-
1
-
-
0027501810
-
Control analysis of microbial interactions in continuous culture: a simulation study
-
doi: 10.1099/00221287-139-10-2309
-
Allison, S. M., Small, J. R., Kacser, H., and Prosser, J. I. (1993). Control analysis of microbial interactions in continuous culture: a simulation study. J. Gen. Microbiol. 139, 2309-2317. doi: 10.1099/00221287-139-10-2309.
-
(1993)
J. Gen. Microbiol.
, vol.139
, pp. 2309-2317
-
-
Allison, S.M.1
Small, J.R.2
Kacser, H.3
Prosser, J.I.4
-
2
-
-
80052687169
-
Is analysing the nitrogen use at the plant canopy level a matter of choosing the right optimization criterion?
-
doi: 10.1007/s00442-011-2011-3
-
Anten, N. P. R., and During, H. J. (2011). Is analysing the nitrogen use at the plant canopy level a matter of choosing the right optimization criterion? Oecologia 167, 293-303. doi: 10.1007/s00442-011-2011-3.
-
(2011)
Oecologia
, vol.167
, pp. 293-303
-
-
Anten, N.P.R.1
During, H.J.2
-
3
-
-
0036042278
-
Network-based selectivity of antiparasitic inhibitors
-
doi: 10.1023/A:1020397513646
-
Bakker, B. M., Assmus, H. E., Bruggeman, F., Haanstra, J. R., Klipp, E., and Westerhoff, H. (2002). Network-based selectivity of antiparasitic inhibitors. Mol. Biol. Rep. 29, 1-5. doi: 10.1023/A:1020397513646.
-
(2002)
Mol. Biol. Rep.
, vol.29
, pp. 1-5
-
-
Bakker, B.M.1
Assmus, H.E.2
Bruggeman, F.3
Haanstra, J.R.4
Klipp, E.5
Westerhoff, H.6
-
4
-
-
0033591259
-
What controls glycolysis in bloodstream form Trypanosoma brucei?
-
doi: 10.1074/jbc.274.21.14551
-
Bakker, B. M., Michels, P. A. M., Opperdoes, F. R., and Westerhoff, H. V. (1999). What controls glycolysis in bloodstream form Trypanosoma brucei? J. Biol. Chem. 274, 14551-14559. doi: 10.1074/jbc.274.21.14551.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 14551-14559
-
-
Bakker, B.M.1
Michels, P.A.M.2
Opperdoes, F.R.3
Westerhoff, H.V.4
-
5
-
-
44949225040
-
Context-specific metabolic networks are consistent with experiments
-
doi: 10.1371/journal.pcbi.1000082
-
Becker, S. A., and Palsson, B. O. (2008). Context-specific metabolic networks are consistent with experiments. PLoS Comput. Biol. 4:e1000082. doi: 10.1371/journal.pcbi.1000082.
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Becker, S.A.1
Palsson, B.O.2
-
6
-
-
34547887655
-
Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity
-
doi: 10.1073/pnas.0609845104
-
Beg, Q. K., Vazquez, A., Ernst, J., De Menezes, M. A., Bar-Joseph, Z., Barabasi, A. L., et al. (2007). Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity. Proc. Nat. Acad. Sci. U.S.A. 104, 12663-12668. doi: 10.1073/pnas.0609845104.
-
(2007)
Proc. Nat. Acad. Sci. U.S.A.
, vol.104
, pp. 12663-12668
-
-
Beg, Q.K.1
Vazquez, A.2
Ernst, J.3
De Menezes, M.A.4
Bar-Joseph, Z.5
Barabasi, A.L.6
-
7
-
-
84856247380
-
FAME, the flux analysis and modeling environment
-
doi: 10.1186/1752-0509-6-8
-
Boele, J., Olivier, B. G., and Teusink, B. (2012). FAME, the flux analysis and modeling environment. BMC Syst. Biol. 6:8. doi: 10.1186/1752-0509-6-8.
-
(2012)
BMC Syst. Biol.
, vol.6
, pp. 8
-
-
Boele, J.1
Olivier, B.G.2
Teusink, B.3
-
8
-
-
59649085782
-
Topological signatures of species interactions in metabolic networks
-
doi: 10.1089/cmb.2008.06TT
-
Borenstein, E., and Feldman, M. W. (2009). Topological signatures of species interactions in metabolic networks. J. Comput. Biol. 16, 191-200. doi: 10.1089/cmb.2008.06TT.
-
(2009)
J. Comput. Biol.
, vol.16
, pp. 191-200
-
-
Borenstein, E.1
Feldman, M.W.2
-
9
-
-
55749087868
-
Large-scale reconstruction and phylogenetic analysis of metabolic environments
-
doi: 10.1073/pnas.0806162105
-
Borenstein, E., Kupiec, M., Feldman, M. W., and Ruppin, E. (2008). Large-scale reconstruction and phylogenetic analysis of metabolic environments. Proc. Natl. Acad. Sci. U.S.A. 105, 14482-14487. doi: 10.1073/pnas.0806162105.
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 14482-14487
-
-
Borenstein, E.1
Kupiec, M.2
Feldman, M.W.3
Ruppin, E.4
-
10
-
-
77953597713
-
Hydrocarbon-degrading bacteria: the oil-spill clean-up crew
-
doi: 10.1111/j.1751-7915.2009.00151.x
-
Brooijmans, R. J. W., Pastink, M. I., and Siezen, S. J. (2009). Hydrocarbon-degrading bacteria: the oil-spill clean-up crew. Microb. Biotechnol. 2, 587-594. doi: 10.1111/j.1751-7915.2009.00151.x.
-
(2009)
Microb. Biotechnol.
, vol.2
, pp. 587-594
-
-
Brooijmans, R.J.W.1
Pastink, M.I.2
Siezen, S.J.3
-
11
-
-
33846017352
-
The nature of systems biology
-
doi: 10.1016/j.tim.2006.11.003
-
Bruggeman, F. J., and Westerhoff, H. V. (2007). The nature of systems biology. Trends Microbiol. 15, 45-50. doi: 10.1016/j.tim.2006.11.003.
-
(2007)
Trends Microbiol.
, vol.15
, pp. 45-50
-
-
Bruggeman, F.J.1
Westerhoff, H.V.2
-
12
-
-
77956311544
-
Tracking hydrocarbon plume transport and biodegradation at deepwater horizon
-
doi: 10.1126/science.1195223
-
Camilli, R., Reddy, C. M., Yoerger, D. R., Van Mooy, B. A. S., Jakuba, M. V., Kinsey, J. C., et al. (2010). Tracking hydrocarbon plume transport and biodegradation at deepwater horizon. Science 330, 201-204. doi: 10.1126/science.1195223.
-
(2010)
Science
, vol.330
, pp. 201-204
-
-
Camilli, R.1
Reddy, C.M.2
Yoerger, D.R.3
Van Mooy, B.A.S.4
Jakuba, M.V.5
Kinsey, J.C.6
-
13
-
-
34447317252
-
Metabolic systems cost-benefit analysis for interpreting network structure and regulation
-
doi: 10.1093/bioinformatics/btm082
-
Carlson, R. P. (2007). Metabolic systems cost-benefit analysis for interpreting network structure and regulation. Bioinformatics 23, 1258-1264. doi: 10.1093/bioinformatics/btm082.
-
(2007)
Bioinformatics
, vol.23
, pp. 1258-1264
-
-
Carlson, R.P.1
-
14
-
-
77954238817
-
A global network of coexisting microbes from environmental and whole-genome sequence data
-
doi: 10.1101/gr.104521.109
-
Chaffron, S., Rehrauer, H., Pernthaler, J., and Von Mering, C. (2010). A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res. 20, 947-959. doi: 10.1101/gr.104521.109.
-
(2010)
Genome Res.
, vol.20
, pp. 947-959
-
-
Chaffron, S.1
Rehrauer, H.2
Pernthaler, J.3
Von Mering, C.4
-
15
-
-
78049255973
-
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis
-
doi: 10.1073/pnas.1005139107
-
Chandrasekaran, S., and Price, N. D. (2010). Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. U.S.A. 107, 17845-17850. doi: 10.1073/pnas.1005139107.
