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Items: 1 to 20 of 200

1.

Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model.

Fang Y, Scheibe TD, Mahadevan R, Garg S, Long PE, Lovley DR.

J Contam Hydrol. 2011 Mar 25;122(1-4):96-103. doi: 10.1016/j.jconhyd.2010.11.007. Epub 2010 Nov 28.

PMID:
21172725
2.

Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation.

Scheibe TD, Mahadevan R, Fang Y, Garg S, Long PE, Lovley DR.

Microb Biotechnol. 2009 Mar;2(2):274-86. doi: 10.1111/j.1751-7915.2009.00087.x.

3.

Model-based analysis of the role of biological, hydrological and geochemical factors affecting uranium bioremediation.

Zhao J, Scheibe TD, Mahadevan R.

Biotechnol Bioeng. 2011 Jul;108(7):1537-48. doi: 10.1002/bit.23096. Epub 2011 Mar 1.

PMID:
21337330
4.

A thermodynamically-based model for predicting microbial growth and community composition coupled to system geochemistry: Application to uranium bioreduction.

Istok JD, Park M, Michalsen M, Spain AM, Krumholz LR, Liu C, McKinley J, Long P, Roden E, Peacock AD, Baldwin B.

J Contam Hydrol. 2010 Mar 1;112(1-4):1-14. doi: 10.1016/j.jconhyd.2009.07.004. Epub 2009 Jul 15.

PMID:
19683832
5.

Geobacter sulfurreducens strain engineered for increased rates of respiration.

Izallalen M, Mahadevan R, Burgard A, Postier B, Didonato R Jr, Sun J, Schilling CH, Lovley DR.

Metab Eng. 2008 Sep;10(5):267-75. doi: 10.1016/j.ymben.2008.06.005. Epub 2008 Jun 27.

PMID:
18644460
6.

Evaluation of a genome-scale in silico metabolic model for Geobacter metallireducens by using proteomic data from a field biostimulation experiment.

Fang Y, Wilkins MJ, Yabusaki SB, Lipton MS, Long PE.

Appl Environ Microbiol. 2012 Dec;78(24):8735-42. doi: 10.1128/AEM.01795-12. Epub 2012 Oct 5.

7.

Variably saturated flow and multicomponent biogeochemical reactive transport modeling of a uranium bioremediation field experiment.

Yabusaki SB, Fang Y, Williams KH, Murray CJ, Ward AL, Dayvault RD, Waichler SR, Newcomer DR, Spane FA, Long PE.

J Contam Hydrol. 2011 Nov 1;126(3-4):271-90. doi: 10.1016/j.jconhyd.2011.09.002. Epub 2011 Sep 17.

PMID:
22115092
8.

Genome-scale constraint-based modeling of Geobacter metallireducens.

Sun J, Sayyar B, Butler JE, Pharkya P, Fahland TR, Famili I, Schilling CH, Lovley DR, Mahadevan R.

BMC Syst Biol. 2009 Jan 28;3:15. doi: 10.1186/1752-0509-3-15.

9.

Molecular analysis of phosphate limitation in Geobacteraceae during the bioremediation of a uranium-contaminated aquifer.

N'Guessan AL, Elifantz H, Nevin KP, Mouser PJ, Methé B, Woodard TL, Manley K, Williams KH, Wilkins MJ, Larsen JT, Long PE, Lovley DR.

ISME J. 2010 Feb;4(2):253-66. doi: 10.1038/ismej.2009.115. Epub 2009 Dec 10.

PMID:
20010635
10.

Use of an uncertainty analysis for genome-scale models as a prediction tool for microbial growth processes in subsurface environments.

Klier C.

Environ Sci Technol. 2012 Mar 6;46(5):2790-8. doi: 10.1021/es203461u. Epub 2012 Feb 27.

PMID:
22335464
11.

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, Lovley DR.

ISME J. 2011 Feb;5(2):305-16. doi: 10.1038/ismej.2010.117. Epub 2010 Jul 29.

12.

Quantifying expression of Geobacter spp. oxidative stress genes in pure culture and during in situ uranium bioremediation.

Mouser PJ, Holmes DE, Perpetua LA, DiDonato R, Postier B, Liu A, Lovley DR.

ISME J. 2009 Apr;3(4):454-65. doi: 10.1038/ismej.2008.126. Epub 2009 Jan 8.

PMID:
19129865
13.

Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments.

Holmes DE, O'Neil RA, Chavan MA, N'Guessan LA, Vrionis HA, Perpetua LA, Larrahondo MJ, DiDonato R, Liu A, Lovley DR.

ISME J. 2009 Feb;3(2):216-30. doi: 10.1038/ismej.2008.89. Epub 2008 Oct 9.

PMID:
18843300
14.

Expression of acetate permease-like (apl ) genes in subsurface communities of Geobacter species under fluctuating acetate concentrations.

Elifantz H, N'Guessan LA, Mouser PJ, Williams KH, Wilkins MJ, Risso C, Holmes DE, Long PE, Lovley DR.

FEMS Microbiol Ecol. 2010 Sep;73(3):441-9. doi: 10.1111/j.1574-6941.2010.00907.x. Epub 2010 May 10.

15.

Mineral transformation and biomass accumulation associated with uranium bioremediation at Rifle, Colorado.

Li L, Steefel CI, Williams KH, Wilkins MJ, Hubbard SS.

Environ Sci Technol. 2009 Jul 15;43(14):5429-35.

PMID:
19708377
16.

Genes for two multicopper proteins required for Fe(III) oxide reduction in Geobacter sulfurreducens have different expression patterns both in the subsurface and on energy-harvesting electrodes.

Holmes DE, Mester T, O'Neil RA, Perpetua LA, Larrahondo MJ, Glaven R, Sharma ML, Ward JE, Nevin KP, Lovley DR.

Microbiology. 2008 May;154(Pt 5):1422-35. doi: 10.1099/mic.0.2007/014365-0.

PMID:
18451051
17.

Uranium removal from groundwater via in situ biostimulation: Field-scale modeling of transport and biological processes.

Yabusaki SB, Fang Y, Long PE, Resch CT, Peacock AD, Komlos J, Jaffe PR, Morrison SJ, Dayvault RD, White DC, Anderson RT.

J Contam Hydrol. 2007 Aug 15;93(1-4):216-35. Epub 2007 Mar 12.

PMID:
17442451
18.

Effects of physical and geochemical heterogeneities on mineral transformation and biomass accumulation during biostimulation experiments at Rifle, Colorado.

Li L, Steefel CI, Kowalsky MB, Englert A, Hubbard SS.

J Contam Hydrol. 2010 Mar 1;112(1-4):45-63. doi: 10.1016/j.jconhyd.2009.10.006. Epub 2009 Oct 31.

PMID:
20036028
19.

Modeling and sensitivity analysis of electron capacitance for Geobacter in sedimentary environments.

Zhao J, Fang Y, Scheibe TD, Lovley DR, Mahadevan R.

J Contam Hydrol. 2010 Mar 1;112(1-4):30-44. doi: 10.1016/j.jconhyd.2009.10.002. Epub 2009 Nov 5.

PMID:
19892431
20.

Simulating bioremediation of uranium-contaminated aquifers; uncertainty assessment of model parameters.

Wang S, Jaffé PR, Li G, Wang SW, Rabitz HA.

J Contam Hydrol. 2003 Jul;64(3-4):283-307.

PMID:
12814885

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