-
1
-
-
77955381783
-
Robustness from flexibility in the fungal circadian clock
-
Ozgur E, Akman, David A. Rand, Paul E. Brown, and Andrew J. Millar. 2010. Robustness from flexibility in the fungal circadian clock. BMC Systems Biology 4, 1 (2010), 88
-
(2010)
BMC Systems Biology
, vol.4
, Issue.1
, pp. 88
-
-
Ozgur, E.A.1
Rand, D.A.2
Brown, P.E.3
Millar, A.J.4
-
2
-
-
0003880161
-
-
Number v. 1 in Molecular Biology of the Cell: Reference Edition Taylor & Francis
-
B. Alberts. 2008. Molecular Biology of the Cell: Reference Edition. Number v. 1 in Molecular Biology of the Cell: Reference Edition. Taylor & Francis
-
(2008)
Molecular Biology of the Cell: Reference Edition
-
-
Alberts, B.1
-
3
-
-
58149464983
-
KINSOLVER: A simulator for computing large ensembles of biochemical and gene regulatory networks
-
Boanerges Aleman-Meza, Yihai Yu, Heinz-Bernd Schüttler, Jonathan Arnold, and Thiab R. Taha. 2009. KINSOLVER: A simulator for computing large ensembles of biochemical and gene regulatory networks. Computers & Mathematics with Applications 57, 3 (2009), 420-435
-
(2009)
Computers & Mathematics with Applications
, vol.57
, Issue.3
, pp. 420-435
-
-
Aleman-Meza, B.1
Yu, Y.2
Schüttler, H.-B.3
Arnold, J.4
Taha, T.R.5
-
4
-
-
77950833499
-
Detailed simulations of cell biology with Smoldyn 2.1
-
Steven S. Andrews, Nathan J. Addy, Roger Brent, and Adam P. Arkin. 2010. Detailed simulations of cell biology with Smoldyn 2.1. PLoS Computational Biology 6, 3 (2010), e1000705
-
(2010)
PLoS Computational Biology
, vol.6
, Issue.3
, pp. e1000705
-
-
Andrews, S.S.1
Addy, N.J.2
Brent, R.3
Arkin, A.P.4
-
5
-
-
79551523678
-
New approaches to modeling complex biochemistry
-
John A. Bachman and Peter Sorger. 2011. New approaches to modeling complex biochemistry. Nature Methods 8, 2 (2011), 130
-
(2011)
Nature Methods
, vol.8
, Issue.2
, pp. 130
-
-
Bachman, J.A.1
Sorger, P.2
-
7
-
-
34447498286
-
Systems biology by the rules: Hybrid intelligent systems for pathway modeling and discovery
-
William J. Bosl. 2007. Systems biology by the rules: Hybrid intelligent systems for pathway modeling and discovery. BMC Systems Biology 1, 1 (2007), 13
-
(2007)
BMC Systems Biology
, vol.1
, Issue.1
, pp. 13
-
-
Bosl, W.J.1
-
8
-
-
0027231876
-
Computer simulation of the phosphorylation cascade controlling bacterial chemotaxis
-
Dennis Bray, Robert B. Bourret, and Melvin I. Simon. 1993. Computer simulation of the phosphorylation cascade controlling bacterial chemotaxis. Molecular Biology of the Cell 4, 5 (1993), 469
-
(1993)
Molecular Biology of the Cell
, vol.4
, Issue.5
, pp. 469
-
-
Bray, D.1
Bourret, R.B.2
Simon, M.I.3
-
9
-
-
0035455635
-
Distributing mcell simulations on the grid
-
Henri Casanova, Thomas M. Bartol, Joel Stiles, and Francine Berman. 2001. DistributingMCell simulations on the Grid. International Journal of High Performance Computing Applications 15, 3 (2001), 243-257.
