-
1
-
-
1342265599
-
Improving the development process for eukaryotic cell cycle models with a modeling support environment
-
Allen, N., C. Shaffer, M. Vass, N. Ramakrishnan, and L. Watson. 2003. Improving the development process for eukaryotic cell cycle models with a modeling support environment. Simulation 79:674-688.
-
(2003)
Simulation
, vol.79
, pp. 674-688
-
-
Allen, N.1
Shaffer, C.2
Vass, M.3
Ramakrishnan, N.4
Watson, L.5
-
2
-
-
0000122278
-
Statistical construction of chemical-reaction mechanisms from measured time-series
-
Arkin, A., and J. Ross. 1995. Statistical construction of chemical-reaction mechanisms from measured time-series. Journal of Physical Chemistry 99 (3): 970-979.
-
(1995)
Journal of Physical Chemistry
, vol.99
, Issue.3
, pp. 970-979
-
-
Arkin, A.1
Ross, J.2
-
3
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
Ashburner, M., C. A. Ball, and J. A. Blake. 2000. Gene ontology: tool for the unification of biology. Nature Genetics 25:25-29.
-
(2000)
Nature Genetics
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
-
4
-
-
85182615482
-
-
Bader, G, E. Brauner, M. Cary, R. Goldberg, C. Hogue, P. Karp, T. Klein, J. Luciano, D. Marks, N. Maltsev, E. Marland, E. Neumann, S. Paley, J. Rick, A. Regev, A. Rzhetsky, C. Sander, V. Schachter, I. Shah, and J. Zucker. 2005. BioPAX-Biological Pathways Exchange language. Level 1, Version 1.4 documentation. Available on the Internet at
-
Bader, G., E. Brauner, M. Cary, R. Goldberg, C. Hogue, P. Karp, T. Klein, J. Luciano, D. Marks, N. Maltsev, E. Marland, E. Neumann, S. Paley, J. Rick, A. Regev, A. Rzhetsky, C. Sander, V. Schachter, I. Shah, and J. Zucker. 2005. BioPAX-Biological Pathways Exchange language. Level 1, Version 1.4 documentation. Available on the Internet at 〈http://www.biopax.org〉.
-
-
-
-
5
-
-
84870503326
-
-
BioModels Database Team, Available on the Internet at
-
BioModels Database Team. 2006. BioModels Database. Available on the Internet at 〈http://www.ebi.ac.uk/biomodels/〉.
-
(2006)
BioModels Database
-
-
-
6
-
-
85182616208
-
-
BioPax
-
BioPax 2006. 〈http://www.biopax.org〉.
-
(2006)
-
-
-
8
-
-
85182611657
-
Quantitative compositional reasoning
-
IEEE CS. To appear
-
Chatterjee, K., L. de Alfaro, M. Faella, T. Henzinger, R. Majumdar, and M. Stoelinga. 2006. Quantitative compositional reasoning. In Proceedings of the 3rd International Conference on Quantitative Evaluation of Systems (QEST'06): IEEE CS. To appear.
-
(2006)
Proceedings of the 3rd International Conference on Quantitative Evaluation of Systems (QEST'06)
-
-
Chatterjee, K.1
de Alfaro, L.2
Faella, M.3
Henzinger, T.4
Majumdar, R.5
Stoelinga, M.6
-
9
-
-
3343020085
-
Integrative analysis of cell cycle control in budding yeast
-
Chen, K., L. Calzone, A. Csikasz-Nagy, F. Cross, B. Novak, and J. Tyson. 2004. Integrative analysis of cell cycle control in budding yeast. Molecular Biology of the Cell 15 (8): 3841-3862.
