-
1
-
-
34147103873
-
Emergent biogeography of microbial communities in a model ocean
-
DOI 10.1126/science.1138544
-
Follows, M. J., Dutkiewicz, S., Grant, S., and Chisholm, S. W. (2007) Emergent biogeography of microbial communities in a model ocean Science 315 (5820) 1843-6 (Pubitemid 46580143)
-
(2007)
Science
, vol.315
, Issue.5820
, pp. 1843-1846
-
-
Follows, M.J.1
Dutkiewicz, S.2
Grant, S.3
Chisholm, S.W.4
-
2
-
-
84862286169
-
A framework for human microbiome research
-
The Human Microbiome Project Consortium
-
The Human Microbiome Project Consortium (2012) A framework for human microbiome research Nature 486 (7402) 215-221
-
(2012)
Nature
, vol.486
, Issue.7402
, pp. 215-221
-
-
-
3
-
-
84862276328
-
Structure, function, and diversity of the healthy human microbiome
-
The Human Microbiome Project Consortium
-
The Human Microbiome Project Consortium (2012) Structure, function, and diversity of the healthy human microbiome Nature 486 (7402) 207-214
-
(2012)
Nature
, vol.486
, Issue.7402
, pp. 207-214
-
-
-
4
-
-
79956157487
-
Prospects for systems biology and modeling of the gut microbiome
-
Karlsson, F. H., Nookaew, I., Petranovic, D., and Nielsen, J. (2011) Prospects for systems biology and modeling of the gut microbiome Trends Biotechnol. 29 (6) 251-8
-
(2011)
Trends Biotechnol.
, vol.29
, Issue.6
, pp. 251-258
-
-
Karlsson, F.H.1
Nookaew, I.2
Petranovic, D.3
Nielsen, J.4
-
5
-
-
80051856839
-
The human gut microbiome: Ecology and recent evolutionary changes
-
Walter, J. and Ley, R. (2011) The human gut microbiome: Ecology and recent evolutionary changes Annu. Rev. Microbiol. 65, 411-29
-
(2011)
Annu. Rev. Microbiol.
, vol.65
, pp. 411-429
-
-
Walter, J.1
Ley, R.2
-
6
-
-
36549000721
-
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
-
DOI 10.1038/nature06269
-
Warnecke, F., Luginbuhl, P., Ivanova, N., Ghassemian, M., Richardson, T. H., Stege, J. T., Cayouette, M., McHardy, A. C., Djordjevic, G., Aboushadi, N., Sorek, R., Tringe, S. G., Podar, M., Martin, H. G., Kunin, V., Dalevi, D., Madejska, J., Kirton, E., Platt, D., Szeto, E., Salamov, A., Barry, K., Mikhailova, N., Kyrpides, N. C., Matson, E. G., Ottesen, E. A., Zhang, X., Hernandez, M., Murillo, C., Acosta, L. G., Rigoutsos, I., Tamayo, G., Green, B. D., Chang, C., Rubin, E. M., Mathur, E. J., Robertson, D. E., Hugenholtz, P., and Leadbetter, J. R. (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite Nature 450 (7169) 560-565 (Pubitemid 350190243)
-
(2007)
Nature
, vol.450
, Issue.7169
, pp. 560-565
-
-
Warnecke, F.1
Luginbuhl, P.2
Ivanova, N.3
Ghassemian, M.4
Richardson, T.H.5
Stege, J.T.6
Cayouette, M.7
McHardy, A.C.8
Djordjevic, G.9
Aboushadi, N.10
Sorek, R.11
Tringe, S.G.12
Podar, M.13
Martin, H.G.14
Kunin, V.15
Dalevi, D.16
Madejska, J.17
Kirton, E.18
Platt, D.19
Szeto, E.20
Salamov, A.21
Barry, K.22
Mikhailova, N.23
Kyrpides, N.C.24
Matson, E.G.25
Ottesen, E.A.26
Zhang, X.27
Hernandez, M.28
Murillo, C.29
Acosta, L.G.30
Rigoutsos, I.31
Tamayo, G.32
Green, B.D.33
Chang, C.34
Rubin, E.M.35
Mathur, E.J.36
Robertson, D.E.37
Hugenholtz, P.38
Leadbetter, J.R.39
more..
-
7
-
-
84861801813
-
Characterization of a biogas-producing microbial community by short-read next generation DNA sequencing
-
Wirth, R., Kovacs, E., Maroti, G., Bagi, Z., Rakhely, G., and Kovacs, K. L. (2012) Characterization of a biogas-producing microbial community by short-read next generation DNA sequencing Biotechnol. Biofuels 5 (1) 41
-
(2012)
Biotechnol. Biofuels
, vol.5
, Issue.1
, pp. 41
-
-
Wirth, R.1
Kovacs, E.2
Maroti, G.3
Bagi, Z.4
Rakhely, G.5
Kovacs, K.L.6
-
8
-
-
58549094275
-
Complementary cooperation between two syntrophic bacteria in pesticide degradation
-
Katsuyama, C., Nakaoka, S., Takeuchi, Y., Tago, K., Hayatsu, M., and Kato, K. (2009) Complementary cooperation between two syntrophic bacteria in pesticide degradation J. Theor. Biol. 256 (4) 644-54
-
(2009)
