-
1
-
-
40549127097
-
Design and application of genome-scale reconstructed metabolic models
-
Rocha, I., Förster, J. and Nielsen, J. (2008) Design and application of genome-scale reconstructed metabolic models. Methods Mol. Biol., 416, 409-431.
-
(2008)
Methods Mol. Biol.
, vol.416
, pp. 409-431
-
-
Rocha, I.1
Förster, J.2
Nielsen, J.3
-
2
-
-
58549108388
-
Reconstruction of biochemical networks in microorganisms
-
Feist, A.M., Herrgård, M.J., Thiele, I., Reed, J.L. and Palsson, B.Ø. (2009) Reconstruction of biochemical networks in microorganisms. Nat. Rev. Microbiol., 7, 129-143.
-
(2009)
Nat. Rev. Microbiol.
, vol.7
, pp. 129-143
-
-
Feist, A.M.1
Herrgård, M.J.2
Thiele, I.3
Reed, J.L.4
Palsson B.Ø5
-
3
-
-
75149129569
-
A protocol for generating a high-quality genome-scale metabolic reconstruction
-
Thiele, I. and Palsson, B.Ø. (2010) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat. Protoc., 5, 93-121.
-
(2010)
Nat. Protoc.
, vol.5
, pp. 93-121
-
-
Thiele, I.1
Palsson B.Ø2
-
4
-
-
27144533653
-
Reconstructing the metabolic network of a bacterium from its genome
-
Francke, C., Siezen, R.J. and Teusink, B. (2005) Reconstructing the metabolic network of a bacterium from its genome. Trends Microbiol., 13, 550-558.
-
(2005)
Trends Microbiol.
, vol.13
, pp. 550-558
-
-
Francke, C.1
Siezen, R.J.2
Teusink, B.3
-
5
-
-
84930230737
-
Systems biology in Fungi
-
Paterson, R (ed). CRC Press, Boca Raton
-
Dias, O. and Rocha, I. (2015) Systems Biology in Fungi. In: Paterson, R (ed). Molecular Biology of Food and Water Borne Mycotoxigenic and Mycotic Fungi. CRC Press, Boca Raton, 69-92.
-
(2015)
Molecular Biology of Food and Water Borne Mycotoxigenic and Mycotic Fungi
, pp. 69-92
-
-
Dias, O.1
Rocha, I.2
-
6
-
-
0003450992
-
-
Webb, EC (ed). Academic Press, San Diego
-
Barrett, A.J., Canter, C.R., Liebecq, C., Moss, G.P., Saenger, W., Sharon, N., Tipton, K.F., Vnetianer, P. and Vliegenthart, V.F.G. (1992) In: Webb, EC (ed). Enzyme Nomenclature NC-ICBMB. Academic Press, San Diego.
-
(1992)
Enzyme Nomenclature NC-ICBMB
-
-
Barrett, A.J.1
Canter, C.R.2
Liebecq, C.3
Moss, G.P.4
Saenger, W.5
Sharon, N.6
Tipton, K.F.7
Vnetianer, P.8
Vliegenthart, V.F.G.9
-
7
-
-
33644873454
-
TCDB: The Transporter Classification Database for membrane transport protein analyses and information
-
Saier, M.H., Tran, C.V. and Barabote, R.D. (2006) TCDB: the Transporter Classification Database for membrane transport protein analyses and information. Nucleic Acids Res., 34, D181-D186.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. D181-D186
-
-
Saier, M.H.1
Tran, C.V.2
Barabote, R.D.3
-
8
-
-
84866782417
-
Genome-wide metabolic (re-) annotation of Kluyveromyces lactis
-
Dias, O., Gombert, A.K., Ferreira, E.C. and Rocha, I. (2012) Genome-wide metabolic (re-) annotation of Kluyveromyces lactis. BMC Genomics, 13, 517.
-
(2012)
BMC Genomics
, vol.13
, pp. 517
-
-
Dias, O.1
Gombert, A.K.2
Ferreira, E.C.3
Rocha, I.4
-
9
-
-
34347230891
-
Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence
-
Gundogdu, O., Bentley, S.D., Holden, M.T., Parkhill, J., Dorrell, N. and Wren, B.W. (2007) Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence. BMC Genomics, 8, 162.
-
(2007)
BMC Genomics
, vol.8
, pp. 162
-
-
Gundogdu, O.1
Bentley, S.D.2
Holden, M.T.3
Parkhill, J.4
Dorrell, N.5
Wren, B.W.6
-
10
-
-
0036774642
-
Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv
-
Camus, J.-C., Pryor, M.J., Médigue, C. and Cole, S.T. (2002) Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. Microbiology, 148, 2967-2973.
