-
1
-
-
33645450631
-
Brief report statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes
-
Abdo, Z., Schüette, U. M., Bent, S. J., Williams, C. J., Forney, L. J., and Joyce, P. (2006). Brief report statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes. Environ. Microbiol. 8, 929-938.
-
(2006)
Environ. Microbiol.
, vol.8
, pp. 929-938
-
-
Abdo, Z.1
Schüette, U.M.2
Bent, S.J.3
Williams, C.J.4
Forney, L.J.5
Joyce, P.6
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J. H., Zhang, Z., Miller, W., and Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.H.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
3
-
-
40549120596
-
The RAST Server: rapid annotations using subsystems technology
-
doi:10.1186/1471-2164-9-75
-
Aziz, R. K., Bartels, D., Best, A. A, DeJongh, M., Disz, T., Edwards, R. A, Formsma, K., Gerdes, S., Glass, E. M., Kubal, M., Meyer, F., Olsen, G. J., Olson, R., Osterman, A. L., Overbeek, R., McNeil, L. K., Paarmann, D., Paczian, T., Parrello, B., Pusch, G. D., Reich, C., Stevens, R., Vassieva, O., Vonstein, V., Wilke, A., and Zagnitko, O. (2008). The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9, 75. doi:10.1186/1471-2164-9-75.
-
(2008)
BMC Genomics
, vol.9
, pp. 75
-
-
Aziz, R.K.1
Bartels, D.2
Best, A.A.3
DeJongh, M.4
Disz, T.5
Edwards, R.A.6
Formsma, K.7
Gerdes, S.8
Glass, E.M.9
Kubal, M.10
Meyer, F.11
Olsen, G.J.12
Olson, R.13
Osterman, A.L.14
Overbeek, R.15
McNeil, L.K.16
Paarmann, D.17
Paczian, T.18
Parrello, B.19
Pusch, G.D.20
Reich, C.21
Stevens, R.22
Vassieva, O.23
Vonstein, V.24
Wilke, A.25
Zagnitko, O.26
more..
-
4
-
-
33644821142
-
Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru
-
Biddle, J. F., Lipp, J. S., Lever, M. A., Lloyd, K. G., Sørensen, K. B., Anderson, R., Fredricks, H. F., Elvert, M., Kelly, T. J., Schrag, D. P., Sogin, M. L., Brenchley, J. E., Teske, A., House, C. H., and Hinrichs, K. (2006). Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. Proc. Natl. Acad. Sci. U.S.A. 103, 3846-3851.
-
(2006)
Proc. Natl. Acad. Sci. U. S. A
, vol.103
, pp. 3846-3851
-
-
Biddle, J.F.1
Lipp, J.S.2
Lever, M.A.3
Lloyd, K.G.4
Sørensen, K.B.5
Anderson, R.6
Fredricks, H.F.7
Elvert, M.8
Kelly, T.J.9
Schrag, D.P.10
Sogin, M.L.11
Brenchley, J.E.12
Teske, A.13
House, C.H.14
Hinrichs, K.15
-
5
-
-
78649448514
-
[FeFe]-Hydrogenase in Yellowstone National Park: evidence for dispersal limitation and phylogenetic niche conservatism
-
Boyd, E. S., Hamilton, T. L., Spear, J. R., Lavin, M., and Peters, J. W. (2010). [FeFe]-Hydrogenase in Yellowstone National Park: evidence for dispersal limitation and phylogenetic niche conservatism. ISME J. 4, 1485-1495.
-
(2010)
ISME J
, vol.4
, pp. 1485-1495
-
-
Boyd, E.S.1
Hamilton, T.L.2
Spear, J.R.3
Lavin, M.4
Peters, J.W.5
-
6
-
-
67649621650
-
[FeFe] Hydrogenase genetic diversity provides insight into molecular adaptation in a saline microbial mat community
-
Boyd, E. S., Spear, J. R., and Peters, J. W. (2009). [FeFe] Hydrogenase genetic diversity provides insight into molecular adaptation in a saline microbial mat community. Appl. Environ. Microbiol. 75, 4620-4623.
-
(2009)
Appl. Environ. Microbiol
, vol.75
, pp. 4620-4623
-
-
Boyd, E.S.1
Spear, J.R.2
Peters, J.W.3
-
8
-
-
72649088719
-
Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm
-
Brazelton, W J., and Baross, J. A. (2009). Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm. ISME J. 3, 1420-1424.
-
(2009)
ISME J
, vol.3
, pp. 1420-1424
-
-
Brazelton, W.J.1
Baross, J.A.2
-
9
-
-
78149422269
-
Metagenomic comparison of two thiomicrospira lineages inhabiting contrasting deep-sea hydrothermal environments
-
doi:10.1371/journal.pone.0013530
-
Brazelton, W J., and Baross, J. A. (2010). Metagenomic comparison of two thiomicrospira lineages inhabiting contrasting deep-sea hydrothermal environments. PLoS ONE 5, e13530. doi:10.1371/journal.pone.0013530.