-
(2001)
International Journal of High Performance Computing Applications
, vol.15
, Issue.3
, pp. 243-257
-
-
Casanova, H.1
Bartol, T.M.2
Stiles, J.3
Berman, F.4
-
10
-
-
71849095864
-
TinkerCell: Modular CAD tool for synthetic biology
-
Deepak Chandran, Frank T. Bergmann, Herbert M. Sauro, and others. 2009. TinkerCell: Modular CAD tool for synthetic biology. Journal of Biological Engineering 3, 1 (2009), 19
-
(2009)
Journal of Biological Engineering
, vol.3
, Issue.1
, pp. 19
-
-
Chandran, D.1
Bergmann, F.T.2
Sauro, H.M.3
-
12
-
-
74049092326
-
The Bio-PEPA tool suite
-
IEEE
-
Federica Ciocchetta, Adam Duguid, Stephen Gilmore, Maria Luisa Guerriero, and Jane Hillston. 2009. The Bio-PEPA tool suite. In Proceedings of the 6th International Conference on the Quantitative Evaluation of Systems (QEST '09). IEEE, 309-310
-
(2009)
Proceedings of the 6th International Conference on the Quantitative Evaluation of Systems (QEST '09)
, pp. 309-310
-
-
Ciocchetta, F.1
Duguid, A.2
Gilmore, S.3
Guerriero, M.L.4
Hillston, J.5
-
13
-
-
84866119498
-
Hybrid models and biological model reduction with PyDSTool
-
Robert Clewley. 2012. Hybrid models and biological model reduction with PyDSTool. PLoS Computational Biology 8, 8 (2012), e1002628
-
(2012)
PLoS Computational Biology
, vol.8
, Issue.8
, pp. e1002628
-
-
Clewley, R.1
-
14
-
-
66649126189
-
A review of overview + detail, zooming, and focus + context interfaces
-
Andy Cockburn, Amy Karlson, and Benjamin B. Bederson. 2008. A review of overview + detail, zooming, and focus + context interfaces. ACM Computing Surveys (CSUR) 41, 1 (2008), 2
-
(2008)
ACM Computing Surveys (CSUR)
, vol.41
, Issue.1
, pp. 2
-
-
Cockburn, A.1
Karlson, A.2
Bederson, B.B.3
-
15
-
-
63549099634
-
Simulation of large-scale rule-based models
-
Apr 2009
-
J. Colvin, M. I. Monine, J. R. Faeder, W. S. Hlavacek, D. D. Von Hoff, and R. G. Posner. 2009. Simulation of large-scale rule-based models. Bioinformatics 25, 7 (Apr 2009), 910-917
-
(2009)
Bioinformatics
, vol.25
, Issue.7
, pp. 910-917
-
-
Colvin, J.1
Monine, M.I.2
Faeder, J.R.3
Hlavacek, W.S.4
Von Hoff, D.D.5
Posner, R.G.6
-
16
-
-
49949112078
-
The Beta Workbench: A computational tool to study the dynamics of biological systems
-
L. Dematté, C. Priami, and A. Romanel. 2008. The Beta Workbench: A computational tool to study the dynamics of biological systems. Briefings in Bioinformatics 9, 5 (2008), 437-449
-
(2008)
Briefings in Bioinformatics
, vol.9
, Issue.5
, pp. 437-449
-
-
Dematté, L.1
Priami, C.2
Romanel, A.3
-
17
-
-
3042595010
-
Cellware: A multi-Algorithmic software for computational systems biology
-
Pawan Dhar, Tan Chee Meng, Sandeep Somani, Li Ye, Anand Sairam, Mandar Chitre, Zhu Hao, and Kishore Sakharkar. 2004. Cellware: A multi-Algorithmic software for computational systems biology. Bioinformatics 20, 8 (2004), 1319-1321
-
(2004)
Bioinformatics
, vol.20
, Issue.8
, pp. 1319-1321
-
-
Dhar, P.1
Meng, T.C.2
Somani, S.3
Ye, L.4
Sairam, A.5
Chitre, M.6
Hao, Z.7
Sakharkar, K.8
-
18
-
-
79961090826
-
Multiscale modeling and interoperability in MOOSE
-
Niraj Dudani, Subhasis Ray, Siji George, and Upinder S. Bhalla. 2009. Multiscale modeling and interoperability in MOOSE. Neuroscience 10, Suppl 1 (2009), 54
-
(2009)
Neuroscience
, vol.10
, pp. 54
-
-
Dudani, N.1
Ray, S.2
George, S.3
Bhalla, U.S.4
-
20
-
-
52649086295
-
FERN-A Java framework for stochastic simulation and evaluation of reaction networks
-
Florian Erhard, Caroline C. Friedel, and Ralf Zimmer. 2008. FERN-A Java framework for stochastic simulation and evaluation of reaction networks. BMC Bioinformatics 9, 1 (2008), 356
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.1
, pp. 356
-
-
Erhard, F.1
Friedel, C.C.2
Zimmer, R.3
-
21
-
-
77953882208
-
Graph drawing and its applications
