-
1
-
-
84885367114
-
Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction
-
O'Brien EJ, Lerman JA, Chang RL, Hyduke DR, Palsson BO, Brien EJO, et al. Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction. Mol Syst Biol. 2013;9(693). doi:10.1038/msb.2013.52.
-
(2013)
Mol Syst Biol.
, vol.9
, Issue.693
-
-
O'Brien, E.J.1
Lerman, J.A.2
Chang, R.L.3
Hyduke, D.R.4
Palsson, B.O.5
Brien, E.J.O.6
-
2
-
-
84864258618
-
A Whole-Cell Computational Model Predicts Phenotype from Genotype
-
Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Jr Bolival B, et al. A Whole-Cell Computational Model Predicts Phenotype from Genotype. Cell. 2012;150(2):389-401. doi:10.1016/j.cell.2012.05.044.
-
(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
Jr. Bolival, B.6
-
3
-
-
25644458211
-
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
-
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, et al. The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes. Nucleic Acids Res. 2005;33(17): 5691-702. doi:10.1093/nar/gki866. http://nar.oxfordjournals.org/content/33/17/5691.full.pdf+html.
-
(2005)
Nucleic Acids Res.
, vol.33
, Issue.17
, pp. 5691-5702
-
-
Overbeek, R.1
Begley, T.2
Butler, R.M.3
Choudhuri, J.V.4
Chuang, H.Y.5
Cohoon, M.6
-
4
-
-
75149129569
-
A protocol for generating a high-quality genome-scale metabolic reconstruction
-
Thiele I, Palsson BØ. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc. 2010;5(1):93-121. doi:10.1038/nprot.2009.203.
-
(2010)
Nat Protoc.
, vol.5
, Issue.1
, pp. 93-121
-
-
Thiele, I.1
Palsson, BØ.2
-
5
-
-
84931269105
-
Kinetic Modeling of Metabolic Networks
-
Wittmann C, Lee SY, editors, Van Godewijckstraat 30 3311 GX Dordrecht Netherlands: Springer Netherlands, Springer Science+Business Media B.V.
-
Zielinski DC, Palsson BØ. Kinetic Modeling of Metabolic Networks. In: Wittmann C, Lee SY, editors. Systems Metabolic Engineering. Van Godewijckstraat 30 3311 GX Dordrecht Netherlands: Springer Netherlands, Springer Science+Business Media B.V.; 2012. p. 25-55. doi:10.1007/978-94-007-4534-6_2.
-
(2012)
Systems Metabolic Engineering
, pp. 25-55
-
-
Zielinski, D.C.1
Palsson, BØ.2
-
6
-
-
63649141014
-
Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies
-
Dräger A, Kronfeld M, Ziller MJ, Supper J, Planatscher H, Magnus JB, et al. Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies. BMC Syst Biol. 2009;3:5. doi:10.1186/1752-0509-3-5.
-
(2009)
BMC Syst Biol.
, vol.3
, pp. 5
-
-
Dräger, A.1
Kronfeld, M.2
Ziller, M.J.3
Supper, J.4
Planatscher, H.5
Magnus, J.B.6
-
7
-
-
33845368513
-
COPASI-a COmplex PAthway SImulator
-
Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, et al. COPASI-a COmplex PAthway SImulator. Bioinforma. 2006;22(24):3067-074. doi:10.1093/bioinformatics/btl485.
-
(2006)
Bioinforma.
, 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
-
8
-
-
34249880382
-
Integration of CellDesigner and SABIO-RK
-
Funahashi A, Jouraku A, Matsuoka Y, Kitano H. Integration of CellDesigner and SABIO-RK. In Silico Biology. 2007;7(2 Suppl):81-90.
-
(2007)
In Silico Biology.
, vol.7
, Issue.2
, pp. 81-90
-
-
Funahashi, A.1
Jouraku, A.2
Matsuoka, Y.3
Kitano, H.4
-
9
-
-
0037461036
-
Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations
-
Shapiro BE, Levchenko A, Meyerowitz EM, Wold BJ, Mjolsness ED. Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations. Bioinforma. 2002;19(5):677-8. doi:10.1093/bioinformatics/btg042.
-
(2002)
Bioinforma.
, vol.19
, Issue.5
, pp. 677-678
-
-
Shapiro, B.E.1
Levchenko, A.2
Meyerowitz, E.M.3
Wold, B.J.4
Mjolsness, E.D.5
-
10
-
-
84862214722
-
SABIO-RK-database for biochemical reaction kinetics
-
Wittig U, Kania R, Golebiewski M, Rey M, Shi L, Jong L, et al. SABIO-RK-database for biochemical reaction kinetics. Nucleic Acids Res. 2012;40(Database issue):790-6. doi:10.1093/nar/gkr1046.