J. Theor. Biol.
, vol.256
, Issue.4
, pp. 644-654
-
-
Katsuyama, C.1
Nakaoka, S.2
Takeuchi, Y.3
Tago, K.4
Hayatsu, M.5
Kato, K.6
-
9
-
-
37249079763
-
Biodegradation of aged polycyclic aromatic hydrocarbons (PAHs) by microbial consortia in soil and slurry phases
-
DOI 10.1016/j.jhazmat.2007.04.040, PII S0304389407005225
-
Li, X., Li, P., Lin, X., Zhang, C., Li, Q., and Gong, Z. (2008) Biodegradation of aged polycyclic aromatic hydrocarbons (PAHs) by microbial consortia in soil and slurry phases J. Hazard. Mater. 150 (1) 21-6 (Pubitemid 350266976)
-
(2008)
Journal of Hazardous Materials
, vol.150
, Issue.1
, pp. 21-26
-
-
Li, X.1
Li, P.2
Lin, X.3
Zhang, C.4
Li, Q.5
Gong, Z.6
-
10
-
-
78650677445
-
Microbial communities involved in anaerobic degradation of alkanes
-
Mbadinga, S. M., Wang, L. Y., Zhou, L., Liu, J. F., Gu, J. D., and Mu, B. Z. (2011) Microbial communities involved in anaerobic degradation of alkanes Int. Biodeter. Biodegr. 65 (1) 1-13
-
(2011)
Int. Biodeter. Biodegr.
, vol.65
, Issue.1
, pp. 1-13
-
-
Mbadinga, S.M.1
Wang, L.Y.2
Zhou, L.3
Liu, J.F.4
Gu, J.D.5
Mu, B.Z.6
-
11
-
-
84865289997
-
Bacterial community dynamics during the preferential degradation of aromatic hydrocarbons by a microbial consortium
-
Bacosa, H. P., Suto, K., and Inoue, C. (2012) Bacterial community dynamics during the preferential degradation of aromatic hydrocarbons by a microbial consortium Int. Biodeter. Biodegr. 74, 109-115
-
(2012)
Int. Biodeter. Biodegr.
, vol.74
, pp. 109-115
-
-
Bacosa, H.P.1
Suto, K.2
Inoue, C.3
-
12
-
-
78751584992
-
Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments
-
Zhuang, K., Izallalen, M., Mouser, P., Richter, H., Risso, C., Mahadevan, R., and Lovley, D. R. (2011) Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments ISME J. 5 (2) 305-16
-
(2011)
ISME J.
, vol.5
, Issue.2
, pp. 305-316
-
-
Zhuang, K.1
Izallalen, M.2
Mouser, P.3
Richter, H.4
Risso, C.5
Mahadevan, R.6
Lovley, D.R.7
-
13
-
-
67449110763
-
Influence of heterogeneous ammonium availability on bacterial community structure and the expression of nitrogen fixation and ammonium transporter genes during in situ bioremediation of uranium-contaminated groundwater
-
Mouser, P. J., N'Guessan, A. L., Elifantz, H., Holmes, D. E., Williams, K. H., Wilkins, M. J., Long, P. E., and Lovley, D. R. (2009) Influence of heterogeneous ammonium availability on bacterial community structure and the expression of nitrogen fixation and ammonium transporter genes during in situ bioremediation of uranium-contaminated groundwater Environ. Sci. Technol. 43 (12) 4386-92
-
(2009)
Environ. Sci. Technol.
, vol.43
, Issue.12
, pp. 4386-4392
-
-
Mouser, P.J.1
N'Guessan, A.L.2
Elifantz, H.3
Holmes, D.E.4
Williams, K.H.5
Wilkins, M.J.6
Long, P.E.7
Lovley, D.R.8
-
14
-
-
79958295322
-
Dynamics of microbial community composition and function during in situ bioremediation of a uranium-contaminated aquifer
-
Van Nostrand, J. D., Wu, L., Wu, W. M., Huang, Z., Gentry, T. J., Deng, Y., Carley, J., Carroll, S., He, Z., Gu, B., Luo, J., Criddle, C. S., Watson, D. B., Jardine, P. M., Marsh, T. L., Tiedje, J. M., Hazen, T. C., and Zhou, J. (2011) Dynamics of microbial community composition and function during in situ bioremediation of a uranium-contaminated aquifer Appl. Environ. Microbiol. 77 (11) 3860-3869
-
(2011)
Appl. Environ. Microbiol.
, vol.77
, Issue.11
, pp. 3860-3869
-
-
Van Nostrand, J.D.1
Wu, L.2
Wu, W.M.3
Huang, Z.4
Gentry, T.J.5
Deng, Y.6
Carley, J.7
Carroll, S.8
He, Z.9
Gu, B.10
Luo, J.11
Criddle, C.S.12
Watson, D.B.13
Jardine, P.M.14
Marsh, T.L.15
Tiedje, J.M.16
Hazen, T.C.17
Zhou, J.18
-
15
-
-
0011309312
-
Microflora of activated-sludge
-
Ueda, S. and Earle, R. L. (1972) Microflora of activated-sludge J. Gen. Appl. Microbiol. 18 (3) 239
-
(1972)
J. Gen. Appl. Microbiol.
, vol.18
, Issue.3
, pp. 239
-
-
Ueda, S.1
Earle, R.L.2
-
16
-
-
0036624935
-
Bacterial community composition and function in sewage treatment systems
-
DOI 10.1016/S0958-1669(02)00315-4
-
Wagner, M. and Loy, A. (2002) Bacterial community composition and function in sewage treatment systems Curr. Opin. Biotechnol. 13 (3) 218-27 (Pubitemid 35299541)
-
(2002)
Current Opinion in Biotechnology
, vol.13
, Issue.3
, pp. 218-227
-
-
Wagner, M.1
Loy, A.2
-
17
-
-
77958571424
-
Biosystems analysis and engineering of microbial consortia for industrial biotechnology
-
Sabra, W., Dietz, D., Tjahjasari, D., and Zeng, A. P. (2010) Biosystems analysis and engineering of microbial consortia for industrial biotechnology Eng. Life Sci. 10 (5) 407-421
-
(2010)
Eng. Life Sci.