-
(2010)
Proc. Natl. Acad. Sci. U.S.A.
, vol.107
, pp. 17845-17850
-
-
Chandrasekaran, S.1
Price, N.D.2
-
16
-
-
2342648924
-
Integrating high-throughput and computational data elucidates bacterial networks
-
doi: 10.1038/nature02456
-
Covert, M. W., Knight, E. M., Reed, J. L., Herrgard, M. J., and Palsson, B. O. (2004). Integrating high-throughput and computational data elucidates bacterial networks. Nature 429, 92-96. doi: 10.1038/nature02456.
-
(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
-
17
-
-
35648972123
-
The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels
-
doi: 10.1073/pnas.0707476104
-
Daran-Lapujade, P., Rossell, S., Van Gulik, W. M., Luttik, M. A. H., De Groot, M. J. L., Slijper, M., et al. (2007). The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels. Proc. Natl. Acad. Sci. U.S.A. 104, 15753-15758. doi: 10.1073/pnas.0707476104.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 15753-15758
-
-
Daran-Lapujade, P.1
Rossell, S.2
Van Gulik, W.M.3
Luttik, M.A.H.4
De Groot, M.J.L.5
Slijper, M.6
-
18
-
-
75149180930
-
Profiling human gut bacterial metabolism and its kinetics using [U-C-13]glucose and NMR
-
doi: 10.1002/nbm.1418
-
De Graaf, A. A., Maathuis, A., De Waard, P., Deutz, N. E. P., Dijkema, C., De Vos, W. M., et al. (2010). Profiling human gut bacterial metabolism and its kinetics using [U-C-13]glucose and NMR. NMR Biomed. 23, 2-12. doi: 10.1002/nbm.1418.
-
(2010)
NMR Biomed.
, vol.23
, pp. 2-12
-
-
De Graaf, A.A.1
Maathuis, A.2
De Waard, P.3
Deutz, N.E.P.4
Dijkema, C.5
De Vos, W.M.6
-
19
-
-
79955015975
-
DNA-, rRNA- and mRNA-based stable isotope probing of aerobic methanotrophs in lake sediment
-
doi: 10.1111/j.1462-2920.2010.02415.x
-
Dumont, M. G., Pommerenke, B., Casper, P., and Conrad, R. (2011). DNA-, rRNA- and mRNA-based stable isotope probing of aerobic methanotrophs in lake sediment. Environ. Microbiol. 13, 1153-1167. doi: 10.1111/j.1462-2920.2010.02415.x.
-
(2011)
Environ. Microbiol.
, vol.13
, pp. 1153-1167
-
-
Dumont, M.G.1
Pommerenke, B.2
Casper, P.3
Conrad, R.4
-
20
-
-
0028797101
-
Cycloclasticus pugetii gen-nov, sp-nov, an aromatic hydrocarbon-degrading bacterium from marine sediments
-
doi: 10.1099/00207713-45-1-116
-
Dyksterhouse, S. E., Gray, J. P., Herwig, R. P., Lara, J. C., and Staley, J. T. (1995). Cycloclasticus pugetii gen-nov, sp-nov, an aromatic hydrocarbon-degrading bacterium from marine sediments. Int. J. Syst. Bacteriol. 45, 116-123. doi: 10.1099/00207713-45-1-116.
-
(1995)
Int. J. Syst. Bacteriol.
, vol.45
, pp. 116-123
-
-
Dyksterhouse, S.E.1
Gray, J.P.2
Herwig, R.P.3
Lara, J.C.4
Staley, J.T.5
-
21
-
-
78650306221
-
Stoichiogenomics: the evolutionary ecology of macromolecular elemental composition
-
doi: 10.1016/j.tree.2010.10.006
-
Elser, J. J., Acquisti, C., and Kumar, S. (2011). Stoichiogenomics: the evolutionary ecology of macromolecular elemental composition. Trends Ecol. Evol. 26, 38-44. doi: 10.1016/j.tree.2010.10.006.
-
(2011)
Trends Ecol. Evol.
, vol.26
, pp. 38-44
-
-
Elser, J.J.1
Acquisti, C.2
Kumar, S.3
-
22
-
-
78650311629
-
Influence of four major plant traits on average height, leaf-area cover net primary productivity, and biomass density in single-species forests: a theoretical investigation
-
doi: 10.1111/j.1365-2745.2010.01735.x
-
Falster, D. S., Brannstrom, A., Dieckmann, U., and Westoby, M. (2012). Influence of four major plant traits on average height, leaf-area cover net primary productivity, and biomass density in single-species forests: a theoretical investigation. J. Ecol. 99, 148-164. doi: 10.1111/j.1365-2745.2010.01735.x.
-
(2012)
J. Ecol.
, vol.99
, pp. 148-164
-
-
Falster, D.S.1
Brannstrom, A.2
Dieckmann, U.3
Westoby, M.4
-
23
-
-
4344698259
-
Distributed control in ecological networks
-
doi: 10.1016/j.ecolmodel.2004.06.007
-
Fath, B. D. (2004). Distributed control in ecological networks. Ecol. Modell. 179, 235-245. doi: 10.1016/j.ecolmodel.2004.06.007.
-
(2004)
Ecol. Modell.
, vol.179
, pp. 235-245
-
-
Fath, B.D.1
-
24
-
-
84863920287
-
Microbial interactions: from networks to models
-
doi: 10.1038/nrmicro2832
-
Faust, K., and Raes, J. (2012). Microbial interactions: from networks to models. Nat. Rev. Microbiol. 10, 538-550. doi: 10.1038/nrmicro2832.
-
(2012)
Nat. Rev. Microbiol.
, vol.10
, pp. 538-550
-
-
Faust, K.1
Raes, J.2
-
25
-
-
34347332311
-
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
-
doi: 10.1038/msb4100155
-
Feist, A. M., Henry, C. S., Reed, J. L., Krummenacker, M., Joyce, A. R., Karp, P. D., et al. (2007). A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol. Syst. Biol. 3:121. doi: 10.1038/msb4100155.
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 121
-
-
Feist, A.M.1
Henry, C.S.2
Reed, J.L.3
Krummenacker, M.4
Joyce, A.R.5
Karp, P.D.6
-
26
-
-
58549108388
-
Reconstruction of biochemical networks in microorganisms
-
doi: 10.1038/nrmicro1949
-
Feist, A. M., Herrgard, M. J., Thiele, I., Reed, J. L., and Palsson, B. O. (2009). Reconstruction of biochemical networks in microorganisms. Nat. Rev. Microbiol. 7, 129-143. doi: 10.1038/nrmicro1949.
-
(2009)
Nat. Rev. Microbiol.
, vol.7
, pp. 129-143
-
-
Feist, A.M.1
Herrgard, M.J.2
Thiele, I.3
Reed, J.L.4
Palsson, B.O.5
-
27
-
-
65549102552
-
Fixation and fate of C and N in the cyanobacterium Trichodesmium using nanometer-scale secondary ion mass spectrometry
-
doi: 10.1073/pnas.0810547106
-
Finzi-Hart, J. A., Pett-Ridge, J., Weber, P. K., Popa, R., Fallon, S. J., Gunderson, T., et al. (2009). Fixation and fate of C and N in the cyanobacterium Trichodesmium using nanometer-scale secondary ion mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 106, 6345-6350. doi: 10.1073/pnas.0810547106.
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 6345-6350
-
-
Finzi-Hart, J.A.1
Pett-Ridge, J.2
Weber, P.K.3
Popa, R.4
Fallon, S.J.5
Gunderson, T.6
-
28
-
-
67649470562
-
Metabolic-network-driven analysis of bacterial ecological strategies
-
doi: 10.1186/gb-2009-10-6-r61
-
Freilich, S., Kreimer, A., Borenstein, E., Yosef, N., Sharan, R., Gophna, U., et al. (2009). Metabolic-network-driven analysis of bacterial ecological strategies. Genome Biol. 10:R61. doi: 10.1186/gb-2009-10-6-r61.
-
(2009)
Genome Biol.
