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1
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33744804299
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Metagenomic analysis of the human distal gut microbiome
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The first large-scale analysis of a human-associated microbiome.
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Gill S.R., Pop M., Deboy R.T., Eckburg P.B., Turnbaugh P.J., Samuel B.S., Gordon J.I., Relman D.A., Fraser-Liggett C.M., and Nelson K.E. Metagenomic analysis of the human distal gut microbiome. Science 312 (2006) 1355-1359. The first large-scale analysis of a human-associated microbiome.
-
(2006)
Science
, vol.312
, pp. 1355-1359
-
-
Gill, S.R.1
Pop, M.2
Deboy, R.T.3
Eckburg, P.B.4
Turnbaugh, P.J.5
Samuel, B.S.6
Gordon, J.I.7
Relman, D.A.8
Fraser-Liggett, C.M.9
Nelson, K.E.10
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2
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33750003359
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Symbiosis
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This 'primer' provides definitions and examples for different forms of symbiosis, and as such lays a framework for comparative studies of different biological systems where coevolution or codiversification is thought to occur.
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Moran N.A. Symbiosis. Curr Biol 16 (2006) R866-R871. This 'primer' provides definitions and examples for different forms of symbiosis, and as such lays a framework for comparative studies of different biological systems where coevolution or codiversification is thought to occur.
-
(2006)
Curr Biol
, vol.16
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Moran, N.A.1
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3
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31344454634
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Traversing the tangle: algorithms and applications for cophylogenetic studies
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Useful recent review of methods for testing codivergence, including the discussion of the strengths and weaknesses of the conceptual underpinnings of several of the methods.
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Charleston M.A., and Perkins S.L. Traversing the tangle: algorithms and applications for cophylogenetic studies. J Biomed Inform 39 (2006) 62-71. Useful recent review of methods for testing codivergence, including the discussion of the strengths and weaknesses of the conceptual underpinnings of several of the methods.
-
(2006)
J Biomed Inform
, vol.39
, pp. 62-71
-
-
Charleston, M.A.1
Perkins, S.L.2
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4
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21644432975
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Computational aspects of host-parasite phylogenies
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Exceptionally clear review of methods for testing for codivergence between hosts and parasites (or symbionts). Includes notes on the availability of the different methods.
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Stevens J. Computational aspects of host-parasite phylogenies. Brief Bioinform 5 (2004) 339-349. Exceptionally clear review of methods for testing for codivergence between hosts and parasites (or symbionts). Includes notes on the availability of the different methods.
-
(2004)
Brief Bioinform
, vol.5
, pp. 339-349
-
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Stevens, J.1
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5
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0027132264
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Microbiological studies of the intestinal microflora of the Koala, Phascolarctos cinereus. 2. Pap, a special maternal feces consumed by Juvenile Koalas
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Osawa R., Blanshard W.H., and Ocallaghan P.G. Microbiological studies of the intestinal microflora of the Koala, Phascolarctos cinereus. 2. Pap, a special maternal feces consumed by Juvenile Koalas. Aust J Zool 41 (1993) 611-620
-
(1993)
Aust J Zool
, vol.41
, pp. 611-620
-
-
Osawa, R.1
Blanshard, W.H.2
Ocallaghan, P.G.3
-
6
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35348961403
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An ecological and evolutionary perspective on human-microbe mutualism and disease
-
Dethlefsen L., McFall-Ngai M., and Relman D.A. An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature 449 (2007) 811-818
-
(2007)
Nature
, vol.449
, pp. 811-818
-
-
Dethlefsen, L.1
McFall-Ngai, M.2
Relman, D.A.3
-
7
-
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29144464937
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UniFrac: a new phylogenetic method for comparing microbial communities
-
Lozupone C., and Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71 (2005) 8228-8235
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 8228-8235
-
-
Lozupone, C.1
Knight, R.2
-
8
-
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0035843908
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Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis
-
Ochman H., and Moran N.A. Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 292 (2001) 1096-1099
-
(2001)
Science
, vol.292
, pp. 1096-1099
-
-
Ochman, H.1
Moran, N.A.2
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9
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33745208719
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Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters
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A fascinating study of the genomic consequences of host-symbiont evolution in insects, showing how the symbiont can allow the host to become a crop pest.
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Wu D., Daugherty S.C., Van Aken S.E., Pai G.H., Watkins K.L., Khouri H., Tallon L.J., Zaborsky J.M., Dunbar H.E., Tran P.L., et al. Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. PLoS Biol 4 (2006) e188. A fascinating study of the genomic consequences of host-symbiont evolution in insects, showing how the symbiont can allow the host to become a crop pest.