, vol.10
, Issue.5
, pp. 407-421
-
-
Sabra, W.1
Dietz, D.2
Tjahjasari, D.3
Zeng, A.P.4
-
19
-
-
33846704237
-
Evolution of species interactions in a biofilm community
-
DOI 10.1038/nature05514, PII NATURE05514
-
Hansen, S. K., Rainey, P. B., Haagensen, J. A. J., and Molin, S. (2007) Evolution of species interactions in a biofilm community Nature 445 (7127) 533-536 (Pubitemid 46197632)
-
(2007)
Nature
, vol.445
, Issue.7127
, pp. 533-536
-
-
Hansen, S.K.1
Rainey, P.B.2
Haagensen, J.A.J.3
Molin, S.4
-
20
-
-
79954515937
-
Social interaction in synthetic and natural microbial communities
-
Xavier, J. B. (2011) Social interaction in synthetic and natural microbial communities Mol. Syst. Biol. 7, 483
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 483
-
-
Xavier, J.B.1
-
21
-
-
66149150877
-
Microbial community structure and its functional implications
-
Fuhrman, J. A. (2009) Microbial community structure and its functional implications Nature 459 (7244) 193-199
-
(2009)
Nature
, vol.459
, Issue.7244
, pp. 193-199
-
-
Fuhrman, J.A.1
-
22
-
-
77956415336
-
Emergent cooperation in microbial metabolism
-
Wintermute, E. H. and Silver, P. A. (2010) Emergent cooperation in microbial metabolism Mol. Syst. Biol. 6, 407
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 407
-
-
Wintermute, E.H.1
Silver, P.A.2
-
23
-
-
84883326386
-
Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass
-
Minty, J. J., Singer, M. E., Scholz, S. A., Bae, C. H., Ahn, J. H., Foster, C. E., Liao, J. C., and Lin, X. N. (2013) Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass Proc. Natl. Acad. Sci. U.S.A. 110 (36) 14592-7
-
(2013)
Proc. Natl. Acad. Sci. U.S.A.
, vol.110
, Issue.36
, pp. 14592-14597
-
-
Minty, J.J.1
Singer, M.E.2
Scholz, S.A.3
Bae, C.H.4
Ahn, J.H.5
Foster, C.E.6
Liao, J.C.7
Lin, X.N.8
-
24
-
-
78649851616
-
Dynamics in the mixed microbial concourse
-
Wintermute, E. H. and Silver, P. A. (2010) Dynamics in the mixed microbial concourse Genes Dev. 24 (23) 2603-14
-
(2010)
Genes Dev.
, vol.24
, Issue.23
, pp. 2603-2614
-
-
Wintermute, E.H.1
Silver, P.A.2
-
25
-
-
0003068294
-
Fermentation process control - Population dynamics of a continuous propagator for microorganisms
-
Finn, R. K. and Wilson, R. E. (1954) Fermentation process control - Population dynamics of a continuous propagator for microorganisms J. Agric. Food Chem. 2 (2) 66-69
-
(1954)
J. Agric. Food Chem.
, vol.2
, Issue.2
, pp. 66-69
-
-
Finn, R.K.1
Wilson, R.E.2
-
26
-
-
27944487902
-
Cell biology: Logic of the yeast metabolic cycle: Temporal compartmentalization of cellular processes
-
DOI 10.1126/science.1120499
-
Tu, B. P., Kudlicki, A., Rowicka, M., and McKnight, S. L. (2005) Logic of the yeast metabolic cycle: Temporal compartmentalization of cellular processes Science 310 (5751) 1152-8 (Pubitemid 41681736)
-
(2005)
Science
, vol.310
, Issue.5751
, pp. 1152-1158
-
-
Tu, B.P.1
Kudlicki, A.2
Rowicka, M.3
McKnight, S.L.4
-
27
-
-
33947276100
-
Metabolic modeling of a mutualistic microbial community
-
Stolyar, S., Van Dien, S., Hillesland, K. L., Pinel, N., Lie, T. J., Leigh, J. A., and Stahl, D. A. (2007) Metabolic modeling of a mutualistic microbial community Mol. Syst. Biol. 3, 92
-
(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
Stahl, D.A.7
-
28
-
-
77953618954
-
Metabolic modelling of syntrophic-like growth of a 1,3-propanediol producer, Clostridium butyricum, and a methanogenic archeon, Methanosarcina mazei, under anaerobic conditions
-
Bizukojc, M., Dietz, D., Sun, J., and Zeng, A. P. (2010) Metabolic modelling of syntrophic-like growth of a 1,3-propanediol producer, Clostridium butyricum, and a methanogenic archeon, Methanosarcina mazei, under anaerobic conditions Bioprocess Biosyst. Eng. 33 (4) 507-23
-
(2010)
Bioprocess Biosyst. Eng.