, vol.10
-
-
Freilich, S.1
Kreimer, A.2
Borenstein, E.3
Yosef, N.4
Sharan, R.5
Gophna, U.6
-
29
-
-
77954241658
-
The large-scale organization of the bacterial network of ecological co-occurrence interactions
-
doi: 10.1093/nar/gkq118
-
Freilich, S., Kreimer, A., Meilijson, I., Gophna, U., Sharan, R., and Ruppin, E. (2010). The large-scale organization of the bacterial network of ecological co-occurrence interactions. Nucleic Acids Res. 38, 3857-3868. doi: 10.1093/nar/gkq118.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 3857-3868
-
-
Freilich, S.1
Kreimer, A.2
Meilijson, I.3
Gophna, U.4
Sharan, R.5
Ruppin, E.6
-
30
-
-
66149150877
-
Microbial community structure and its functional implications
-
doi: 10.1038/nature08058
-
Fuhrman, J. A. (2009). Microbial community structure and its functional implications. Nature 459, 193-199. doi: 10.1038/nature08058.
-
(2009)
Nature
, vol.459
, pp. 193-199
-
-
Fuhrman, J.A.1
-
31
-
-
0347365859
-
Control analysis of trophic chains
-
doi: 10.1016/S0304-3800(03)00208-4
-
Getz, W. M., Westerhoff, H. V., Hofmeyr, J. H. S., and Snoep, J. L. (2003). Control analysis of trophic chains. Ecol. Modell. 168, 153-171. doi: 10.1016/S0304-3800(03)00208-4.
-
(2003)
Ecol. Modell.
, vol.168
, pp. 153-171
-
-
Getz, W.M.1
Westerhoff, H.V.2
Hofmeyr, J.H.S.3
Snoep, J.L.4
-
32
-
-
43649084234
-
An environmental perspective on metabolism
-
doi: 10.1016/j.jtbi.2007.10.036
-
Handorf, T., Christian, N., Ebenhoh, O., and Kahn, D. (2008). An environmental perspective on metabolism. J. Theor. Biol. 252, 530-537. doi: 10.1016/j.jtbi.2007.10.036.
-
(2008)
J. Theor. Biol.
, vol.252
, pp. 530-537
-
-
Handorf, T.1
Christian, N.2
Ebenhoh, O.3
Kahn, D.4
-
33
-
-
77956299931
-
Deep-sea oil plume enriches indigenous oil-degrading bacteria
-
doi: 10.1126/science.1195979
-
Hazen, T. C., Dubinsky, E. A., Desantis, T. Z., Andersen, G. L., Piceno, Y. M., Singh, N., et al. (2010). Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 330, 204-208. doi: 10.1126/science.1195979.
-
(2010)
Science
, vol.330
, pp. 204-208
-
-
Hazen, T.C.1
Dubinsky, E.A.2
Desantis, T.Z.3
Andersen, G.L.4
Piceno, Y.M.5
Singh, N.6
-
34
-
-
33645994824
-
Marine microorganisms make a meal of oil
-
doi: 10.1038/nrmicro1348
-
Head, I. M., Jones, D. M., and Röling, W. F. M. (2006). Marine microorganisms make a meal of oil. Nat. Rev. Microb. 4, 173-182. doi: 10.1038/nrmicro1348.
-
(2006)
Nat. Rev. Microb.
, vol.4
, pp. 173-182
-
-
Head, I.M.1
Jones, D.M.2
Röling, W.F.M.3
-
35
-
-
33847797256
-
Thermodynamics-based metabolic flux analysis
-
doi: 10.1529/biophysj.106.093138
-
Henry, C. S., Broadbelt, L. J., and Hatzimanikatis, V. (2007). Thermodynamics-based metabolic flux analysis. Biophys. J. 92, 1792-1805. doi: 10.1529/biophysj.106.093138.
-
(2007)
Biophys. J.
, vol.92
, pp. 1792-1805
-
-
Henry, C.S.1
Broadbelt, L.J.2
Hatzimanikatis, V.3
-
36
-
-
77956696072
-
High-throughput generation, optimization and analysis of genome-scale metabolic models
-
doi: 10.1038/nbt.1672
-
Henry, C. S., Dejongh, M., Best, A. A., Frybarger, P. M., Linsay, B., and Stevens, R. L. (2010). High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat. Biotechnol. 28, 977-U922. doi: 10.1038/nbt.1672.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 922-977
-
-
Henry, C.S.1
Dejongh, M.2
Best, A.A.3
Frybarger, P.M.4
Linsay, B.5
Stevens, R.L.6
-
37
-
-
0036229317
-
Metabolic engineering of lactic acid bacteria, the combined approach: kinetic modelling, metabolic control and experimental analysis
-
Hoefnagel, M. H. N., Starrenburg, M. J. C., Martens, D. E., Hugenholtz, J., Kleerebezem, M., Van Swam, I. I., et al. (2002). Metabolic engineering of lactic acid bacteria, the combined approach: kinetic modelling, metabolic control and experimental analysis. Microbiology 148, 1003-1013.
-
(2002)
Microbiology
, vol.148
, pp. 1003-1013
-
-
Hoefnagel, M.H.N.1
Starrenburg, M.J.C.2
Martens, D.E.3
Hugenholtz, J.4
Kleerebezem, M.5
Van Swam, I.I.6
-
38
-
-
50549104615
-
Geobacter sulfurreducens strain engineered for increased rates of respiration
-
doi: 10.1016/j.ymben.2008.06.005
-
Izallalen, M., Mahadevan, R., Burgard, A., Postier, B., Didonato, R., Sun, J., et al. (2008). Geobacter sulfurreducens strain engineered for increased rates of respiration. Metab. Eng. 10, 267-275. doi: 10.1016/j.ymben.2008.06.005.
-
(2008)
Metab. Eng.
, vol.10
, pp. 267-275
-
-
Izallalen, M.1
Mahadevan, R.2
Burgard, A.3
Postier, B.4
Didonato, R.5
Sun, J.6
-
39
-
-
67149131864
-
Comparison of methods for simultaneous identification of bacterial species and determination of metabolic activity by protein-based stable isotope probing (Protein-SIP) experiments
-
doi: 10.1002/rcm.4084
-
Jehmlich, N., Schmidt, F., Taubert, M., Seifert, J., Von Bergen, M., Richnow, H. H., et al. (2009). Comparison of methods for simultaneous identification of bacterial species and determination of metabolic activity by protein-based stable isotope probing (Protein-SIP) experiments. Rapid Commun. Mass Spectrom. 23, 1871-1878. doi: 10.1002/rcm.4084.
-
(2009)
Rapid Commun. Mass Spectrom.
, vol.23
, pp. 1871-1878
-
-
Jehmlich, N.1
Schmidt, F.2
Taubert, M.3
Seifert, J.4
Von Bergen, M.5
Richnow, H.H.6
-
40
-
-
85013930125
-
-
Amsterdam: Elsevier
-
Jørgensen, S. E., Fath, B., Bastianoni, S., Marques, J., Muller, F., Nielsen, S. N., et al. (eds.). (2007). A New Ecology: Systems Perspective. Amsterdam: Elsevier.
-
(2007)
A New Ecology: Systems Perspective
-
-
Jørgensen, S.E.1
Fath, B.2
Bastianoni, S.3
Marques, J.4
Muller, F.5
Nielsen, S.N.6
-
41
-
-
0029055565
-
The control of flux
-
Kacser, H., Burns, J. A., and Fell, D. A. (1995). The control of flux. Biochem. Soc. Trans. 23, 341-366.
-
(1995)
Biochem. Soc. Trans.
, vol.23
, pp. 341-366
-
-
Kacser, H.1
Burns, J.A.2
Fell, D.A.3
-
42
-
-
0036951676
-
Rhodanobacter sp. strain BPC1 in a benzo[a]pyrene-mineralizing bacterial consortium
-
doi: 10.1128/AEM.68.12.5826-5833.2002
-
Kanaly, R. A., Harayama, S., and Watanabe, K. (2002). Rhodanobacter sp. strain BPC1 in a benzo[a]pyrene-mineralizing bacterial consortium. Appl. Environ. Microbiol. 68, 5826-5833. doi: 10.1128/AEM.68.12.5826-5833.2002.