-
(2012)
Nucleic Acids Res.
, vol.40
, Issue.DATABASE ISSUE
, pp. 790-796
-
-
Wittig, U.1
Kania, R.2
Golebiewski, M.3
Rey, M.4
Shi, L.5
Jong, L.6
-
11
-
-
84871681271
-
Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0
-
Weber M, Henkel SG, Vlaic S, Guthke R, van Zoelen EJ, Driesch D. Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0. BMC Syst Biol. 2013;7(1):1. doi:10.1186/1752-0509-7-1.
-
(2013)
BMC Syst Biol.
, vol.7
, Issue.1
, pp. 1
-
-
Weber, M.1
Henkel, S.G.2
Vlaic, S.3
Guthke, R.4
van Zoelen, E.J.5
Driesch, D.6
-
12
-
-
84882677184
-
GRN2SBML: Automated encoding and annotation of inferred gene regulatory networks complying with SBML
-
Vlaic S, Hoffmann B, Kupfer P, Weber M, Dräger A. GRN2SBML: Automated encoding and annotation of inferred gene regulatory networks complying with SBML. Bioinforma. 2013;29(17):2216-217. doi:10.1093/bioinformatics/btt370.
-
(2013)
Bioinforma.
, vol.29
, Issue.17
, pp. 2216-2217
-
-
Vlaic, S.1
Hoffmann, B.2
Kupfer, P.3
Weber, M.4
Dräger, A.5
-
14
-
-
0003043542
-
The possible effects of the aggregation of the molecules of haemoglobin on its dissociation curves
-
Hill AV. The possible effects of the aggregation of the molecules of haemoglobin on its dissociation curves. J Physiol. 1910;40(4):iv-vii.
-
(1910)
J Physiol.
, vol.40
, Issue.4
, pp. iv-vii
-
-
Hill, A.V.1
-
15
-
-
84991905414
-
Improving collaboration by standardization efforts in systems biology
-
Dräger A, Palsson BØ. Improving collaboration by standardization efforts in systems biology. Front Bioeng. 2014;2(61). doi:10.3389/fbioe.2014.00061.
-
(2014)
Front Bioeng.
, vol.2
, Issue.61
-
-
Dräger, A.1
Palsson, BØ.2
-
16
-
-
33846617808
-
Bringing metabolic networks to life: convenience rate law and thermodynamic constraints
-
Liebermeister W, Klipp E. Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. Theor Biol Med Model. 2006;3(42):41. doi:10.1186/1742-4682-3-41.
-
(2006)
Theor Biol Med Model.
, vol.3
, Issue.42
, pp. 41
-
-
Liebermeister, W.1
Klipp, E.2
-
17
-
-
10644250404
-
Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project
-
Hucka M, Finney A, Bornstein BJ, Keating SM, Shapiro BE, Matthews J, et al. Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project. Syst Biol IEE. 2004;1(1):41-53.
-
(2004)
Syst Biol IEE.
, vol.1
, Issue.1
, pp. 41-53
-
-
Hucka, M.1
Finney, A.2
Bornstein, B.J.3
Keating, S.M.4
Shapiro, B.E.5
Matthews, J.6
-
18
-
-
79960423002
-
JSBML: a flexible Java library for working with SBML
-
Dräger A, Rodriguez N, Dumousseau M, Dörr A, Wrzodek C, Le Novère N, et al. JSBML: a flexible Java library for working with SBML. Bioinforma. 2011;27(15):2167-168. doi:10.1093/bioinformatics/btr361. http://bioinformatics.oxfordjournals.org/content/27/15/2167.full.pdf+ html.
-
(2011)
Bioinforma.
, vol.27
, Issue.15
, pp. 2167-2168
-
-
Dräger, A.1
Rodriguez, N.2
Dumousseau, M.3
Dörr, A.4
Wrzodek, C.5
Le Novère, N.6
-
19
-
-
84940750593
-
JSBML 1.0: providing a smorgasbord of options to encode systems biology models
-
Rodriguez N, Thomas A, Watanabe L, Vazirabad IY, Kofia V, Gómez HF, et al. JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinforma. 2015. doi:10.1093/bioinformatics/btv341. http://bioinformatics.oxfordjournals.org/content/early/2015/06/30/bioinformatics.btv341.