, vol.33
, Issue.4
, pp. 507-523
-
-
Bizukojc, M.1
Dietz, D.2
Sun, J.3
Zeng, A.P.4
-
29
-
-
78650002545
-
Large-scale in silico modeling of metabolic interactions between cell types in the human brain
-
Lewis, N. E., Schramm, G., Bordbar, A., Schellenberger, J., Andersen, M. P., Cheng, J. K., Patel, N., Yee, A., Lewis, R. A., Eils, R., Konig, R., and Palsson, B. O. (2010) Large-scale in silico modeling of metabolic interactions between cell types in the human brain Nat. Biotechnol. 28 (12) 1279-85
-
(2010)
Nat. Biotechnol.
, vol.28
, Issue.12
, pp. 1279-1285
-
-
Lewis, N.E.1
Schramm, G.2
Bordbar, A.3
Schellenberger, J.4
Andersen, M.P.5
Cheng, J.K.6
Patel, N.7
Yee, A.8
Lewis, R.A.9
Eils, R.10
Konig, R.11
Palsson, B.O.12
-
30
-
-
84898972470
-
Computational identification of bacterial communities
-
Tzamali, E., Poirazi, P., Tollis, I. G., and Reczko, M. (2009) Computational identification of bacterial communities World Acad. Sci. Eng. Technol. 52, 269
-
(2009)
World Acad. Sci. Eng. Technol.
, vol.52
, pp. 269
-
-
Tzamali, E.1
Poirazi, P.2
Tollis, I.G.3
Reczko, M.4
-
31
-
-
84888371682
-
Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association
-
Nagarajan, H., Embree, M., Rotaru, A. E., Shrestha, P. M., Feist, A. M., Palsson, B. O., Lovley, D. R., and Zengler, K. (2013) Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association Nat. Commun. 4, 2809
-
(2013)
Nat. Commun.
, vol.4
, pp. 2809
-
-
Nagarajan, H.1
Embree, M.2
Rotaru, A.E.3
Shrestha, P.M.4
Feist, A.M.5
Palsson, B.O.6
Lovley, D.R.7
Zengler, K.8
-
32
-
-
1642588336
-
Quantitative analysis of Escherichia coli metabolic phenotypes within the context of phenotypic phase planes
-
DOI 10.1159/000076740
-
Ibarra, R. U., Fu, P., Palsson, B. O., DiTonno, J. R., and Edwards, J. S. (2003) Quantitative analysis of Escherichia coli metabolic phenotypes within the context of phenotypic phase planes J. Mol. Microbiol. Biotechnol. 6 (2) 101-8 (Pubitemid 38410694)
-
(2003)
Journal of Molecular Microbiology and Biotechnology
, vol.6
, Issue.2
, pp. 101-108
-
-
Ibarra, R.U.1
Fu, P.2
Palsson, B.O.3
DiTonno, J.R.4
Edwards, J.S.5
-
33
-
-
80054115962
-
A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities
-
Tzamali, E., Poirazi, P., Tollis, I. G., and Reczko, M. (2011) A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities BMC Syst. Biol. 5, 167
-
(2011)
BMC Syst. Biol.
, vol.5
, pp. 167
-
-
Tzamali, E.1
Poirazi, P.2
Tollis, I.G.3
Reczko, M.4
-
34
-
-
0037069467
-
Analysis of optimality in natural and perturbed metabolic networks
-
DOI 10.1073/pnas.232349399
-
Segre, D., Vitkup, D., and Church, G. M. (2002) Analysis of optimality in natural and perturbed metabolic networks Proc. Natl. Acad. Sci. U.S.A. 99 (23) 15112-7 (Pubitemid 35334618)
-
(2002)
Proceedings of the National Academy of Sciences of the United States of America
, vol.99
, Issue.23
, pp. 15112-15117
-
-
Segre, D.1
Vitkup, D.2
Church, G.M.3
-
35
-
-
59649085782
-
Topological signatures of species interactions in metabolic networks
-
Borenstein, E. and Feldman, M. W. (2009) Topological signatures of species interactions in metabolic networks J. Comput. Biol. 16 (2) 191-200
-
(2009)
J. Comput. Biol.
, vol.16
, Issue.2
, pp. 191-200
-
-
Borenstein, E.1
Feldman, M.W.2
-
36
-
-
67649470562
-
Metabolic-network-driven analysis of bacterial ecological strategies
-
Freilich, S., Kreimer, A., Borenstein, E., Yosef, N., Sharan, R., Gophna, U., and Ruppin, E. (2009) Metabolic-network-driven analysis of bacterial ecological strategies Genome Biol. 10 (6) R61
-
(2009)
Genome Biol.
, vol.10
, Issue.6
, pp. 61
-
-
Freilich, S.1
Kreimer, A.2
Borenstein, E.3
Yosef, N.4
Sharan, R.5
Gophna, U.6
Ruppin, E.7
-
37
-
-
33747314412
-
The evolution of cooperation and altruism - A general framework and a classification of models
-
Lehmann, L. and Keller, L. (2006) The evolution of cooperation and altruism - A general framework and a classification of models J. Evol. Biol. 19 (5) 1365-76
-
(2006)
J. Evol. Biol.
, vol.19
, Issue.5
, pp. 1365-1376
-
-
Lehmann, L.1
Keller, L.2
-
38
-
-
77950831062
-
Emergence of spatial structure in cell groups and the evolution of cooperation
-
Nadell, C. D., Foster, K. R., and Xavier, J. B. (2010) Emergence of spatial structure in cell groups and the evolution of cooperation PLoS Comput. Biol. 6 (3) e1000716
-
(2010)
PLoS Comput. Biol.