-
(2002)
Appl. Environ. Microbiol.
, vol.68
, pp. 5826-5833
-
-
Kanaly, R.A.1
Harayama, S.2
Watanabe, K.3
-
43
-
-
84866090747
-
Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks
-
doi: 10.1038/srep00580
-
Kelk, S. M., Olivier, B. G., Stougie, L., and Bruggeman, F. J. (2012). Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks. Sci. Rep. 2:e580. doi: 10.1038/srep00580.
-
(2012)
Sci. Rep.
, vol.2
-
-
Kelk, S.M.1
Olivier, B.G.2
Stougie, L.3
Bruggeman, F.J.4
-
44
-
-
84878575301
-
Community flux balance analysis for microbial consortia at balanced growth
-
doi: 10.1371/journal.pone.0064567
-
Khandelwal, R. A., Olivier, B. G., Röling, W. F. M., Teusink, B., and Bruggeman, F. J. (2013). Community flux balance analysis for microbial consortia at balanced growth. PLoS ONE 8:10. doi: 10.1371/journal.pone.0064567.
-
(2013)
PLoS ONE
, vol.8
, pp. 10
-
-
Khandelwal, R.A.1
Olivier, B.G.2
Röling, W.F.M.3
Teusink, B.4
Bruggeman, F.J.5
-
45
-
-
77952404373
-
Maximum entropy production in environmental and ecological systems
-
doi: 10.1098/rstb.2010.0018
-
Kleidon, A., Malhi, Y., and Cox, P. M. (2010). Maximum entropy production in environmental and ecological systems. Philos. Trans. R. Soc. B Biol. Sci. 365, 1297-1302. doi: 10.1098/rstb.2010.0018.
-
(2010)
Philos. Trans. R. Soc. B Biol. Sci.
, vol.365
, pp. 1297-1302
-
-
Kleidon, A.1
Malhi, Y.2
Cox, P.M.3
-
46
-
-
0031719199
-
Growth kinetics of suspended microbial cells: from single-substrate-controlled growth to mixed-substrate kinetics
-
Kovarova-Kovar, K., and Egli, T. (1998). Growth kinetics of suspended microbial cells: from single-substrate-controlled growth to mixed-substrate kinetics. Microbiol. Mol. Biol. Rev. 62, 646-666.
-
(1998)
Microbiol. Mol. Biol. Rev.
, vol.62
, pp. 646-666
-
-
Kovarova-Kovar, K.1
Egli, T.2
-
47
-
-
63849262393
-
Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing
-
doi: 10.1111/j.1462-2920.2008.01815.x
-
Kovatcheva-Datchary, P., Egert, M., Maathuis, A., Rajilic-Stojanovic, M., De Graaf, A. A., Smidt, H., et al. (2009). Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing. Environ. Microbiol. 11, 914-926. doi: 10.1111/j.1462-2920.2008.01815.x.
-
(2009)
Environ. Microbiol.
, vol.11
, pp. 914-926
-
-
Kovatcheva-Datchary, P.1
Egert, M.2
Maathuis, A.3
Rajilic-Stojanovic, M.4
De Graaf, A.A.5
Smidt, H.6
-
48
-
-
15844368293
-
The evolution of groups of cooperating bacteria and the growth rate versus yield trade-off
-
doi: 10.1099/mic.0.27415-0
-
Kreft, J. U., and Bonhoeffer, S. (2005). The evolution of groups of cooperating bacteria and the growth rate versus yield trade-off. Microbiology 151, 637-641. doi: 10.1099/mic.0.27415-0.
-
(2005)
Microbiology
, vol.151
, pp. 637-641
-
-
Kreft, J.U.1
Bonhoeffer, S.2
-
49
-
-
80052333923
-
Polycyclic aromatic hydrocarbon metabolic network in Mycobacterium vanbaalenii PYR-1
-
doi: 10.1128/JB.00215-11
-
Kweon, O., Kim, S.-J., Holland, R. D., Chen, H., Kim, D.-W., Gao, Y., et al. (2011). Polycyclic aromatic hydrocarbon metabolic network in Mycobacterium vanbaalenii PYR-1. J. Bacteriol. 193, 4326-4337. doi: 10.1128/JB.00215-11.
-
(2011)
J. Bacteriol.
, vol.193
, pp. 4326-4337
-
-
Kweon, O.1
Kim, S.-J.2
Holland, R.D.3
Chen, H.4
Kim, D.-W.5
Gao, Y.6
-
50
-
-
84884127512
-
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
-
doi: 10.1038/nbt.2676
-
Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., et al. (2013). Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 31, 814-821. doi: 10.1038/nbt.2676.
-
(2013)
Nat. Biotechnol.
, vol.31
, pp. 814-821
-
-
Langille, M.G.I.1
Zaneveld, J.2
Caporaso, J.G.3
McDonald, D.4
Knights, D.5
Reyes, J.A.6
-
51
-
-
84867102878
-
A predictive model of community assembly that incorporates intraspecific trait variation
-
doi: 10.1111/j.1461-0248.2012.01852.x
-
Laughlin, D. C., Joshi, C., van Bodegom, P. M., Bastow, Z. A., and Fule, P. Z. (2012). A predictive model of community assembly that incorporates intraspecific trait variation. Ecol. Lett. 15, 1291-1299. doi: 10.1111/j.1461-0248.2012.01852.x.
-
(2012)
Ecol. Lett.
, vol.15
, pp. 1291-1299
-
-
Laughlin, D.C.1
Joshi, C.2
van Bodegom, P.M.3
Bastow, Z.A.4
Fule, P.Z.5
-
52
-
-
84855964551
-
Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume
-
doi: 10.1038/ismej.2011.91
-
Lu, Z. M., Deng, Y., Van Nostrand, J. D., He, Z. L., Voordeckers, J., Zhou, A. F., et al. (2012). Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume. ISME J. 6, 451-460. doi: 10.1038/ismej.2011.91.
-
(2012)
ISME J.
, vol.6
, pp. 451-460
-
-
Lu, Z.M.1
Deng, Y.2
Van Nostrand, J.D.3
He, Z.L.4
Voordeckers, J.5
Zhou, A.F.6
-
53
-
-
33747348104
-
Identification of bacterial micropredators distinctively active in a soil microbial food web
-
doi: 10.1128/AEM.00400-06
-
Lueders, T., Kindler, R., Miltner, A., Friedrich, M. W., and Kaestner, M. (2006). Identification of bacterial micropredators distinctively active in a soil microbial food web. Appl. Environ. Microbiol. 72, 5342-5348. doi: 10.1128/AEM.00400-06.
-
(2006)
Appl. Environ. Microbiol.
, vol.72
, pp. 5342-5348
-
-
Lueders, T.1
Kindler, R.2
Miltner, A.3
Friedrich, M.W.4
Kaestner, M.5
-
54
-
-
0036708443
-
Dynamic flux balance analysis of diauxic growth in Escherichia coli
-
doi: 10.1016/S0006-3495(02)73903-9
-
Mahadevan, R., Edwards, J. S., and Doyle, F. J. (2002). Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophys. J. 83, 1331-1340. doi: 10.1016/S0006-3495(02)73903-9.
-
(2002)
Biophys. J.
, vol.83
, pp. 1331-1340
-
-
Mahadevan, R.1
Edwards, J.S.2
Doyle, F.J.3
-
55
-
-
84865318505
-
Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill
-
doi: 10.1038/ismej.2012.59
-
Mason, O. U., Hazen, T. C., Borglin, S., Chain, P. S. G., Dubinsky, E. A., Fortney, J. L., et al. (2012). Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. ISME J. 6, 1715-1727. doi: 10.1038/ismej.2012.59.
-
(2012)
ISME J.
, vol.6
, pp. 1715-1727
-
-
Mason, O.U.1
Hazen, T.C.2
Borglin, S.3
Chain, P.S.G.4
Dubinsky, E.A.5
Fortney, J.L.6
-
56
-
-
21244452656
-
Off the hook-how bacteria survive protozoan grazing
-
doi: 10.1016/j.tim.2005.05.009
-
Matz, C., and Kjelleberg, S. (2005). Off the hook-how bacteria survive protozoan grazing. Trends Microbiol. 13, 302-307. doi: 10.1016/j.tim.2005.05.009.