-
(2015)
Bioinforma
-
-
Rodriguez, N.1
Thomas, A.2
Watanabe, L.3
Vazirabad, I.Y.4
Kofia, V.5
Gómez, H.F.6
-
20
-
-
40749162829
-
LibSBML: an API library for SBML
-
Bornstein BJ, Keating SM, Jouraku A, Hucka M. LibSBML: an API library for SBML. Bioinforma. 2008;24(6):880-1. doi:10.1093/bioinformatics/btn051.
-
(2008)
Bioinforma.
, vol.24
, Issue.6
, pp. 880-881
-
-
Bornstein, B.J.1
Keating, S.M.2
Jouraku, A.3
Hucka, M.4
-
21
-
-
47949099328
-
CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks
-
IEEE
-
Funahashi A, Matsuoka Y, Jouraku A, Morohashi M, Kikuchi N, Kitano H. CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks. In: Proceedings of the IEEE. IEEE; 2008 vol 96: p. 1254-1265.
-
(2008)
Proceedings of the IEEE
, vol.96
, pp. 1254-1265
-
-
Funahashi, A.1
Matsuoka, Y.2
Jouraku, A.3
Morohashi, M.4
Kikuchi, N.5
Kitano, H.6
-
22
-
-
77955801615
-
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
-
Goecks J, Nekrutenko A, Taylor J, Team G. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010;11(8):86. doi:10.1186/gb-2010-11-8-r86.
-
(2010)
Genome Biol.
, vol.11
, Issue.8
, pp. 86
-
-
Goecks, J.1
Nekrutenko, A.2
Taylor, J.3
Team, G.4
-
23
-
-
65649112429
-
SBML2LATEX: Conversion of SBML files into human-readable reports
-
Dräger A, Planatscher H, Wouamba DM, Schröder A, Hucka M, Endler L, et al. SBML2LATEX: Conversion of SBML files into human-readable reports. Bioinforma. 2009;25(11):1455-1456. doi:10.1093/bioinformatics/btp170. http://bioinformatics.oxfordjournals.org/content/25/11/1455.full.pdf+ html.
-
(2009)
Bioinforma.
, vol.25
, Issue.11
, pp. 1455-1456
-
-
Dräger, A.1
Planatscher, H.2
Wouamba, D.M.3
Schröder, A.4
Hucka, M.5
Endler, L.6
-
24
-
-
81355123249
-
Software for systems biology: from tools to integrated platforms
-
Ghosh S, Matsuoka Y, Asai Y, Hsin KY, Kitano H. Software for systems biology: from tools to integrated platforms. Nat Rev Genet. 2011;12(12): 821-32.
-
(2011)
Nat Rev Genet.
, vol.12
, Issue.12
, pp. 821-832
-
-
Ghosh, S.1
Matsuoka, Y.2
Asai, Y.3
Hsin, K.Y.4
Kitano, H.5
-
25
-
-
80155212661
-
Controlled vocabularies and semantics in systems biology
-
Courtot M, Juty N, Knüpfer C, Waltemath D, Zhukova A, Dräger A, et al. Controlled vocabularies and semantics in systems biology. Mol Syst Biol. 2011;7:543. doi:10.1038/msb.2011.77.
-
(2011)
Mol Syst Biol.
, vol.7
, pp. 543
-
-
Courtot, M.1
Juty, N.2
Knüpfer, C.3
Waltemath, D.4
Zhukova, A.5
Dräger, A.6
-
26
-
-
0033982936
-
KEGG: Kyoto Encyclopedia of Genes and Genomes
-
Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 2000;28(1):27-30. doi:10.1093/nar/28.1.27 http://nar. oxfordjournals.org/cgi/reprint/28/1/27.pdf.
-
(2000)
Nucleic Acids Res.
, vol.28
, Issue.1
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
27
-
-
28644433993
-
Minimum information requested in the annotation of biochemical models (MIRIAM)
-
Le Novère N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, et al. Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol. 2005;23(12):1509-1515. doi:10.1038/nbt1156.
-
(2005)
Nat Biotechnol.
, vol.23
, Issue.12
, pp. 1509-1515
-
-
Le Novère, N.1
Finney, A.2
Hucka, M.3
Bhalla, U.S.4
Campagne, F.5
Collado-Vides, J.6
-
28
-
-
70249107803
-
The Systems Biology Graphical Notation
-
Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, et al. The Systems Biology Graphical Notation. Nat Biotechnol. 2009;27(8):735-41. doi:10.1038/nbt0909-864d.
-
(2009)
Nat Biotechnol.
