-
1
-
-
84885776383
-
-
Department of Computer Science, University of Helsinki
-
BMVis graph visualisation tool. Department of Computer Science, University of Helsinki, http://www.cs.helsinki.fi/group/biomine
-
BMVis graph visualisation tool
-
-
-
2
-
-
0030801002
-
Gapped blast and psi-blast: A new generation of protein database search programs
-
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Research 25, 3389-3402 (1997)
-
(1997)
Nucleic Acids Research
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
3
-
-
85048766375
-
-
Version 5.1.0.0 dated 1 May 2004. GNU LGPL (Lesser General Public Licence)
-
Berkelaar, M., Eikland, K., Notebaert, P.: lp solve: Open source (mixed-integer) linear programming system, Multi-platform, pure ANSI C/POSIX source code, Lex/Yacc based parsing. Version 5.1.0.0 dated 1 May 2004. GNU LGPL (Lesser General Public Licence) (2005), http://groups.yahoo.com/group/lp solve
-
(2005)
Lp solve: Open source (mixed-integer) linear programming system, Multi-platform, pure ANSI C/POSIX source code, Lex/Yacc based parsing
-
-
Berkelaar, M.1
Eikland, K.2
Notebaert, P.3
-
4
-
-
15444350252
-
The complete genome sequence of escherichia coli k-12
-
Blattner, F.R., Plunkett 3rd, G., Bloch, C.A., Perna, N.T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J.D., Rode, C.K., Mayhew, G.F., Gregor, J., Davis, N.W., Kirkpatrick, H.A., Goeden, M.A., Rose, D.J., Mau, B., Shao, Y.: The complete genome sequence of escherichia coli k-12. Science 277, 1453-1474 (1997)
-
(1997)
Science
, vol.277
, pp. 1453-1474
-
-
Blattner, F.R.1
Plunkett III, G.2
Bloch, C.A.3
Perna, N.T.4
Burland, V.5
Riley, M.6
Collado-Vides, J.7
Glasner, J.D.8
Rode, C.K.9
Mayhew, G.F.10
Gregor, J.11
Davis, N.W.12
Kirkpatrick, H.A.13
Goeden, M.A.14
Rose, D.J.15
Mau, B.16
Shao, Y.17
-
5
-
-
1242274402
-
Flux coupling analysis of genome-scale metabolic network reconstructions
-
Burgard, A.P., Nikolaev, E.V., Schilling, C.H., Maranas, C.D.: Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Research 14(2), 301-312 (2004)
-
(2004)
Genome Research
, vol.14
, Issue.2
, pp. 301-312
-
-
Burgard, A.P.1
Nikolaev, E.V.2
Schilling, C.H.3
Maranas, C.D.4
-
6
-
-
33644877904
-
Metacyc: A multiorganism database of metabolic pathways and enzymes
-
Caspi, R., Foerster, H., Fulcher, C.A., Hopkinson, R., Ingraham, J., Kaipa, P., Krummenacker, M., Paley, S., Pick, J., Rhee, S.Y., Tissier, C., Zhang, P., Karp, P.D.: Metacyc: A multiorganism database of metabolic pathways and enzymes. Nucleic Acids Research 516, D511-D516 (2006)
-
(2006)
Nucleic Acids Research
, vol.516
-
-
Caspi, R.1
Foerster, H.2
Fulcher, C.A.3
Hopkinson, R.4
Ingraham, J.5
Kaipa, P.6
Krummenacker, M.7
Paley, S.8
Pick, J.9
Rhee, S.Y.10
Tissier, C.11
Zhang, P.12
Karp, P.D.13
-
7
-
-
33745035630
-
Predicting genes for orphan metabolic activities using phylogenetic profiles
-
Chen, L., Vitkup, D.: Predicting genes for orphan metabolic activities using phylogenetic profiles. Genome Biology 7(R17), 1777-1782 (2006)
-
(2006)
Genome Biology
, vol.7
, Issue.R17
, pp. 1777-1782
-
-
Chen, L.1
Vitkup, D.2
-
8
-
-
33846041078
-
The universal protein resource (uniprot)
-
The UniProt Consortium
-
The UniProt Consortium. The universal protein resource (uniprot). Nucleic Acids Research 35, D193-D197 (2007)
-
(2007)
Nucleic Acids Research
, vol.35
-
-
-
9
-
-
0032702286
-
Microbial genomes and "missing" enzymes: Redefining biochemical pathways