-
(2004)
Molecular Biology of the Cell
, vol.15
, Issue.8
, pp. 3841-3862
-
-
Chen, K.1
Calzone, L.2
Csikasz-Nagy, A.3
Cross, F.4
Novak, B.5
Tyson, J.6
-
11
-
-
0037464588
-
A vision for the future of genomics research: A blueprint for the genomic era
-
Collins, F. S., E. D. Green, and A. E. Guttmacher. 2003. A vision for the future of genomics research: a blueprint for the genomic era. Nature 422:835-847.
-
(2003)
Nature
, vol.422
, pp. 835-847
-
-
Collins, F.S.1
Green, E.D.2
Guttmacher, A.E.3
-
12
-
-
33846205068
-
-
Conrad, E. 2006. Oscill8. 〈http://oscill8.sourceforge.net/〉.
-
(2006)
Oscill8
-
-
Conrad, E.1
-
13
-
-
85182614940
-
-
Copasi. 2006. 〈http://www.copasi.org/tiki-index.php〉.
-
(2006)
-
-
-
14
-
-
1342329447
-
An overview of CellML 1.1, a biological model description language
-
Cuellar, A., C. Lloyd, P. Nielsen, D. Bullivant, D. Nickerson, and P. Hunter. 2003. An overview of CellML 1.1, a biological model description language. Simulation: Transactions of the Society for Modeling and Simulation International 79 (12): 740-747.
-
(2003)
Simulation: Transactions of the Society for Modeling and Simulation International
, vol.79
, Issue.12
, pp. 740-747
-
-
Cuellar, A.1
Lloyd, C.2
Nielsen, P.3
Bullivant, D.4
Nickerson, D.5
Hunter, P.6
-
15
-
-
0036683181
-
Linking the genes: Inferring quantitative gene networks from microarray data
-
de la Fuente, A., P. Brazhnik, and P. Mendes. 2002. Linking the genes: inferring quantitative gene networks from microarray data. Trends in Genetics 18:395-398.
-
(2002)
Trends in Genetics
, vol.18
, pp. 395-398
-
-
de la Fuente, A.1
Brazhnik, P.2
Mendes, P.3
-
17
-
-
0242574975
-
Towards rigorous comprehension of biological complexity: Modeling, execution and visualization of thymic T cell maturation
-
Efroni, S., D. Harel, and I. Cohen. 2003. Towards rigorous comprehension of biological complexity: modeling, execution and visualization of thymic T cell maturation. Genome Research 13:2485-2497.
-
(2003)
Genome Research
, vol.13
, pp. 2485-2497
-
-
Efroni, S.1
Harel, D.2
Cohen, I.3
-
18
-
-
70049106280
-
Software infrastructure for effective communication and reuse of computational models
-
ed. Z. Szallasi, J. Stelling, and V. Periwal, Chapter 17. MIT Press
-
Finney, A., M. Hucka, B. Bornstein, S. Keating, B. Shapiro, J. Matthews, B. Kovitz, M. Schilstra, A. Funahashi, J. Doyle, and H. Kitano. 2006. Software infrastructure for effective communication and reuse of computational models. In System Modeling in Cellular Biology, ed. Z. Szallasi, J. Stelling, and V. Periwal, Chapter 17. MIT Press.
-
(2006)
System Modeling in Cellular Biology
-
-
Finney, A.1
Hucka, M.2
Bornstein, B.3
Keating, S.4
Shapiro, B.5
Matthews, J.6
Kovitz, B.7
Schilstra, M.8
Funahashi, A.9
Doyle, J.10
Kitano, H.11
-
19
-
-
13844309568
-
Computational insights into C. elegans vulval development
-
Fisher, J., N. Piterman, E. Hubbard, M. Stern, and D. Harel. 2005. Computational insights into C. elegans vulval development. Proceedings of the National Academy of Sciences 6 (102): 1951-1956.
-
(2005)
Proceedings of the National Academy of Sciences
, vol.6
, Issue.102
, pp. 1951-1956
-
-
Fisher, J.1
Piterman, N.2
Hubbard, E.3
Stern, M.4
Harel, D.5
-
20
-
-
0038048325
-
Inferring genetic networks and identifying compound mode of action via expression profiling
-
Gardner, T. S., D. di Bernardo, D. Lorenz, and J. J. Collins. 2003. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301 (5629): 102-105.