, vol.6
, Issue.3
, pp. 1000716
-
-
Nadell, C.D.1
Foster, K.R.2
Xavier, J.B.3
-
39
-
-
33846936445
-
Synthetic cooperation in engineered yeast populations
-
DOI 10.1073/pnas.0610575104
-
Shou, W., Ram, S., and Vilar, J. M. (2007) Synthetic cooperation in engineered yeast populations Proc. Natl. Acad. Sci. U.S.A. 104 (6) 1877-82 (Pubitemid 46239872)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.6
, pp. 1877-1882
-
-
Shou, W.1
Ram, S.2
Vilar, J.M.G.3
-
40
-
-
0037396770
-
Modeling microbial consortiums as distributed metabolic networks
-
Vallino, J. J. (2003) Modeling microbial consortiums as distributed metabolic networks Biol. Bull. 204 (2) 174-9 (Pubitemid 36516704)
-
(2003)
Biological Bulletin
, vol.204
, Issue.2
, pp. 174-179
-
-
Vallino, J.J.1
-
41
-
-
77955711148
-
Evolutionary game theory: Theoretical concepts and applications to microbial communities
-
Frey, E. (2010) Evolutionary game theory: Theoretical concepts and applications to microbial communities Phys. A 389 (20) 4265-4298
-
(2010)
Phys. A
, vol.389
, Issue.20
, pp. 4265-4298
-
-
Frey, E.1
-
42
-
-
0036708443
-
Dynamic Flux Balance Analysis of diauxic growth in Escherichia coli
-
Mahadevan, R., Edwards, J. S., and Doyle, F. J., 3rd (2002) Dynamic flux balance analysis of diauxic growth Biophys. J. 83 (3) 1331-40 (Pubitemid 34977706)
-
(2002)
Biophysical Journal
, vol.83
, Issue.3
, pp. 1331-1340
-
-
Mahadevan, R.1
Edwards, J.S.2
Doyle III, F.J.3
-
43
-
-
84899912216
-
Modeling metabolic systems: The need for dynamics
-
Song, H.-S., DeVilbiss, F., and Ramkrishna, D. (2013) Modeling metabolic systems: The need for dynamics Curr. Opin. Chem. Eng. 2, 373
-
(2013)
Curr. Opin. Chem. Eng.
, vol.2
, pp. 373
-
-
Song, H.-S.1
Devilbiss, F.2
Ramkrishna, D.3
-
44
-
-
84865358026
-
The design of long-term effective uranium bioremediation strategy using a community metabolic model
-
Zhuang, K., Ma, E., Lovley, D. R., and Mahadevan, R. (2012) The design of long-term effective uranium bioremediation strategy using a community metabolic model Biotechnol. Bioeng. 109 (10) 2475-83
-
(2012)
Biotechnol. Bioeng.
, vol.109
, Issue.10
, pp. 2475-2483
-
-
Zhuang, K.1
Ma, E.2
Lovley, D.R.3
Mahadevan, R.4
-
45
-
-
77954724818
-
Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing
-
Salimi, F., Zhuang, K., and Mahadevan, R. (2010) Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing Biotechnol. J. 5 (7) 726-38
-
(2010)
Biotechnol. J.
, vol.5
, Issue.7
, pp. 726-738
-
-
Salimi, F.1
Zhuang, K.2
Mahadevan, R.3
-
46
-
-
78650215306
-
Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures
-
Hanly, T. J. and Henson, M. A. (2011) Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures Biotechnol. Bioeng. 108 (2) 376-85
-
(2011)
Biotechnol. Bioeng.
, vol.108
, Issue.2
, pp. 376-385
-
-
Hanly, T.J.1
Henson, M.A.2
-
47
-
-
84875495658
-
Dynamic metabolic modeling of a microaerobic yeast co-culture: Predicting and optimizing ethanol production from glucose/xylose mixtures
-
Hanly, T. J. and Henson, M. A. (2013) Dynamic metabolic modeling of a microaerobic yeast co-culture: Predicting and optimizing ethanol production from glucose/xylose mixtures Biotechnol. Biofuels 6 (1) 44
-
(2013)
Biotechnol. Biofuels
, vol.6
, Issue.1
, pp. 44
-
-
Hanly, T.J.1
Henson, M.A.2
-
48
-
-
84861180223
-
OptCom: A multi-level optimization framework for the metabolic modeling and analysis of microbial communities
-
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 (2) e1002363
-
(2012)
PLoS Comput. Biol.