-
Cordwell, S.J.: Microbial genomes and "missing" enzymes: redefining biochemical pathways. Arch Microbiol 172, 269-279 (1999)
-
(1999)
Arch Microbiol
, vol.172
, pp. 269-279
-
-
Cordwell, S.J.1
-
10
-
-
4344670936
-
Bow ties, metabolism and disease
-
Csete, M., Doyle, J.: Bow ties, metabolism and disease. TRENDS in Biotechnology 22(9), 446-450 (2004)
-
(2004)
TRENDS in Biotechnology
, vol.22
, Issue.9
, pp. 446-450
-
-
Csete, M.1
Doyle, J.2
-
11
-
-
33846910173
-
Global reconstruction of the human metabolic network based on genomic and bibliomic data
-
Duarte, N., Becker, S., Jamshidi, N., Thiele, I., Mo, M., Vo, T., Srivas, R., Palsson, B.: Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proceedings of National Academy of Science, USA 104(6), 1777-1782 (2007)
-
(2007)
Proceedings of National Academy of Science, USA
, vol.104
, Issue.6
, pp. 1777-1782
-
-
Duarte, N.1
Becker, S.2
Jamshidi, N.3
Thiele, I.4
Mo, M.5
Vo, T.6
Srivas, R.7
Palsson, B.8
-
12
-
-
3843128481
-
Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model
-
Duarte, N., Herrgård, M., Palsson, B.: Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Research 14(7), 1298-1309 (2004)
-
(2004)
Genome Research
, vol.14
, Issue.7
, pp. 1298-1309
-
-
Duarte, N.1
Herrgård, M.2
Palsson, B.3
-
13
-
-
0034625143
-
The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
-
Edwards, J., Palsson, B.: The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proceedings of National Academy of Science, USA 97(10), 5528-5533 (2000)
-
(2000)
Proceedings of National Academy of Science, USA
, vol.97
, Issue.10
, pp. 5528-5533
-
-
Edwards, J.1
Palsson, B.2
-
14
-
-
31544443526
-
Escherichia coli k-12: A cooperatively developed annotation snapshot
-
Riley, M., et al.: Escherichia coli k-12: a cooperatively developed annotation snapshot. Nucleic Acids Res. 34(1), 1-9 (2006)
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.1
, pp. 1-9
-
-
Riley, M.1
-
15
-
-
38549117301
-
The metacyc database of metabolic pathways and enzymes and the biocyc collection of pathway/genome databases
-
Caspi, R., et al.: The metacyc database of metabolic pathways and enzymes and the biocyc collection of pathway/genome databases. Nucleic Acids Research 36(Database issue), 623-631 (2008)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.Database issue
, pp. 623-631
-
-
Caspi, R.1
-
16
-
-
0037313750
-
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
-
Förster, J., Famili, I., Fu, P., Palsson, B., Nielsen, J.: Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Research 13(2), 244-253 (2003)
-
(2003)
Genome Research
, vol.13
, Issue.2
, pp. 244-253
-
-
Förster, J.1
Famili, I.2
Fu, P.3
Palsson, B.4
Nielsen, J.5
-
17
-
-
27144533653
-
Reconstructing the metabolic network of a bacterium from its genome
-
Francke, C., Siezen, R.J., Teusink, B.: Reconstructing the metabolic network of a bacterium from its genome. Trends Microbiol 13(11), 550-558 (2005)
-
(2005)
Trends Microbiol
, vol.13
, Issue.11
, pp. 550-558
-
-
Francke, C.1
Siezen, R.J.2
Teusink, B.3
-
18
-
-
0034084865
-
Who's your neighbor? new computational approaches for functional genomics
-
Galperin, M., Koonin, E.: Who's your neighbor? new computational approaches for functional genomics. Nat. Biotechnol. 18, 609-613 (2000)
-
(2000)
Nat. Biotechnol
, vol.18
, pp. 609-613
-
-
Galperin, M.1
Koonin, E.2
-
19
-
-
13244268322
-
