-
1
-
-
0036500993
-
Systems biology: A brief overview
-
Kitano H: Systems biology: a brief overview. Science 2002, 295:1662-1664.
-
(2002)
Science
, vol.295
, pp. 1662-1664
-
-
Kitano, H.1
-
2
-
-
0029876941
-
Application of biochemical systems theory to metabolism in human red blood cells. Signal propagation and accuracy of representation
-
Ni TC, Savageau MA: Application of biochemical systems theory to metabolism in human red blood cells. Signal propagation and accuracy of representation. J Biol Chem 1996, 271:7927-7941.
-
(1996)
J Biol Chem
, vol.271
, pp. 7927-7941
-
-
Ni, T.C.1
Savageau, M.A.2
-
3
-
-
2342648924
-
Integrating high-throughput and computational data elucidates bacterial networks
-
Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO: Integrating high-throughput and computational data elucidates bacterial networks. Nature 2004, 429:92-96.
-
(2004)
Nature
, vol.429
, pp. 92-96
-
-
Covert, M.W.1
Knight, E.M.2
Reed, J.L.3
Herrgard, M.J.4
Palsson, B.O.5
-
4
-
-
0033515250
-
Building working cells 'in silico'
-
Normile D: Building working cells 'in silico'. Science 1999, 284:80-81.
-
(1999)
Science
, vol.284
, pp. 80-81
-
-
Normile, D.1
-
5
-
-
0037079054
-
Computational systems biology
-
Kitano H: Computational systems biology. Nature 2002, 420:206-210.
-
(2002)
Nature
, vol.420
, pp. 206-210
-
-
Kitano, H.1
-
6
-
-
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, 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 JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, 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..
-
7
-
-
0141837071
-
Computational Challenges in Cell Simulation
-
Takahashi K, Yugi K, Hashimoto K, Yamada Y, Pickett CJF, Tomita M: Computational Challenges in Cell Simulation. IEEE Intelligent Systems 2002, 17:64-71.
-
(2002)
IEEE Intelligent Systems
, vol.17
, pp. 64-71
-
-
Takahashi, K.1
Yugi, K.2
Hashimoto, K.3
Yamada, Y.4
Pickett, C.J.F.5
Tomita, M.6
-
8
-
-
0027370376
-
GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems
-
Mendes P: GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems. Comput Appl Biosci 1993, 9:563-571.
-
(1993)
Comput Appl Biosci
, vol.9
, pp. 563-571
-
-
Mendes, P.1
-
9
-
-
14844349363
-
metaSIHARK: Software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella
-
Pinney JW, Shirley MW, McConkey GA, Westhead DR: metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella. Nucleic Acids Res 2005, 3 3:1399-1409.
-
(2005)
Nucleic Acids Res
, vol.3
, Issue.3
, pp. 1399-1409
-
-
Pinney, J.W.1
Shirley, M.W.2
McConkey, G.A.3
Westhead, D.R.4
-
10
-
-
13244265575
-
IdentiCS - Identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence
-
Sun J, Zeng AP: IdentiCS - identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence. BMC Bioinformatics 2004, 5:112.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 112
-
-
Sun, J.1
Zeng, A.P.2
-
12
-
-
2442636351
-
Computational analysis of Plasmodium falciparum metabolism: Organizing genomic information to facilitate drug discovery
-
Yeh I, Hanekamp T, Tsoka S, Karp PD, Altman RB: Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery. Genome Res 2004, 14:917-924.
-
(2004)
Genome Res
, vol.14
, pp. 917-924
-
-
Yeh, I.1
Hanekamp, T.2
Tsoka, S.3
Karp, P.D.4
Altman, R.B.5
-
13
-
-
0142219725
-
Quantitative cell biology with the Virtual Cell
-
Slepchenko BM, Schaff JC, Macara I, Loew LM: Quantitative cell biology with the Virtual Cell. Trends Cell Biol 2003, 13:570-576.
