-
1
-
-
0242490780
-
Cytoscape: a software environment for integrated models of biomolecular interaction networks
-
10.1101/gr.1239303, 403769, 14597658
-
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks Genome Res 2003, 13(11):2498-2504. 10.1101/gr.1239303, 403769, 14597658.
-
(2003)
Genome Res
, vol.13
, Issue.11
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
3
-
-
2942609149
-
VisANT: an online visualization and analysis tool for biological interaction data
-
10.1186/1471-2105-5-17, 368431, 15028117
-
Hu Z, Mellor J, Wu J, Delisi C. VisANT: an online visualization and analysis tool for biological interaction data BMC Bioinformatics 2004, 5(1):17. 10.1186/1471-2105-5-17, 368431, 15028117.
-
(2004)
BMC Bioinformatics
, vol.5
, Issue.1
, pp. 17
-
-
Hu, Z.1
Mellor, J.2
Wu, J.3
Delisi, C.4
-
4
-
-
68449103579
-
The systems biology graphical notation
-
10.1038/nbt.1558, 19668183
-
Novère NL, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, et al. The systems biology graphical notation Nat Biotechnol 2009, 27(8):735-741. 10.1038/nbt.1558, 19668183.
-
(2009)
Nat Biotechnol
, vol.27
, Issue.8
, pp. 735-741
-
-
Novère, N.L.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
more..
-
5
-
-
30044440098
-
Molecular interaction maps of bioregulatory networks: a general rubric for systems biology
-
1345641, 16267266
-
Kohn KW, Aladjem MI, Weinstein JN, Pommier Y. Molecular interaction maps of bioregulatory networks: a general rubric for systems biology Mol Biol Cell 2006, 17(1):1-13. 1345641, 16267266.
-
(2006)
Mol Biol Cell
, vol.17
, Issue.1
, pp. 1-13
-
-
Kohn, K.W.1
Aladjem, M.I.2
Weinstein, J.N.3
Pommier, Y.4
-
6
-
-
79955968330
-
A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method
-
10.1186/1471-2105-12-167, 3118169, 21586134
-
Luna A, Karac EI, Sunshine M, Chang L, Nussinov R, Aladjem MI, Kohn KW. A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method BMC Bioinformatics 2011, 12:167. 10.1186/1471-2105-12-167, 3118169, 21586134.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 167
-
-
Luna, A.1
Karac, E.I.2
Sunshine, M.3
Chang, L.4
Nussinov, R.5
Aladjem, M.I.6
Kohn, K.W.7
-
7
-
-
65649154507
-
Rule-based modeling of biochemical systems with, BioNetGen
-
Totowa: Humana Press, Maly IV
-
Faeder JR, Blinov ML, Hlavacek WS. Rule-based modeling of biochemical systems with, BioNetGen Systems Biology. Volume 500 2009,113-167. Totowa: Humana Press, Maly IV.
-
(2009)
Systems Biology. Volume 500
, pp. 113-167
-
-
Faeder, J.R.1
Blinov, M.L.2
Hlavacek, W.S.3
-
8
-
-
77956393134
-
Multiscale modeling for biologists
-
10.1002/wsbm.33, 2862646, 20448808
-
Meier-Schellersheim M, Fraser IDC, Klauschen F. Multiscale modeling for biologists Wiley Interdiscip Rev Syst Biol Med 2009, 1(1):4-14. 10.1002/wsbm.33, 2862646, 20448808.
-
(2009)
Wiley Interdiscip Rev Syst Biol Med
, vol.1
, Issue.1
, pp. 4-14
-
-
Meier-Schellersheim, M.1
Fraser, I.D.C.2
Klauschen, F.3
-
9
-
-
66149151035
-
Internal coarse-graining of molecular systems
-
10.1073/pnas.0809908106, 2672529, 19346467
-
Feret J, Danos V, Krivine J, Harmer R, Fontana W. Internal coarse-graining of molecular systems Proc Natl Acad Sci USA 2009, 106(16):6453-6458. 10.1073/pnas.0809908106, 2672529, 19346467.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, Issue.16
, pp. 6453-6458
-
-
Feret, J.1
Danos, V.2
Krivine, J.3
Harmer, R.4
Fontana, W.5
-
11
-
-
65649104062
-
GetBonNie for building, analyzing and sharing rule-based models
-
10.1093/bioinformatics/btp173, 2682519, 19321734
-
Hu B, Fricke GM, Faeder JR, Posner RG, Hlavacek WS. GetBonNie for building, analyzing and sharing rule-based models Bioinformatics 2009, 25(11):1457-1460. 10.1093/bioinformatics/btp173, 2682519, 19321734.