-
M. Kaufmann and D. Wagner, Eds. Springer
-
Rudolf Fleischer and Colin Hirsch. 2001. Graph drawing and its applications. In Drawing Graphs. M. Kaufmann and D. Wagner, Eds., Springer, 1-22
-
(2001)
Drawing Graphs
, pp. 1-22
-
-
Fleischer, R.1
Hirsch, C.2
-
23
-
-
47949099328
-
CellDesigner 3.5: A versatile modeling tool for biochemical networks
-
Akira Funahashi, Yukiko Matsuoka, Akiya Jouraku, Mineo Morohashi, Norihiro Kikuchi, and Hiroaki Kitano. 2008. CellDesigner 3.5: A versatile modeling tool for biochemical networks. Proceedings of the IEEE 96, 8 (2008), 1254-1265
-
(2008)
Proceedings of the IEEE
, vol.96
, Issue.8
, pp. 1254-1265
-
-
Funahashi, A.1
Matsuoka, Y.2
Jouraku, A.3
Morohashi, M.4
Kikuchi, N.5
Kitano, H.6
-
24
-
-
0346250869
-
BioSPICE: Access to the most current computational tools for biologists
-
T. D. Garvey, P. Lincoln, C. J. Pedersen, D. Martin, and M. Johnson. 2003. BioSPICE: Access to the most current computational tools for biologists. OMICS 7, 4 (2003), 411-420
-
(2003)
OMICS
, vol.7
, Issue.4
, pp. 411-420
-
-
Garvey, T.D.1
Lincoln, P.2
Pedersen, C.J.3
Martin, D.4
Johnson, M.5
-
25
-
-
77955290623
-
DBSolve Optimum: A software package for kinetic modeling which allows dynamic visualization of simulation results
-
Nail M. Gizzatkulov, Igor I. Goryanin, Eugeny A. Metelkin, Ekaterina A. Mogilevskaya, Kirill V. Peskov, and Oleg V. Demin. 2010. DBSolve Optimum: A software package for kinetic modeling which allows dynamic visualization of simulation results. BMC Systems Biology 4, 1 (2010), 109
-
(2010)
BMC Systems Biology
, vol.4
, Issue.1
, pp. 109
-
-
Gizzatkulov, N.M.1
Goryanin, I.I.2
Metelkin, E.A.3
Mogilevskaya, E.A.4
Peskov, K.V.5
Demin, O.V.6
-
26
-
-
85206048306
-
Using the SRSim software for spatial and rule-based modeling of combinatorially complex biochemical reaction systems
-
M. Gheorghe, T.Hinze, G. Paun, G. Rozenberg, and A. Salomaa, Eds. Springer
-
Gerd Grünert and Peter Dittrich. 2011. Using the SRSim software for spatial and rule-based modeling of combinatorially complex biochemical reaction systems. In Membrane Computing.M. Gheorghe, T.Hinze, G. Paun, G. Rozenberg, and A. Salomaa, Eds., Springer, 240-256
-
(2011)
Membrane Computing
, pp. 240-256
-
-
Grünert, G.1
Dittrich, P.2
-
27
-
-
54949133752
-
SynBioSS: The synthetic biology modeling suite
-
Anthony D. Hill, Jonathan R. Tomshine, Emma M. B. Weeding, Vassilios Sotiropoulos, and Yiannis N. Kaznessis. 2008. SynBioSS: The synthetic biology modeling suite. Bioinformatics 24, 21 (2008), 2551-2553
-
(2008)
Bioinformatics
, vol.24
, Issue.21
, pp. 2551-2553
-
-
Hill, A.D.1
Tomshine, J.R.2
Weeding, E.M.B.3
Sotiropoulos, V.4
Kaznessis, Y.N.5
-
28
-
-
33845368513
-
COPASI-A Complex pathway simulator
-
Dec 2006
-
S. Hoops, S. Sahle, R. Gauges, C. Lee, J. Pahle, N. Simus, M. Singhal, L. Xu, P. Mendes, and U. Kummer. 2006. COPASI-A COmplex PAthway SImulator. Bioinformatics 22, 24 (Dec 2006), 3067-3074
-
(2006)
Bioinformatics
, vol.22
, Issue.24
, pp. 3067-3074
-
-
Hoops, S.1
Sahle, S.2
Gauges, R.3
Lee, C.4
Pahle, J.5
Simus, N.6
Singhal, M.7
Xu, L.8
Mendes, P.9
Kummer, U.10
-
29
-
-
34247540849
-
A new algorithm for removing node overlapping in graph visualization
-
Xiaodi Huang,Wei Lai, A. S.M. Sajeev, and Junbin Gao. 2007. A new algorithm for removing node overlapping in graph visualization. Information Sciences 177, 14 (2007), 2821-2844
-
(2007)
Information Sciences
, vol.177
, Issue.14
, pp. 2821-2844
-
-
Huang, X.1
Lai, W.2
Sajeev, A.S.M.3
Gao, J.4
-
30
-
-
0037342537
-
The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
-
Michael Hucka, Andrew Finney, Herbert M. Sauro, Hamid Bolouri, John C. Doyle, Hiroaki Kitano, Adam P. Arkin, Benjamin J. Bornstein, Dennis Bray, Athel Cornish-Bowden, and others. 2003. The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 19, 4 (2003), 524-531