-
(2003)
Trends Cell Biol
, vol.13
, pp. 570-576
-
-
Slepchenko, B.M.1
Schaff, J.C.2
Macara, I.3
Loew, L.M.4
-
14
-
-
0033485517
-
Improved microbial gene identification with GLIMMER
-
Delcher AL, Harmon D, Kasif S, White O, Salzberg SL: Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999, 27:4636-4641.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 4636-4641
-
-
Delcher, A.L.1
Harmon, D.2
Kasif, S.3
White, O.4
Salzberg, S.L.5
-
15
-
-
0037561991
-
GenDB - An open source genome annotation system for prokaryote genomes
-
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A: GenDB - an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 2003, 31:2187-2195.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 2187-2195
-
-
Meyer, F.1
Goesmann, A.2
McHardy, A.C.3
Bartels, D.4
Bekel, T.5
Clausen, J.6
Kalinowski, J.7
Linke, B.8
Rupp, O.9
Giegerich, R.10
Puhler, A.11
-
16
-
-
0033034745
-
Automated genome sequence analysis and annotation
-
Andrade MA, Brown NP, Leroy C, Hoersch S, de Daruvar A, Reich C, Franchini A, Tamames J, Valencia A, Ouzounis C, Sander C: Automated genome sequence analysis and annotation. Bioinformatics 1999, 15:391-412.
-
(1999)
Bioinformatics
, vol.15
, pp. 391-412
-
-
Andrade, M.A.1
Brown, N.P.2
Leroy, C.3
Hoersch, S.4
de Daruvar, A.5
Reich, C.6
Franchini, A.7
Tamames, J.8
Valencia, A.9
Ouzounis, C.10
Sander, C.11
-
17
-
-
13444251422
-
Ensembl 2005
-
Database issue
-
Hubbard T, Andrews D, Caccamo M, Cameron G, Chen Y, Clamp M, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Gilbert J, Hammond M, Herrero J, Hotz H, Howe K, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Kokocinsci F, London D, Longden 1, McVicker G, Melsopp C, Meidl P, Potter S, Proctor G, Rae M, Rios D, Schuster M, Searle S, Severin J, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Birney E: Ensembl 2005. Nucleic Acids Res 2005, 33 Database issue:D447-53.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Hubbard, T.1
Andrews, D.2
Caccamo, M.3
Cameron, G.4
Chen, Y.5
Clamp, M.6
Clarke, L.7
Coates, G.8
Cox, T.9
Cunningham, F.10
Curwen, V.11
Cutts, T.12
Down, T.13
Durbin, R.14
Fernandez-Suarez, X.M.15
Gilbert, J.16
Hammond, M.17
Herrero, J.18
Hotz, H.19
Howe, K.20
Iyer, V.21
Jekosch, K.22
Kahari, A.23
Kasprzyk, A.24
Keefe, D.25
Keenan, S.26
Kokocinsci, F.27
London, D.28
Longden, I.29
McVicker, G.30
Melsopp, C.31
Meidl, P.32
Potter, S.33
Proctor, G.34
Rae, M.35
Rios, D.36
Schuster, M.37
Searle, S.38
Severin, J.39
Slater, G.40
Smedley, D.41
Smith, J.42
Spooner, W.43
Stabenau, A.44
Stalker, J.45
Storey, R.46
Trevanion, S.47
Ureta-Vidal, A.48
Vogel, J.49
White, S.50
Woodwark, C.51
Birney, E.52
more..