-
(2002)
Microbiology
, vol.148
, pp. 2967-2973
-
-
Camus, J.-C.1
Pryor, M.J.2
Médigue, C.3
Cole, S.T.4
-
11
-
-
78651330012
-
BRENDA, the enzyme information system in 2011
-
Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Söhngen, C., Stelzer, M., Thiele, J. and Schomburg, D. (2011) BRENDA, the enzyme information system in 2011. Nucleic Acids Res., 39, D670-D676.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D670-D676
-
-
Scheer, M.1
Grote, A.2
Chang, A.3
Schomburg, I.4
Munaretto, C.5
Rother, M.6
Söhngen, C.7
Stelzer, M.8
Thiele, J.9
Schomburg, D.10
-
12
-
-
79961121106
-
BKM-react, an integrated biochemical reaction database
-
Lang, M., Stelzer, M. and Schomburg, D. (2011) BKM-react, an integrated biochemical reaction database. BMC Biochem., 12, 42.
-
(2011)
BMC Biochem.
, vol.12
, pp. 42
-
-
Lang, M.1
Stelzer, M.2
Schomburg, D.3
-
13
-
-
84860490976
-
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
-
Caspi, R., Altman, T., Dreher, K., Fulcher, C.A., Subhraveti, P., Keseler, I.M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L.A. et al. (2012) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res., 40, D742-D753.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D742-D753
-
-
Caspi, R.1
Altman, T.2
Dreher, K.3
Fulcher, C.A.4
Subhraveti, P.5
Keseler, I.M.6
Kothari, A.7
Krummenacker, M.8
Latendresse, M.9
Mueller, L.A.10
-
14
-
-
0033580813
-
Systems properties of the Haemophilus influenzae Rd metabolic genotype
-
Edwards, J.S. and Palsson, B.O. (1999) Systems properties of the Haemophilus influenzae Rd metabolic genotype. J. Biol. Chem., 274, 17410-17416.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 17410-17416
-
-
Edwards, J.S.1
Palsson, B.O.2
-
15
-
-
84856247380
-
FAME, the flux analysis and modeling environment
-
Boele, J., Olivier, B.G. and Teusink, B. (2012) FAME, the Flux Analysis and Modeling Environment. BMC Syst. Biol., 6, 8.
-
(2012)
BMC Syst. Biol.
, vol.6
, pp. 8
-
-
Boele, J.1
Olivier, B.G.2
Teusink, B.3
-
16
-
-
79251546728
-
MEMOSys: Bioinformatics platform for genome-scale metabolic models
-
Pabinger, S., Rader, R., Agren, R., Nielsen, J. and Trajanoski, Z. (2011) MEMOSys: Bioinformatics platform for genome-scale metabolic models. BMC Syst. Biol., 5, 20.
-
(2011)
BMC Syst. Biol.
, vol.5
, pp. 20
-
-
Pabinger, S.1
Rader, R.2
Agren, R.3
Nielsen, J.4
Trajanoski, Z.5
-
17
-
-
84864464109
-
MicrobesFlux: A web platform for drafting metabolic models from the KEGG database
-
Feng, X., Xu, Y., Chen, Y. and Tang, Y.J. (2012) MicrobesFlux: a web platform for drafting metabolic models from the KEGG database. BMC Syst. Biol., 6, 94.
-
(2012)
BMC Syst. Biol.
, vol.6
, pp. 94
-
-
Feng, X.1
Xu, Y.2
Chen, Y.3
Tang, Y.J.4
-
18
-
-
11244328060
-
The pathway tools software
-
Karp, P.D., Paley, S. and Romero, P. (2002) The Pathway Tools software. Bioinformatics, 18 (Suppl. 1), S225-S232.
-
(2002)
Bioinformatics
, vol.18
, pp. S225-S232
-
-
Karp, P.D.1
Paley, S.2
Romero, P.3
-
19
-
-
84895735489
-
Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species
-
Pitkänen, E., Jouhten, P., Hou, J., Syed, M.F., Blomberg, P., Kludas, J., Oja, M., Holm, L., Penttilä, M., Rousu, J. et al. (2014) Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species. PLoS Comput. Biol., 10, e1003465.
-
(2014)
PLoS Comput. Biol.
, vol.10
, pp. e1003465
-
-
Pitkänen, E.1
Jouhten, P.2
Hou, J.3
Syed, M.F.4
Blomberg, P.5
Kludas, J.6
Oja, M.7
Holm, L.8
Penttilä, M.9
Rousu, J.10
-
20
-
-
84875973063
-
The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum
-
Agren, R., Liu, L., Shoaie, S., Vongsangnak, W., Nookaew, I. and Nielsen, J. (2013) The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PLoS Comput. Biol., 9, e1002980.
-
(2013)
PLoS Comput. Biol.
