-
1
-
-
77956333400
-
Systematic integration of experimental data and models in systems biology
-
Li P, Dada JO, Jameson D, Spasic I, Swainston N, Carroll K, Dunn W, Khan F, Malys N, Messiha HL, Simeonidis E, Weichart D, Winder C, Wishart J, Broomhead DS, Goble CA, Gaskell SJ, Kell DB, Westerhoff HV, Mendes P, Paton NW. Systematic integration of experimental data and models in systems biology. BMC Bioinformatics 2010, 11:582.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 582
-
-
Li, P.1
Dada, J.O.2
Jameson, D.3
Spasic, I.4
Swainston, N.5
Carroll, K.6
Dunn, W.7
Khan, F.8
Malys, N.9
Messiha, H.L.10
Simeonidis, E.11
Weichart, D.12
Winder, C.13
Wishart, J.14
Broomhead, D.S.15
Goble, C.A.16
Gaskell, S.J.17
Kell, D.B.18
Westerhoff, H.V.19
Mendes, P.20
Paton, N.W.21
more..
-
2
-
-
0037342537
-
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
-
10.1093/bioinformatics/btg015, 12611808
-
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr J-HS, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19:524-531. 10.1093/bioinformatics/btg015, 12611808.
-
(2003)
Bioinformatics
, vol.19
, 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
Cuellar, A.A.11
Dronov, S.12
Gilles, E.D.13
Ginkel, M.14
Gor, V.15
Goryanin, I.I.16
Hedley, W.J.17
Hodgman, T.C.18
Hofmeyr, J.-.H.S.19
Hunter, P.J.20
Juty, N.S.21
Kasberger, J.L.22
Kremling, A.23
Kummer, U.24
Le Novère, N.25
Loew, L.M.26
Lucio, D.27
Mendes, P.28
Minch, E.29
Mjolsness, E.D.30
more..
-
3
-
-
9444266171
-
CellDesigner: a process diagram editor for gene-regulatory and biochemical networks
-
Funahashi A, Tanimura N, Morohashi M, Kitano H. CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. BioSilico 2003, 1:159-162.
-
(2003)
BioSilico
, vol.1
, pp. 159-162
-
-
Funahashi, A.1
Tanimura, N.2
Morohashi, M.3
Kitano, H.4
-
4
-
-
33845368513
-
COPASI - a COmplex PAthway SImulator
-
10.1093/bioinformatics/btl485, 17032683
-
Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U. COPASI - a COmplex PAthway SImulator. Bioinformatics 2006, 22:3067-3074. 10.1093/bioinformatics/btl485, 17032683.
-
(2006)
Bioinformatics
, vol.22
, 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
-
5
-
-
0030739712
-
A general computational framework for modeling cellular structure and function
-
10.1016/S0006-3495(97)78146-3, 1181013, 9284281
-
Schaff J, Fink CC, Slepchenko B, Carson JH, Loew LM. A general computational framework for modeling cellular structure and function. Biophys J 1997, 73:1135-1146. 10.1016/S0006-3495(97)78146-3, 1181013, 9284281.
-
(1997)
Biophys J
, vol.73
, pp. 1135-1146
-
-
Schaff, J.1
Fink, C.C.2
Slepchenko, B.3
Carson, J.H.4
Loew, L.M.5
-
6
-
-
77953934646
-
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
-
10.1186/1752-0509-4-92, 2909940, 20587024
-
Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He EU, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C. BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 2010, 4:92. 10.1186/1752-0509-4-92, 2909940, 20587024.
-
(2010)
BMC Syst Biol
, vol.4
, pp. 92
-
-
Li, C.1
Donizelli, M.2
Rodriguez, N.3
Dharuri, H.4
Endler, L.5
Chelliah, V.6
Li, L.7
He, E.U.8
Henry, A.9
Stefan, M.I.10
Snoep, J.L.11
Hucka, M.12
Le Novère, N.13
Laibe, C.14
-
7
-
-
77956511014
-
MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format
-
10.1093/bioinformatics/btq425, 20671147
-
Forth T, McConkey GA, Westhead DR. MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format. Bioinformatics 2010, 26:2352-2353. 10.1093/bioinformatics/btq425, 20671147.
