메뉴 건너뛰기




Volumn 3, Issue , 2009, Pages

In Silico approaches to study mass and energy flows in microbial consortia: A syntrophic case study

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); BASIDIOMYCOTA; OCTOPUS;

EID: 74049119822     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-3-114     Document Type: Article
Times cited : (95)

References (67)
  • 1
    • 44449137093 scopus 로고    scopus 로고
    • The microbial engines that drive Earth's biogeochemical cycles
    • 10.1126/science.1153213, 18497287
    • Falkowski PG, Fenchel T, Delong EF. The microbial engines that drive Earth's biogeochemical cycles. Science 2008, 320(5879):1034-1039. 10.1126/science.1153213, 18497287.
    • (2008) Science , vol.320 , Issue.5879 , pp. 1034-1039
    • Falkowski, P.G.1    Fenchel, T.2    Delong, E.F.3
  • 2
    • 34249952423 scopus 로고    scopus 로고
    • Mixed culture biotechnology for bioenergy production
    • 10.1016/j.copbio.2007.05.001, 17509864
    • Kleerebezem R, van Loosdrecht MCM. Mixed culture biotechnology for bioenergy production. Curr Opin Biotechnol 2007, 18(3):207-212. 10.1016/j.copbio.2007.05.001, 17509864.
    • (2007) Curr Opin Biotechnol , vol.18 , Issue.3 , pp. 207-212
    • Kleerebezem, R.1    van Loosdrecht, M.C.M.2
  • 3
    • 0031737291 scopus 로고    scopus 로고
    • A natural view of microbial biodiversity within hot spring cyanobacterial mat communities
    • 98949, 9841675
    • Ward DM, Ferris MJ, Nold SC, Bateson MM. A natural view of microbial biodiversity within hot spring cyanobacterial mat communities. Microbiol Mol Biol Rev 1998, 62(4):1353-1370. 98949, 9841675.
    • (1998) Microbiol Mol Biol Rev , vol.62 , Issue.4 , pp. 1353-1370
    • Ward, D.M.1    Ferris, M.J.2    Nold, S.C.3    Bateson, M.M.4
  • 4
    • 38549155995 scopus 로고    scopus 로고
    • Genomics, environmental genomics and the issue of microbial species
    • 10.1038/sj.hdy.6801011, 17551524
    • Ward DM, Cohan FM, Bhaya D, Heidelberg JF, Kuhl M, Grossman A. Genomics, environmental genomics and the issue of microbial species. Heredity 2008, 100(2):207-219. 10.1038/sj.hdy.6801011, 17551524.
    • (2008) Heredity , vol.100 , Issue.2 , pp. 207-219
    • Ward, D.M.1    Cohan, F.M.2    Bhaya, D.3    Heidelberg, J.F.4    Kuhl, M.5    Grossman, A.6
  • 5
    • 42049096529 scopus 로고    scopus 로고
    • Regulation of nif gene expression and the energetics of N2 fixation over the diel cycle in a hot spring microbial mat
    • 10.1038/ismej.2007.117, 18323780
    • Steunou AS, Jensen SI, Brecht E, Becraft ED, Bateson MM, Kilian O, Bhaya D, Ward DM, Peters JW, Grossman AR. Regulation of nif gene expression and the energetics of N2 fixation over the diel cycle in a hot spring microbial mat. ISME J 2008, 2(4):364-378. 10.1038/ismej.2007.117, 18323780.
    • (2008) ISME J , vol.2 , Issue.4 , pp. 364-378
    • Steunou, A.S.1    Jensen, S.I.2    Brecht, E.3    Becraft, E.D.4    Bateson, M.M.5    Kilian, O.6    Bhaya, D.7    Ward, D.M.8    Peters, J.W.9    Grossman, A.R.10
  • 6
    • 34548230983 scopus 로고    scopus 로고
    • High rates of sulfate reduction in a low-sulfate hot spring microbial mat are driven by a low level of diversity of sulfate-respiring microorganisms
    • 10.1128/AEM.00357-07, 1950965, 17575000
    • Dillon JG, Fishbain S, Miller SR, Bebout BM, Habicht KS, Webb SM, Stahl DA. High rates of sulfate reduction in a low-sulfate hot spring microbial mat are driven by a low level of diversity of sulfate-respiring microorganisms. Appl Environ Microbiol 2007, 73(16):5218-5226. 10.1128/AEM.00357-07, 1950965, 17575000.