-
18
-
-
0037255072
-
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
-
Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin Mj, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 2003, 31:365-370.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 365-370
-
-
Boeckmann, B.1
Bairoch, A.2
Apweiler, R.3
Blatter, M.C.4
Estreicher, A.5
Gasteiger, E.6
Martin, M.J.7
Michoud, K.8
O'Donovan, C.9
Phan, I.10
Pilbout, S.11
Schneider, M.12
-
19
-
-
0037245986
-
The European Bioinformatics Institute's data resources
-
Brooksbank C, Camon E, Harris MA, Magrane M, Martin MJ, Mulder N, O'Donovan C, Parkinson H, Tuli MA, Apweiler R, Birney E, Brazma A, Henrick K, Lopez R, Stoesser G, Stoehr P, Cameron G: The European Bioinformatics Institute's data resources. Nucleic Acids Res 2003, 31:43-50.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 43-50
-
-
Brooksbank, C.1
Camon, E.2
Harris, M.A.3
Magrane, M.4
Martin, M.J.5
Mulder, N.6
O'Donovan, C.7
Parkinson, H.8
Tuli, M.A.9
Apweiler, R.10
Birney, E.11
Brazma, A.12
Henrick, K.13
Lopez, R.14
Stoesser, G.15
Stoehr, P.16
Cameron, G.17
-
20
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman Dj: Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
21
-
-
0036807946
-
Comparative bioinformatic analysis of complete proteomes and protein parameters for cross-species identification in proteomics
-
Lester PJ, Hubbard SJ: Comparative bioinformatic analysis of complete proteomes and protein parameters for cross-species identification in proteomics. Proteomics 2002, 2:1392-1405.
-
(2002)
Proteomics
, vol.2
, pp. 1392-1405
-
-
Lester, P.J.1
Hubbard, S.J.2
-
22
-
-
0035162592
-
The COG database: New developments in phylogenetic classification of proteins from complete genomes
-
Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV: The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 2001, 29:22-28.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 22-28
-
-
Tatusov, R.L.1
Natale, D.A.2
Garkavtsev, I.V.3
Tatusova, T.A.4
Shankavaram, U.T.5
Rao, B.S.6
Kiryutin, B.7
Galperin, M.Y.8
Fedorova, N.D.9
Koonin, E.V.10
-
23
-
-
0345865009
-
GenBank: Update
-
Database issue
-
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL: GenBank: update. Nucleic Acids Res 2004, 32 Database issue:D23-6.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Benson, D.A.1
Karsch-Mizrachi, I.2
Lipman, D.J.3
Ostell, J.4
Wheeler, D.L.5
-
24
-
-
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
-
25
-
-
0033977576
-
WIT: Integrated system for high-throughput genome sequence analysis and metabolic reconstruction
-
Overbeek R, Larsen N, Pusch GD, D'Souza M, Selkov EJ, Kyrpides N, Fonstein M, Maltsev N, Selkov E: WIT: Integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res 2000, 28:123-125.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 123-125
-
-
Overbeek, R.1
Larsen, N.2
Pusch, G.D.3
D'Souza, M.4
Selkov, E.J.5
Kyrpides, N.6
Fonstein, M.7
Maltsev, N.8
Selkov, E.9
-
26
-
-
16544365827
-
Additional paper, computational resources for metabolornics
-
Arita M: Additional paper, computational resources for metabolornics. Brief Funct Genomic Proteomic 2004, 3:84-93.
-
(2004)
Brief Funct Genomic Proteomic
, vol.3
, pp. 84-93
-
-
Arita, M.1
-
27
-
-
0036165418
-
BRENDA: A resource for enzyme data and metabolic information
-
Schomburg I, Chang A, Hofmann O, Ebeling C, Ehrentreich F, Schomburg D: BRENDA. a resource for enzyme data and metabolic information. Trends Biochem Sci 2002, 27:54-56.