-
(2006)
PLoS Biol
, vol.4
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Wu, D.1
Daugherty, S.C.2
Van Aken, S.E.3
Pai, G.H.4
Watkins, K.L.5
Khouri, H.6
Tallon, L.J.7
Zaborsky, J.M.8
Dunbar, H.E.9
Tran, P.L.10
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10
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34547163007
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Obligate symbiont involved in pest status of host insect
-
Hosokawa T., Kikuchi Y., Shimada M., and Fukatsu T. Obligate symbiont involved in pest status of host insect. Proc Biol Sci 274 (2007) 1979-1984
-
(2007)
Proc Biol Sci
, vol.274
, pp. 1979-1984
-
-
Hosokawa, T.1
Kikuchi, Y.2
Shimada, M.3
Fukatsu, T.4
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11
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34447516925
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Evolution of symbiotic bacteria in the distal human intestine
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A comparative genomic analysis of multiple human gut symbionts that demonstrates the importance of horizontal gene transfer in shaping gut genomes.
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Xu J., Mahowald M.A., Ley R.E., Lozupone C.A., Hamady M., Martens E.C., Henrissat B., Coutinho P.M., Minx P., Latreille P., et al. Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol 5 (2007) e156. A comparative genomic analysis of multiple human gut symbionts that demonstrates the importance of horizontal gene transfer in shaping gut genomes.
-
(2007)
PLoS Biol
, vol.5
-
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Xu, J.1
Mahowald, M.A.2
Ley, R.E.3
Lozupone, C.A.4
Hamady, M.5
Martens, E.C.6
Henrissat, B.7
Coutinho, P.M.8
Minx, P.9
Latreille, P.10
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12
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15544376418
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Glycan foraging in vivo by an intestine-adapted bacterial symbiont
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Functional genomic analyses of a prominent human gut symbiont in gnotobiotic mice.
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Sonnenburg J.L., Xu J., Leip D.D., Chen C.H., Westover B.P., Weatherford J., Buhler J.D., and Gordon J.I. Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 307 (2005) 1955-1959. Functional genomic analyses of a prominent human gut symbiont in gnotobiotic mice.
-
(2005)
Science
, vol.307
, pp. 1955-1959
-
-
Sonnenburg, J.L.1
Xu, J.2
Leip, D.D.3
Chen, C.H.4
Westover, B.P.5
Weatherford, J.6
Buhler, J.D.7
Gordon, J.I.8
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13
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34447296622
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Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut
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Samuel B.S., Hansen E.E., Manchester J.K., Coutinho P.M., Henrissat B., Fulton R., Latreille P., Kim K., Wilson R.K., and Gordon J.I. Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc Natl Acad Sci U S A 104 (2007) 10643-10648
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 10643-10648
-
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Samuel, B.S.1
Hansen, E.E.2
Manchester, J.K.3
Coutinho, P.M.4
Henrissat, B.5
Fulton, R.6
Latreille, P.7
Kim, K.8
Wilson, R.K.9
Gordon, J.I.10
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14
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35348968286
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The human microbiome project
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A overview and prospectus of the recently initiated international effort to understand the microbiome of multiple human-associated habitats.
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Turnbaugh P.J., Ley R.E., Hamady M., Fraser-Liggett C.M., Knight R., and Gordon J.I. The human microbiome project. Nature 449 (2007) 804-810. A overview and prospectus of the recently initiated international effort to understand the microbiome of multiple human-associated habitats.
-
(2007)
Nature
, vol.449
, pp. 804-810
-
-
Turnbaugh, P.J.1
Ley, R.E.2
Hamady, M.3
Fraser-Liggett, C.M.4
Knight, R.5
Gordon, J.I.6
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15
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38449088143
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Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
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Kurokawa K., Itoh T., Kuwahara T., Oshima K., Toh H., Toyoda A., Takami H., Morita H., Sharma V.K., Srivastava T.P., et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 14 (2007) 169-181
-
(2007)
DNA Res
, vol.14
, pp. 169-181
-
-
Kurokawa, K.1
Itoh, T.2
Kuwahara, T.3
Oshima, K.4
Toh, H.5
Toyoda, A.6
Takami, H.7
Morita, H.8
Sharma, V.K.9
Srivastava, T.P.10
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16
-
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0036176262
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Analyses of the evolutionary distribution of Salmonella translocated effectors
-
Hansen-Wester I., Stecher B., and Hensel M. Analyses of the evolutionary distribution of Salmonella translocated effectors. Infect Immun 70 (2002) 1619-1622
-
(2002)
Infect Immun
, vol.70
, pp. 1619-1622
-
-
Hansen-Wester, I.1
Stecher, B.2
Hensel, M.3
-
17
-
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4644369350
-
Evolution of pathogenicity islands of Salmonella enterica
-
Hensel M. Evolution of pathogenicity islands of Salmonella enterica. Int J Med Microbiol 294 (2004) 95-102
-
(2004)
Int J Med Microbiol
, vol.294
, pp. 95-102
-
-
Hensel, M.1
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18
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34547632567
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Disrupting antibiotic resistance propagation by inhibiting the conjugative DNA relaxase
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This study demonstrates that several bisphosphonate compounds, including two already in clinical use in other applications, serve as inhibitors of the TraI relaxase in vitro and conjugative F plasmid transfer in vivo.