-
(2005)
Trends Microbiol.
, vol.13
, pp. 302-307
-
-
Matz, C.1
Kjelleberg, S.2
-
57
-
-
67349255256
-
Trade-offs between efficiency and robustness in bacterial metabolic networks are associated with niche breadth
-
doi: 10.1007/s00239-009-9226-5
-
Morine, M. J., Gu, H., Myers, R. A., and Bielawski, J. P. (2009). Trade-offs between efficiency and robustness in bacterial metabolic networks are associated with niche breadth. J. Mol. Evol. 68, 506-515. doi: 10.1007/s00239-009-9226-5.
-
(2009)
J. Mol. Evol.
, vol.68
, pp. 506-515
-
-
Morine, M.J.1
Gu, H.2
Myers, R.A.3
Bielawski, J.P.4
-
58
-
-
0000568637
-
Bioavailability of energy and its relationship to growth and starvation survival in nature
-
doi: 10.1139/m88-076
-
Morita, R. Y. (1988). Bioavailability of energy and its relationship to growth and starvation survival in nature. Can. J. Microbiol. 34, 436-441. doi: 10.1139/m88-076.
-
(1988)
Can. J. Microbiol.
, vol.34
, pp. 436-441
-
-
Morita, R.Y.1
-
59
-
-
77953254182
-
Functional single-cell analyses: flow cytometry and cell sorting of microbial populations and communities
-
doi: 10.1111/j.1574-6976.2010.00214.x
-
Muller, S., and Nebe-Von-Caron, G. (2010). Functional single-cell analyses: flow cytometry and cell sorting of microbial populations and communities. FEMS Microbiol. Rev. 34, 554-587. doi: 10.1111/j.1574-6976.2010.00214.x.
-
(2010)
FEMS Microbiol. Rev.
, vol.34
, pp. 554-587
-
-
Muller, S.1
Nebe-Von-Caron, G.2
-
60
-
-
56649097491
-
A single-cell view on the ecophysiology of anaerobic phototrophic bacteria
-
doi: 10.1073/pnas.0809329105
-
Musat, N., Halm, H., Winterholler, B., Hoppe, P., Peduzzi, S., Hillion, F., et al. (2008). A single-cell view on the ecophysiology of anaerobic phototrophic bacteria. Proc. Natl. Acad. Sci. U.S.A. 105, 17861-17866. doi: 10.1073/pnas.0809329105.
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 17861-17866
-
-
Musat, N.1
Halm, H.2
Winterholler, B.3
Hoppe, P.4
Peduzzi, S.5
Hillion, F.6
-
61
-
-
0037347176
-
Quantification of cell-specific substrate uptake by probe-defined bacteria under in situ conditions by microautoradiography and fluorescence in situ hybridization
-
doi: 10.1046/j.1462-2920.2003.00402.x
-
Nielsen, J. L., Christensen, D., Kloppenborg, M., and Nielsen, P. H. (2003). Quantification of cell-specific substrate uptake by probe-defined bacteria under in situ conditions by microautoradiography and fluorescence in situ hybridization. Environ. Microbiol. 5, 202-211. doi: 10.1046/j.1462-2920.2003.00402.x.
-
(2003)
Environ. Microbiol.
, vol.5
, pp. 202-211
-
-
Nielsen, J.L.1
Christensen, D.2
Kloppenborg, M.3
Nielsen, P.H.4
-
62
-
-
6344262034
-
Linking flow cytometric cell sorting and compound-specific C-13-analysis to determine population-specific isotopic signatures and growth rates in cyanobacteria-dominated lake plankton
-
doi: 10.1111/j.1529-8817.2004.03176.x
-
Pel, R., Floris, V., Gons, H. J., and Hoogveld, H. L. (2004). Linking flow cytometric cell sorting and compound-specific C-13-analysis to determine population-specific isotopic signatures and growth rates in cyanobacteria-dominated lake plankton. J. Phycol. 40, 857-866. doi: 10.1111/j.1529-8817.2004.03176.x.
-
(2004)
J. Phycol.
, vol.40
, pp. 857-866
-
-
Pel, R.1
Floris, V.2
Gons, H.J.3
Hoogveld, H.L.4
-
63
-
-
0033108071
-
Towards elucidation of microbial community metabolic pathways: unravelling the network of carbon sharing in a pollutant-degrading bacterial consortium by immunocapture and isotopic ratio mass spectrometry
-
doi: 10.1046/j.1462-2920.1999.00023.x
-
Pelz, O., Tesar, M., Wittich, R. M., Moore, E. R. B., Timmis, K. N., and Abraham, W. R. (1999). Towards elucidation of microbial community metabolic pathways: unravelling the network of carbon sharing in a pollutant-degrading bacterial consortium by immunocapture and isotopic ratio mass spectrometry. Environ. Microbiol. 1, 167-174. doi: 10.1046/j.1462-2920.1999.00023.x.
-
(1999)
Environ. Microbiol.
, vol.1
, pp. 167-174
-
-
Pelz, O.1
Tesar, M.2
Wittich, R.M.3
Moore, E.R.B.4
Timmis, K.N.5
Abraham, W.R.6
-
64
-
-
71449096836
-
Strategies for cellular decision-making
-
doi: 10.1038/msb.2009.83
-
Perkins, T. J., and Swain, P. S. (2009). Strategies for cellular decision-making. Mol. Syst. Biol. 5:326. doi: 10.1038/msb.2009.83.
-
(2009)
Mol. Syst. Biol.
, vol.5
, pp. 326
-
-
Perkins, T.J.1
Swain, P.S.2
-
65
-
-
11844280852
-
Game-theoretical approaches to studying the evolution of biochemical systems
-
doi: 10.1016/j.tibs.2004.11.006
-
Pfeiffer, T., and Schuster, S. (2005). Game-theoretical approaches to studying the evolution of biochemical systems. Trends Biochem. Sci. 30, 20-25. doi: 10.1016/j.tibs.2004.11.006.
-
(2005)
Trends Biochem. Sci.
, vol.30
, pp. 20-25
-
-
Pfeiffer, T.1
Schuster, S.2
-
66
-
-
0035917865
-
Cooperation and competition in the evolution of ATP-producing pathways
-
doi: 10.1126/science.1058079
-
Pfeiffer, T., Schuster, S., and Bonhoeffer, S. (2001). Cooperation and competition in the evolution of ATP-producing pathways. Science 292, 504-507. doi: 10.1126/science.1058079.
-
(2001)
Science
, vol.292
, pp. 504-507
-
-
Pfeiffer, T.1
Schuster, S.2
Bonhoeffer, S.3
-
67
-
-
27944446350
-
Maximum entropy modeling of species geographic distributions
-
doi: 10.1016/j.ecolmodel.2005.03.026
-
Phillips, S. J., Anderson, R. P., and Schapire, R. E. (2006). Maximum entropy modeling of species geographic distributions. Ecol. Modell. 190, 231-259. doi: 10.1016/j.ecolmodel.2005.03.026.
-
(2006)
Ecol. Modell.
, vol.190
, pp. 231-259
-
-
Phillips, S.J.1
Anderson, R.P.2
Schapire, R.E.3
-
68
-
-
80052609854
-
Electron acceptor-dependent identification of key anaerobic toluene degraders at a tar-oil-contaminated aquifer by Pyro-SIP
-
doi: 10.1111/j.1574-6941.2011.01083.x
-
Pilloni, G., Von Netzer, F., Engel, M., and Lueders, T. (2011). Electron acceptor-dependent identification of key anaerobic toluene degraders at a tar-oil-contaminated aquifer by Pyro-SIP. FEMS Microbiol. Ecol. 78, 165-175. doi: 10.1111/j.1574-6941.2011.01083.x.
-
(2011)
FEMS Microbiol. Ecol.