-
(2003)
Bioinformatics
, vol.19
, Issue.4
, pp. 524-531
-
-
Hucka, M.1
Finney, A.2
Sauro, H.M.3
Bolouri, H.4
Doyle, J.C.5
Kitano, H.6
Arkin, A.P.7
Bornstein, B.J.8
Bray, D.9
Cornish-Bowden, A.10
-
31
-
-
84864258618
-
A whole-cell computational model predicts phenotype from genotype
-
Jonathan R. Karr, Jayodita C. Sanghvi, Derek N. Macklin, Miriam V. Gutschow, Jared M. Jacobs, Benjamin Bolival Jr., Nacyra Assad-Garcia, John I. Glass, and MarkusW. Covert. 2012. A whole-cell computational model predicts phenotype from genotype. Cell 150, 2 (2012), 389-401
-
(2012)
Cell
, vol.150
, Issue.2
, pp. 389-401
-
-
Karr, J.R.1
Sanghvi, J.C.2
Macklin, D.N.3
Gutschow, M.V.4
Jacobs, J.M.5
Bolival, B.6
Assad-Garcia, N.7
Glass, J.I.8
Covert, M.W.9
-
33
-
-
0036204115
-
STOCKS: STOChastic kinetic simulations of biochemical systems with Gillespie algorithm
-
Andrzej M. Kierzek. 2002. STOCKS: STOChastic kinetic simulations of biochemical systems with Gillespie algorithm. Bioinformatics 18, 3 (2002), 470-481
-
(2002)
Bioinformatics
, vol.18
, Issue.3
, pp. 470-481
-
-
Kierzek, A.M.1
-
34
-
-
0036500993
-
Systems biology: A brief overview
-
Hiroaki Kitano. 2002. Systems biology: A brief overview. Science 295, 5560 (2002), 1662-1664
-
(2002)
Science
, vol.295
, Issue.5560
, pp. 1662-1664
-
-
Kitano, H.1
-
36
-
-
61349127270
-
ALC: Automated reduction of rule-based models
-
Markus Koschorreck and Ernst D. Gilles. 2008. ALC: Automated reduction of rule-based models. BMC Systems Biology 2, 1 (2008), 91
-
(2008)
BMC Systems Biology
, vol.2
, Issue.1
, pp. 91
-
-
Koschorreck, M.1
Gilles, E.D.2
-
37
-
-
77951962279
-
Odefy-from discrete to continuous models
-
J. Krumsiek, S. Polsterl, D. M. Wittmann, and F. J. Theis. 2010. Odefy-from discrete to continuous models. BMC Bioinformatics 11 (2010), 233
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 233
-
-
Krumsiek, J.1
Polsterl, S.2
Wittmann, D.M.3
Theis, F.J.4
-
38
-
-
36749043657
-
Extended CADLIVE: A novel graphical notation for design of biochemical network maps and computational pathway analysis
-
Hiroyuki Kurata, Kentaro Inoue, Kazuhiro Maeda, Koichi Masaki, Yuki Shimokawa, and Quanyu Zhao. 2007. Extended CADLIVE: A novel graphical notation for design of biochemical network maps and computational pathway analysis. Nucleic Acids Research 35, 20 (2007), e134-e134
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.20
, pp. e134-e134
-
-
Kurata, H.1
Inoue, K.2
Maeda, K.3
Masaki, K.4
Shimokawa, Y.5
Zhao, Q.6
-
39
-
-
68449103579
-
The systems biology graphical notation
-
N. Le Novère, M. Hucka, H. Mi, S. Moodie, F. Schreiber, A. Sorokin, E. Demir, K. Wegner, M. I. Aladjem, S. M.Wimalaratne, F. T. Bergman, R. Gauges, P. Ghazal, H. Kawaji, L. Li, Y. Matsuoka, A. Villéger, S. E. Boyd, L. Calzone, M. Courtot, U. Dogrusoz, T. C. Freeman, A. Funahashi, S. Ghosh, A. Jouraku, S. Kim, F. Kolpakov, A. Luna, S. Sahle, E. Schmidt, S. Watterson, G. Wu, I. Goryanin, D. B. Kell, C. Sander, H. Sauro, J. L. Snoep, K. Kohn, and H. Kitano. 2009. The systems biology graphical notation. Nature Biotechnology 27 (2009), 735-741
-
(2009)
Nature Biotechnology
, vol.27
, pp. 735-741
-
-
Le Novère, N.1
Hucka, M.2
Mi, H.3
Moodie, S.4
Schreiber, F.5
Sorokin, A.6
Demir, E.7
Wegner, K.8
Aladjem, M.I.9
Wimalaratne, S.M.10
Bergman, F.T.11
Gauges, R.12
Ghazal, P.13
Kawaji, H.14
Li, L.15
Matsuoka, Y.16
Villéger, A.17
Boyd, S.E.18
Calzone, L.19
Courtot, M.20
Dogrusoz, U.21
Freeman, T.C.22
Funahashi, A.23
Ghosh, S.24
Jouraku, A.25
Kim, S.26
Kolpakov, F.27
Luna, A.28
Sahle, S.29
Schmidt, E.30
Watterson, S.31
Wu, G.32
Goryanin, I.33
Kell, D.B.34
Sander, C.35
Sauro, H.36
Snoep, J.L.37
Kohn, K.38
Kitano, H.39
more..