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Lujan S.A., Guogas L.M., Ragonese H., Matson S.W., and Redinbo M.R. Disrupting antibiotic resistance propagation by inhibiting the conjugative DNA relaxase. Proc Natl Acad Sci U S A 104 (2007) 12282-12287. This study demonstrates that several bisphosphonate compounds, including two already in clinical use in other applications, serve as inhibitors of the TraI relaxase in vitro and conjugative F plasmid transfer in vivo.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 12282-12287
-
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Lujan, S.A.1
Guogas, L.M.2
Ragonese, H.3
Matson, S.W.4
Redinbo, M.R.5
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19
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37849049329
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Design, synthesis, and multivariate quantitative structure-activity relationship of salicylanilides-potent inhibitors of type III secretion in yersinia
-
Dahlgren M.K., Kauppi A.M., Olsson I.M., Linusson A., and Elofsson M. Design, synthesis, and multivariate quantitative structure-activity relationship of salicylanilides-potent inhibitors of type III secretion in yersinia. J Med Chem 50 (2007) 6177-6188
-
(2007)
J Med Chem
, vol.50
, pp. 6177-6188
-
-
Dahlgren, M.K.1
Kauppi, A.M.2
Olsson, I.M.3
Linusson, A.4
Elofsson, M.5
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20
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55449094978
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Evidence of a large novel gene pool associated with prokaryotic genomic islands
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This bioinformatics study demonstrates that genomic islands are enriched in genes of unknown function.
-
Hsiao W.W., Ung K., Aeschliman D., Bryan J., Finlay B.B., and Brinkman F.S. Evidence of a large novel gene pool associated with prokaryotic genomic islands. PLoS Genet 1 (2005) e62. This bioinformatics study demonstrates that genomic islands are enriched in genes of unknown function.
-
(2005)
PLoS Genet
, vol.1
-
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Hsiao, W.W.1
Ung, K.2
Aeschliman, D.3
Bryan, J.4
Finlay, B.B.5
Brinkman, F.S.6
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21
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34247237333
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Identification of novel genes in genomic islands that contribute to Salmonella typhimurium replication in macrophages
-
Klumpp J., and Fuchs T.M. Identification of novel genes in genomic islands that contribute to Salmonella typhimurium replication in macrophages. Microbiology 153 (2007) 1207-1220
-
(2007)
Microbiology
, vol.153
, pp. 1207-1220
-
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Klumpp, J.1
Fuchs, T.M.2
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22
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35549007148
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Short pyrosequencing reads suffice for accurate microbial community analysis
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Liu Z., Lozupone C., Hamady M., Bushman F.D., and Knight R. Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res 35 (2007) e120
-
(2007)
Nucleic Acids Res
, vol.35
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Liu, Z.1
Lozupone, C.2
Hamady, M.3
Bushman, F.D.4
Knight, R.5
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23
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33845874101
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An obesity-associated gut microbiome with increased capacity for energy harvest
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A demonstration that comparative metagenomics of complex microbial communities using short pyrosequencing reads, coupled to gnotobiotics, can be used to identify and test novel hypotheses.
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Turnbaugh P.J., Ley R.E., Mahowald M.A., Magrini V., Mardis E.R., and Gordon J.I. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444 (2006) 1027-1031. A demonstration that comparative metagenomics of complex microbial communities using short pyrosequencing reads, coupled to gnotobiotics, can be used to identify and test novel hypotheses.
-
(2006)
Nature
, vol.444
, pp. 1027-1031
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Turnbaugh, P.J.1
Ley, R.E.2
Mahowald, M.A.3
Magrini, V.4
Mardis, E.R.5
Gordon, J.I.6
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24
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20244376755
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Comparative metagenomics of microbial communities
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An early demonstration that comparative metagenomics can reveal specific genes that are important for the microorganisms in a specific environment.
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Tringe S.G., von Mering C., Kobayashi A., Salamov A.A., Chen K., Chang H.W., Podar M., Short J.M., Mathur E.J., Detter J.C., et al. Comparative metagenomics of microbial communities. Science 308 (2005) 554-557. An early demonstration that comparative metagenomics can reveal specific genes that are important for the microorganisms in a specific environment.
-
(2005)
Science
, vol.308
, pp. 554-557
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Tringe, S.G.1
von Mering, C.2
Kobayashi, A.3
Salamov, A.A.4
Chen, K.5
Chang, H.W.6
Podar, M.7
Short, J.M.8
Mathur, E.J.9
Detter, J.C.10
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