    • (2007) Appl Environ Microbiol , vol.73 , Issue.16 , pp. 5218-5226
    • Dillon, J.G.1    Fishbain, S.2    Miller, S.R.3    Bebout, B.M.4    Habicht, K.S.5    Webb, S.M.6    Stahl, D.A.7
  • 7
    • 0003410448 scopus 로고
    • Thermophilic microorganisms and life at high temperatures
    • New York: Springer-Verlag
    • Brock TD. Thermophilic microorganisms and life at high temperatures. 1978, New York: Springer-Verlag.
    • (1978)
    • Brock, T.D.1
  • 8
    • 0014148305 scopus 로고
    • Life at high temperatures: evolutionary ecological and biochemical significance of organisms living in hot springs is discussed
    • 10.1126/science.158.3804.1012, 4861476
    • Brock TD. Life at high temperatures: evolutionary ecological and biochemical significance of organisms living in hot springs is discussed. Science 1967, 158(3804):1012-1019. 10.1126/science.158.3804.1012, 4861476.
    • (1967) Science , vol.158 , Issue.3804 , pp. 1012-1019
    • Brock, T.D.1
  • 9
    • 0000651747 scopus 로고
    • Photoexcretion and fate of glycolate in a hot spring cyanobacterial mat
    • 202738, 16347684
    • Bateson MM, Ward DM. Photoexcretion and fate of glycolate in a hot spring cyanobacterial mat. Appl Environ Microbiol 1988, 54(7):1738-1743. 202738, 16347684.
    • (1988) Appl Environ Microbiol , vol.54 , Issue.7 , pp. 1738-1743
    • Bateson, M.M.1    Ward, D.M.2
  • 10
    • 0029908371 scopus 로고    scopus 로고
    • Photosynthate partitioning and fermentation in hot spring microbial mat communities
    • 1389010, 16535472
    • Nold SC, Ward DM. Photosynthate partitioning and fermentation in hot spring microbial mat communities. Appl Environ Microbiol 1996, 62(12):4598-4607. 1389010, 16535472.
    • (1996) Appl Environ Microbiol , vol.62 , Issue.12 , pp. 4598-4607
    • Nold, S.C.1    Ward, D.M.2
  • 11
    • 33144476814 scopus 로고    scopus 로고
    • In situ analysis of nitrogen fixation and metabolic switching in unicellular thermophilic cyanobacteria inhabiting hot spring microbial mats
    • 10.1073/pnas.0507513103, 1413695, 16467157
    • Steunou AS, Bhaya D, Bateson MM, Melendrez MC, Ward DM, Brecht E, Peters JW, Kühl M, Grossman AR. In situ analysis of nitrogen fixation and metabolic switching in unicellular thermophilic cyanobacteria inhabiting hot spring microbial mats. Proc Natl Acad Sci USA 2006, 103(7):2398-2403. 10.1073/pnas.0507513103, 1413695, 16467157.
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.7 , pp. 2398-2403
    • Steunou, A.S.1    Bhaya, D.2    Bateson, M.M.3    Melendrez, M.C.4    Ward, D.M.5    Brecht, E.6    Peters, J.W.7    Kühl, M.8    Grossman, A.R.9
  • 12
    • 22144448928 scopus 로고    scopus 로고
    • Diel variations in carbon metabolism by green nonsulfur-like bacteria in alkaline siliceous hot spring microbial mats from Yellowstone National Park
    • 10.1128/AEM.71.7.3978-3986.2005, 1168979, 16000812
    • Meer MTJ, Schouten S, Bateson MM, Nübel U, Wieland A, Kühl M, de Leeuw JW, Damste JSS, Ward DM. Diel variations in carbon metabolism by green nonsulfur-like bacteria in alkaline siliceous hot spring microbial mats from Yellowstone National Park. Appl Environ Microbiol 2005, 71(7):3978-3986. 10.1128/AEM.71.7.3978-3986.2005, 1168979, 16000812.
    • (2005) Appl Environ Microbiol , vol.71 , Issue.7 , pp. 3978-3986
    • Meer, M.T.J.1    Schouten, S.2    Bateson, M.M.3    Nübel, U.4    Wieland, A.5    Kühl, M.6    de Leeuw, J.W.7    Damste, J.S.S.8    Ward, D.M.9
  • 13
    • 0004122931 scopus 로고    scopus 로고
    • Biochemistry
    • Belmont, CA: Thomson Brooks/Cole, 3
    • Garrett R, Grisham CM. Biochemistry. 2005, Belmont, CA: Thomson Brooks/Cole, 3.