-
(2003)
Science
, vol.301
, Issue.5629
, pp. 102-105
-
-
Gardner, T.S.1
di Bernardo, D.2
Lorenz, D.3
Collins, J.J.4
-
21
-
-
33745451921
-
Oscillations and variability in the p53 system
-
Geva-Zatorsky, N., N. Rosenfeld, S. Itzkovitz, R. Milo, A. Sigal, E. Dekel, T. Yarnitzky, Y. Liron, P. Polak, G. Lahav, and U. Alon. 2006. Oscillations and variability in the p53 system. Molecular Systems Biology 2:2006-2006.
-
(2006)
Molecular Systems Biology
, vol.2
, pp. 2006-2006
-
-
Geva-Zatorsky, N.1
Rosenfeld, N.2
Itzkovitz, S.3
Milo, R.4
Sigal, A.5
Dekel, E.6
Yarnitzky, T.7
Liron, Y.8
Polak, P.9
Lahav, G.10
Alon, U.11
-
23
-
-
46149098874
-
-
Reprinted in, Algorithms and Complexity, Paun, Rozenberg and Salomaa, eds, World Scientific, pp
-
(Reprinted in Current Trends in Theoretical Computer Science: The Challenge of the New Century, Algorithms and Complexity, Vol I (Paun, Rozenberg and Salomaa, eds.), World Scientific, pp. 559-568, 2004).
-
(2004)
Current Trends in Theoretical Computer Science: The Challenge of the New Century
, vol.1
, pp. 559-568
-
-
-
24
-
-
23644440995
-
A turing-like test for biological modeling
-
Harel, D. 2005. A turing-like test for biological modeling. Nature Biotechnology 23:495-496.
-
(2005)
Nature Biotechnology
, vol.23
, pp. 495-496
-
-
Harel, D.1
-
25
-
-
0033518234
-
From molecular to modular cell biology
-
Hartwell, L. H., J. J. Hopfield, S. Leibler, and A. W. Murray. 1999. From molecular to modular cell biology. Nature 402 (6761 Supplement): C47-C52.
-
(1999)
Nature
, vol.402
, Issue.6761 SUPPL.EMENT
-
-
Hartwell, L.H.1
Hopfield, J.J.2
Leibler, S.3
Murray, A.W.4
-
26
-
-
57249083893
-
A short introduction to CellML
-
Hedley, W., M. Nelson, D. P. Bullivant, and P. Nielson. 2001. A short introduction to CellML. Philosophical Transactions of the Royal Society of London A 359:1073-1089.
-
(2001)
Philosophical Transactions of the Royal Society of London A
, vol.359
, pp. 1073-1089
-
-
Hedley, W.1
Nelson, M.2
Bullivant, D.P.3
Nielson, P.4
-
27
-
-
0742323374
-
The HUPO PSI's molecular interaction format - a community standard for the representation of protein interaction data
-
Hermjakob, H., L. Montecchi-Palazzi, and G. Baden 2004. The HUPO PSI's molecular interaction format - a community standard for the representation of protein interaction data. Nature Biotechnology 22:177-183.
-
(2004)
Nature Biotechnology
, vol.22
, pp. 177-183
-
-
Hermjakob, H.1
Montecchi-Palazzi, L.2
Baden, G.3
-
29
-
-
0037342537
-
The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
-
Hucka, M., A. Finney, and H. M. Sauro. 2003. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19:524-531.