A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases
-
Green, M., Karp, P.D.: A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics 5(76) (2004)
-
(2004)
BMC Bioinformatics
, vol.5
, Issue.76
-
-
Green, M.1
Karp, P.D.2
-
20
-
-
17444382016
-
Exploring the diversity of complex metabolic networks
-
Hatzimanikatis, V., Li, C., Ionita, J.A., Henry, C.S., Jankowski, M.D., Broadbelt, L.J.: Exploring the diversity of complex metabolic networks. Bioinformatics 21(8) (2005)
-
(2005)
Bioinformatics
, vol.21
, Issue.8
-
-
Hatzimanikatis, V.1
Li, C.2
Ionita, J.A.3
Henry, C.S.4
Jankowski, M.D.5
Broadbelt, L.J.6
-
21
-
-
33746660425
-
Identification of genome-scale metabolic network models using experimentally measured flux profiles
-
Herrgård, M., Fong, S., Palsson, B.: Identification of genome-scale metabolic network models using experimentally measured flux profiles. PLoS Computational Biology 2(7), 72 (2006)
-
(2006)
PLoS Computational Biology
, vol.2
, Issue.7
, pp. 72
-
-
Herrgård, M.1
Fong, S.2
Palsson, B.3
-
22
-
-
0003450992
-
-
IUBMB, Academic Press
-
IUBMB. Enzyme Nomenclature. Academic Press (1992)
-
(1992)
Enzyme Nomenclature
-
-
-
23
-
-
11244328060
-
The pathway tools software
-
Karp, P., Paley, S., Romero, P.: The pathway tools software. Bioinformatics 232, S225-S232 (2002)
-
(2002)
Bioinformatics
, vol.232
-
-
Karp, P.1
Paley, S.2
Romero, P.3
-
24
-
-
13444262374
-
EcoCyc: A comprehensive database resource for Escherichia coli
-
Keseler, I.M., Collado-Vides, J., Gama-Castro, S., Ingraham, J., Paley, S., Paulsen, I.T., Peralta-Gil, M., Karp, P.D.: EcoCyc: A comprehensive database resource for Escherichia coli. Nucleic Acids Research 337, D334-D337 (2005)
-
(2005)
Nucleic Acids Research
, vol.337
-
-
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
-
25
-
-
33646171940
-
Identifying metabolic enzymes with multiple types of association evidence
-
Kharchenko, P., Chen, L., Freund, Y., Vitkup, D., Church, G.M.: Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics 7(177) (2006)
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.177
-
-
Kharchenko, P.1
Chen, L.2
Freund, Y.3
Vitkup, D.4
Church, G.M.5
-
26
-
-
24744467372
-
Filling gaps in a metabolic network using expression information
-
Kharchenko, P., Church, G.M., Vitkup, D.: Filling gaps in a metabolic network using expression information. Bioinformatics 185, I178-I185 (2004)
-
(2004)
Bioinformatics
, vol.185
-
-
Kharchenko, P.1
Church, G.M.2
Vitkup, D.3
-
27
-
-
35348893696
-
Metabolite essentiality elucidates robustness of escherichia coli metabolism
-
Kim, P.-J., Lee, D.-Y., Kim, T., Lee, K., Jeong, H., Lee, S., Park, S.: Metabolite essentiality elucidates robustness of escherichia coli metabolism. Proceedings of National Academy of Science, USA 104(34), 13638-13642 (2007)
-
(2007)
Proceedings of National Academy of Science, USA
, vol.104
, Issue.34
, pp. 13638-13642
-
-
Kim, P.-J.1
Lee, D.-Y.2
Kim, T.3
Lee, K.4
Jeong, H.5
Lee, S.6
Park, S.7
-
28
-
-
34547676311
-
Optimization based automated curation of metabolic reconstructions
-
Kumar, V., Dasika, M., Maranas, C.: Optimization based automated curation of metabolic reconstructions. BMC Bioinformatics 8(212), 13638-13642 (2007)
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.212
, pp. 13638-13642
-
-
Kumar, V.1
Dasika, M.2
Maranas, C.3
-
29
-
-
0034027595
-
Computational genetics: Finding protein function by nonhomology methods
-