    • (2005)
    • Garrett, R.1    Grisham, C.M.2
  • 14
    • 0004110426 scopus 로고    scopus 로고
    • Principles of biochemistry
    • Upper Saddle River, NJ: Prentice Hall, 3
    • Horton HR. Principles of biochemistry. 2002, Upper Saddle River, NJ: Prentice Hall, 3.
    • (2002)
    • Horton, H.R.1
  • 15
    • 0001451404 scopus 로고
    • Formation and fate of fermentation products in hot spring cyanobacterial mats
    • 204111, 16347455
    • Anderson KL, Tayne TA, Ward DM. Formation and fate of fermentation products in hot spring cyanobacterial mats. Appl Environ Microbiol 1987, 53(10):2343-2352. 204111, 16347455.
    • (1987) Appl Environ Microbiol , vol.53 , Issue.10 , pp. 2343-2352
    • Anderson, K.L.1    Tayne, T.A.2    Ward, D.M.3
  • 16
    • 0026458643 scopus 로고
    • Accumulation and utilization of polysaccharide by hot spring phototrophs during a light-dark transition
    • Konopka A. Accumulation and utilization of polysaccharide by hot spring phototrophs during a light-dark transition. FEMS Microbiol Ecol 1992, 102(1):27-32.
    • (1992) FEMS Microbiol Ecol , vol.102 , Issue.1 , pp. 27-32
    • Konopka, A.1
  • 17
    • 0000793839 scopus 로고
    • Fate of immediate methane precursors in low-sulfate, hot-spring algal-bacterial mats
    • 243774, 16345736
    • Sandbeck KA, Ward DM. Fate of immediate methane precursors in low-sulfate, hot-spring algal-bacterial mats. Appl Environ Microbiol 1981, 41(3):775-782. 243774, 16345736.
    • (1981) Appl Environ Microbiol , vol.41 , Issue.3 , pp. 775-782
    • Sandbeck, K.A.1    Ward, D.M.2
  • 18
    • 0026613944 scopus 로고
    • Diurnal cycles of sulfate reduction under oxic conditions in cyanobacterial mats
    • 195174, 16348641
    • Fründ C, Cohen Y. Diurnal cycles of sulfate reduction under oxic conditions in cyanobacterial mats. Appl Environ Microbiol 1992, 58(1):70-77. 195174, 16348641.
    • (1992) Appl Environ Microbiol , vol.58 , Issue.1 , pp. 70-77
    • Fründ, C.1    Cohen, Y.2
  • 19
    • 33645075319 scopus 로고    scopus 로고
    • Ecology: from individuals to ecosystems
    • Malden, MA: Blackwell Pub, 4
    • Begon M, Townsend CR, Harper JL. Ecology: from individuals to ecosystems. 2006, Malden, MA: Blackwell Pub, 4.
    • (2006)
    • Begon, M.1    Townsend, C.R.2    Harper, J.L.3
  • 20
    • 0033080396 scopus 로고    scopus 로고
    • Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering
    • 10.1016/S0167-7799(98)01290-6, 10087604
    • Schuster S, Dandekar T, Fell DA. Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering. Trends Biotechnol 1999, 17(2):53-60. 10.1016/S0167-7799(98)01290-6, 10087604.
    • (1999) Trends Biotechnol , vol.17 , Issue.2 , pp. 53-60
    • Schuster, S.1    Dandekar, T.2    Fell, D.A.3
  • 21
    • 0034064689 scopus 로고    scopus 로고
    • A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
    • 10.1038/73786, 10700151
    • Schuster S, Fell DA, Dandekar T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat Biotechnol 2000, 18(3):326-332. 10.1038/73786, 10700151.
    • (2000) Nat Biotechnol , vol.18 , Issue.3 , pp. 326-332
    • Schuster, S.1    Fell, D.A.2    Dandekar, T.3
  • 22
    • 0000029295 scopus 로고
    • On elementary flux modes in biochemical reaction systems at steady state
    • Schuster S, Hilgetag C. On elementary flux modes in biochemical reaction systems at steady state. Journal of Biological Systems 1994, 2(2):165-182.
    • (1994) Journal of Biological Systems , vol.2 , Issue.2 , pp. 165-182
    • Schuster, S.1    Hilgetag, C.2
  • 23
    • 34447317252 scopus 로고    scopus 로고
    • Metabolic systems cost-benefit analysis for interpreting network structure and regulation
    • 10.1093/bioinformatics/btm082, 17344237
    • Carlson RP. Metabolic systems cost-benefit analysis for interpreting network structure and regulation. Bioinformatics 2007, 23(10):1258-1264. 10.1093/bioinformatics/btm082, 17344237.