-
(2010)
Bioinformatics
, vol.26
, pp. 2352-2353
-
-
Forth, T.1
McConkey, G.A.2
Westhead, D.R.3
-
8
-
-
0033982936
-
KEGG: Kyoto Encyclopedia of Genes and Genomes
-
10.1093/nar/28.1.27, 102409, 10592173
-
Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 2000, 28:27-30. 10.1093/nar/28.1.27, 102409, 10592173.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
9
-
-
77949508535
-
Annotation and merging of SBML models with semanticSBML
-
10.1093/bioinformatics/btp642, 19933161
-
Krause F, Uhlendorf J, Lubitz T, Schulz M, Klipp E, Liebermeister W. Annotation and merging of SBML models with semanticSBML. Bioinformatics 2010, 26:421-422. 10.1093/bioinformatics/btp642, 19933161.
-
(2010)
Bioinformatics
, vol.26
, pp. 421-422
-
-
Krause, F.1
Uhlendorf, J.2
Lubitz, T.3
Schulz, M.4
Klipp, E.5
Liebermeister, W.6
-
10
-
-
53749085229
-
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
-
10.1038/nbt1492, 18846089
-
Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Ki{dotless}rdar B, Penttilä M, Klipp E, Palsson B, Sauer U, Oliver SG, et al. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol 2008, 26:1155-1160. 10.1038/nbt1492, 18846089.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1155-1160
-
-
Herrgård, M.J.1
Swainston, N.2
Dobson, P.3
Dunn, W.B.4
Arga, K.Y.5
Arvas, M.6
Blüthgen, N.7
Borger, S.8
Costenoble, R.9
Heinemann, M.10
Hucka, M.11
Le Novère, N.12
Li, P.13
Liebermeister, W.14
Mo, M.L.15
Oliveira, A.P.16
Petranovic, D.17
Pettifer, S.18
Simeonidis, E.19
Smallbone, K.20
Spasić, I.21
Weichart, D.22
Brent, R.23
Broomhead, D.S.24
Westerhoff, H.V.25
Kirdar, B.26
Penttilä, M.27
Klipp, E.28
Palsson, B.29
Sauer, U.30
Oliver, S.G.31
more..
-
11
-
-
57049184135
-
SED-ML - an XML format for the implementation of the MIASE guidelines
-
Berlin/Heidelberg: Springer, Heiner M, Uhrmacher A
-
Köhn D, Le Novère N. SED-ML - an XML format for the implementation of the MIASE guidelines. Computational Methods in Systems Biology 2008, 176-190. Berlin/Heidelberg: Springer, Heiner M, Uhrmacher A.
-
(2008)
Computational Methods in Systems Biology
, pp. 176-190
-
-
Köhn, D.1
Le Novère, N.2
-
12
-
-
28644433993
-
Minimum Information Requested In the Annotation of biochemical Models (MIRIAM)
-
10.1038/nbt1156, 16333295
-
Le Novère N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin E, Halstead M, Klipp E, Mendes P, Nielsen P, Sauro H, Shapiro B, Snoep JL, Spence HD, Wanner BL. Minimum Information Requested In the Annotation of biochemical Models (MIRIAM). Nat Biotechnol 2005, 23:1509-1515. 10.1038/nbt1156, 16333295.
-
(2005)
Nat Biotechnol
, vol.23
, pp. 1509-1515
-
-
Le Novère, N.1
Finney, A.2
Hucka, M.3
Bhalla, U.S.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.L.14
Spence, H.D.15
Wanner, B.L.16
-
13
-
-
33746675631
-
SABIO-RK: integration and curation of reaction kinetics data
-
Berlin/Heidelberg, Springer, Leser U, Naumann F, Eckman B
-
Wittig U, Golebiewski M, Kania R, Krebs O, Mir S, Weidemann A, Anstein S, Saric J, Rojas I. SABIO-RK: integration and curation of reaction kinetics data. Data Integration in the Life Sciences 2006, 94-103. Berlin/Heidelberg, Springer, Leser U, Naumann F, Eckman B.
-
(2006)
Data Integration in the Life Sciences
, pp. 94-103
-
-
Wittig, U.1
Golebiewski, M.2
Kania, R.3
Krebs, O.4
Mir, S.5
Weidemann, A.6
Anstein, S.7
Saric, J.8
Rojas, I.9
|