Marcotte, E.: Computational genetics: finding protein function by nonhomology methods. Curr. Opin. Struct. Biol. 10, 359-365 (2000)
-
(2000)
Curr. Opin. Struct. Biol
, vol.10
, pp. 359-365
-
-
Marcotte, E.1
-
30
-
-
0033918228
-
Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes
-
McGuire, A., Hughes, J., Church, G.: Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res. 10, 744-757 (2000)
-
(2000)
Genome Res
, vol.10
, pp. 744-757
-
-
McGuire, A.1
Hughes, J.2
Church, G.3
-
31
-
-
0037398732
-
Missing genes in metabolic pathways: A comparative genomics approach
-
Osterman, A., Overbeek, R.: Missing genes in metabolic pathways: a comparative genomics approach. Current Opinion in Chemical Biology 7, 238-251 (2003)
-
(2003)
Current Opinion in Chemical Biology
, vol.7
, pp. 238-251
-
-
Osterman, A.1
Overbeek, R.2
-
32
-
-
29544436058
-
An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems
-
Pharkya, P., Maranas, C.D.: An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. Metabolic Engineering 8(1), 1-13 (2006)
-
(2006)
Metabolic Engineering
, vol.8
, Issue.1
, pp. 1-13
-
-
Pharkya, P.1
Maranas, C.D.2
-
33
-
-
33646527159
-
Finding feasible pathways in metabolic networks
-
In: Bozanis, P., Houstis, E.N. (eds.), LNCS, Springer, Heidelberg
-
Pitkänen, E., Rantanen, A., Rousu, J., Ukkonen, E.: Finding feasible pathways in metabolic networks. In: Bozanis, P., Houstis, E.N. (eds.) PCI 2005. LNCS, vol. 3746, pp. 123-133. Springer, Heidelberg (2005)
-
(2005)
PCI 2005
, vol.3746
, pp. 123-133
-
-
Pitkänen, E.1
Rantanen, A.2
Rousu, J.3
Ukkonen, E.4
-
34
-
-
35748961978
-
Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli
-
Resendis-Antonio, O., Reed, J., Encarnación, S., Collado-Vides, J., Palsson, B.: Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli. PLoS Computational Biology 3(10), 13638-13642 (2007)
-
(2007)
PLoS Computational Biology
, vol.3
, Issue.10
, pp. 13638-13642
-
-
Resendis-Antonio, O.1
Reed, J.2
Encarnación, S.3
Collado-Vides, J.4
Palsson, B.5
-
35
-
-
0034615791
-
Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective
-
Schilling, C.H., Letscher, D., Palsson, B.: Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. Journal of Theoretical Biology 203(3), 228-248 (2003)
-
(2003)
Journal of Theoretical Biology
, vol.203
, Issue.3
, pp. 228-248
-
-
Schilling, C.H.1
Letscher, D.2
Palsson, B.3
-
36
-
-
0034064689
-
A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic network
-
Schuster, S., Fell, D.A., Dandekar, T.: A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic network. Nature Biotechnology 18, 326-332 (2000)
-
(2000)
Nature Biotechnology
, vol.18
, pp. 326-332
-
-
Schuster, S.1
Fell, D.A.2
Dandekar, T.3
-
37
-
-
0037079050
-
Metabolic network structure determines key aspects of functionality and regulation
-
Stelling, J., Klamt, S., Bettenbrock, K., Schuster, S., Gilles, E.D.: Metabolic network structure determines key aspects of functionality and regulation. Nature 420, 190-193 (2002)
-
(2002)
Nature
, vol.420
, pp. 190-193
-
-
Stelling, J.1
Klamt, S.2
Bettenbrock, K.3
Schuster, S.4
Gilles, E.D.5
-
39
-
-
0035085816
-
Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context
-
Wolf, Y., Rogozin, I., Kondrashov, A., Koonin, E.: Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res. 11, 356-372 (2001)
-
(2001)
Genome Res
, vol.11
, pp. 356-372
-
-
Wolf, Y.1
Rogozin, I.2
Kondrashov, A.3
Koonin, E.4
|