, vol.78
, pp. 165-175
-
-
Pilloni, G.1
Von Netzer, F.2
Engel, M.3
Lueders, T.4
-
69
-
-
0343035686
-
Stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirements
-
doi: 10.1002/(SICI)1097-0290(19971120)56:4%3C398::AID-BIT6%3E3.3.CO;2-F
-
Pramanik, J., and Keasling, J. D. (1997). Stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirements. Biotechnol. Bioeng. 56, 398-421. doi: 10.1002/(SICI)1097-0290(19971120)56:4%3C398::AID-BIT6%3E3.3.CO;2-F.
-
(1997)
Biotechnol. Bioeng.
, vol.56
, pp. 398-421
-
-
Pramanik, J.1
Keasling, J.D.2
-
70
-
-
0032552815
-
Effect of Escherichia coli biomass composition on central metabolic fluxes predicted by a stoichiometric model
-
Pramanik, J., and Keasling, J. D. (1998). Effect of Escherichia coli biomass composition on central metabolic fluxes predicted by a stoichiometric model. Biotechnol. Bioeng. 60, 230-238.
-
(1998)
Biotechnol. Bioeng.
, vol.60
, pp. 230-238
-
-
Pramanik, J.1
Keasling, J.D.2
-
71
-
-
85019470992
-
Think before you sequence
-
Prosser, J. I. (2013). Think before you sequence. Nature 494, 41-41.
-
(2013)
Nature
, vol.494
, pp. 41-41
-
-
Prosser, J.I.1
-
72
-
-
34247221045
-
The role of ecological theory in microbial ecology
-
doi: 10.1038/nrmicro1643
-
Prosser, J. I., Bohannan, B. J. M., Curtis, T. P., Ellis, R. J., Firestone, M. K., Freckleton, R. P., et al. (2007). The role of ecological theory in microbial ecology. Nat. Rev. Microbiol. 5, 384-392. doi: 10.1038/nrmicro1643.
-
(2007)
Nat. Rev. Microbiol.
, vol.5
, pp. 384-392
-
-
Prosser, J.I.1
Bohannan, B.J.M.2
Curtis, T.P.3
Ellis, R.J.4
Firestone, M.K.5
Freckleton, R.P.6
-
73
-
-
49649089054
-
Molecular eco-systems biology: towards an understanding of community function
-
doi: 10.1038/nrmicro1935
-
Raes, J., and Bork, P. (2008). Molecular eco-systems biology: towards an understanding of community function. Nat. Rev. Microbiol. 6, 693-699. doi: 10.1038/nrmicro1935.
-
(2008)
Nat. Rev. Microbiol.
, vol.6
, pp. 693-699
-
-
Raes, J.1
Bork, P.2
-
74
-
-
79953232381
-
Thermodynamics of microbial growth coupled to metabolism of glucose, ethanol, short-chain organic acids, and hydrogen
-
doi: 10.1128/AEM.02425-10
-
Roden, E. E., and Jin, Q. S. (2011). Thermodynamics of microbial growth coupled to metabolism of glucose, ethanol, short-chain organic acids, and hydrogen. Appl. Environ. Microbiol. 77, 1907-1909. doi: 10.1128/AEM.02425-10.
-
(2011)
Appl. Environ. Microbiol.
, vol.77
, pp. 1907-1909
-
-
Roden, E.E.1
Jin, Q.S.2
-
75
-
-
35349030830
-
Do microbial numbers count? Quantifying the regulation of biogeochemical fluxes by population size and cellular activity
-
doi: 10.1111/j.1574-6941.2007.00350.x
-
Röling, W. F. M. (2007). Do microbial numbers count? Quantifying the regulation of biogeochemical fluxes by population size and cellular activity. FEMS Microbiol. Ecol. 62, 202-210. doi: 10.1111/j.1574-6941.2007.00350.x.
-
(2007)
FEMS Microbiol. Ecol.
, vol.62
, pp. 202-210
-
-
Röling, W.F.M.1
-
76
-
-
77956647726
-
Systems approaches to microbial communities and their functioning
-
doi: 10.1016/j.copbio.2010.06.007
-
Röling, W. F. M., Ferrer, M., and Golyshin, P. N. (2010). Systems approaches to microbial communities and their functioning. Curr. Opin. Biotechnol. 21, 532-538. doi: 10.1016/j.copbio.2010.06.007.
-
(2010)
Curr. Opin. Biotechnol.
, vol.21
, pp. 532-538
-
-
Röling, W.F.M.1
Ferrer, M.2
Golyshin, P.N.3
-
77
-
-
0036840898
-
Robust hydrocarbon degradation and dynamics of bacterial communities during nutrient-enhanced oil spill bioremediation
-
doi: 10.1128/AEM.68.11.5537-5548.2002
-
Röling, W. F. M., Milner, M. G., Jones, D. M., Lee, K., Daniel, F., Swannell, R. J. P., et al. (2002). Robust hydrocarbon degradation and dynamics of bacterial communities during nutrient-enhanced oil spill bioremediation. Appl. Environ. Microbiol. 68, 5537-5548. doi: 10.1128/AEM.68.11.5537-5548.2002.
-
(2002)
Appl. Environ. Microbiol.
, vol.68
, pp. 5537-5548
-
-
Röling, W.F.M.1
Milner, M.G.2
Jones, D.M.3
Lee, K.4
Daniel, F.5
Swannell, R.J.P.6
-
78
-
-
33846088428
-
Ecological control analysis: being(s) in control of mass flux and metabolite concentrations in anaerobic degradation processes
-
doi: 10.1111/j.1462-2920.2006.01167.x
-
Röling, W. F. M., Van Breukelen, B. M., Bruggeman, F. J., and Westerhoff, H. V. (2007). Ecological control analysis: being(s) in control of mass flux and metabolite concentrations in anaerobic degradation processes. Environ. Microbiol. 9, 500-511. doi: 10.1111/j.1462-2920.2006.01167.x.
-
(2007)
Environ. Microbiol.
, vol.9
, pp. 500-511
-
-
Röling, W.F.M.1
Van Breukelen, B.M.2
Bruggeman, F.J.3
Westerhoff, H.V.4
-
79
-
-
33846061120
-
Metabolic networks in motion: C-13-based flux analysis
-
doi: 10.1038/msb4100109
-
Sauer, U. (2006). Metabolic networks in motion: C-13-based flux analysis. Mol. Sys. Biol. 2, 62. doi: 10.1038/msb4100109.
-
(2006)
Mol. Sys. Biol.
, vol.2
, pp. 62
-
-
Sauer, U.1
-
80
-
-
69849084132
-
Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation
-
doi: 10.1111/j.1751-7915.2009.00087.x
-
Scheibe, T. D., Mahadevan, R., Fang, Y., Garg, S., Long, P. E., and Lovley, D. R. (2009). Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation. Microb. Biotech. 2, 274-286. doi: 10.1111/j.1751-7915.2009.00087.x.
-
(2009)
Microb. Biotech.
, vol.2
, pp. 274-286
-
-
Scheibe, T.D.1
Mahadevan, R.2
Fang, Y.3
Garg, S.4
Long, P.E.5
Lovley, D.R.6
-
81
-
-
33747043510
-
Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis
-
doi: 10.1038/nbt1232
-
Schneiker, S., Dos Santos, V., Bartels, D., Bekel, T., Brecht, M., Buhrmester, J., et al. (2006). Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat. Biotechnol. 24, 997-1004. doi: 10.1038/nbt1232.
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 997-1004
-
-
Schneiker, S.1
Dos Santos, V.2
Bartels, D.3
Bekel, T.4
Brecht, M.5
Buhrmester, J.6
-
82
-
-
84876522835
-
BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA
-
doi: 10.1093/nar/gks1049
-
Schomburg, I., Chang, A., Placzek, S., Sohngen, C., Rother, M., Lang, M., et al. (2013). BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. Nucleic Acids Res. 41, D764-D772. doi: 10.1093/nar/gks1049.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Schomburg, I.1
Chang, A.2
Placzek, S.3
Sohngen, C.4
Rother, M.5
Lang, M.6
-
83
-
-
34447523907
-
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
-
doi: 10.1038/msb4100162
-
Schuetz, R., Kuepfer, L., and Sauer, U. (2007). Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol. Syst. Biol. 3, 119. doi: 10.1038/msb4100162.