, vol.27
, Issue.8
, pp. 735-741
-
-
Le Novère, N.1
Hucka, M.2
Mi, H.3
Moodie, S.4
Schreiber, F.5
Sorokin, A.6
-
31
-
-
84982130923
-
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core
-
Hucka M, Bergmann FT, Hoops S, Keating SM, Sahle S, SchaffJC, et al. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J Integr Bioinforma. 2015;12(2):266. doi:10.23 90/biecoll-jib-2015-266.
-
(2015)
J Integr Bioinforma.
, vol.12
, Issue.2
, pp. 266
-
-
Hucka, M.1
Bergmann, F.T.2
Hoops, S.3
Keating, S.M.4
Sahle, S.5
Schaff, J.C.6
-
32
-
-
0037342537
-
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
-
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinforma. 2003;19(4): 524-31. doi:10.1093/bioinformatics/btg015.
-
(2003)
Bioinforma.
, 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
-
33
-
-
84978259965
-
Metabolic
-
Dubitzky W, Wolkenhauer O, Yokota H, Cho K-H, editors, Networks. Springer New York Heidelberg Dorodrecht London: Springer
-
Dräger A, Planatscher H. Metabolic In: Dubitzky W, Wolkenhauer O, Yokota H, Cho K-H, editors. Metabolic. Networks. Springer New York Heidelberg Dorodrecht London: Springer; 2013. p. 1249-1251. doi:10.1007/978-1-4419-9863-7_1277. http://link.springer.com/referenceworkentry/10.1007/978-1-4419-9863-7_100849.
-
(2013)
Metabolic
, pp. 1249-1251
-
-
Dräger, A.1
Planatscher, H.2
-
34
-
-
85051838387
-
Parameter
-
Dubitzky W, Wolkenhauer O, Yokota H, Cho K-H, editors. Springer New York Heidelberg Dorodrecht London: Springer
-
Dräger A, Planatscher H. Parameter. In: Dubitzky W, Wolkenhauer O, Yokota H, Cho K-H, editors. Parameter Estimation, Metabolic Network Modeling. Springer New York Heidelberg Dorodrecht London: Springer; 2013 p. 1627-1631. doi:10.1007/978-1-4419-9863-7_1174. http://link. springer.com/referenceworkentry/10.1007/978-1-4419-9863-7_1174.
-
(2013)
Parameter Estimation, Metabolic Network Modeling
, pp. 1627-1631
-
-
Dräger, A.1
Planatscher, H.2
-
35
-
-
77954196484
-
Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation
-
Liebermeister W, Uhlendorf J, Klipp E. Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation. Bioinformatics. 2010;26(12):1528-1534. doi:10.1093/bioinformatics/btq141, http://bioinformatics.oxfordjournals. org/content/26/12/1528.abstract.
-
(2010)
Bioinformatics.
, vol.26
, Issue.12
, pp. 1528-1534
-
-
Liebermeister, W.1
Uhlendorf, J.2
Klipp, E.3
-
36
-
-
40349100409
-
MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology
-
Laible C, Le Novère N. MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology. BMC Systems Biology. 2007;13(58):58-67. doi:10.1186/1752-0509-1-58.
-
(2007)
BMC Systems Biology.
, vol.13
, Issue.58
, pp. 58-67
-
-
Laible, C.1
Le Novère, N.2
-
37
-
-
84862156032
-
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification
-
Juty N, Le Novère N, Laibe C. Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. Nucleic Acids Res. 2012;40(D1):580-6.
-
(2012)
Nucleic Acids Res.
, vol.40
, Issue.D1
, pp. 580-586
-
-
Juty, N.1
Le Novère, N.2
Laibe, C.3
-
38
-
-
84883258975
-
Controlled annotations for systems biology
-
Schneider MV, editor, Springer
-
Juty N, Laibe C, Le Novère N. Controlled annotations for systems biology In: Schneider MV, editor. In Silico Systems Biology. Springer; 2013. p. 227-45. doi:10.1007/978-1-62703-450-0_12, http://link.springer.com/protocol/10.1007/978-1-62703-450-0_12.
-
(2013)
In Silico Systems Biology
, pp. 227-245
-
-
Juty, N.1
Laibe, C.2
Le Novère, N.3
-
39
-
-
84982126079
-
Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions
-
Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, et al. Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. J Integr Bioinforma. 2015;12(2):271. doi:10.2390/biecoll-jib-2015-271.
-
(2015)
J Integr Bioinforma.