-
(2003)
Bioinformatics
, vol.19
, pp. 524-531
-
-
Hucka, M.1
Finney, A.2
Sauro, H.M.3
-
30
-
-
85182616770
-
-
Hucka, M., A. Finney, H. M. Sauro, H. Bolouri, J. Doyle, H. Kitano, A. Arkin, B. J. Bornstein, D. Bray, A. Cornish-Bowden, A. A. Cuellar, S. Dronov, E. D. Gilles, M. Ginkel, V. Gor, I. I. Goryanin, W. J. Hedley, T. Hodgman, J. H. Hofmeyr, P. J. Hunter, N. Juty, J. L. Kasberger, A. Kremling, U. Kummer, N. Le Novere, L. M. Loew, D. Lucio, P. Mendes, E. Minch, E. D. Mjolsness, Y. Nakayama, M. R. Nelson, P. F. Nielsen, T. Sakurada, J. C. Schaff, B. Shapiro, T. S. Shimizu, H. D. Spence, J. Stelling, K. Takahashi, M. Tomita, J. Wagner, and J. Wang. 2003. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19 (4): 524-531.
-
Hucka, M., A. Finney, H. M. Sauro, H. Bolouri, J. Doyle, H. Kitano, A. Arkin, B. J. Bornstein, D. Bray, A. Cornish-Bowden, A. A. Cuellar, S. Dronov, E. D. Gilles, M. Ginkel, V. Gor, I. I. Goryanin, W. J. Hedley, T. Hodgman, J. H. Hofmeyr, P. J. Hunter, N. Juty, J. L. Kasberger, A. Kremling, U. Kummer, N. Le Novere, L. M. Loew, D. Lucio, P. Mendes, E. Minch, E. D. Mjolsness, Y. Nakayama, M. R. Nelson, P. F. Nielsen, T. Sakurada, J. C. Schaff, B. Shapiro, T. S. Shimizu, H. D. Spence, J. Stelling, K. Takahashi, M. Tomita, J. Wagner, and J. Wang. 2003. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19 (4): 524-531.
-
-
-
-
31
-
-
33750979409
-
Synthetic gene regulatory systems
-
ed. Z. Szallasi, J. Stelling, and V. Periwal, Chapter 13, 269-298. MIT Press
-
Kaern, M., and R. Weiss. 2006. Synthetic gene regulatory systems. In System Modeling in Cellular BiologyFrom Concepts to Nuts and Bolts, ed. Z. Szallasi, J. Stelling, and V. Periwal, Chapter 13, 269-298. MIT Press.
-
(2006)
System Modeling in Cellular BiologyFrom Concepts to Nuts and Bolts
-
-
Kaern, M.1
Weiss, R.2
-
32
-
-
84883592668
-
Formal modeling of C. elegans development: A scenario-based approach
-
Proceedings of the 1st International Workshop on Computational Methods in Systems Biology ICMSB 2003, Number in, Springer
-
Kam, N., D. Harel, H. Kugler, R. Marelly, A. Pnueli, E. Hubbard, and M. Stern. 2002. Formal modeling of C. elegans development: a scenario-based approach. In Proceedings of the 1st International Workshop on Computational Methods in Systems Biology (ICMSB 2003), Number 2602 in LNCS, 4-20: Springer.
-
(2002)
LNCS
, vol.2602
, pp. 4-20
-
-
Kam, N.1
Harel, D.2
Kugler, H.3
Marelly, R.4
Pnueli, A.5
Hubbard, E.6
Stern, M.7
-
33
-
-
85182616967
-
-
(Revised version in Modeling in Molecular Biology (G. Ciobanu and G. Rozenberg, eds.), Springer, Berlin, 2004, pp. 151-173.).
-
(Revised version in Modeling in Molecular Biology (G. Ciobanu and G. Rozenberg, eds.), Springer, Berlin, 2004, pp. 151-173.).
-
-
-
-
34
-
-
0036500993
-
Systems biology: A brief overview
-
Kitano, H. 2002. Systems biology: a brief overview. Science 295 (5560): 1662-1664.