    • (2007) Bioinformatics , vol.23 , Issue.10 , pp. 1258-1264
    • Carlson, R.P.1
  • 24
    • 58049200682 scopus 로고    scopus 로고
    • Decomposition of complex microbial behaviors into resource-based stress responses
    • 10.1093/bioinformatics/btn589, 19008248
    • Carlson RP. Decomposition of complex microbial behaviors into resource-based stress responses. Bioinformatics 2009, 25(1):90-97. 10.1093/bioinformatics/btn589, 19008248.
    • (2009) Bioinformatics , vol.25 , Issue.1 , pp. 90-97
    • Carlson, R.P.1
  • 25
    • 0142122303 scopus 로고    scopus 로고
    • Advances in flux balance analysis
    • 10.1016/j.copbio.2003.08.001, 14580578
    • Kauffman KJ, Prakash P, Edwards JS. Advances in flux balance analysis. Curr Opin Biotechnol 2003, 14(5):491-496. 10.1016/j.copbio.2003.08.001, 14580578.
    • (2003) Curr Opin Biotechnol , vol.14 , Issue.5 , pp. 491-496
    • Kauffman, K.J.1    Prakash, P.2    Edwards, J.S.3
  • 26
    • 0004218135 scopus 로고    scopus 로고
    • Metabolic engineering: Principles and methodologies
    • San Diego: Academic Press
    • Stephanopoulos GN, Aristidou AA, Nielsen JH. Metabolic engineering: Principles and methodologies. 1998, San Diego: Academic Press.
    • (1998)
    • Stephanopoulos, G.N.1    Aristidou, A.A.2    Nielsen, J.H.3
  • 28
    • 0037142769 scopus 로고    scopus 로고
    • Metabolic pathway analysis of a recombinant yeast for rational strain development
    • 10.1002/bit.10305, 12115428
    • Carlson RP, Fell DA, Srienc F. Metabolic pathway analysis of a recombinant yeast for rational strain development. Biotechnol Bioeng 2002, 79(2):121-134. 10.1002/bit.10305, 12115428.
    • (2002) Biotechnol Bioeng , vol.79 , Issue.2 , pp. 121-134
    • Carlson, R.P.1    Fell, D.A.2    Srienc, F.3
  • 29
    • 0022493181 scopus 로고
    • Fat synthesis in adipose tissue: An examination of stoichiometric constraints
    • 1147204, 3800960
    • Fell DA, Small JR. Fat synthesis in adipose tissue: An examination of stoichiometric constraints. Biochem J 1986, 238(3):781-786. 1147204, 3800960.
    • (1986) Biochem J , vol.238 , Issue.3 , pp. 781-786
    • Fell, D.A.1    Small, J.R.2
  • 30
    • 59649085782 scopus 로고    scopus 로고
    • Topological signatures of species interactions in metabolic networks
    • 10.1089/cmb.2008.06TT, 19178139
    • Borenstein E, Feldman MW. Topological signatures of species interactions in metabolic networks. J Comput Biol 2009, 16(2):191-200. 10.1089/cmb.2008.06TT, 19178139.
    • (2009) J Comput Biol , vol.16 , Issue.2 , pp. 191-200
    • Borenstein, E.1    Feldman, M.W.2
  • 31
    • 59449106950 scopus 로고    scopus 로고
    • Network-based approaches for linking metabolism with environment
    • 2614483, 19040774
    • Janga SC, Babu MM. Network-based approaches for linking metabolism with environment. Genome Biol 2008, 9(11):239. 2614483, 19040774.
    • (2008) Genome Biol , vol.9 , Issue.11 , pp. 239
    • Janga, S.C.1    Babu, M.M.2
  • 32
    • 0037316239 scopus 로고    scopus 로고
    • Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms
    • 10.1093/bioinformatics/19.2.270, 12538249
    • Ma HW, Zeng AP. Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 2003, 19(2):270-277. 10.1093/bioinformatics/19.2.270, 12538249.
    • (2003) Bioinformatics , vol.19 , Issue.2 , pp. 270-277
    • Ma, H.W.1    Zeng, A.P.2
  • 33
    • 1642465370 scopus 로고    scopus 로고
    • Phylogenetic comparison of metabolic capacities of organisms at genome level
    • 10.1016/j.ympev.2003.08.011, 15019620
    • Ma HW, Zeng AP. Phylogenetic comparison of metabolic capacities of organisms at genome level. Molecular Phylogenetics and Evolution 2004, 31(1):204-213. 10.1016/j.ympev.2003.08.011, 15019620.