, vol.12
, Issue.2
, pp. 271
-
-
Hucka, M.1
Bergmann, F.T.2
Dräger, A.3
Hoops, S.4
Keating, S.M.5
Le Novère, N.6
-
40
-
-
44949099336
-
SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks
-
Dräger A, Hassis N, Supper J, Schröder A, Zell A. SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks. BMC Syst Biol. 2008;2(1):39. doi:10.1186/1752-0509-2-39.
-
(2008)
BMC Syst Biol.
, vol.2
, Issue.1
, pp. 39
-
-
Dräger, A.1
Hassis, N.2
Supper, J.3
Schröder, A.4
Zell, A.5
-
41
-
-
84908454823
-
Automating mathematical modeling of biochemical reaction networks
-
New York: Springer
-
Dräger A, Schröder A, Zell A. Automating mathematical modeling of biochemical reaction networks. In: Systems Biology for Signaling Networks. New York: Springer; 2010. vol. 2. doi: 10.1007/978-1-4419-5797-9_7, http://link.springer.com/chapter/10.1007 %2F978-1-4419-5797-9_7.
-
(2010)
Systems Biology for Signaling Networks
, vol.2
-
-
Dräger, A.1
Schröder, A.2
Zell, A.3
-
42
-
-
38549159888
-
Hill Kinetics meets P Systems: A Case Study on Gene Regulatory Networks as Computing Agents in silico and in vivo
-
Eleftherakis G, Kefalas P, Paun G, editors, SEERC. Berlin Heidelberg: Springer
-
Hinze T, Hayat S, Lenser T, Matsumaru N, Dittrich P. Hill Kinetics meets P Systems: A Case Study on Gene Regulatory Networks as Computing Agents in silico and in vivo In: Eleftherakis G, Kefalas P, Paun G, editors. Proceedings of the Eight Workshop on Membrane Computing. SEERC. Berlin Heidelberg: Springer; 2007. p. 363-81. doi: 10.1007/978-3-540-77312-2_20, http://link.springer.com/chapter/10.1007 %2F978-3-540-77312-2_20.
-
(2007)
Proceedings of the Eight Workshop on Membrane Computing
, pp. 363-381
-
-
Hinze, T.1
Hayat, S.2
Lenser, T.3
Matsumaru, N.4
Dittrich, P.5
-
43
-
-
56249106676
-
-
PhD thesis, Faculty of Mathematics and Natural Sciences. Germany: University of Cologne; January
-
Radde N. Modeling Non-Linear Dynamic Phenomena in Biochemical Networks. PhD thesis, Faculty of Mathematics and Natural Sciences. Germany: University of Cologne; January 2007. http://kups.ub.uni-koeln. de/volltexte/2008/2221/.
-
(2007)
Modeling Non-Linear Dynamic Phenomena in Biochemical Networks
-
-
Radde, N.1
-
44
-
-
34548060998
-
Bayesian Inference of Gene Regulatory Networks Using Gene Expression Time Series Data
-
Hochreiter S, Wagner R, editors, Berlin Heidelberg: Springer
-
Radde N, Kaderali L. Bayesian Inference of Gene Regulatory Networks Using Gene Expression Time Series Data In: Hochreiter S, Wagner R, editors. Bioinformatics Research and Development. Berlin Heidelberg: Springer; 2007. vol. 4414. p. 1-15. doi:10.1007/978-3-540-71233-6_1 http://dx.doi.org/10.1007/978-3-540-71233-6_1.
-
(2007)
Bioinformatics Research and Development
, vol.4414
, pp. 1-15
-
-
Radde, N.1
Kaderali, L.2
-
46
-
-
38349047954
-
The NetGenerator Algorithm: reconstruction of gene regulatory networks
-
Tuyls K, Westra R, Saeys Y, Nowé A, editors. Lecture Notes in Computer Science
-
Töpfer S, Guthke R, Driesch D, Wötzel D, PfaffM. The NetGenerator Algorithm: reconstruction of gene regulatory networks. In: Tuyls K, Westra R, Saeys Y, Nowé A, editors. Knowledge Discovery and Emergent Complexity in Bioinformatics. Lecture Notes in Computer Science; 2007. vol. 4366. doi:10.1007/978-3-540-71037-0_8 http://www.springerlink. com/content/f0u6757h2186075x/.
-
(2007)
Knowledge Discovery and Emergent Complexity in Bioinformatics
, vol.4366
-
-
Töpfer, S.1
Guthke, R.2
Driesch, D.3
Wötzel, D.4
Pfaff, M.5
-
47
-
-
0035082045
-
Neural network model of gene expression
-
Vohradskỳ J. Neural network model of gene expression. FASEB Journal. 2001;15(3):846-54. doi:10.1096/fj.00-0361com. http://www.fasebj.org/cgi/reprint/15/3/846.pdf.