-
(2002)
Science
, vol.295
, Issue.5560
, pp. 1662-1664
-
-
Kitano, H.1
-
35
-
-
23444439817
-
Using process diagrams for the graphical representation of biological networks
-
Kitano, H., A. Funahashi, Y. Matsuoka, and K. Oda. 2005. Using process diagrams for the graphical representation of biological networks. Nature Biotechnology 23 (8): 961-966.
-
(2005)
Nature Biotechnology
, vol.23
, Issue.8
, pp. 961-966
-
-
Kitano, H.1
Funahashi, A.2
Matsuoka, Y.3
Oda, K.4
-
36
-
-
0142042996
-
BioSPICE: A computational infrastructure for integrative biology
-
Kumar, S., and J. Feidler. 2003. BioSPICE: A computational infrastructure for integrative biology. OMICS7 (3): 225.
-
(2003)
OMICS7
, vol.225
-
-
Kumar, S.1
Feidler, J.2
-
37
-
-
46149099541
-
Computational modelling of signalling pathways: Comparing simulation, verification and differential equation approaches
-
ed. L. Perrone, F. Wieland, J. Liu, B. Lawson, D. Nicol, and R. Fujimoto. Monterey, California, USA
-
Kwiatkowska, M., O. Tymchishyn, G. Norman, E. Gaffney, and J. Heath. 2006. Computational modelling of signalling pathways: comparing simulation, verification and differential equation approaches. In Proceedings of the 2006 Winter Simulation Conference, ed. L. Perrone, F. Wieland, J. Liu, B. Lawson, D. Nicol, and R. Fujimoto. Monterey, California, USA.
-
(2006)
Proceedings of the 2006 Winter Simulation Conference
-
-
Kwiatkowska, M.1
Tymchishyn, O.2
Norman, G.3
Gaffney, E.4
Heath, J.5
-
38
-
-
0842332406
-
Dynamics of the p53-mdm2 feedback loop in individual cells
-
Lahav, G., N. Rosenfeld, A. Sigal, N. Geva-Zatorsky, A. Levine, M. Elowitz, and U. Alon. 2004. Dynamics of the p53-mdm2 feedback loop in individual cells. Nature Genetics 36 (2): 147-150.
-
(2004)
Nature Genetics
, vol.36
, Issue.2
, pp. 147-150
-
-
Lahav, G.1
Rosenfeld, N.2
Sigal, A.3
Geva-Zatorsky, N.4
Levine, A.5
Elowitz, M.6
Alon, U.7
-
40
-
-
3042799574
-
A computational algebra approach to the reverse engineering of gene regulatory networks
-
Laubenbacher, R., and B. Stigler. 2004. A computational algebra approach to the reverse engineering of gene regulatory networks. Journal of Theoretical Biology 229 (4): 523-537.
-
(2004)
Journal of Theoretical Biology
, vol.229
, Issue.4
, pp. 523-537
-
-
Laubenbacher, R.1
Stigler, B.2
-
41
-
-
33644877164
-
BioModels Database: A free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
-
Le Novère, N., B. Bornstein, A. Broicher, M. Courtot, M. Donizelli, H. Dharuri, L. Li, H. Sauro, M. Schilstra, B. Shapiro, J. Snoep, and M. Hucka. 2006. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Research 34 (suppl-1): D689-691.
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.SUPPL.-1
-
-
Le Novère, N.1
Bornstein, B.2
Broicher, A.3
Courtot, M.4
Donizelli, M.5
Dharuri, H.6
Li, L.7
Sauro, H.8
Schilstra, M.9
Shapiro, B.10
Snoep, J.11
Hucka, M.12
-
42
-
-
0032406131
-
Non-linear optimization of biochemical pathways: Applications to metabolic engineering and parameter estimation
-
Mendes, P., and D. Kell. 1998. Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics 14:869-883.