    • (2004) Molecular Phylogenetics and Evolution , vol.31 , Issue.1 , pp. 204-213
    • Ma, H.W.1    Zeng, A.P.2
  • 34
    • 0042093610 scopus 로고    scopus 로고
    • The connectivity structure, giant strong component and centrality of metabolic networks
    • 10.1093/bioinformatics/btg177, 12874056
    • Ma HW, Zeng AP. The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics 2003, 19(11):1423-1430. 10.1093/bioinformatics/btg177, 12874056.
    • (2003) Bioinformatics , vol.19 , Issue.11 , pp. 1423-1430
    • Ma, H.W.1    Zeng, A.P.2
  • 35
    • 0036039060 scopus 로고    scopus 로고
    • Combinatorial complexity of pathway analysis in metabolic networks
    • 10.1023/A:1020390132244, 12241063
    • Klamt S, Stelling J. Combinatorial complexity of pathway analysis in metabolic networks. Molecular Biology Reports 2002, 29(1-2):233-236. 10.1023/A:1020390132244, 12241063.
    • (2002) Molecular Biology Reports , vol.29 , Issue.1-2 , pp. 233-236
    • Klamt, S.1    Stelling, J.2
  • 36
    • 0028946084 scopus 로고
    • Phylogenetic Identification and in situ Detection of Individual Microbial Cells without Cultivation
    • 239358, 7535888
    • Amann RI, Ludwig W, Schleifer KH. Phylogenetic Identification and in situ Detection of Individual Microbial Cells without Cultivation. Microbiological Reviews 1995, 59(1):143-169. 239358, 7535888.
    • (1995) Microbiological Reviews , vol.59 , Issue.1 , pp. 143-169
    • Amann, R.I.1    Ludwig, W.2    Schleifer, K.H.3
  • 37
    • 52949098408 scopus 로고    scopus 로고
    • Large-scale computation of elementary flux modes with bit pattern trees
    • 10.1093/bioinformatics/btn401, 18676417
    • Terzer M, Stelling J. Large-scale computation of elementary flux modes with bit pattern trees. Bioinformatics 2008, 24(19):2229-2235. 10.1093/bioinformatics/btn401, 18676417.
    • (2008) Bioinformatics , vol.24 , Issue.19 , pp. 2229-2235
    • Terzer, M.1    Stelling, J.2
  • 38
    • 0036188159 scopus 로고    scopus 로고
    • Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae
    • 10.1093/bioinformatics/18.2.351, 11847093
    • Schuster S, Pfeiffer T, Moldenhauer F, Koch I, Dandekar T. Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics 2002, 18(2):351-361. 10.1093/bioinformatics/18.2.351, 11847093.
    • (2002) Bioinformatics , vol.18 , Issue.2 , pp. 351-361
    • Schuster, S.1    Pfeiffer, T.2    Moldenhauer, F.3    Koch, I.4    Dandekar, T.5
  • 39
    • 4444233112 scopus 로고    scopus 로고
    • Biofilms promote altruism
    • 10.1099/mic.0.26829-0, 15289571
    • Kreft J-U. Biofilms promote altruism. Microbiology 2004, 150:2751-2760. 10.1099/mic.0.26829-0, 15289571.
    • (2004) Microbiology , vol.150 , pp. 2751-2760
    • Kreft, J.-.U.1
  • 40
    • 0035917865 scopus 로고    scopus 로고
    • Cooperation and competition in the evolution of ATP-producing pathways
    • 10.1126/science.1058079, 11283355
    • Pfeiffer T, Schuster S, Bonhoeffer S. Cooperation and competition in the evolution of ATP-producing pathways. Science 2001, 292(5516):504-507. 10.1126/science.1058079, 11283355.
    • (2001) Science , vol.292 , Issue.5516 , pp. 504-507
    • Pfeiffer, T.1    Schuster, S.2    Bonhoeffer, S.3
  • 41
    • 1842525835 scopus 로고    scopus 로고
    • Fundamental Escherichia coli biochemical pathways for biomass and energy production: Creation of overall flux states
    • 10.1002/bit.20044, 15052634
    • Carlson R, Srienc F. Fundamental Escherichia coli biochemical pathways for biomass and energy production: Creation of overall flux states. Biotechnol Bioeng 2004, 86(2):149-162. 10.1002/bit.20044, 15052634.
    • (2004) Biotechnol Bioeng , vol.86 , Issue.2 , pp. 149-162
    • Carlson, R.1    Srienc, F.2
  • 42
    • 0026052565 scopus 로고
    • Enzymology of the acetyl-coA pathway of CO2 fixation
    • 10.3109/10409239109114070, 1935170
    • Ragsdale SW. Enzymology of the acetyl-coA pathway of CO2 fixation. Crit Rev Biochem Mol Biol 1991, 26:261-300. 10.3109/10409239109114070, 1935170.