-
(2001)
FASEB Journal.
, vol.15
, Issue.3
, pp. 846-854
-
-
Vohradskỳ, J.1
-
48
-
-
33846703173
-
Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of saccharomyces cerevisiae
-
Vu TT, Vohradskỳ J. Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of saccharomyces cerevisiae. Nucleic Acids Res. 2007;35(1):279-87. doi:10.1093/nar/gkl1001.
-
(2007)
Nucleic Acids Res.
, vol.35
, Issue.1
, pp. 279-287
-
-
Vu, T.T.1
Vohradskỳ, J.2
-
50
-
-
0014649230
-
Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions
-
Savageau MA. Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions. J Theor Biol. 1969;25(3):365-9.
-
(1969)
J Theor Biol.
, vol.25
, Issue.3
, pp. 365-369
-
-
Savageau, M.A.1
-
51
-
-
33750271082
-
Comparing Mathematical Models on the Problem of Network Inference
-
GECCO '06. New York, NY, USA: ACM
-
Spieth C, Hassis N, Streichert F, Supper J, Beyreuther K, Zell A. Comparing Mathematical Models on the Problem of Network Inference. In: Proceedings of the 8th Annual Conference on Genetic and Evolutionary Computation. GECCO '06. New York, NY, USA: ACM; 2006. p. 279-86. doi:10.1145/1143997.1144045. http://doi.acm.org/10.1145/1143997.1144045.
-
(2006)
Proceedings of the 8th Annual Conference on Genetic and Evolutionary Computation
, pp. 279-286
-
-
Spieth, C.1
Hassis, N.2
Streichert, F.3
Supper, J.4
Beyreuther, K.5
Zell, A.6
-
52
-
-
77951612556
-
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
-
Schellenberger J, Park JO, Conrad TM, Palsson BO. BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC bioinformatics. 2010;11:213. doi:10.1186/1471-2105-11-213.
-
(2010)
BMC bioinformatics.
, vol.11
, pp. 213
-
-
Schellenberger, J.1
Park, J.O.2
Conrad, T.M.3
Palsson, B.O.4
-
53
-
-
79961195281
-
KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats
-
Wrzodek C, Dräger A, Zell A. KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats. Bioinformatics. 2011;27(16):2314-315. doi:10.1093/bioinformatics/btr377.
-
(2011)
Bioinformatics.
, vol.27
, Issue.16
, pp. 2314-2315
-
-
Wrzodek, C.1
Dräger, A.2
Zell, A.3
-
54
-
-
84874016103
-
Precise generation of systems biology models from KEGG pathways
-
Wrzodek C, Büchel F, RuffM, Dräger A, Zell A. Precise generation of systems biology models from KEGG pathways. BMC Systems Biology. 2013;7(1):15. doi:10.1186/1752-0509-7-15.
-
(2013)
BMC Systems Biology.
, vol.7
, Issue.1
, pp. 15
-
-
Wrzodek, C.1
Büchel, F.2
Ruff, M.3
Dräger, A.4
Zell, A.5
-
55
-
-
84879801381
-
The systems biology simulation core algorithm
-
Keller R, Dörr A, Tabira A, Funahashi A, Ziller MJ, Adams R, Rodriguez N, Le Novère N, Hiroi N, Planatscher H, Zell A, Dräger A. The systems biology simulation core algorithm. BMC Syst Biol. 2013;7(1):55. doi:10.1186/1752-0509-7-55.
-
(2013)
BMC Syst Biol.
, vol.7
, Issue.1
, pp. 55
-
-
Keller, R.1
Dörr, A.2
Tabira, A.3
Funahashi, A.4
Ziller, M.J.5
Adams, R.6
Rodriguez, N.7
Le Novère, N.8
Hiroi, N.9
Planatscher, H.10
Zell, A.11
Dräger, A.12
-
56
-
-
84966367307
-
SBMLsimulator: a Java tool for model simulation and parameter estimation in systems biology
-
Dörr A, Keller R, Zell A, Dräger A. SBMLsimulator: a Java tool for model simulation and parameter estimation in systems biology. Computation. 2014;2(4):246-57. doi:10.3390/computation2040246.
-
(2014)
Computation.
, vol.2
, Issue.4
, pp. 246-257
-
-
Dörr, A.1
Keller, R.2
Zell, A.3
Dräger, A.4
-
57
-
-
84889794047
-
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
-
Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, et al. SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Systems Biology. 2013;7:135. doi:10.1186/1752-0509-7-135. 1309.1910.