-
(1998)
Bioinformatics
, vol.14
, pp. 869-883
-
-
Mendes, P.1
Kell, D.2
-
43
-
-
85182617767
-
-
Newman, M., and M. Girvan. 2004. Finding and evaluating community structure in networks. Physical Review E Statistcal, Nonlinear, and Soft Matter Physics 69 (2 Pt 2): 026113-026113.
-
Newman, M., and M. Girvan. 2004. Finding and evaluating community structure in networks. Physical Review E Statistcal, Nonlinear, and Soft Matter Physics 69 (2 Pt 2): 026113-026113.
-
-
-
-
44
-
-
0027716813
-
Numerical analysis of a comprehensive model of m-phase control in xenopus oocyte extracts and intact embryos
-
Novak, B., and J. J. Tyson. 1993. Numerical analysis of a comprehensive model of m-phase control in xenopus oocyte extracts and intact embryos. Journal of Cell Science 106 (Pt 4):1153-1168.
-
(1993)
Journal of Cell Science
, vol.106
, Issue.PART 4
, pp. 1153-1168
-
-
Novak, B.1
Tyson, J.J.2
-
45
-
-
28644433993
-
Minimum information requested in the annotation of biochemical models (MIRIAM)
-
Novre, N., A. Finney, M. Hucka, U. Bhalla, F. Campagne, J. Collado-Vides, E. Crampin, M. Halstead, E. Klipp, P. Mendes, P. Nielsen, H. Sauro, B. Shapiro, J. Snoep, H. Spence, and B. Wanner. 2005. Minimum information requested in the annotation of biochemical models (MIRIAM). Nature Biotechnology 23 (12): 1509-1515.
-
(2005)
Nature Biotechnology
, vol.23
, Issue.12
, pp. 1509-1515
-
-
Novre, N.1
Finney, A.2
Hucka, M.3
Bhalla, U.4
Campagne, F.5
Collado-Vides, J.6
Crampin, E.7
Halstead, M.8
Klipp, E.9
Mendes, P.10
Nielsen, P.11
Sauro, H.12
Shapiro, B.13
Snoep, J.14
Spence, H.15
Wanner, B.16
-
47
-
-
27844465352
-
Issues in enhancing model reuse
-
San Antonio, Texas, USA
-
Overstreet, C. M., R. E. Nance, and O. Balci. 2002. Issues in enhancing model reuse. In International Conference on Grand Challenges for Modeling and Simulation. San Antonio, Texas, USA.
-
(2002)
International Conference on Grand Challenges for Modeling and Simulation
-
-
Overstreet, C.M.1
Nance, R.E.2
Balci, O.3
-
48
-
-
85182612078
-
Deterministic parallel global parameter estimation for a model of the budding yeast cell cycle
-
Panning, T., L. Watson, N. Allen, C. Shaffer, and J. Tyson. 2006. Deterministic parallel global parameter estimation for a model of the budding yeast cell cycle. In Proceedings of the 2006 High Performance Computing Symposium (HPC'06), 195-201.
-
(2006)
Proceedings of the 2006 High Performance Computing Symposium (HPC'06)
, pp. 195-201
-
-
Panning, T.1
Watson, L.2
Allen, N.3
Shaffer, C.4
Tyson, J.5
-
50
-
-
0035888407
-
Application of a stochastic name-passing calculus to representation and simulation of molecular processes
-
Priami, C., A. Regev, E. Shapiro, and W. Silverman. 2001. Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters 80:25-31.
-
(2001)
Information Processing Letters
, vol.80
, pp. 25-31
-
-
Priami, C.1
Regev, A.2
Shapiro, E.3
Silverman, W.4
-
51
-
-
85093293677
-
Top-down standards will not serve systems biology
-
Quackenbush, J. 2006. Top-down standards will not serve systems biology. Nature 440:24.