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 119
-
-
Schuetz, R.1
Kuepfer, L.2
Sauer, U.3
-
84
-
-
84860487758
-
Multidimensional optimality of microbial metabolism
-
doi: 10.1126/science.1216882
-
Schuetz, R., Zamboni, N., Zampieri, M., Heinemann, M., and Sauer, U. (2012). Multidimensional optimality of microbial metabolism. Science 336, 601-604. doi: 10.1126/science.1216882.
-
(2012)
Science
, vol.336
, pp. 601-604
-
-
Schuetz, R.1
Zamboni, N.2
Zampieri, M.3
Heinemann, M.4
Sauer, U.5
-
85
-
-
43449132092
-
Is maximization of molar yield in metabolic networks favoured by evolution?
-
doi: 10.1016/j.jtbi.2007.12.008
-
Schuster, S., Pfeiffer, T., and Fell, D. A. (2008). Is maximization of molar yield in metabolic networks favoured by evolution? J. Theor. Biol. 252, 497-504. doi: 10.1016/j.jtbi.2007.12.008.
-
(2008)
J. Theor. Biol.
, vol.252
, pp. 497-504
-
-
Schuster, S.1
Pfeiffer, T.2
Fell, D.A.3
-
86
-
-
77951570815
-
Forces that influence the evolution of codon bias
-
doi: 10.1098/rstb.2009.0305
-
Sharp, P. M., Emery, L. R., and Zeng, K. (2010). Forces that influence the evolution of codon bias. Philos. Trans. R. Soc. B Biol. Sci. 365, 1203-1212. doi: 10.1098/rstb.2009.0305.
-
(2010)
Philos. Trans. R. Soc. B Biol. Sci.
, vol.365
, pp. 1203-1212
-
-
Sharp, P.M.1
Emery, L.R.2
Zeng, K.3
-
87
-
-
33750723839
-
From plant traits to plant communities: a statistical mechanistic approach to biodiversity
-
doi: 10.1126/science.1131344
-
Shipley, B., Vile, D., and Garnier, E. (2006). From plant traits to plant communities: a statistical mechanistic approach to biodiversity. Science 314, 812-814. doi: 10.1126/science.1131344.
-
(2006)
Science
, vol.314
, pp. 812-814
-
-
Shipley, B.1
Vile, D.2
Garnier, E.3
-
88
-
-
51349092391
-
Network-based prediction of human tissue-specific metabolism
-
doi: 10.1038/nbt.1487
-
Shlomi, T., Cabili, M. N., Herrgard, M. J., Palsson, B. O., and Ruppin, E. (2008). Network-based prediction of human tissue-specific metabolism. Nat. Biotechnol. 26, 1003-1010. doi: 10.1038/nbt.1487.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1003-1010
-
-
Shlomi, T.1
Cabili, M.N.2
Herrgard, M.J.3
Palsson, B.O.4
Ruppin, E.5
-
89
-
-
33947276100
-
Metabolic modeling of a mutualistic microbial community
-
doi: 10.1038/msb4100131
-
Stolyar, S., Van Dien, S., Hillesland, K. L., Pinel, N., Lie, T. J., Leigh, J. A., et al. (2007). Metabolic modeling of a mutualistic microbial community. Mol. Syst. Biol. 3, 92. doi: 10.1038/msb4100131.
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 92
-
-
Stolyar, S.1
Van Dien, S.2
Hillesland, K.L.3
Pinel, N.4
Lie, T.J.5
Leigh, J.A.6
-
90
-
-
0015910716
-
Theoretical study on amount of atp required for synthesis of microbial cell material
-
doi: 10.1007/BF02578899
-
Stouthamer, A. H. (1973). Theoretical study on amount of atp required for synthesis of microbial cell material. Antonie Van Leeuwenhoek 39, 545-565. doi: 10.1007/BF02578899.
-
(1973)
Antonie Van Leeuwenhoek
, vol.39
, pp. 545-565
-
-
Stouthamer, A.H.1
-
91
-
-
74049119822
-
In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study
-
doi: 10.1186/1752-0509-3-114
-
Taffs, R., Aston, J. E., Brileya, K., Jay, Z., Klatt, C. G., McGlynn, S., et al. (2009). In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study. BMC Syst. Biol. 3:114. doi: 10.1186/1752-0509-3-114.
-
(2009)
BMC Syst. Biol.
, vol.3
, pp. 114
-
-
Taffs, R.1
Aston, J.E.2
Brileya, K.3
Jay, Z.4
Klatt, C.G.5
McGlynn, S.6
-
92
-
-
33846912964
-
Shewanella oneidensis MR-1 fluxome under various oxygen conditions
-
doi: 10.1128/AEM.01532-06
-
Tang, Y. J., Hwang, J. S., Wemmer, D. E., and Keasling, J. D. (2007). Shewanella oneidensis MR-1 fluxome under various oxygen conditions. Appl. Environ. Microbiol. 73, 718-729. doi: 10.1128/AEM.01532-06.
-
(2007)
Appl. Environ. Microbiol.
, vol.73
, pp. 718-729
-
-
Tang, Y.J.1
Hwang, J.S.2
Wemmer, D.E.3
Keasling, J.D.4
-
93
-
-
60549117294
-
Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central carbon metabolism
-
doi: 10.1002/bit.22129
-
Tang, Y. J., Martin, H. G., Dehal, P. S., Deutschbauer, A., Llora, X., Meadows, A., et al. (2009). Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central carbon metabolism. Biotech. Bioeng. 102, 1161-1169. doi: 10.1002/bit.22129.
-
(2009)
Biotech. Bioeng.
, vol.102
, pp. 1161-1169
-
-
Tang, Y.J.1
Martin, H.G.2
Dehal, P.S.3
Deutschbauer, A.4
Llora, X.5
Meadows, A.6
-
94
-
-
0035816464
-
Transcriptome meets metabolome: hierarchical and metabolic regulation of the glycolytic pathway
-
doi: 10.1016/S0014-5793(01)02613-8
-
Ter Kuile, B. H., and Westerhoff, H. V. (2001). Transcriptome meets metabolome: hierarchical and metabolic regulation of the glycolytic pathway. FEBS Lett. 500, 169-171. doi: 10.1016/S0014-5793(01)02613-8.
-
(2001)
FEBS Lett.
, vol.500
, pp. 169-171
-
-
Ter Kuile, B.H.1
Westerhoff, H.V.2
-
95
-
-
0027909730
-
A thermodynamically based correlation for maintenance gibbs energy-requirements in aerobic and anaerobic chemotropic growth
-
doi: 10.1002/bit.260420415
-
Tijhuis, L., Vanloosdrecht, M. C. M., and Heijnen, J. J. (1993). A thermodynamically based correlation for maintenance gibbs energy-requirements in aerobic and anaerobic chemotropic growth. Biotechnol. Bioeng. 42, 509-519. doi: 10.1002/bit.260420415.
-
(1993)
Biotechnol. Bioeng.
, vol.42
, pp. 509-519
-
-
Tijhuis, L.1
Vanloosdrecht, M.C.M.2
Heijnen, J.J.3
-
96
-
-
33748781707
-
Exergy, information and aggradation: an ecosystems reconciliation
-
doi: 10.1016/j.ecolmodel.2006.06.004
-
Ulanowicz, R. E., Jorgensen, S. E., and Fath, B. D. (2006). Exergy, information and aggradation: an ecosystems reconciliation. Ecol. Modell. 198, 520-524. doi: 10.1016/j.ecolmodel.2006.06.004.
-
(2006)
Ecol. Modell.
, vol.198
, pp. 520-524
-
-
Ulanowicz, R.E.1
Jorgensen, S.E.2
Fath, B.D.3
-
97
-
-
79952769971
-
Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging
-
doi: 10.1073/pnas.1101134108
-
Valm, A. M., Welch, J. L. M., Rieken, C. W., Hasegawa, Y., Sogin, M. L., Oldenbourg, R., et al. (2011). Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging. Proc. Natl. Acad. Sci. U.S.A. 108, 4152-4157. doi: 10.1073/pnas.1101134108.