-
(2013)
BMC Systems Biology.
, vol.7
, pp. 135
-
-
Chaouiya, C.1
Bérenguier, D.2
Keating, S.M.3
Naldi, A.4
van Iersel, M.P.5
Rodriguez, N.6
-
58
-
-
84982145073
-
The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1
-
Chaouiya C, Keating SM, Berenguier D, Naldi A, Thieffry D, van Iersel MP, et al. The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1. Journal of Integrative Bioinformatics. 2015;12(2):270. doi:10.2390/biecoll-jib-2015-270.
-
(2015)
Journal of Integrative Bioinformatics.
, vol.12
, Issue.2
, pp. 270
-
-
Chaouiya, C.1
Keating, S.M.2
Berenguier, D.3
Naldi, A.4
Thieffry, D.5
van Iersel, M.P.6
-
59
-
-
67650674074
-
Designing and encoding models for synthetic biology
-
Endler L, Rodriguez N, Juty N, Chelliah V, Laibe C, Li C, Le Novère N. Designing and encoding models for synthetic biology. Journal of The Royal Society Interface. 2009;6(Suppl 4):405-17. doi:10.1098/rsif.2009.0176.focus.
-
(2009)
Journal of The Royal Society Interface.
, vol.6
, pp. 405-417
-
-
Endler, L.1
Rodriguez, N.2
Juty, N.3
Chelliah, V.4
Laibe, C.5
Li, C.6
Le Novère, N.7
-
60
-
-
67650677053
-
Modeling of the bacterial mechanism of methicillin-resistance by a systems biology approach
-
Autiero I, Costantini S, Colonna G. Modeling of the bacterial mechanism of methicillin-resistance by a systems biology approach. PLoS One. 2009;4(7):6226. doi:10.1371/journal.pone.0006226.
-
(2009)
PLoS One.
, vol.4
, Issue.7
, pp. 6226
-
-
Autiero, I.1
Costantini, S.2
Colonna, G.3
-
61
-
-
84873551843
-
Systems Modelling of NHEJ Reveals the Importance of Redox Regulation of Ku70/80 in the Dynamics of DNA Damage Foci
-
Dolan D, Nelson G, Zupanic A, Smith G, Shanley D. Systems Modelling of NHEJ Reveals the Importance of Redox Regulation of Ku70/80 in the Dynamics of DNA Damage Foci. PLoS ONE. 2013;8(2):55190. doi:10.1371/journal.pone.0055190.
-
(2013)
PLoS ONE.
, vol.8
, Issue.2
, pp. 55190
-
-
Dolan, D.1
Nelson, G.2
Zupanic, A.3
Smith, G.4
Shanley, D.5
-
62
-
-
84874715571
-
Biological network inference for drug discovery
-
Lecca P, Priami C. Biological network inference for drug discovery. Drug Discovery Today. 2013;18(5-6):256-64. doi:10.1016/j.drudis.2012.11.001.
-
(2013)
Drug Discovery Today.
, vol.18
, Issue.5-6
, pp. 256-264
-
-
Lecca, P.1
Priami, C.2
-
63
-
-
84887084426
-
Metabolic Modeling and Simulation Analysis of Thyroid Disorder Pathway
-
Gupta MK. Metabolic Modeling and Simulation Analysis of Thyroid Disorder Pathway. JCSB. 2012;05(02):52-61. doi:10.4172/jcsb.1000090.
-
(2012)
JCSB.
, vol.5
, Issue.2
, pp. 52-61
-
-
Gupta, M.K.1
-
64
-
-
85048746506
-
Modeling and simulation analysis of propyl-thiouracil (PTU), an anti-thyroid drug on thyroid peroxidase (TPO), thyroid stimulating hormone receptor (TSHR), and sodium iodide (NIS) symporter based on systems biology approach
-
Gupta MK, Misra K. Modeling and simulation analysis of propyl-thiouracil (PTU), an anti-thyroid drug on thyroid peroxidase (TPO), thyroid stimulating hormone receptor (TSHR), and sodium iodide (NIS) symporter based on systems biology approach. Network Modeling Analysis in Health Informatics and Bioinformatics. 2013;2(1):45-57. doi:10.1007/s13721-013-0023-0.
-
(2013)
Network Modeling Analysis in Health Informatics and Bioinformatics.