, vol.8
, Issue.2
, pp. 1002363
-
-
Zomorrodi, A.R.1
Maranas, C.D.2
-
49
-
-
0000318768
-
BARON: A general purpose global optimization software package
-
Sahinidis, N. V. (1996) BARON: A general purpose global optimization software package J, Global Optim, 8 (2) 201-205
-
(1996)
J, Global Optim
, vol.8
, Issue.2
, pp. 201-205
-
-
Sahinidis, N.V.1
-
50
-
-
34347332311
-
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
-
Feist, A. M., Henry, C. S., Reed, J. L., Krummenacker, M., Joyce, A. R., Karp, P. D., Broadbelt, L. J., Hatzimanikatis, V., and Palsson, B. O. (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
-
(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
Broadbelt, L.J.7
Hatzimanikatis, V.8
Palsson, B.O.9
-
51
-
-
7044222207
-
Dissimilatory Fe(III) and Mn(IV) reduction
-
DOI 10.1016/S0065-2911(04)49005-5, PII S0065291104490055
-
Lovley, D. R., Holmes, D. E., and Nevin, K. P. (2004) Dissimilatory Fe(III) and Mn(IV) reduction Adv. Microb. Physiol. 49, 219-86 (Pubitemid 39424008)
-
(2004)
Advances in Microbial Physiology
, vol.49
, pp. 219-286
-
-
Lovley, D.R.1
Holmes, D.E.2
Nevin, K.P.3
-
53
-
-
10744231694
-
Stimulating the In Situ Activity of Geobacter Species to Remove Uranium from the Groundwater of a Uranium-Contaminated Aquifer
-
DOI 10.1128/AEM.69.10.5884-5891.2003
-
Anderson, R. T., Vrionis, H. A., Ortiz-Bernad, I., Resch, C. T., Long, P. E., Dayvault, R., Karp, K., Marutzky, S., Metzler, D. R., Peacock, A., White, D. C., Lowe, M., and Lovley, D. R. (2003) Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer Appl. Environ. Microbiol. 69 (10) 5884-91 (Pubitemid 37280308)
-
(2003)
Applied and Environmental Microbiology
, vol.69
, Issue.10
, pp. 5884-5891
-
-
Anderson, R.T.1
Vrionis, H.A.2
Ortiz-Bernad, I.3
Resch, C.T.4
Long, P.E.5
Dayvault, R.6
Karp, K.7
Marutzky, S.8
Metzler, D.R.9
Peacock, A.10
White, D.C.11
Lowe, M.12
Lovley, D.R.13
-
54
-
-
26844471341
-
Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site
-
DOI 10.1128/AEM.71.10.6308-6318.2005
-
Vrionis, H. A., Anderson, R. T., Ortiz-Bernad, I., O'Neill, K. R., Resch, C. T., Peacock, A. D., Dayvault, R., White, D. C., Long, P. E., and Lovley, D. R. (2005) Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site Appl. Environ. Microbiol. 71 (10) 6308-18 (Pubitemid 41460528)
-
(2005)
Applied and Environmental Microbiology
, vol.71
, Issue.10
, pp. 6308-6318
-
-
Vrionis, H.A.1
Anderson, R.T.2
Ortiz-Bernad, I.3
O'Neill, K.R.4
Resch, C.T.5
Peacock, A.D.6
Dayvault, R.7
White, D.C.8
Long, P.E.9
Lovley, D.R.10
-
55
-
-
62949105310
-
Ethanol and acetate production by Clostridium ljungdahlii and Clostridium autoethanogenum using resting cells
-
Cotter, J. L., Chinn, M. S., and Grunden, A. M. (2009) Ethanol and acetate production by Clostridium ljungdahlii and Clostridium autoethanogenum using resting cells Bioprocess Biosyst. Eng. 32 (3) 369-80
-
(2009)
Bioprocess Biosyst. Eng.
, vol.32
, Issue.3
, pp. 369-380
-
-
Cotter, J.L.1
Chinn, M.S.2
Grunden, A.M.3
-
56
-
-
60849099919
-
Genome-scale constraint-based modeling of Geobacter metallireducens
-
Sun, J., Sayyar, B., Butler, J. E., Pharkya, P., Fahland, T. R., Famili, I., Schilling, C. H., Lovley, D. R., and Mahadevan, R. (2009) Genome-scale constraint-based modeling of Geobacter metallireducens BMC Syst. Biol. 3, 15
-
(2009)
BMC Syst. Biol.
, vol.3
, pp. 15
-
-
Sun, J.1
Sayyar, B.2
Butler, J.E.3
Pharkya, P.4
Fahland, T.R.5
Famili, I.6
Schilling, C.H.7
Lovley, D.R.8
Mahadevan, R.9
-
57
-
-
33144470047
-
Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling
-
DOI 10.1128/AEM.72.2.1558-1568.2006
-
Mahadevan, R., Bond, D. R., Butler, J. E., Esteve-Nunez, A., Coppi, M. V., Palsson, B. O., Schilling, C. H., and Lovley, D. R. (2006) Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling Appl. Environ. Microbiol. 72 (2) 1558-68 (Pubitemid 43271271)
-
(2006)
Applied and Environmental Microbiology
, vol.72
, Issue.2
, pp. 1558-1568
-
-
Mahadevan, R.1
Bond, D.R.2
Butler, J.E.3
Esteve-Nunez, A.4
Coppi, M.V.5
Palsson, B.O.6
Schilling, C.H.7
Lovley, D.R.8
-
58
-
-
70350460030
-
Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens
-
Risso, C., Sun, J., Zhuang, K., Mahadevan, R., DeBoy, R., Ismail, W., Shrivastava, S., Huot, H., Kothari, S., Daugherty, S., Bui, O., Schilling, C. H., Lovley, D. R., and Methe, B. A. (2009) Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens BMC Genomics 10, 447
-
(2009)
BMC Genomics
, vol.10
, pp. 447
-
-
Risso, C.1
Sun, J.2
Zhuang, K.3
Mahadevan, R.4
Deboy, R.5
Ismail, W.6
Shrivastava, S.7
Huot, H.8
Kothari, S.9
Daugherty, S.10
Bui, O.11
Schilling, C.H.12
Lovley, D.R.13
Methe, B.A.14
-
59
-
-
77955495197
-
Constraint-based model of Shewanella oneidensis MR-1 metabolism: A tool for data analysis and hypothesis generation
-
Pinchuk, G. E., Hill, E. A., Geydebrekht, O. V., De Ingeniis, J., Zhang, X., Osterman, A., Scott, J. H., Reed, S. B., Romine, M. F., Konopka, A. E., Beliaev, A. S., Fredrickson, J. K., and Reed, J. L. (2010) Constraint-based model of Shewanella oneidensis MR-1 metabolism: A tool for data analysis and hypothesis generation PLoS Comput. Biol. 6 (6) e1000822
-
(2010)
PLoS Comput. Biol.