    • (1991) Crit Rev Biochem Mol Biol , vol.26 , pp. 261-300
    • Ragsdale, S.W.1
  • 43
    • 0034609791 scopus 로고    scopus 로고
    • The large-scale organization of metabolic networks
    • 10.1038/35036627, 11034217
    • Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi A-L. The large-scale organization of metabolic networks. Nature 2000, 407(6804):651-654. 10.1038/35036627, 11034217.
    • (2000) Nature , vol.407 , Issue.6804 , pp. 651-654
    • Jeong, H.1    Tombor, B.2    Albert, R.3    Oltvai, Z.N.4    Barabasi, A.-.L.5
  • 44
    • 0035823264 scopus 로고    scopus 로고
    • The small world inside large metabolic networks
    • Wagner A, Fell DA. The small world inside large metabolic networks. Proc R Soc Lond Ser B-Biol Sci 2001, 268(1478):1803-1810.
    • (2001) Proc R Soc Lond Ser B-Biol Sci , vol.268 , Issue.1478 , pp. 1803-1810
    • Wagner, A.1    Fell, D.A.2
  • 45
    • 34547684426 scopus 로고    scopus 로고
    • Computational approaches to the topology, stability and dynamics of metabolic networks
    • 10.1016/j.phytochem.2007.04.041, 17574639
    • Steuer R. Computational approaches to the topology, stability and dynamics of metabolic networks. Phytochemistry 2007, 68(16-18):2139-2151. 10.1016/j.phytochem.2007.04.041, 17574639.
    • (2007) Phytochemistry , vol.68 , Issue.16-18 , pp. 2139-2151
    • Steuer, R.1
  • 46
    • 13244292328 scopus 로고    scopus 로고
    • Computation of elementary modes: a unifying framework and the new binary approach
    • Gagneur J, Klamt S. Computation of elementary modes: a unifying framework and the new binary approach. BMC Bioinformatics 2004, 5:e175.
    • (2004) BMC Bioinformatics , vol.5
    • Gagneur, J.1    Klamt, S.2
  • 47
    • 0037079050 scopus 로고    scopus 로고
    • Metabolic network structure determines key aspects of functionality and regulation
    • 10.1038/nature01166, 12432396
    • Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED. Metabolic network structure determines key aspects of functionality and regulation. Nature 2002, 420(6912):190-193. 10.1038/nature01166, 12432396.
    • (2002) Nature , vol.420 , Issue.6912 , pp. 190-193
    • Stelling, J.1    Klamt, S.2    Bettenbrock, K.3    Schuster, S.4    Gilles, E.D.5
  • 48
    • 0027723421 scopus 로고
    • Metabolic capabilities of Escherichia coli: II. Optimal growth patterns
    • Varma A, Palsson B. Metabolic capabilities of Escherichia coli: II. Optimal growth patterns. J Theor Biol 1993, 165(4):503-522.
    • (1993) J Theor Biol , vol.165 , Issue.4 , pp. 503-522
    • Varma, A.1    Palsson, B.2
  • 49
    • 0036001069 scopus 로고    scopus 로고
    • Metabolic modelling of microbes: the flux-balance approach
    • 10.1046/j.1462-2920.2002.00282.x, 12000313
    • Edwards JS, Covert M, Palsson B. Metabolic modelling of microbes: the flux-balance approach. Environ Microbiol 2002, 4(3):133-140. 10.1046/j.1462-2920.2002.00282.x, 12000313.
    • (2002) Environ Microbiol , vol.4 , Issue.3 , pp. 133-140
    • Edwards, J.S.1    Covert, M.2    Palsson, B.3
  • 50
    • 0034625143 scopus 로고    scopus 로고
    • The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
    • 10.1073/pnas.97.10.5528, 25862, 10805808
    • Edwards JS, Palsson B. The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proc Natl Acad Sci USA 2000, 97(10):5528-5533. 10.1073/pnas.97.10.5528, 25862, 10805808.
    • (2000) Proc Natl Acad Sci USA , vol.97 , Issue.10 , pp. 5528-5533
    • Edwards, J.S.1    Palsson, B.2
  • 51
    • 15844365500 scopus 로고    scopus 로고
    • Phenotype phase plane analysis using interior point methods
    • Bell SL, Palsson B. Phenotype phase plane analysis using interior point methods. Comput Chem Eng 2005, 29(3):481-486.