-
40
-
-
0034961694
-
STOCHSIM: Modelling of stochastic biomolecular processes
-
Nicolas Le Novere and Thomas Simon Shimizu. 2001. STOCHSIM: Modelling of stochastic biomolecular processes. Bioinformatics 17, 6 (2001), 575-576
-
(2001)
Bioinformatics
, vol.17
, Issue.6
, pp. 575-576
-
-
Le Novere, N.1
Shimizu, T.S.2
-
41
-
-
33646203362
-
WebCell: A web-based environment for kinetic modeling and dynamic simulation of cellular networks
-
Dong-Yup Lee, Choamun Yun, Ayoun Cho, Bo Kyeng Hou, Sunwon Park, and Sang Yup Lee. 2006. WebCell: A web-based environment for kinetic modeling and dynamic simulation of cellular networks. Bioinformatics 22, 9 (2006), 1150-1151
-
(2006)
Bioinformatics
, vol.22
, Issue.9
, pp. 1150-1151
-
-
Lee, D.-Y.1
Yun, C.2
Cho, A.3
Hou, B.K.4
Park, S.5
Lee, S.Y.6
-
42
-
-
80555153990
-
BioTapestry: A tool to visualize the dynamic properties of gene regulatory networks
-
W. J. Longabaugh. 2012. BioTapestry: A tool to visualize the dynamic properties of gene regulatory networks. Methods in Molecular Biology (Clifton, NJ) 786 (2012), 359
-
(2012)
Methods in Molecular Biology (Clifton, NJ)
, vol.786
, pp. 359
-
-
Longabaugh, W.J.1
-
43
-
-
84882758675
-
Programming biological models in Python using PySB
-
Carlos F. Lopez, Jeremy L. Muhlich, John A. Bachman, and Peter K. Sorger. 2013. Programming biological models in Python using PySB. Molecular Systems Biology 9, 1 (2013)
-
(2013)
Molecular Systems Biology
, vol.9
, pp. 1
-
-
Lopez, C.F.1
Muhlich, J.L.2
Bachman, J.A.3
Sorger, P.K.4
-
45
-
-
57149106822
-
-
Pearson Prentice Hall
-
Anthea Maton, David Lahart, Jean Hopkins, Maryanna Quon Warner, Susan Johnson, and Jill D. Wright. 1997. Cells: Building Blocks of Life. Pearson Prentice Hall
-
(1997)
Cells: Building Blocks of Life
-
-
Maton, A.1
Lahart, D.2
Hopkins, J.3
Warner, M.Q.4
Johnson, S.5
Wright, J.D.6
-
46
-
-
33746595848
-
Key role of local regulation in chemosensing revealed by a new molecular interactionbased modeling method
-
Martin Meier-Schellersheim, Xuehua Xu, Bastian Angermann, Eric J. Kunkel, Tian Jin, and Ronald N. Germain. 2006. Key role of local regulation in chemosensing revealed by a new molecular interactionbased modeling method. PLoS Computational Biology 2, 7 (2006), e82
-
(2006)
PLoS Computational Biology
, vol.2
, Issue.7
, pp. e82
-
-
Meier-Schellersheim, M.1
Xu, X.2
Angermann, B.3
Kunkel, E.J.4
Jin, T.5
Germain, R.N.6
-
47
-
-
0027370376
-
GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems
-
Pedro Mendes. 1993. GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems. Computer Applications in the Biosciences: CABIOS 9, 5 (1993), 563-571.