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 4152-4157
-
-
Valm, A.M.1
Welch, J.L.M.2
Rieken, C.W.3
Hasegawa, Y.4
Sogin, M.L.5
Oldenbourg, R.6
-
98
-
-
34248582999
-
Microbial maintenance: a critical review on its quantification
-
doi: 10.1007/s00248-006-9049-5
-
Van Bodegom, P. (2007). Microbial maintenance: a critical review on its quantification. Microb. Ecol. 53, 513-523. doi: 10.1007/s00248-006-9049-5.
-
(2007)
Microb. Ecol.
, vol.53
, pp. 513-523
-
-
Van Bodegom, P.1
-
99
-
-
0036439074
-
Evaluation of methods to predict bacterial yield using thermodynamics
-
doi: 10.1023/A:1020887214879
-
Vanbriesen, J. M. (2002). Evaluation of methods to predict bacterial yield using thermodynamics. Biodegradation 13, 171-190. doi: 10.1023/A:1020887214879.
-
(2002)
Biodegradation
, vol.13
, pp. 171-190
-
-
Vanbriesen, J.M.1
-
100
-
-
38749088283
-
Assessing nutrient limitation of Prochlorococcus in the North Pacific subtropical gyre by using an RNA capture method
-
doi: 10.4319/lo.2008.53.1.0078
-
Van Mooy, B. A. S., and Devol, A. H. (2008). Assessing nutrient limitation of Prochlorococcus in the North Pacific subtropical gyre by using an RNA capture method. Limnol. Oceanogr. 53, 78-88. doi: 10.4319/lo.2008.53.1.0078.
-
(2008)
Limnol. Oceanogr.
, vol.53
, pp. 78-88
-
-
Van Mooy, B.A.S.1
Devol, A.H.2
-
101
-
-
4644275488
-
Quantifying H-3-thymidine incorporation rates by a phylogenetically defined group of marine planktonic bacteria (Bacteriodetes phylum)
-
doi: 10.1111/j.1462-2920.2004.00636.x
-
Van Mooy, B. A. S., Devol, A. H., and Keil, R. G. (2004). Quantifying H-3-thymidine incorporation rates by a phylogenetically defined group of marine planktonic bacteria (Bacteriodetes phylum). Environ. Microbiol. 6, 1061-1069. doi: 10.1111/j.1462-2920.2004.00636.x.
-
(2004)
Environ. Microbiol.
, vol.6
, pp. 1061-1069
-
-
Van Mooy, B.A.S.1
Devol, A.H.2
Keil, R.G.3
-
102
-
-
0021365651
-
Eubacteria have 3 growth modes keyed to nutrient flow:consequences for the concept of maintenance and maximal growth yield
-
doi: 10.1007/BF00414463
-
Van Verseveld, H. W., Chesbro, W. R., Braster, M., and Stouthamer, A. H. (1984). Eubacteria have 3 growth modes keyed to nutrient flow:consequences for the concept of maintenance and maximal growth yield. Arch. Microbiol. 137, 176-184. doi: 10.1007/BF00414463.
-
(1984)
Arch. Microbiol.
, vol.137
, pp. 176-184
-
-
Van Verseveld, H.W.1
Chesbro, W.R.2
Braster, M.3
Stouthamer, A.H.4
-
103
-
-
76749155783
-
The systemic imprint of growth and its uses in ecological (Meta) genomics
-
doi: 10.1371/journal.pgen.1000808
-
Vieira-Silva, S., and Rocha, E. P. C. (2010). The systemic imprint of growth and its uses in ecological (Meta) genomics. PLoS Genet. 6:e1000808. doi: 10.1371/journal.pgen.1000808.
-
(2010)
PLoS Genet.
, vol.6
-
-
Vieira-Silva, S.1
Rocha, E.P.C.2
-
104
-
-
0020687005
-
Thermodynamic efficiency of microbial-growth is low but optimal for maximal growth-rate
-
doi: 10.1073/pnas.80.1.305
-
Westerhoff, H. V., Hellingwerf, K. J., and Vandam, K. (1983). Thermodynamic efficiency of microbial-growth is low but optimal for maximal growth-rate. Proc. Natl. Acad. Sci. U.S.A. 80, 305-309. doi: 10.1073/pnas.80.1.305.
-
(1983)
Proc. Natl. Acad. Sci. U.S.A.
, vol.80
, pp. 305-309
-
-
Westerhoff, H.V.1
Hellingwerf, K.J.2
Vandam, K.3
-
105
-
-
0031778521
-
Alcanivorax borkumensis gen. nov., sp. nov., a new, hydrocarbon-degrading and surfactant-producing marine bacterium
-
doi: 10.1099/00207713-48-2-339
-
Yakimov, M. M., Golyshin, P. N., Lang, S., Moore, E. R. B., Abraham, W. R., Lunsdorf, H., et al. (1998). Alcanivorax borkumensis gen. nov., sp. nov., a new, hydrocarbon-degrading and surfactant-producing marine bacterium. Int. J. Syst. Bacteriol. 48, 339-348. doi: 10.1099/00207713-48-2-339.
-
(1998)
Int. J. Syst. Bacteriol.
, vol.48
, pp. 339-348
-
-
Yakimov, M.M.1
Golyshin, P.N.2
Lang, S.3
Moore, E.R.B.4
Abraham, W.R.5
Lunsdorf, H.6
-
106
-
-
79955787125
-
Single-cell genomics reveals organismal interactions in uncultivated marine protists
-
doi: 10.1126/science.1203163
-
Yoon, H. S., Price, D. C., Stepanauskas, R., Rajah, V. D., Sieracki, M. E., Wilson, W. H., et al. (2011). Single-cell genomics reveals organismal interactions in uncultivated marine protists. Science 332, 714-717. doi: 10.1126/science.1203163.
-
(2011)
Science
, vol.332
, pp. 714-717
-
-
Yoon, H.S.1
Price, D.C.2
Stepanauskas, R.3
Rajah, V.D.4
Sieracki, M.E.5
Wilson, W.H.6
-
107
-
-
84859907317
-
A road map for the development of community systems (CoSy) biology
-
doi: 10.1038/nrmicro2763
-
Zengler, K., and Palsson, B. O. (2012). A road map for the development of community systems (CoSy) biology. Nat. Rev. Microbiol. 10, 366-372. doi: 10.1038/nrmicro2763.
-
(2012)
Nat. Rev. Microbiol.
, vol.10
, pp. 366-372
-
-
Zengler, K.1
Palsson, B.O.2
-
108
-
-
78751584992
-
Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments
-
doi: 10.1038/ismej.2010.117
-
Zhuang, K., Izallalen, M., Mouser, P., Richter, H., Risso, C., Mahadevan, R., et al. (2011). Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments. ISME J. 5, 305-316. doi: 10.1038/ismej.2010.117.
-
(2011)
ISME J.
, vol.5
, pp. 305-316
-
-
Zhuang, K.1
Izallalen, M.2
Mouser, P.3
Richter, H.4
Risso, C.5
Mahadevan, R.6
-
109
-
-
84870775587
-
Relationships between kinetic constants and amino acid composition of enzymes from the yeast Saccharomyces cerevisiae glycolysis pathway
-
doi: 10.1186/1687-4153-2012-11
-
Zikmanis, P., and Kampenusa, I. (2012). Relationships between kinetic constants and amino acid composition of enzymes from the yeast Saccharomyces cerevisiae glycolysis pathway. EURASIP J. Bioinform. Syst. Biol. 1:11. doi: 10.1186/1687-4153-2012-11.
-
(2012)
EURASIP J. Bioinform. Syst. Biol.
, vol.1
, pp. 11
-
-
Zikmanis, P.1
Kampenusa, I.2
-
110
-
-
84861180223
-
OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities
-
doi: 10.1371/journal.pcbi.1002363
-
Zomorrodi, A. R., and Maranas, C. D. (2012). OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities. PLoS Comput. Biol. 8:e1002363. doi: 10.1371/journal.pcbi.1002363.
-
(2012)
PLoS Comput. Biol.
, vol.8
-
-
Zomorrodi, A.R.1
Maranas, C.D.2
|