, vol.6
, Issue.6
, pp. 1000822
-
-
Pinchuk, G.E.1
Hill, E.A.2
Geydebrekht, O.V.3
De Ingeniis, J.4
Zhang, X.5
Osterman, A.6
Scott, J.H.7
Reed, S.B.8
Romine, M.F.9
Konopka, A.E.10
Beliaev, A.S.11
Fredrickson, J.K.12
Reed, J.L.13
-
60
-
-
83255192314
-
Pyruvate and lactate metabolism by Shewanella oneidensis MR-1 under fermentation, oxygen limitation, and fumarate respiration conditions
-
Pinchuk, G. E., Geydebrekht, O. V., Hill, E. A., Reed, J. L., Konopka, A. E., Beliaev, A. S., and Fredrickson, J. K. (2011) Pyruvate and lactate metabolism by Shewanella oneidensis MR-1 under fermentation, oxygen limitation, and fumarate respiration conditions Appl. Environ. Microbiol. 77 (23) 8234-40
-
(2011)
Appl. Environ. Microbiol.
, vol.77
, Issue.23
, pp. 8234-8240
-
-
Pinchuk, G.E.1
Geydebrekht, O.V.2
Hill, E.A.3
Reed, J.L.4
Konopka, A.E.5
Beliaev, A.S.6
Fredrickson, J.K.7
-
61
-
-
33846561094
-
Anaerobic central metabolic pathways in Shewanella oneidensis MR-1 reinterpreted in the light of isotopic metabolite labeling
-
DOI 10.1128/JB.00926-06
-
Tang, Y. J., Meadows, A. L., Kirby, J., and Keasling, J. D. (2007) Anaerobic central metabolic pathways in Shewanella oneidensis MR-1 reinterpreted in the light of isotopic metabolite labeling J. Bacteriol. 189 (3) 894-901 (Pubitemid 46183864)
-
(2007)
Journal of Bacteriology
, vol.189
, Issue.3
, pp. 894-901
-
-
Tang, Y.J.1
Meadows, A.L.2
Kirby, J.3
Keasling, J.D.4
-
62
-
-
33846031603
-
A kinetic model describing Shewanella oneidensis MR-1 growth, substrate consumption, and product secretion
-
DOI 10.1002/bit.21101
-
Tang, Y. J., Meadows, A. L., and Keasling, J. D. (2007) A kinetic model describing Shewanella oneidensis MR-1 growth, substrate consumption, and product secretion Biotechnol. Bioeng. 96 (1) 125-33 (Pubitemid 46043222)
-
(2007)
Biotechnology and Bioengineering
, vol.96
, Issue.1
, pp. 125-133
-
-
Tang, Y.J.1
Meadows, A.L.2
Keasling, J.D.3
-
63
-
-
84898958171
-
Biostimulated uranium immobilization within aquifers: From bench scale to field experiments
-
Rüde, R. T. Freund, A. and Wolkersdorfer, C. IMWA, Aachen, Germany
-
Ulrich, K., Veeramani, H., Schofield, E. J., Sharp, J. O., Suvorova, E. T., Stubbs, J. E., Lezama-Pacheco, J. S., Barrows, C. J., Cerrato, J. M., Campbell, K. M., Yabusaki, S. B., Long, P. L., Bernier-Latmani, R., Giammar, D. E., and Bargar, J. R. Biostimulated uranium immobilization within aquifers: From bench scale to field experiments. In Mine Water - Managing the Challenges, Rüde, R. T., Freund, A., and Wolkersdorfer, C., Eds.; IMWA, Aachen, Germany, 2011; pp 627-631.
-
(2011)
Mine Water - Managing the Challenges
, pp. 627-631
-
-
Ulrich, K.1
Veeramani, H.2
Schofield, E.J.3
Sharp, J.O.4
Suvorova, E.T.5
Stubbs, J.E.6
Lezama-Pacheco, J.S.7
Barrows, C.J.8
Cerrato, J.M.9
Campbell, K.M.10
Yabusaki, S.B.11
Long, P.L.12
Bernier-Latmani, R.13
Giammar, D.E.14
Bargar, J.R.15
-
64
-
-
81855210028
-
-
U.S. Nuclear Regulatory Commission, Office of Nuclear Regulatory Research, Richland, WA.