-
(1993)
Computer Applications in the Biosciences: CABIOS
, vol.9
, Issue.5
, pp. 563-571
-
-
Mendes, P.1
-
48
-
-
0034288444
-
The JSIM web-based simulation environment
-
John A. Miller, Andrew F. Seila, and Xuewei Xiang. 2000. The JSIM web-based simulation environment. Future Generation Computer Systems 17, 2 (2000), 119-133
-
(2000)
Future Generation Computer Systems
, vol.17
, Issue.2
, pp. 119-133
-
-
Miller, J.A.1
Seila, A.F.2
Xiang, X.3
-
49
-
-
33646023496
-
Simpathica: A computational systems biology tool within the valis bioinformatics environment
-
Bud Mishra, Marco Antoniotti, Salvatore Paxia, and Nadia Ugel. 2005. Simpathica: A computational systems biology tool within the valis bioinformatics environment. Computational Systems Biology (2005)
-
(2005)
Computational Systems Biology
-
-
Mishra, B.1
Antoniotti, M.2
Paxia, S.3
Ugel, N.4
-
50
-
-
54049114302
-
Virtual cell modelling and simulation software environment
-
I. I. Moraru, J. C. Schaff, B. M. Slepchenko, M. L. Blinov, F. Morgan, A. Lakshminarayana, F. Gao, Y. Li, and L. M. Loew. 2008. Virtual cell modelling and simulation software environment. IET Systems Biology 2, 5 (2008), 352-362
-
(2008)
IET Systems Biology
, vol.2
, Issue.5
, pp. 352-362
-
-
Moraru, I.I.1
Schaff, J.C.2
Slepchenko, B.M.3
Blinov, M.L.4
Morgan, F.5
Lakshminarayana, A.6
Gao, F.7
Li, Y.8
Loew, L.M.9
-
51
-
-
81355164232
-
Transcriptomic coordination in the human metabolic network reveals links between n-3 fat intake adipose tissue gene expression and metabolic health
-
M. J. Morine, A. C. Tierney, B. van Ommen, H. Daniel, S. Toomey, I. M. F. Gjelstad, I. C. Gormley, P. Prez-Martinez, C. A. Drevon, J. L-pez-Miranda, and H. M. Roche. 2011. Transcriptomic coordination in the human metabolic network reveals links between n-3 fat intake, adipose tissue gene expression and metabolic health. PLoS Computational Biology 7, 11 (2011)
-
(2011)
PLoS Computational Biology
, vol.7
, pp. 11
-
-
Morine, M.J.1
Tierney, A.C.2
Van Ommen, B.3
Daniel, H.4
Toomey, S.5
Gjelstad, I.M.F.6
Gormley, I.C.7
Prez-Martinez, P.8
Drevon, C.A.9
L-Pez-Miranda, J.10
Roche, H.M.11
-
52
-
-
77952851181
-
BoolNet: An R package for generation, reconstruction and analysis of Boolean networks
-
Christoph Müssel, Martin Hopfensitz, and Hans A. Kestler. 2010. BoolNet: An R package for generation, reconstruction and analysis of Boolean networks. Bioinformatics 26, 10 (2010), 1378-1380
-
(2010)
Bioinformatics
, vol.26
, Issue.10
, pp. 1378-1380
-
-
Müssel, C.1
Hopfensitz, M.2
Kestler, H.A.3
-
53
-
-
70350669878
-
IBioSim: A tool for the analysis and design of genetic circuits
-
Nov
-
C. J. Myers, N. Barker, K. Jones, H. Kuwahara, C. Madsen, and N. P. Nguyen. 2009. iBioSim: A tool for the analysis and design of genetic circuits. Bioinformatics 25, 21 (Nov 2009), 2848-2849
-
(2009)
Bioinformatics
, vol.25
, Issue.21
, pp. 2848-2849
-
-
Myers, C.J.1
Barker, N.2
Jones, K.3
Kuwahara, H.4
Madsen, C.5
Nguyen, N.P.6
-
54
-
-
34247473881
-
Python unleashed on systems biology
-
Christopher R. Myers, Ryan N. Gutenkunst, and James P. Sethna. 2007. Python unleashed on systems biology. Computing in Science & Engineering 9, 3 (2007), 34-37
-
(2007)
Computing in Science & Engineering
, vol.9
, Issue.3
, pp. 34-37
-
-
Myers, C.R.1
Gutenkunst, R.N.2
Sethna, J.P.3
-
55
-
-
8844244248
-
Map labeling with application to graph drawing
-
M. Kaufmann and D. Wagner, Eds. Springer
-
