-
1
-
-
66149172363
-
Diversity-based, model-guided construction of synthetic gene networks with predicted functions
-
Ellis T., Wang X., Collins J.J. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat. Biotechnol. 2009, 27:465-471.
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 465-471
-
-
Ellis, T.1
Wang, X.2
Collins, J.J.3
-
2
-
-
38349066180
-
Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli
-
Nishio Y., Usuda Y., Matsui K., Kurata H. Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli. Mol. Syst. Biol. 2008, 4:160.
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 160
-
-
Nishio, Y.1
Usuda, Y.2
Matsui, K.3
Kurata, H.4
-
3
-
-
28544440364
-
Reconstruction of genetic circuits
-
Sprinzak D., Elowitz M.B. Reconstruction of genetic circuits. Nature 2005, 438:443-448.
-
(2005)
Nature
, vol.438
, pp. 443-448
-
-
Sprinzak, D.1
Elowitz, M.B.2
-
4
-
-
0742305866
-
Network biology: understanding the cell's functional organization
-
Barabasi A.L., Oltvai Z.N. Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 2004, 5:101-113.
-
(2004)
Nat. Rev. Genet.
, vol.5
, pp. 101-113
-
-
Barabasi, A.L.1
Oltvai, Z.N.2
-
5
-
-
0242490780
-
Cytoscape: a software environment for integrated models of biomolecular interaction networks
-
Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., Amin N., Schwikowski B., Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13:2498-2504.
-
(2003)
Genome Res.
, vol.13
, 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
-
6
-
-
47949099328
-
CellDesigner 3.5: a versatile modeling tool for biochemical networks
-
Funahashi A., Matsuoka Y., Jouraku A., Morohashi M., Kikuchi N., Kitano H. CellDesigner 3.5: a versatile modeling tool for biochemical networks. Proc. IEEE 2008, 96:1254-1265.
-
(2008)
Proc. IEEE
, vol.96
, pp. 1254-1265
-
-
Funahashi, A.1
Matsuoka, Y.2
Jouraku, A.3
Morohashi, M.4
Kikuchi, N.5
Kitano, H.6
-
7
-
-
23444439817
-
Using process diagrams for the graphical representation of biological networks
-
Kitano H., Funahashi A., Matsuoka Y., Oda K. Using process diagrams for the graphical representation of biological networks. Nat. Biotechnol. 2005, 23:961-966.
-
(2005)
Nat. Biotechnol.
, vol.23
, pp. 961-966
-
-
Kitano, H.1
Funahashi, A.2
Matsuoka, Y.3
Oda, K.4
-
8
-
-
2642527148
-
Genomic Object Net: II. Modelling biopathways by hybrid functional Petri net with extension
-
Doi A., Nagasaki M., Fujita S., Matsuno H., Miyano S. Genomic Object Net: II. Modelling biopathways by hybrid functional Petri net with extension. Appl. Bioinformatics 2003, 2:185-188.
-
(2003)
Appl. Bioinformatics
, vol.2
, pp. 185-188
-
-
Doi, A.1
Nagasaki, M.2
Fujita, S.3
Matsuno, H.4
Miyano, S.5
-
9
-
-
2642533799
-
Genomic Object Net: I. A platform for modelling and simulating biopathways
-
Nagasaki M., Doi A., Matsuno H., Miyano S. Genomic Object Net: I. A platform for modelling and simulating biopathways. Appl. Bioinformatics 2003, 2:181-184.
-
(2003)
Appl. Bioinformatics
, vol.2
, pp. 181-184
-
-
Nagasaki, M.1
Doi, A.2
Matsuno, H.3
Miyano, S.4
-
10
-
-
36749043657
-
Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis
-
Kurata H., Inoue K., Maeda K., Masaki K., Shimokawa Y., Zhao Q. Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis. Nucleic Acids Res. 2007, 35:e134.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Kurata, H.1
Inoue, K.2
Maeda, K.3
Masaki, K.4
Shimokawa, Y.5
Zhao, Q.6
-
11
-
-
17844397967
-
CADLIVE dynamic simulator: direct link of biochemical networks to dynamic models
-
Kurata H., Masaki K., Sumida Y., Iwasaki R. CADLIVE dynamic simulator: direct link of biochemical networks to dynamic models. Genome Res. 2005, 15:590-600.
-
(2005)
Genome Res.