, vol.2
, Issue.1
, pp. 45-57
-
-
Gupta, M.K.1
Misra, K.2
-
65
-
-
84930976266
-
Modeling of the MAPK machinery activation in response to various abiotic and biotic stresses in plants by a system biology approach
-
Pathak RK, Taj G, Pandey D, Arora S, Kumar A. Modeling of the MAPK machinery activation in response to various abiotic and biotic stresses in plants by a system biology approach. Bioinformation. 2013;9(9):443-9. doi:10.6026/97320630009443.
-
(2013)
Bioinformation.
, vol.9
, Issue.9
, pp. 443-449
-
-
Pathak, R.K.1
Taj, G.2
Pandey, D.3
Arora, S.4
Kumar, A.5
-
66
-
-
84886740491
-
Large-scale generation of computational models from biochemical pathway maps
-
Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, et al. Large-scale generation of computational models from biochemical pathway maps. BMC Syst Biol. 2013;7(1):116. doi:10.1186/1752-0509-7-116.
-
(2013)
BMC Syst Biol.
, vol.7
, Issue.1
, pp. 116
-
-
Büchel, F.1
Rodriguez, N.2
Swainston, N.3
Wrzodek, C.4
Czauderna, T.5
Keller, R.6
-
67
-
-
85051836456
-
-
PhD thesis, University of Tuebingen, Tübingen, Germany (January 2011).
-
Dräger A. Computational modeling of biochemical networks. PhD thesis, University of Tuebingen, Tübingen, Germany (January 2011). http://www. dr.hut-verlag.de/978-3-86853-850-2.html.
-
Computational modeling of biochemical networks
-
-
Dräger, A.1
-
68
-
-
84859524818
-
-
PhD thesis, Eberhard-Karls-Universität Tübingen, Tübingen, Germany:July 2009
-
Blum T. Computational approaches for analyzing metabolic pathways. PhD thesis, Eberhard-Karls-Universität Tübingen, Tübingen, Germany:July 2009 http://nbn-resolving.de/urn:nbn:de:bsz:21-opus-41532.
-
Computational approaches for analyzing metabolic pathways
-
-
Blum, T.1
-
69
-
-
80054069179
-
A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011
-
Orth JD, Conrad TM, Na J, Lerman JA, Nam H, Feist AM, et al. A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011. Mol Syst Biol. 2011;7(1):535. doi:10.1038/msb.2011.65.
-
(2011)
Mol Syst Biol.
, vol.7
, Issue.1
, pp. 535
-
-
Orth, J.D.1
Conrad, T.M.2
Na, J.3
Lerman, J.A.4
Nam, H.5
Feist, A.M.6
-
71
-
-
0000870544
-
Kinetik der Invertinwirkung
-
Michaelis L, Menten ML. Kinetik der Invertinwirkung. Biochem Z. 1913;49: 333-69.
-
(1913)
Biochem Z.
, vol.49
, pp. 333-369
-
-
Michaelis, L.1
Menten, M.L.2
-
74
-
-
33749538696
-
Approximation of dynamical systems using s-systems theory: application to biological systems
-
New York, NY, USA: ACM press
-
Tournier L. Approximation of dynamical systems using s-systems theory: application to biological systems. In: ISSAC '05: Proceedings of the 2005 International Symposium on Symbolic and Algebraic Computation. New York, NY, USA: ACM press; 2005. p. 317-24. doi:10.1145/1073884.1073928. http://portal.acm.org/citation.cfm?id=1073884.1073928.
-
(2005)
ISSAC '05: Proceedings of the 2005 International Symposium on Symbolic and Algebraic Computation
, pp. 317-324
-
-
Tournier, L.1
-
76
-
-
61349180117
-
Gene regulatory network inference: data integration in dynamic models-a review
-
Hecker M, Lambeck S, Töpfer S, Someren EV, Guthke R. Gene regulatory network inference: data integration in dynamic models-a review. Biosystems. 2009;96(1):86-103. doi:10.1016/j.biosystems.2008.12.004.
-
(2009)
Biosystems.
, vol.96
, Issue.1
, pp. 86-103
-
-
Hecker, M.1
Lambeck, S.2
Töpfer, S.3
Someren, E.V.4
Guthke, R.5
-
77
-
-
83055187942
-
A quantitative comparison of calvin-benson cycle models
-
Arnold A, Nikoloski Z. A quantitative comparison of calvin-benson cycle models. Trends Plant Sci. 2011;16(12):676-83. doi:10.1016/j.tplants.2011.09.004.
-
(2011)
Trends Plant Sci.
, vol.16
, Issue.12
, pp. 676-683
-
-
Arnold, A.1
Nikoloski, Z.2
|