-
(2009)
Bioinformatics
, vol.25
, Issue.11
, pp. 1457-1460
-
-
Hu, B.1
Fricke, G.M.2
Faeder, J.R.3
Posner, R.G.4
Hlavacek, W.S.5
-
12
-
-
84886430663
-
The Simmune Modeler visual interface for creating signaling networks based on bi-molecular interactions
-
10.1093/bioinformatics/btt134, 3634183, 23508970
-
Zhang F, Angermann BR, Meier-Schellersheim M. The Simmune Modeler visual interface for creating signaling networks based on bi-molecular interactions Bioinformatics 2013, 29(9):1229-1230. 10.1093/bioinformatics/btt134, 3634183, 23508970.
-
(2013)
Bioinformatics
, vol.29
, Issue.9
, pp. 1229-1230
-
-
Zhang, F.1
Angermann, B.R.2
Meier-Schellersheim, M.3
-
13
-
-
84872841992
-
RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry
-
10.1186/1471-2105-13-S8-S3, 3267649, 22221313
-
Smith AM, Xu W, Sun Y, Faeder JR, Marai GE. RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry BMC Bioinformatics 2012, 13(Suppl 8):3. 10.1186/1471-2105-13-S8-S3, 3267649, 22221313.
-
(2012)
BMC Bioinformatics
, vol.13
, Issue.SUPPL. 8
, pp. 3
-
-
Smith, A.M.1
Xu, W.2
Sun, Y.3
Faeder, J.R.4
Marai, G.E.5
-
14
-
-
80052771333
-
Guidelines for visualizing and annotating rule-based models
-
10.1039/c1mb05077j, 3168731, 21647530
-
Chylek LA, Hu B, Blinov ML, Emonet T, Faeder JR, Goldstein B, Gutenkunst RN, Haugh JM, Lipniacki T, Posner RG, Yang J, Hlavacek WS. Guidelines for visualizing and annotating rule-based models Mol BioSyst 2011, 7(10):2779-2795. 10.1039/c1mb05077j, 3168731, 21647530.
-
(2011)
Mol BioSyst
, vol.7
, Issue.10
, pp. 2779-2795
-
-
Chylek, L.A.1
Hu, B.2
Blinov, M.L.3
Emonet, T.4
Faeder, J.R.5
Goldstein, B.6
Gutenkunst, R.N.7
Haugh, J.M.8
Lipniacki, T.9
Posner, R.G.10
Yang, J.11
Hlavacek, W.S.12
-
15
-
-
84860315246
-
A framework for mapping, visualisation and automatic model creation of signal-transduction networks
-
3361003, 22531118
-
Tiger C-F, Krause F, Cedersund G, Palmer R, Klipp E, Hohmann S, Kitano H, Krantz M. A framework for mapping, visualisation and automatic model creation of signal-transduction networks Mol Syst Biol 2012, 8:578. 3361003, 22531118.
-
(2012)
Mol Syst Biol
, vol.8
, pp. 578
-
-
Tiger, C.-F.1
Krause, F.2
Cedersund, G.3
Palmer, R.4
Klipp, E.5
Hohmann, S.6
Kitano, H.7
Krantz, M.8
-
16
-
-
33746595848
-
Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method
-
Meier-Schellersheim M, Xu X, Angermann B, Kunkel EJ, Jin T, Germain RN. Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method PLoS Comput Biol 2006, 2(7):82.
-
(2006)
PLoS Comput Biol
, vol.2
, Issue.7
, pp. 82
-
-
Meier-Schellersheim, M.1
Xu, X.2
Angermann, B.3
Kunkel, E.J.4
Jin, T.5
Germain, R.N.6
-
17
-
-
84862777639
-
Computational modeling of cellular signaling processes embedded into dynamic spatial contexts
-
10.1038/nmeth.1861, 3448286, 22286385
-
Angermann BR, Klauschen F, Garcia AD, Prustel T, Zhang F, Germain RN, Meier-Schellersheim M. Computational modeling of cellular signaling processes embedded into dynamic spatial contexts Nat Methods 2012, 9(3):283-289. 10.1038/nmeth.1861, 3448286, 22286385.