, vol.15
, pp. 590-600
-
-
Kurata, H.1
Masaki, K.2
Sumida, Y.3
Iwasaki, R.4
-
12
-
-
0242380634
-
CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle
-
Kurata H., Matoba N., Shimizu N. CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle. Nucleic Acids Res. 2003, 31:4071-4084.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 4071-4084
-
-
Kurata, H.1
Matoba, N.2
Shimizu, N.3
-
13
-
-
0036326896
-
PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways
-
Demir E., Babur O., Dogrusoz U., Gursoy A., Nisanci G., Cetin-Atalay R., Ozturk M. PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways. Bioinformatics 2002, 18:996-1003.
-
(2002)
Bioinformatics
, vol.18
, pp. 996-1003
-
-
Demir, E.1
Babur, O.2
Dogrusoz, U.3
Gursoy, A.4
Nisanci, G.5
Cetin-Atalay, R.6
Ozturk, M.7
-
14
-
-
0037342537
-
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
-
Hucka M., Finney A., Sauro H.M., Bolouri H., Doyle J.C., Kitano H., Arkin A.P., Bornstein B.J., Bray D., Cornish-Bowden A., Cuellar A.A., Dronov S., Gilles E.D., Ginkel M., Gor V., Goryanin I.I., Hedley W.J., Hodgman T.C., Hofmeyr J.H., Hunter P.J., Juty N.S., Kasberger J.L., Kremling A., Kummer U., Le Novere N., Loew L.M., Lucio D., Mendes P., Minch E., Mjolsness E.D., Nakayama Y., Nelson M.R., Nielsen P.F., Sakurada T., Schaff J.C., Shapiro B.E., Shimizu T.S., Spence H.D., Stelling J., Takahashi K., Tomita M., Wagner J., Wang J. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19:524-531.
-
(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.19
Hunter, P.J.20
Juty, N.S.21
Kasberger, J.L.22
Kremling, A.23
Kummer, U.24
Le Novere, N.25
Loew, L.M.26
Lucio, D.27
Mendes, P.28
Minch, E.29
Mjolsness, E.D.30
Nakayama, Y.31
Nelson, M.R.32
Nielsen, P.F.33
Sakurada, T.34
Schaff, J.C.35
Shapiro, B.E.36
Shimizu, T.S.37
Spence, H.D.38
Stelling, J.39
Takahashi, K.40
Tomita, M.41
Wagner, J.42
Wang, J.43
more..
-
15
-
-
79953775804
-
-
BioPAX-Biological Pathways Exchange Language Level 2, Version 1.0 Documentation
-
G. Bader, M. Cary, BioPAX-Biological Pathways Exchange Language Level 2, Version 1.0 Documentation, 2005.
-
(2005)
-
-
Bader, G.1
Cary, M.2
-
16
-
-
18744387729
-
A grid layout algorithm for automatic drawing of biochemical networks
-
Li W., Kurata H. A grid layout algorithm for automatic drawing of biochemical networks. Bioinformatics 2005, 21:2036-2042.
-
(2005)
Bioinformatics
, vol.21
, pp. 2036-2042
-
-
Li, W.1
Kurata, H.2
-
17
-
-
0036081062
-
The KEGG databases at GenomeNet
-
Kanehisa M., Goto S., Kawashima S., Nakaya A. The KEGG databases at GenomeNet. Nucleic Acids Res. 2002, 30:42-46.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 42-46
-
-
Kanehisa, M.1
Goto, S.2
Kawashima, S.3
Nakaya, A.4
-
18
-
-
0037245913
-
BIND: the biomolecular interaction network database
-
Bader G.D., Betel D., Hogue C.W. BIND: the biomolecular interaction network database. Nucleic Acids Res. 2003, 31:248-250.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 248-250
-
-
Bader, G.D.1
Betel, D.2
Hogue, C.W.3
-
19
-
-
0347755535
-
The database of interacting proteins: 2004 update
-
Salwinski L., Miller C.S., Smith A.J., Pettit F.K., Bowie J.U., Eisenberg D. The database of interacting proteins: 2004 update. Nucleic Acids Res. 2004, 32:D449-451.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Salwinski, L.1
Miller, C.S.2
Smith, A.J.3
Pettit, F.K.4
Bowie, J.U.5
Eisenberg, D.6
-
20
-
-
38549170927
-
MIPS: analysis and annotation of genome information in 2007
-
Mewes H.W., Dietmann S., Frishman D., Gregory R., Mannhaupt G., Mayer K.F., Munsterkotter M., Ruepp A., Spannagl M., Stumpflen V., Rattei T. MIPS: analysis and annotation of genome information in 2007. Nucleic Acids Res. 2008, 36:D196-201.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Mewes, H.W.1
Dietmann, S.2
Frishman, D.3
Gregory, R.4
Mannhaupt, G.5
Mayer, K.F.6
Munsterkotter, M.7
Ruepp, A.8
Spannagl, M.9
Stumpflen, V.10
Rattei, T.11
-
21
-
-
58149193222
-
Human protein reference database-2009 update
-