, vol.9
, pp. e1002980
-
-
Agren, R.1
Liu, L.2
Shoaie, S.3
Vongsangnak, W.4
Nookaew, I.5
Nielsen, J.6
-
21
-
-
34248632008
-
Toward the automated generation of genome-scale metabolic networks in the SEED
-
DeJongh, M., Formsma, K., Boillot, P., Gould, J., Rycenga, M. and Best, A. (2007) Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics, 8, 139.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 139
-
-
Dejongh, M.1
Formsma, K.2
Boillot, P.3
Gould, J.4
Rycenga, M.5
Best, A.6
-
22
-
-
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. et al. (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics, 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
-
23
-
-
0032919364
-
KEGG: Kyoto encyclopedia of genes and genomes
-
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H. and Kanehisa, M. (1999) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 27, 29-34.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 29-34
-
-
Ogata, H.1
Goto, S.2
Sato, K.3
Fujibuchi, W.4
Bono, H.5
Kanehisa, M.6
-
24
-
-
77952010788
-
AIBench: A rapid application development framework for translational research in biomedicine
-
Glez-Peña, D., Reboiro-Jato, M., Maia, P., Rocha, M., Díaz, F. and Fdez-Riverola, F. (2010) AIBench: a rapid application development framework for translational research in biomedicine. Comput. Methods Programs Biomed., 98, 191-203.
-
(2010)
Comput. Methods Programs Biomed.
, vol.98
, pp. 191-203
-
-
Glez-Peña, D.1
Reboiro-Jato, M.2
Maia, P.3
Rocha, M.4
Díaz, F.5
Fdez-Riverola, F.6
-
25
-
-
51749088608
-
BioJava: An open-source framework for bioinformatics
-
Holland, R.C.G., Down, T.A., Pocock, M., Prlić, A., Huen, D., James, K., Foisy, S., Dräger, A., Yates, A., Heuer, M. et al. (2008) BioJava: an open-source framework for bioinformatics. Bioinformatics, 24, 2096-2097.
-
(2008)
Bioinformatics
, vol.24
, pp. 2096-2097
-
-
Holland, R.C.G.1
Down, T.A.2
Pocock, M.3
Prlić, A.4
Huen, D.5
James, K.6
Foisy, S.7
Dräger, A.8
Yates, A.9
Heuer, M.10
-
26
-
-
43349101483
-
UniProtJAPI: A remote API for accessing UniProt data
-
Patient, S., Wieser, D., Kleen, M., Kretschmann, E., Martin, M. and Apweiler, R. (2008) UniProtJAPI: a remote API for accessing UniProt data. Bioinformatics, 24, 1321-1322.
-
(2008)
Bioinformatics
, vol.24
, pp. 1321-1322
-
-
Patient, S.1
Wieser, D.2
Kleen, M.3
Kretschmann, E.4
Martin, M.5
Apweiler, R.6
-
27
-
-
79960423002
-
JSBML: A flexible Java library for working with SBML
-
Dräger, A., Rodriguez, N., Dumousseau, M., Dörr, A., Wrzodek, C., Le Novère, N., Zell, A. and Hucka, M. (2011) JSBML: a flexible Java library for working with SBML. Bioinformatics, 27, 2167-2168.
-
(2011)
Bioinformatics
, vol.27
, pp. 2167-2168
-
-
Dräger, A.1
Rodriguez, N.2
Dumousseau, M.3
Dörr, A.4
Wrzodek, C.5
Le Novère, N.6
Zell, A.7
Hucka, M.8
-
28
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 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
-
29
-
-
0031743421
-
Profile hidden markov models
-
Eddy, S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
-
30
-
-
0343603660
-
A functional-phylogenetic classification system for transmembrane solute transporters
-
Saier, M.H. (2000) A functional-phylogenetic classification system for transmembrane solute transporters. Microbiol. Mol. Biol. Rev., 64, 354-411.
-
(2000)
Microbiol. Mol. Biol. Rev.
, vol.64
, pp. 354-411
-
-
Saier, M.H.1
-
31
-
-
0035910270
-
Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
-
Krogh, A., Larsson, B., von Heijne, G. and Sonnhammer, E.L. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol., 305, 567-580.
-
(2001)
J. Mol. Biol.
, vol.305
, pp. 567-580
-
-
Krogh, A.1
Larsson, B.2
Von Heijne, G.3
Sonnhammer, E.L.4
-
32
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
-
(1981)
J. Mol. Biol.
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
33
-
-
77949508535
-
Annotation and merging of SBML models with semanticSBML
-
Krause, F., Uhlendorf, J., Lubitz, T., Schulz, M., Klipp, E. and Liebermeister, W. (2010) Annotation and merging of SBML models with semanticSBML. Bioinformatics, 26, 421-422.
