF).
[Madar-2009-TI2]
Aviv Madar, Alex Greenfield, Harry Ostrer, Eric Vanden-Eijnden and Richard Bonneau, "The Inferelator 2.0: A Scalable Framework for Reconstruction of Dynamic Regulatory Network Models", , Vol. 1(0), pp. 0--0, 2009. (pdf) (bibtex: Madar-2009-TI2).
[Marai-2010-BWD]
Liz Marai, James Faeder, "BioNetGen workflow description", , Vol. 0(6), pp. 0--0, Jun 2010. (pdf) (bibtex: Marai-2010-BWD).
[Novère-2009-TSB]
Nicolas Le Novère, Michael Hucka, Huaiyu Mi, Stuart Moodie, Falk Schreiber, Anatoly Sorokin, Emek Demir, Katja Wegner, Mirit I Aladjem, Sarala M Wimalaratne, Frank T Bergman, Ralph Gauges, Peter Ghaza, "The Systems Biology Graphical Notation", Nature Biotechnology, Vol. 27(0), pp. 735--741, 2009. (pdf) (bibtex: Novère-2009-TSB).
[O-2004-MAU]
Thimm O, Bläsing O, Gibon Y, Nagel A, Meyer S, Krüger P, Selbig J, Müller LA, Rhee SY, Stitt M, "Mapman: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes", Plant J., Vol. 0(0), pp. 0--0, 2004. (pdf) (bibtex: O-2004-MAU).
[Ruebenacker-2009-IBK]
O. Ruebenacker, I.I. Moraru, J.S. Schaff, M. L. Blinov, "Integrating BioPAX knowledge with SBML models", IET Systems Biology, Vol. 0(0), pp. 0--0, 2009. (pdf) (bibtex: Ruebenacker-2009-IBK).
[S-2008-KAM]
Okuda S, Yamada T, Hamajima M, Itoh M, Katayama T, Bork P, Goto S, Kanehisa M., "Kegg atlas mapping for global analysis of metabolic pathways", Nucleic Acids Res., Vol. 0(0), pp. 0--0, 2008. (pdf) (bibtex: S-2008-KAM).
[Saraiya-2005-VBP]

Saraiya, Purvi and North, Chris and Duca, Karen, "Visualizing Biological Pathways: Requirements Analysis, Systems Evaluation and Research Agenda", Information Visualization, pp. 191--205, 2005. (pdf) (bibtex: Saraiya-2005-VBP).
[Saraiya-2006-AIB]
P. Saraiya, C. North, V. Lam, K. A. Duca, "An Insight-Based Longitudinal Study of Visual Analytics", IEEE Transactions on Visualization and Computer Graphics, Vol. 0(0), pp. 0--0, 2006. (pdf) (bibtex: Saraiya-2006-AIB).
[Sekar-2009-BCM]
Johnarul Sekar, "BioNetGen Contact Map Basics", , Vol. 0(3), pp. 0--0, Mar 2009. (pdf) (bibtex: Sekar-2009-BCM).
[Shannon-2003-CAS]
P. Shannon, A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker, "Cytoscape: A software environment for integrated models of biomolecular interaction networks", Genome Research, Vol. 0(0), pp. 0--0, 2003. (pdf) (bibtex: Shannon-2003-CAS).
[Tominski-2006-FTV]

Tominski, Christian, Abello, James, van Ham, Frank, Schumann, and Heidrun, "Fisheye tree views and lenses for graph visualization", Proceedings of the conference on Information Visualization, pp. 0--0, 2006. (pdf) (bibtex: Tominski-2006-FTV).
[Tsay-2010-HOL]
Jyh-Jong Tsay, Bo-Liang Wu, Yu-Sen Jeng, "Hierarchically organized layout for visualization of biochemical pathways", Artificial Intelligence in Medicine, Vol. 48(0), pp. 107--117, 2010. (pdf) (bibtex: Tsay-2010-HOL).
[Wills-2007-NIV]

G. J. Wills, "Nicheworks: interactive visualization of very large graphs", Proceedings of Graph Drawing, pp. 0--0, 2007. (pdf) (bibtex: Wills-2007-NIV).