Keshava Prasad T.S., Goel R., Kandasamy K., Keerthikumar S., Kumar S., Mathivanan S., Telikicherla D., Raju R., Shafreen B., Venugopal A., Balakrishnan L., Marimuthu A., Banerjee S., Somanathan D.S., Sebastian A., Rani S., Ray S., Harrys Kishore C.J., Kanth S., Ahmed M., Kashyap M.K., Mohmood R., Ramachandra Y.L., Krishna V., Rahiman B.A., Mohan S., Ranganathan P., Ramabadran S., Chaerkady R., Pandey A. Human protein reference database-2009 update. Nucleic Acids Res. 2009, 37:D767-772.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Keshava Prasad, T.S.1
Goel, R.2
Kandasamy, K.3
Keerthikumar, S.4
Kumar, S.5
Mathivanan, S.6
Telikicherla, D.7
Raju, R.8
Shafreen, B.9
Venugopal, A.10
Balakrishnan, L.11
Marimuthu, A.12
Banerjee, S.13
Somanathan, D.S.14
Sebastian, A.15
Rani, S.16
Ray, S.17
Harrys Kishore, C.J.18
Kanth, S.19
Ahmed, M.20
Kashyap, M.K.21
Mohmood, R.22
Ramachandra, Y.L.23
Krishna, V.24
Rahiman, B.A.25
Mohan, S.26
Ranganathan, P.27
Ramabadran, S.28
Chaerkady, R.29
Pandey, A.30
more..
-
22
-
-
38549173606
-
The BioGRID interaction database: 2008 update
-
Breitkreutz B.J., Stark C., Reguly T., Boucher L., Breitkreutz A., Livstone M., Oughtred R., Lackner D.H., Bahler J., Wood V., Dolinski K., Tyers M. The BioGRID interaction database: 2008 update. Nucleic Acids Res. 2008, 36:D637-640.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Breitkreutz, B.J.1
Stark, C.2
Reguly, T.3
Boucher, L.4
Breitkreutz, A.5
Livstone, M.6
Oughtred, R.7
Lackner, D.H.8
Bahler, J.9
Wood, V.10
Dolinski, K.11
Tyers, M.12
-
23
-
-
46049087782
-
The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
-
Wingender E. The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief Bioinformatics 2008, 9:326-332.
-
(2008)
Brief Bioinformatics
, vol.9
, pp. 326-332
-
-
Wingender, E.1
-
24
-
-
38549162091
-
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information
-
Sierro N., Makita Y., de Hoon M., Nakai K. DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res. 2008, 36:D93-96.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Sierro, N.1
Makita, Y.2
de Hoon, M.3
Nakai, K.4
-
25
-
-
38549140094
-
RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
-
Gama-Castro S., Jimenez-Jacinto V., Peralta-Gil M., Santos-Zavaleta A., Penaloza-Spinola M.I., Contreras-Moreira B., Segura-Salazar J., Muniz-Rascado L., Martinez-Flores I., Salgado H., Bonavides-Martinez C., Abreu-Goodger C., Rodriguez-Penagos C., Miranda-Rios J., Morett E., Merino E., Huerta A.M., Trevino-Quintanilla L., Collado-Vides J. RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res. 2008, 36:D120-124.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Gama-Castro, S.1
Jimenez-Jacinto, V.2
Peralta-Gil, M.3
Santos-Zavaleta, A.4
Penaloza-Spinola, M.I.5
Contreras-Moreira, B.6
Segura-Salazar, J.7
Muniz-Rascado, L.8
Martinez-Flores, I.9
Salgado, H.10
Bonavides-Martinez, C.11
Abreu-Goodger, C.12
Rodriguez-Penagos, C.13
Miranda-Rios, J.14
Morett, E.15
Merino, E.16
Huerta, A.M.17
Trevino-Quintanilla, L.18
Collado-Vides, J.19
-
26
-
-
58149185126
-
BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009
-
Chang A., Scheer M., Grote A., Schomburg I., Schomburg D. BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. Nucleic Acids Res. 2009, 37:D588-592.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Chang, A.1
Scheer, M.2
Grote, A.3
Schomburg, I.4
Schomburg, D.5
-
27
-
-
70449515104
-
KEGGconverter: a tool for the in silico modelling of metabolic networks of the KEGG Pathways database
-
Moutselos K., Kanaris I., Chatziioannou A., Maglogiannis I., Kolisis F.N. KEGGconverter: a tool for the in silico modelling of metabolic networks of the KEGG Pathways database. BMC Bioinformatics 2009, 10:324.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 324
-
-
Moutselos, K.1
Kanaris, I.2
Chatziioannou, A.3
Maglogiannis, I.4
Kolisis, F.N.5
-
28
-
-
40749087306
-
BiNoM: a cytoscape plugin for manipulating and analyzing biological networks
-
Zinovyev A., Viara E., Calzone L., Barillot E. BiNoM: a cytoscape plugin for manipulating and analyzing biological networks. Bioinformatics 2008, 24:876-877.