-
(2006)
Nature
, vol.440
, pp. 24
-
-
Quackenbush, J.1
-
52
-
-
33644516416
-
The pi-calculus as an abstraction for biomolecular systems
-
Springer
-
Regev, A., and E. Shapiro. 2004. The pi-calculus as an abstraction for biomolecular systems. In Modelling in Molecular Biology, 219-266. Springer.
-
(2004)
Modelling in Molecular Biology
, pp. 219-266
-
-
Regev, A.1
Shapiro, E.2
-
53
-
-
27144527964
-
Mathematical techniques for analyzing concurrent and probabilistic systems
-
ed. P. Panangaden and F. van Breugel, of, American Mathematical Society
-
Rutten, J., M. Kwiatkowska, G. Norman, and D. Parker. 2004. Mathematical techniques for analyzing concurrent and probabilistic systems, ed. P. Panangaden and F. van Breugel, Volume 23 of CRM Monograph Series. American Mathematical Society.
-
(2004)
CRM Monograph Series
, vol.23
-
-
Rutten, J.1
Kwiatkowska, M.2
Norman, G.3
Parker, D.4
-
54
-
-
0347511691
-
Next generation simulation tools: The systems biology workbench and BioSPICE integration
-
Sauro, H. M., M. Hucka, A. Finney, C. Wellock, H. Bolouri, J. Doyle, and H. Kitano. 2003. Next generation simulation tools: the systems biology workbench and BioSPICE integration. OMICS 7(4):355-372.
-
(2003)
OMICS
, vol.7
, Issue.4
, pp. 355-372
-
-
Sauro, H.M.1
Hucka, M.2
Finney, A.3
Wellock, C.4
Bolouri, H.5
Doyle, J.6
Kitano, H.7
-
56
-
-
0037417803
-
Hysteresis drives cell-cycle transitions in xenopus laevis egg extracts
-
Sha, W., J. Moore, K. Chen, A. Lassaletta, C. Yi, J. Tyson, and J. Sible. 2003. Hysteresis drives cell-cycle transitions in xenopus laevis egg extracts. Proceedings of the National Academy of Sciences 100 (3): 975-980.
-
(2003)
Proceedings of the National Academy of Sciences
, vol.100
, Issue.3
, pp. 975-980
-
-
Sha, W.1
Moore, J.2
Chen, K.3
Lassaletta, A.4
Yi, C.5
Tyson, J.6
Sible, J.7
-
57
-
-
46149110545
-
The role of composition and aggregation in modeling macromolecular regulatory networks
-
ed. L. Perrone, F. Wieland, J. Liu, B. Lawson, D. Nicol, and R. Fujimoto. Monterey, California, USA
-
Shaffer, C., R. Randhawa, and J. Tyson. 2006. The role of composition and aggregation in modeling macromolecular regulatory networks. In Proceedings of the 2006 Winter Simulation Conference, ed. L. Perrone, F. Wieland, J. Liu, B. Lawson, D. Nicol, and R. Fujimoto. Monterey, California, USA.
-
(2006)
Proceedings of the 2006 Winter Simulation Conference
-
-
Shaffer, C.1
Randhawa, R.2
Tyson, J.3
-
59
-
-
46149093738
-
A method for alignment of standardised XML information within systems biology
-
ed. L. Perrone, F. Wieland, J. Liu, B. Lawson, D. Nicol, and R. Fujimoto. Monterey, California, USA
-
Strömbäck, L. 2006. A method for alignment of standardised XML information within systems biology. In Proceedings of the 2006 Winter Simulation Conference, ed. L. Perrone, F. Wieland, J. Liu, B. Lawson, D. Nicol, and R. Fujimoto. Monterey, California, USA.
-
(2006)
Proceedings of the 2006 Winter Simulation Conference
-
-
Strömbäck, L.1
-
60
-
-
85182617347
-
An evaluation of the use of XML for representation, querying, and analysis of molecular interactions
-
ed. L. Perrone, F. Wieland, J. Liu, B. Lawson, D. Nicol, and R. Fujimoto
-
Strömbäck, L., and D. Hall. 2006. An evaluation of the use of XML for representation, querying, and analysis of molecular interactions. In Proceedings of the 2006 Winter Simulation Conference, ed. L. Perrone, F. Wieland, J. Liu, B. Lawson, D. Nicol, and R. Fujimoto.