    • (2005) Comput Chem Eng , vol.29 , Issue.3 , pp. 481-486
    • Bell, S.L.1    Palsson, B.2
  • 52
    • 34447523907 scopus 로고    scopus 로고
    • Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
    • Schuetz R, Kuepfer L, Sauer U. Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol Syst Biol 2007, 3:15.
    • (2007) Mol Syst Biol , vol.3 , pp. 15
    • Schuetz, R.1    Kuepfer, L.2    Sauer, U.3
  • 53
    • 43449132092 scopus 로고    scopus 로고
    • Is maximization of molar yield in metabolic networks favoured by evolution?
    • 10.1016/j.jtbi.2007.12.008, 18249414
    • Schuster S, Pfeiffer T, Fell DA. Is maximization of molar yield in metabolic networks favoured by evolution?. J Theor Biol 2008, 252(3):497-504. 10.1016/j.jtbi.2007.12.008, 18249414.
    • (2008) J Theor Biol , vol.252 , Issue.3 , pp. 497-504
    • Schuster, S.1    Pfeiffer, T.2    Fell, D.A.3
  • 54
    • 84906625278 scopus 로고    scopus 로고
    • Environment: The science behind the stories
    • San Francisco: Pearson Benjamin Cummings, 2
    • Withgott J, Brennan SR. Environment: The science behind the stories. 2007, San Francisco: Pearson Benjamin Cummings, 2.
    • (2007)
    • Withgott, J.1    Brennan, S.R.2
  • 55
    • 33751210106 scopus 로고    scopus 로고
    • Cyanobacterial ecotypes in the microbial mat community of Mushroom Spring (Yellowstone National Park, Wyoming) as species-like units linking microbial community composition, structure and function
    • 10.1098/rstb.2006.1919, 1764927, 17028085
    • Ward DM, Bateson MM, Ferris MJ, Kühl M, Wieland A, Koeppel A, Cohan FM. Cyanobacterial ecotypes in the microbial mat community of Mushroom Spring (Yellowstone National Park, Wyoming) as species-like units linking microbial community composition, structure and function. Philos Trans R Soc Lond B Biol Sci 2006, 361(1475):1997-2008. 10.1098/rstb.2006.1919, 1764927, 17028085.
    • (2006) Philos Trans R Soc Lond B Biol Sci , vol.361 , Issue.1475 , pp. 1997-2008
    • Ward, D.M.1    Bateson, M.M.2    Ferris, M.J.3    Kühl, M.4    Wieland, A.5    Koeppel, A.6    Cohan, F.M.7
  • 56
    • 0019255001 scopus 로고
    • Selective Neutrality of 6pgd Allozymes in Escherichia coli and the Effects of Genetic Background
    • 1219302, 7021316
    • Dykhuizen D, Hartl DL. Selective Neutrality of 6pgd Allozymes in Escherichia coli and the Effects of Genetic Background. Genetics 1980, 96(4):801-817. 1219302, 7021316.
    • (1980) Genetics , vol.96 , Issue.4 , pp. 801-817
    • Dykhuizen, D.1    Hartl, D.L.2
  • 57
    • 33845369271 scopus 로고    scopus 로고
    • Occurrence of hydrogenases in cyanobacteria and anoxygenic photosynthetic bacteria: Implications for the phylogenetic origin of cyanobacterial and algal hydrogenases
    • 10.1007/s00239-006-0001-6, 17103058
    • Ludwig M, Schulz-Friedrich R, Appel J. Occurrence of hydrogenases in cyanobacteria and anoxygenic photosynthetic bacteria: Implications for the phylogenetic origin of cyanobacterial and algal hydrogenases. J Mol Evol 2006, 63(6):758-768. 10.1007/s00239-006-0001-6, 17103058.
    • (2006) J Mol Evol , vol.63 , Issue.6 , pp. 758-768
    • Ludwig, M.1    Schulz-Friedrich, R.2    Appel, J.3
  • 59
    • 34447321098 scopus 로고    scopus 로고
    • Comparative genomics provides evidence for the 3-hydroxypropionate autotrophic pathway in filamentous anoxygenic phototrophic bacteria and in hot spring microbial mats
    • 10.1111/j.1462-2920.2007.01323.x, 17635550
    • Klatt CG, Bryant DA, Ward DM. Comparative genomics provides evidence for the 3-hydroxypropionate autotrophic pathway in filamentous anoxygenic phototrophic bacteria and in hot spring microbial mats. Environ Microbiol 2007, 9(8):2067-2078. 10.1111/j.1462-2920.2007.01323.x, 17635550.