-
(2012)
Nat Methods
, vol.9
, Issue.3
, pp. 283-289
-
-
Angermann, B.R.1
Klauschen, F.2
Garcia, A.D.3
Prustel, T.4
Zhang, F.5
Germain, R.N.6
Meier-Schellersheim, M.7
-
18
-
-
84865123095
-
Software support for SBGN maps: SBGN-ML and LibSBGN
-
10.1093/bioinformatics/bts270, 3400951, 22581176
-
van Iersel MP, Villéger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A, Demir E, Sorokin A, Dogrusoz U, Matsuoka Y, Funahashi A, Aladjem MI, Mi H, Moodie SL, Kitano H, Le Novère N, Schreiber F. Software support for SBGN maps: SBGN-ML and LibSBGN Bioinformatics 2012, 28(15):2016-2021. 10.1093/bioinformatics/bts270, 3400951, 22581176.
-
(2012)
Bioinformatics
, vol.28
, Issue.15
, pp. 2016-2021
-
-
van Iersel, M.P.1
Villéger, A.C.2
Czauderna, T.3
Boyd, S.E.4
Bergmann, F.T.5
Luna, A.6
Demir, E.7
Sorokin, A.8
Dogrusoz, U.9
Matsuoka, Y.10
Funahashi, A.11
Aladjem, M.I.12
Mi, H.13
Moodie, S.L.14
Kitano, H.15
Le Novère, N.16
Schreiber, F.17
-
19
-
-
68049104164
-
Network architecture of signaling from uncoupled helicase-polymerase to cell cycle checkpoints and trans-lesion DNA synthesis
-
10.4161/cc.8.14.9102, 4018747, 19556879
-
Kohn KW, Aladjem MI, Weinstein JN, Pommier Y. Network architecture of signaling from uncoupled helicase-polymerase to cell cycle checkpoints and trans-lesion DNA synthesis Cell Cycle 2009, 8(14):2281-2299. 10.4161/cc.8.14.9102, 4018747, 19556879.
-
(2009)
Cell Cycle
, vol.8
, Issue.14
, pp. 2281-2299
-
-
Kohn, K.W.1
Aladjem, M.I.2
Weinstein, J.N.3
Pommier, Y.4
-
20
-
-
79960377397
-
Drawing graphs with NEATO
-
North S. Drawing graphs with NEATO 2004,[http://ftp.graphviz.org/pdf/neatoguide.pdf].
-
(2004)
-
-
North, S.1
-
21
-
-
84867453337
-
Graphviz-open source graph drawing tools
-
Berlin Heidelberg: Springer, Mutzel P, Jünger M, Leipert S
-
Ellson J, Gansner E, Koutsofios L, North SC, Woodhull G. Graphviz-open source graph drawing tools Graph Drawing. Lecture Notes in Computer Science 2002,483-484. Berlin Heidelberg: Springer, Mutzel P, Jünger M, Leipert S.
-
(2002)
Graph Drawing. Lecture Notes in Computer Science
, pp. 483-484
-
-
Ellson, J.1
Gansner, E.2
Koutsofios, L.3
North, S.C.4
Woodhull, G.5
-
22
-
-
0027553807
-
A technique for drawing directed graphs
-
Gansner ER, Koutsofios E, North SC, Vo K-P. A technique for drawing directed graphs IEEE Trans on Softw Eng 1993, 19(3):214-230.
-
(1993)
IEEE Trans on Softw Eng
, vol.19
, Issue.3
, pp. 214-230
-
-
Gansner, E.R.1
Koutsofios, E.2
North, S.C.3
Vo, K.-P.4
-
23
-
-
77951876275
-
Spatio-temporal modeling of signaling protein recruitment to EGFR
-
10.1186/1752-0509-4-57, 2877007, 20459599
-
Hsieh M-Y, Yang S, Raymond-Stinz MA, Edwards JS, Wilson BS. Spatio-temporal modeling of signaling protein recruitment to EGFR BMC Syst Biol 2010, 4:57. 10.1186/1752-0509-4-57, 2877007, 20459599.
-
(2010)
BMC Syst Biol
, vol.4
, pp. 57
-
-
Hsieh, M.-Y.1
Yang, S.2
Raymond-Stinz, M.A.3
Edwards, J.S.4
Wilson, B.S.5
-
24
-
-
84904112485
-
SBML3 Multi-state, Multi-component
-
SBML3 Multi-state, Multi-component [http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Multistate_and_Multicomponent_Species_(multi)].
-
-
-
|