-
(2006)
Proceedings of the 2006 Winter Simulation Conference
-
-
Strömbäck, L.1
Hall, D.2
-
61
-
-
28944444766
-
Representations of molecular pathways: An evaluation of SBML, PSI MI, and BioPAX
-
Strömbäck, L., and P. Lambrix. 2005. Representations of molecular pathways: an evaluation of SBML, PSI MI, and BioPAX. Bioinformatics 21:4401-4407.
-
(2005)
Bioinformatics
, vol.21
, pp. 4401-4407
-
-
Strömbäck, L.1
Lambrix, P.2
-
62
-
-
35348879370
-
Towards an in-silico lymph node: A realistic approach to modeling dynamic behavior of lymphocytes
-
Submitted
-
Swerdlin, N., I. Cohen, and D. Harel. 2006. Towards an in-silico lymph node: a realistic approach to modeling dynamic behavior of lymphocytes. Submitted.
-
(2006)
-
-
Swerdlin, N.1
Cohen, I.2
Harel, D.3
-
63
-
-
1542400036
-
A multi-algorithm, multi-timescale method for cell simulation
-
Takahashi, K., K. Kaizu, B. Hu, and M. Tomita. 2004. A multi-algorithm, multi-timescale method for cell simulation. Bioinformatics 20 (4): 538-546.
-
(2004)
Bioinformatics
, vol.20
, Issue.4
, pp. 538-546
-
-
Takahashi, K.1
Kaizu, K.2
Hu, B.3
Tomita, M.4
-
64
-
-
46149124308
-
Pathway logic: A logical approach to modeling cellular processes
-
ed. L. Perrone, F. Wieland, J. Liu, B. Lawson, D. Nicol, and R. Fujimoto. Monterey, California, USA
-
Talcott, C. 2006. Pathway logic: a logical approach to modeling cellular processes. In Proceedings of the 2006 Winter Simulation Conference, ed. L. Perrone, F. Wieland, J. Liu, B. Lawson, D. Nicol, and R. Fujimoto. Monterey, California, USA.
-
(2006)
Proceedings of the 2006 Winter Simulation Conference
-
-
Talcott, C.1
-
65
-
-
0037376655
-
Sniffers, buzzers, toggles and blinkers: Dynamics of regulatory and signaling pathways in the cell
-
Tyson, J., K. C. Chen, and B. Novak. 2003. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Current Opinion in Cell Biology 15:221-231.
-
(2003)
Current Opinion in Cell Biology
, vol.15
, pp. 221-231
-
-
Tyson, J.1
Chen, K.C.2
Novak, B.3
-
67
-
-
33646746237
-
The JigCell model builder: A spread-sheet interface for creating biochemical reaction network models
-
Vass, M., C. Shaffer, N. Ramakrishnan, L. Watson, and J. Tyson. 2006. The JigCell model builder: a spread-sheet interface for creating biochemical reaction network models. IEEE/ACM Transactions on Computational Biology and Bioinformatics 3:155-164.
-
(2006)
IEEE/ACM Transactions on Computational Biology and Bioinformatics
, vol.3
, pp. 155-164
-
-
Vass, M.1
Shaffer, C.2
Ramakrishnan, N.3
Watson, L.4
Tyson, J.5
-
69
-
-
85182621047
-
-
Available on the Internet at
-
Zwolak, J. 2006. Parameter estimation tool (PET). Available on the Internet at 〈http://jigcell.biol.vt.edu/parameter.html〉.
-
(2006)
Parameter estimation tool (PET)
-
-
Zwolak, J.1
|