-
Yabusaki, S. B., Fang, Y., Waichler, S. R., and Long, P. E. (2010) Processes, Properties, and Conditions Controlling In Situ Bioremediation of Uranium in Shallow, Alluvial Aquifers, U.S. Nuclear Regulatory Commission, Office of Nuclear Regulatory Research, Richland, WA.
-
(2010)
Processes, Properties, and Conditions Controlling in Situ Bioremediation of Uranium in Shallow, Alluvial Aquifers
-
-
Yabusaki, S.B.1
Fang, Y.2
Waichler, S.R.3
Long, P.E.4
-
65
-
-
32044437563
-
Global transcriptional profiling of Shewanella oneidensis MR-1 during Cr(VI) and U(VI) reduction
-
DOI 10.1128/AEM.71.11.7453-7460.2005
-
Bencheikh-Latmani, R., Williams, S. M., Haucke, L., Criddle, C. S., Wu, L., Zhou, J., and Tebo, B. M. (2005) Global transcriptional profiling of Shewanella oneidensis MR-1 during Cr(VI) and U(VI) reduction Appl. Environ. Microbiol. 71 (11) 7453-60 (Pubitemid 43194239)
-
(2005)
Applied and Environmental Microbiology
, vol.71
, Issue.11
, pp. 7453-7460
-
-
Bencheikh-Latmani, R.1
Williams, S.M.2
Haucke, L.3
Criddle, C.S.4
Wu, L.5
Zhou, J.6
Tebo, B.M.7
-
66
-
-
81855210028
-
-
U.S. Nuclear Regulatory Commission. Office of Nuclear Regulatory Research. U.S. Nuclear Regulatory Commission, Office of Nuclear Regulatory Research, Washington, DC, p online resource (111 p.) col. ill.
-
Yabusaki, S. B., and U.S. Nuclear Regulatory Commission. Office of Nuclear Regulatory Research. (2010) Processes, Properties, and Conditions Controlling In Situ Bioremediation of Uranium in Shallow, Alluvial Aquifers, U.S. Nuclear Regulatory Commission, Office of Nuclear Regulatory Research, Washington, DC, p 1 online resource (111 p.) col. ill. http://purl.fdlp.gov/GPO/ gpo6097.
-
(2010)
Processes, Properties, and Conditions Controlling in Situ Bioremediation of Uranium in Shallow, Alluvial Aquifers
, pp. 1
-
-
Yabusaki, S.B.1
-
67
-
-
76049103018
-
Modeling and sensitivity analysis of electron capacitance for Geobacter in sedimentary environments
-
Zhao, J., Fang, Y., Scheibe, T. D., Lovley, D. R., and Mahadevan, R. (2010) Modeling and sensitivity analysis of electron capacitance for Geobacter in sedimentary environments J. Contamin. Hydrol. 112 (1-4) 30-44
-
(2010)
J. Contamin. Hydrol.
, vol.112
, Issue.14
, pp. 30-44
-
-
Zhao, J.1
Fang, Y.2
Scheibe, T.D.3
Lovley, D.R.4
Mahadevan, R.5
-
68
-
-
79956121413
-
Model-based analysis of the role of biological, hydrological and geochemical factors affecting uranium bioremediation
-
Zhao, J., Scheibe, T. D., and Mahadevan, R. (2011) Model-based analysis of the role of biological, hydrological and geochemical factors affecting uranium bioremediation Biotechnol. Bioeng. 108 (7) 1537-48
-
(2011)
Biotechnol. Bioeng.
, vol.108
, Issue.7
, pp. 1537-1548
-
-
Zhao, J.1
Scheibe, T.D.2
Mahadevan, R.3
-
69
-
-
0026545972
-
Enzymatic uranium precipitation
-
YA, G. and DR, L. (1992) Enzymatic uranium precipitation Environ. Sci. Technol. 26, 205-207
-
(1992)
Environ. Sci. Technol.
, vol.26
, pp. 205-207
-
-
Ya, G.1
Dr, L.2
-
70
-
-
80053080692
-
Extracellular reduction of uranium via Geobacter conductive pili as a protective cellular mechanism
-
Cologgi, D. L., Lampa-Pastirk, S., Speers, A. M., Kelly, S. D., and Reguera, G. (2011) Extracellular reduction of uranium via Geobacter conductive pili as a protective cellular mechanism Proc. Natl. Acad. Sci. U.S.A. 108 (37) 15248-52
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, Issue.37
, pp. 15248-15252
-
-
Cologgi, D.L.1
Lampa-Pastirk, S.2
Speers, A.M.3
Kelly, S.D.4
Reguera, G.5
-
71
-
-
35148851430
-
Hexavalent uranium supports growth of Anaeromyxobacter dehalogenans and Geobacter spp. with lower than predicted biomass yields
-
DOI 10.1111/j.1462-2920.2007.01405.x
-
Sanford, R. A., Wu, Q., Sung, Y., Thomas, S. H., Amos, B. K., Prince, E. K., and Loffler, F. E. (2007) Hexavalent uranium supports growth of Anaeromyxobacter dehalogenans and Geobacter spp. with lower than predicted biomass yields Environ. Microbiol. 9 (11) 2885-93 (Pubitemid 47547555)
-
(2007)
Environmental Microbiology
, vol.9
, Issue.11
, pp. 2885-2893
-
-
Sanford, R.A.1
Wu, Q.2
Sung, Y.3
Thomas, S.H.4
Amos, B.K.5
Prince, E.K.6
Loffler, F.E.7
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