    • (2007) Environ Microbiol , vol.9 , Issue.8 , pp. 2067-2078
    • Klatt, C.G.1    Bryant, D.A.2    Ward, D.M.3
  • 60
    • 84928648280 scopus 로고    scopus 로고
    • Sulphate-reducing bacteria: Environmental and engineered systems
    • Cambridge; New York: Cambridge University Press
    • Barton L, Hamilton WA. Sulphate-reducing bacteria: Environmental and engineered systems. 2007, Cambridge; New York: Cambridge University Press.
    • (2007)
    • Barton, L.1    Hamilton, W.A.2
  • 61
    • 0027954493 scopus 로고
    • Characterization of a new thermophilic sulfate-reducing bacterium Thermodesulfovibrio yellowstonii, gen. nov. and sp. nov.: Its phylogenetic relationship to Thermodesulfobacterium commune and their origins deep within the bacterial domain
    • 10.1007/BF00248894, 11541228
    • Henry EA, Devereux R, Maki JS, Gilmour CC, Woese CR, Mandelco L, Schauder R, Remsen CC, Mitchell R. Characterization of a new thermophilic sulfate-reducing bacterium Thermodesulfovibrio yellowstonii, gen. nov. and sp. nov.: Its phylogenetic relationship to Thermodesulfobacterium commune and their origins deep within the bacterial domain. Arch Microbiol 1994, 161(1):62-69. 10.1007/BF00248894, 11541228.
    • (1994) Arch Microbiol , vol.161 , Issue.1 , pp. 62-69
    • Henry, E.A.1    Devereux, R.2    Maki, J.S.3    Gilmour, C.C.4    Woese, C.R.5    Mandelco, L.6    Schauder, R.7    Remsen, C.C.8    Mitchell, R.9
  • 62
    • 33644520519 scopus 로고    scopus 로고
    • The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide
    • 10.1093/nar/gkj145, 1347507, 16381880
    • Liolios K, Tavernarakis N, Hugenholtz P, Kyrpides NC. The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res 2006, 34:D332-D334. 10.1093/nar/gkj145, 1347507, 16381880.
    • (2006) Nucleic Acids Res , vol.34
    • Liolios, K.1    Tavernarakis, N.2    Hugenholtz, P.3    Kyrpides, N.C.4
  • 63
    • 0004143241 scopus 로고    scopus 로고
    • The physiology and biochemistry of prokaryotes
    • New York: Oxford University Press, 3
    • White D. The physiology and biochemistry of prokaryotes. 2007, New York: Oxford University Press, 3.
    • (2007)
    • White, D.1
  • 64
    • 34547840249 scopus 로고    scopus 로고
    • Using genome-context data to identify specific types of functional associations in pathway/genome databases
    • 10.1093/bioinformatics/btm213, 17646298
    • Green ML, Karp PD. Using genome-context data to identify specific types of functional associations in pathway/genome databases. Bioinformatics 2007, 23(13):I205-I211. 10.1093/bioinformatics/btm213, 17646298.
    • (2007) Bioinformatics , vol.23 , Issue.13
    • Green, M.L.1    Karp, P.D.2
  • 65
    • 0001030739 scopus 로고
    • Microelectrode studies of interstitial water chemistry and photosynthetic activity in a hot spring microbial mat
    • 241501, 16346607
    • Revsbech NP, Ward DM. Microelectrode studies of interstitial water chemistry and photosynthetic activity in a hot spring microbial mat. Appl Environ Microbiol 1984, 48(2):270-275. 241501, 16346607.
    • (1984) Appl Environ Microbiol , vol.48 , Issue.2 , pp. 270-275
    • Revsbech, N.P.1    Ward, D.M.2
  • 66
    • 34447551397 scopus 로고    scopus 로고
    • Structural and functional analysis of cellular networks with CellNetAnalyzer
    • Klamt S, Saez-Rodriguez J, Gilles ED. Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Systems Biology 2007, 1:e2.
    • (2007) BMC Systems Biology , vol.1
    • Klamt, S.1    Saez-Rodriguez, J.2    Gilles, E.D.3
  • 67
    • 31144448020 scopus 로고    scopus 로고
    • Algorithmic approaches for computing elementary modes in large biochemical reaction networks
    • Klamt S, Gagneur J, von Kamp A. Algorithmic approaches for computing elementary modes in large biochemical reaction networks. Syst Biol (Stevenage) 2005, 152(4):249-255.
    • (2005) Syst Biol (Stevenage) , vol.152 , Issue.4 , pp. 249-255
    • Klamt, S.1    Gagneur, J.2    von Kamp, A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.