-
(2002)
Trends Biochem Sci
, vol.27
, pp. 54-56
-
-
Schomburg, I.1
Chang, A.2
Hofmann, O.3
Ebeling, C.4
Ehrentreich, F.5
Schomburg, D.6
-
28
-
-
0346494819
-
MetaCyc: A multiorganism database of metabolic pathways and enzymes
-
Database issue
-
Krieger CJ, Zhang P, Mueller LA, Wang A, Paley S, Arnaud M, Pick J, Rhee SY, Karp PD: MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res 2004, 32 Database issue:D438-42.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Krieger, C.J.1
Zhang, P.2
Mueller, L.A.3
Wang, A.4
Paley, S.5
Arnaud, M.6
Pick, J.7
Rhee, S.Y.8
Karp, P.D.9
-
29
-
-
84886757766
-
GEM System Database
-
Arakawa K: GEM System Database. [rhttp://www.g-language.org/gem/].
-
-
-
Arakawa, K.1
-
31
-
-
13444262374
-
EcoCyc: A comprehensive database resource for Escherichia coli
-
Database Issue
-
Keseler IM, Collado-Vides J, Gama-Castro S, Ingraham J, Paley S, Paulsen IT, Peralta-Gil M, Karp PD: EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res 2005, 33 Database Issue:D334-7.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Keseler, I.M.1
Collado-Vides, J.2
Gama-Castro, S.3
Ingraham, J.4
Paley, S.5
Paulsen, I.T.6
Peralta-Gil, M.7
Karp, P.D.8
-
32
-
-
0034908282
-
A Java applet for visualizing protein-protein interaction
-
Mrowka R: A Java applet for visualizing protein-protein interaction. Bioinformatics 2001, 17:669-671.
-
(2001)
Bioinformatics
, vol.17
, pp. 669-671
-
-
Mrowka, R.1
-
33
-
-
0033987329
-
Metabolic network analysis. A powerful tool in metabolic engineering
-
Christensen B, Nielsen J: Metabolic network analysis. A powerful tool in metabolic engineering. Adv Biochem Eng Biotechnol 2000, 66:209-231.
-
(2000)
Adv Biochem Eng Biotechnol
, vol.66
, pp. 209-231
-
-
Christensen, B.1
Nielsen, J.2
-
34
-
-
9544253891
-
Palsson BO: Genome-scale models of microbial cells: Evaluating the consequences of constraints
-
Price ND, Reed JL, Palsson BO: Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2004, 2:886-897.
-
(2004)
Nat Rev Microbiol
, vol.2
, pp. 886-897
-
-
Price, N.D.1
Reed, J.L.2
-
35
-
-
26844531259
-
Hybrid dynamic/static method for large-scale simulation of metabolism
-
Yugi K, Nakayama Y, Kinoshita A, Tomita M: Hybrid dynamic/ static method for large-scale simulation of metabolism. Theor Biol Med Model 2005, 2:42.
-
(2005)
Theor Biol Med Model
, vol.2
, pp. 42
-
-
Yugi, K.1
Nakayama, Y.2
Kinoshita, A.3
Tomita, M.4
-
36
-
-
0037316319
-
G-language Genome Analysis Environment: A workbench for nucleotide sequence data mining
-
Arakawa K, Mori K, Ikeda K, Matsuzaki T, Kobayashi Y, Tomita M: G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining. Bioinformotics 2003, 19:305-306.
-
(2003)
Bioinformotics
, vol.19
, pp. 305-306
-
-
Arakawa, K.1
Mori, K.2
Ikeda, K.3
Matsuzaki, T.4
Kobayashi, Y.5
Tomita, M.6
-
37
-
-
24644450611
-
Predicting protein subcellular localization: Past, present, and future
-
Donnes P, Hoglund A: Predicting protein subcellular localization: past, present, and future. Genomics Proteomics Bioinformatics 2004, 2:209-215.
-
(2004)
Genomics Proteomics Bioinformatics
, vol.2
, pp. 209-215
-
-
Donnes, P.1
Hoglund, A.2
-
38
-
-
0033909566
-
Protein sorting signals and prediction of subcellular localization
-
Nakai K: Protein sorting signals and prediction of subcellular localization. Adv Protein Chem 2000, 54:277-344.
-
(2000)
Adv Protein Chem
, vol.54
, pp. 277-344
-
-
Nakai, K.1
|