-
(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
-
34
-
-
34547560275
-
WoLF PSORT: Protein localization predictor
-
Horton, P., Park, K.-J., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C.J. and Nakai, K. (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res., 35, W585-W587.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. W585-W587
-
-
Horton, P.1
Park, K.-J.2
Obayashi, T.3
Fujita, N.4
Harada, H.5
Adams-Collier, C.J.6
Nakai, K.7
-
35
-
-
77954199597
-
PSORTb 3.0: Improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes
-
Yu, N.Y., Wagner, J.R., Laird, M.R., Melli, G., Rey, S., Lo, R., Dao, P., Sahinalp, S.C., Ester, M., Foster, L.J. et al. (2010) PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics, 26, 1608-1615.
-
(2010)
Bioinformatics
, vol.26
, pp. 1608-1615
-
-
Yu, N.Y.1
Wagner, J.R.2
Laird, M.R.3
Melli, G.4
Rey, S.5
Lo, R.6
Dao, P.7
Sahinalp, S.C.8
Ester, M.9
Foster, L.J.10
-
37
-
-
28644433993
-
Minimum information requested in the annotation of biochemical models (MIRIAM)
-
Le Novère, N., Finney, A., Hucka, M., Bhalla, U.S., Campagne, F., Collado-Vides, J., Crampin, E.J., Halstead, M., Klipp, E., Mendes, P. et al. (2005) Minimum information requested in the annotation of biochemical models (MIRIAM). Nat. Biotechnol., 23, 1509-1515.
-
(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.J.7
Halstead, M.8
Klipp, E.9
Mendes, P.10
-
38
-
-
77950960250
-
OptFlux: An open-source software platform for in silico metabolic engineering
-
Rocha, I., Maia, P., Evangelista, P., Vilaça, P., Soares, S., Pinto, J.P., Nielsen, J., Patil, K.R., Ferreira, E.C. and Rocha, M. (2010) OptFlux: an open-source software platform for in silico metabolic engineering. BMC Syst. Biol., 4, 45.
-
(2010)
BMC Syst. Biol.
, vol.4
, pp. 45
-
-
Rocha, I.1
Maia, P.2
Evangelista, P.3
Vilaça, P.4
Soares, S.5
Pinto, J.P.6
Nielsen, J.7
Patil, K.R.8
Ferreira, E.C.9
Rocha, M.10
-
39
-
-
84908419443
-
Genome-wide metabolic re-annotation of Ashbya gossypii: New insights into its metabolism through a comparative analysis with Saccharomyces cerevisiae and Kluyveromyces lactis
-
Gomes, D., Aguiar, T.Q., Dias, O., Ferreira, E.C., Domingues, L. and Rocha, I. (2014) Genome-wide metabolic re-annotation of Ashbya gossypii: new insights into its metabolism through a comparative analysis with Saccharomyces cerevisiae and Kluyveromyces lactis. BMC Genomics, 15, 810.
-
(2014)
BMC Genomics
, vol.15
, pp. 810
-
-
Gomes, D.1
Aguiar, T.Q.2
Dias, O.3
Ferreira, E.C.4
Domingues, L.5
Rocha, I.6
-
40
-
-
84902927742
-
Re-annotation of the genome sequence of Helicobacter pylori 26695
-
Resende, T., Correia, D.M., Rocha, M. and Rocha, I. (2013) Re-annotation of the genome sequence of Helicobacter pylori 26695. J. Integr. Bioinform., 10, 233.
-
(2013)
J. Integr. Bioinform.
, vol.10
, pp. 233
-
-
Resende, T.1
Correia, D.M.2
Rocha, M.3
Rocha, I.4
-
41
-
-
84901679540
-
IOD907, the first genome-scale metabolic model for the milk yeast Kluyveromyces lactis
-
Dias, O., Pereira, R., Gombert, A.K., Ferreira, E.C. and Rocha, I. (2014) iOD907, the first genome-scale metabolic model for the milk yeast Kluyveromyces lactis. Biotechnol. J., 9, 776-790.
-
(2014)
Biotechnol. J.
, vol.9
, pp. 776-790
-
-
Dias, O.1
Pereira, R.2
Gombert, A.K.3
Ferreira, E.C.4
Rocha, I.5
-
43
-
-
0032753923
-
Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism
-
Sauer, U., Lasko, D.R., Fiaux, J., Hochuli, M., Glaser, R., Szyperski, T., Wuthrich, K. and Bailey, J.E. (1999) Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism. J. Bacteriol., 181, 6679-6688.
-
(1999)
J. Bacteriol.
, vol.181
, pp. 6679-6688
-
-
Sauer, U.1
Lasko, D.R.2
Fiaux, J.3
Hochuli, M.4
Glaser, R.5
Szyperski, T.6
Wuthrich, K.7
Bailey, J.E.8
|