Gabriele Neyer. 2001. Map labeling with application to graph drawing. In Drawing Graphs. M. Kaufmann and D. Wagner, Eds., Springer, 247-273
-
(2001)
Drawing Graphs
, pp. 247-273
-
-
Neyer, G.1
-
56
-
-
4544344218
-
Web-based kinetic modelling using JWS Online
-
Brett G. Olivier and Jacky L. Snoep. 2004. Web-based kinetic modelling using JWS Online. Bioinformatics 20, 13 (2004), 2143-2144
-
(2004)
Bioinformatics
, vol.20
, Issue.13
, pp. 2143-2144
-
-
Olivier, B.G.1
Snoep, J.L.2
-
57
-
-
78649682240
-
Scalable rule-based modelling of allosteric proteins and biochemical networks
-
Julien F. Ollivier, Vahid Shahrezaei, and Peter S. Swain. 2010. Scalable rule-based modelling of allosteric proteins and biochemical networks. PLoS Computational Biology 6, 11 (2010), e1000975
-
(2010)
PLoS Computational Biology
, vol.6
, Issue.11
, pp. e1000975
-
-
Ollivier, J.F.1
Shahrezaei, V.2
Swain, P.S.3
-
59
-
-
67049143968
-
Algorithmic systems biology
-
Corrado Priami. 2009. Algorithmic systems biology. CACM 52, 5 (2009), 80-88
-
(2009)
CACM
, vol.52
, Issue.5
, pp. 80-88
-
-
Priami, C.1
-
60
-
-
0035888407
-
Application of a stochastic name-passing calculus to representation and simulation ofmolecular processes
-
C. Priami, A. Regev, E. Shapiro, and W. Silverman. 2001. Application of a stochastic name-passing calculus to representation and simulation ofmolecular processes. Information Processing Letter 80 (2001), 25-31
-
(2001)
Information Processing Letter
, vol.80
, pp. 25-31
-
-
Priami, C.1
Regev, A.2
Shapiro, E.3
Silverman, W.4
-
61
-
-
84958540357
-
User preference of graph layout aesthetics: A UML study
-
M. Kaufmann and D. Wagner, Eds., Springer
-
Helen C. Purchase, Jo-Anne Allder, and David Carrington. 2001. User preference of graph layout aesthetics: A UML study. In Graph Drawing. M. Kaufmann and D. Wagner, Eds., Springer, 5-18
-
Graph Drawing
, pp. 5-18
-
-
Purchase, H.C.1
Allder, J.-A.2
Carrington, D.3
-
62
-
-
17644372713
-
Dizzy: Stochastic simulation of large-scale genetic regulatory networks
-
Apr
-
S. Ramsey, D. Orrell, and H. Bolouri. 2005. Dizzy: Stochastic simulation of large-scale genetic regulatory networks. Journal of Bioinformatics Computing Biology 3, 2 (Apr 2005), 415-436
-
(2005)
Journal of Bioinformatics Computing Biology
, vol.3
, Issue.2
, pp. 415-436
-
-
Ramsey, S.1
Orrell, D.2
Bolouri, H.3
-
63
-
-
84884265362
-
Decoding information in cell shape
-
P. Rangamani, A. Lipshtat, E. U. Azeloglu, R. C. Calizo, M. Hu, S. Ghassemi, J. Hone, S. Scarlata, S. R. Neves, and R. Iyengar. 2013. Decoding information in cell shape. Cell 154, 6 (2013), 1356-69
-
(2013)
Cell
, vol.154
, Issue.6
, pp. 1356-1369
-
-
Rangamani, P.1
Lipshtat, A.2
Azeloglu, E.U.3
Calizo, R.C.4
Hu, M.5
Ghassemi, S.6
Hone, J.7
Scarlata, S.8
Neves, S.R.9
Iyengar, R.10
-
64
-
-
36949004095
-
CellLine, a stochastic cell lineage simulator
-
Andre S. Ribeiro, Daniel A. Charlebois, and Jason Lloyd-Price. 2007. CellLine, a stochastic cell lineage simulator. Bioinformatics 23, 24 (2007), 3409-3411
-
(2007)
Bioinformatics
, vol.23
, Issue.24
, pp. 3409-3411
-
-
Ribeiro, A.S.1
Charlebois, D.A.2
Lloyd-Price, J.3
-
65
-
-
34147106039
-
SGN Sim, a stochastic genetic networks simulator
-
Andre S. Ribeiro and Jason Lloyd-Price. 2007. SGN Sim, a stochastic genetic networks simulator. Bioinformatics 23, 6 (2007), 777-779
-
(2007)
Bioinformatics
, vol.23
, Issue.6
, pp. 777-779
-
-
Ribeiro, A.S.1
Lloyd-Price, J.2