-
(2008)
Bioinformatics
, vol.24
, pp. 876-877
-
-
Zinovyev, A.1
Viara, E.2
Calzone, L.3
Barillot, E.4
-
29
-
-
58149279036
-
Maximum entropy decomposition of flux distribution at steady state to elementary modes
-
Zhao Q., Kurata H. Maximum entropy decomposition of flux distribution at steady state to elementary modes. J. Biosci. Bioeng. 2009, 107:84-89.
-
(2009)
J. Biosci. Bioeng.
, vol.107
, pp. 84-89
-
-
Zhao, Q.1
Kurata, H.2
-
30
-
-
67649218402
-
Genetic modification of flux for flux prediction of mutants
-
Zhao Q., Kurata H. Genetic modification of flux for flux prediction of mutants. Bioinformatics 2009, 25:1702-1708.
-
(2009)
Bioinformatics
, vol.25
, pp. 1702-1708
-
-
Zhao, Q.1
Kurata, H.2
-
31
-
-
77954313563
-
Use of maximum entropy principle with Lagrange multipliers extends the feasibility of elementary mode analysis
-
Zhao Q., Kurata H. Use of maximum entropy principle with Lagrange multipliers extends the feasibility of elementary mode analysis. J. Biosci. Bioeng. 2010, 110:254-261.
-
(2010)
J. Biosci. Bioeng.
, vol.110
, pp. 254-261
-
-
Zhao, Q.1
Kurata, H.2
-
32
-
-
0032776303
-
Molecular interaction map of the mammalian cell cycle control and DNA repair systems
-
Kohn K.W. Molecular interaction map of the mammalian cell cycle control and DNA repair systems. Mol. Biol. Cell 1999, 10:2703-2734.
-
(1999)
Mol. Biol. Cell
, vol.10
, pp. 2703-2734
-
-
Kohn, K.W.1
-
33
-
-
27244436714
-
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes
-
Karp P.D., Ouzounis C.A., Moore-Kochlacs C., Goldovsky L., Kaipa P., Ahren D., Tsoka S., Darzentas N., Kunin V., Lopez-Bigas N. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res. 2005, 33:6083-6089.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 6083-6089
-
-
Karp, P.D.1
Ouzounis, C.A.2
Moore-Kochlacs, C.3
Goldovsky, L.4
Kaipa, P.5
Ahren, D.6
Tsoka, S.7
Darzentas, N.8
Kunin, V.9
Lopez-Bigas, N.10
-
34
-
-
77349107936
-
LucidDraw: efficiently visualizing complex biochemical networks within MATLAB
-
He S., Mei J., Shi G., Wang Z., Li W. LucidDraw: efficiently visualizing complex biochemical networks within MATLAB. BMC Bioinformatics 2010, 11:31.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 31
-
-
He, S.1
Mei, J.2
Shi, G.3
Wang, Z.4
Li, W.5
-
35
-
-
0001860685
-
The shortest path through a maze
-
Harvard University Press, Cambridge, Massachusetts
-
Moore E.F. The shortest path through a maze. Proceedings of an International Symposium on the Theory of Switching, 2-5 April 1957 1959, Harvard University Press, Cambridge, Massachusetts, pp. 285-292.
-
(1959)
Proceedings of an International Symposium on the Theory of Switching, 2-5 April 1957
, pp. 285-292
-
-
Moore, E.F.1
-
36
-
-
33846892994
-
IDconverter and IDClight: conversion and annotation of gene and protein IDs
-
Alibes A., Yankilevich P., Canada A., Diaz-Uriarte R. IDconverter and IDClight: conversion and annotation of gene and protein IDs. BMC Bioinformatics 2007, 8:9.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 9
-
-
Alibes, A.1
Yankilevich, P.2
Canada, A.3
Diaz-Uriarte, R.4
-
37
-
-
67849110019
-
Hyperlink Management System and ID Converter System: enabling maintenance-free hyperlinks among major biological databases
-
Imanishi T., Nakaoka H. Hyperlink Management System and ID Converter System: enabling maintenance-free hyperlinks among major biological databases. Nucleic Acids Res. 2009, 37:W17-22.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Imanishi, T.1
Nakaoka, H.2
|