-
66
-
-
84872926726
-
Molecular modeling and simulation of membrane lipid-mediated effects on GPCRs
-
S. K. Sadiq, R. Guixa-Gonzalez, E. Dainese, M. Pastor, G. De Fabritiis, and J. Selent. 2013. Molecular modeling and simulation of membrane lipid-mediated effects on GPCRs. Current Medicinal Chemistry 20, 1 (2013), 22-38
-
(2013)
Current Medicinal Chemistry
, vol.20
, Issue.1
, pp. 22-38
-
-
Sadiq, S.K.1
Guixa-Gonzalez, R.2
Dainese, E.3
Pastor, M.4
De Fabritiis, G.5
Selent, J.6
-
67
-
-
84993730733
-
Visualizing biological pathways: Requirements analysis, systems evaluation and research agenda
-
June
-
Purvi Saraiya, Chris North, and Karen Duca. 2005. Visualizing biological pathways: Requirements analysis, systems evaluation and research agenda. Information Visualization 4, 3 (June 2005), 191-205. DOI:http://dx.doi.org/10.1057/palgrave.ivs.9500102
-
(2005)
Information Visualization
, vol.4
, Issue.3
, pp. 191-205
-
-
Saraiya, P.1
North, C.2
Duca, K.3
-
68
-
-
84872841992
-
RuleBender: Integratedmodeling simulation and visualization for rule-based intracellular biochemistry
-
A. M. Smith,W. Xu, Y. Sun, J. R. Faeder, and G. E. Marai. 2012. RuleBender: Integratedmodeling, simulation and visualization for rule-based intracellular biochemistry. BMC Bioinformatics 13 Suppl 8 (2012), S3.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. S3
-
-
Smith, A.M.1
Xu, W.2
Sun, Y.3
Faeder, J.R.4
Marai, G.E.5
-
69
-
-
33646746237
-
The JigCell model builder: A spreadsheet interface for creating biochemical reaction network models
-
Marc T. Vass, Clifford A. Shaffer, Naren Ramakrishnan, Layne T. Watson, and John J. Tyson. 2006. The JigCell model builder: A spreadsheet interface for creating biochemical reaction network models. IEEE/ACM Transactions on Computational Biology and Bioinformatics on 3, 2 (2006), 155-164
-
(2006)
IEEE/ACM Transactions on Computational Biology and Bioinformatics on
, vol.3
, Issue.2
, pp. 155-164
-
-
Vass, M.T.1
Shaffer, C.A.2
Ramakrishnan, N.3
Watson, L.T.4
Tyson, J.J.5
-
71
-
-
84996727238
-
The NetBuilder'project: Development of a tool for constructing, simulating, evolving, and analysing complex regulatory networks
-
Katja Wegner, Johannes Knabe, Mark Robinson, Attila Egri-Nagy, Maria Schilstra, and Chrystopher Nehaniv. 2007. The NetBuilder'project: Development of a tool for constructing, simulating, evolving, and analysing complex regulatory networks. BMC Systems Biology 1, Suppl 1 (2007), P72
-
(2007)
BMC Systems Biology
, vol.1
, pp. P72
-
-
Wegner, K.1
Knabe, J.2
Robinson, M.3
Egri-Nagy, A.4
Schilstra, M.5
Nehaniv, C.6
-
72
-
-
5044227742
-
The evolution of molecular biology into systems biology
-
Hans V. Westerhoff and Bernhard O. Palsson. 2004. The evolution of molecular biology into systems biology. Nature Biotechnology 22, 10 (2004), 1249-1252
-
(2004)
Nature Biotechnology
, vol.22
, Issue.10
, pp. 1249-1252
-
-
Westerhoff, H.V.1
Palsson, B.O.2
-
73
-
-
75249087912
-
SimBoolNet-A Cytoscape plugin for dynamic simulation of signaling networks
-
J. Zheng, D. Zhang, P. F. Przytycki, R. Zielinski, J. Capala, and T. M. Przytycka. 2010. SimBoolNet-A Cytoscape plugin for dynamic simulation of signaling networks. Bioinformatics 26, 1 (2010), 141-142
-
(2010)
Bioinformatics
, vol.26
, Issue.1
, pp. 141-142
-
-
Zheng, J.1
Zhang, D.2
Przytycki, P.F.3
Zielinski, R.4
Capala, J.5
Przytycka, T.M.6
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