-
(2010)
PLoS ONE
, vol.5
-
-
Brazelton, W.J.1
Baross, J.A.2
-
10
-
-
76549087358
-
Archaea and bacteria with surprising microdiversity show shifts in dominance over 1000-year time scales in hydrothermal chimneys
-
Brazelton, W J., Ludwig, K. A., Sogin, M. L., Andreishcheva, E. N., Kelley, D. S., Shen, C.-C., Edwards, R. L., and Baross, J. A. (2010). Archaea and bacteria with surprising microdiversity show shifts in dominance over 1000-year time scales in hydrothermal chimneys. Proc. Natl. Acad. Sci. U.S.A. 107, 1612-1617.
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, pp. 1612-1617
-
-
Brazelton, W.J.1
Ludwig, K.A.2
Sogin, M.L.3
Andreishcheva, E.N.4
Kelley, D.S.5
Shen, C.-C.6
Edwards, R.L.7
Baross, J.A.8
-
11
-
-
80052574209
-
Physiological differentiation within a single-species biofilm fueled by serpentinization
-
127-11
-
Brazelton, W J., Mehta, M. P., Kelley, D. S., and Baross, J. A. (2011). Physiological differentiation within a single-species biofilm fueled by serpentinization. MBio. 2, e00 127-11.
-
(2011)
MBio
, vol.2
-
-
Brazelton, W.J.1
Mehta, M.P.2
Kelley, D.S.3
Baross, J.A.4
-
12
-
-
33748777657
-
Methane- and sulfur-metabolizing microbial communities dominate the Lost City hydrothermal field ecosystem
-
Brazelton, W J., Schrenk, M. O., Kelley, D. S., and Baross, J. A. (2006). Methane- and sulfur-metabolizing microbial communities dominate the Lost City hydrothermal field ecosystem. Appl. Environ. Microbiol. 72, 6257-6270.
-
(2006)
Appl. Environ. Microbiol.
, vol.72
, pp. 6257-6270
-
-
Brazelton, W.J.1
Schrenk, M.O.2
Kelley, D.S.3
Baross, J.A.4
-
13
-
-
0347823003
-
MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences
-
doi:10.1186/1471-2105-4-29
-
Campanella, J. J., Bitincka, L., and Smalley, J. (2003). MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. BMC Bioinformatics 4, 29. doi:10.1186/1471-2105-4-29.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 29
-
-
Campanella, J.J.1
Bitincka, L.2
Smalley, J.3
-
14
-
-
53749096964
-
Environmental genomics reveals a single-species ecosystem deep within Earth
-
Chivian, D., Brodie, E. L, Aim, E. J., Culley, D. E., Dehal, P. S., DeSantis, T. Z., Gihring, T. M., Lapidus, A., Lin, L.-H., Lowry, S. R., Moser, D. P., Richardson, P. M., Southam, G., Wanger, G., Pratt, L. M., Andersen, G. L., Hazen, T. C., Brockman, E J., Arkin, A. P., and Onstott, T. C. (2008). Environmental genomics reveals a single-species ecosystem deep within Earth. Science 322, 275-278.
-
(2008)
Science
, vol.322
, pp. 275-278
-
-
Chivian, D.1
Brodie, E.L.2
Aim, E.J.3
Culley, D.E.4
Dehal, P.S.5
DeSantis, T.Z.6
Gihring, T.M.7
Lapidus, A.8
Lin, L.-H.9
Lowry, S.R.10
Moser, D.P.11
Richardson, P.M.12
Southam, G.13
Wanger, G.14
Pratt, L.M.15
Andersen, G.L.16
Hazen, T.C.17
Brockman, E.J.18
Arkin, A.P.19
Onstott, T.C.20
more..
-
15
-
-
79953029156
-
Correlating carbon monoxide oxidation with cox genes in the abundant Marine Roseobacter Clade
-
Cunliffe, M. (2011). Correlating carbon monoxide oxidation with cox genes in the abundant Marine Roseobacter Clade. ISME J. 5, 685-691.
-
(2011)
ISME J
, vol.5
, pp. 685-691
-
-
Cunliffe, M.1
-
16
-
-
46749108474
-
Phylogenetic and functional gene analysis of the bacterial and archaeal communities associated with the surface micro -layer of an estuary
-
Cunliffe, M., Schäfer, H., Harrison, E., Cleave, S., Upstill-Goddard, R., and Murrell, J. C. (2008). Phylogenetic and functional gene analysis of the bacterial and archaeal communities associated with the surface micro -layer of an estuary. ISME J. 2, 776-789.
-
(2008)
ISME J
, vol.2
, pp. 776-789
-
-
Cunliffe, M.1
Schäfer, H.2
Harrison, E.3
Cleave, S.4
Upstill-Goddard, R.5
Murrell, J.C.6
-
17
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
18
-
-
38549146894
-
The Pfam protein fami lies database
-
Finn, R. D., Tate, J., Mistry, J., Coggill, P. C., Sammut, S. J., Hotz, H.-R., Ceric, G., Forslund, K., Eddy, S. R., Sonnhammer, E. L, and Bateman, A. (2008). The Pfam protein fami lies database. Nucleic Acids Res. 36, D281-D288.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Finn, R.D.1
Tate, J.2
Mistry, J.3
Coggill, P.C.4
Sammut, S.J.5
Hotz, H.-R.6
Ceric, G.7
Forslund, K.8
Eddy, S.R.9
Sonnhammer, E.L.10
Bateman, A.11
-
19
-
-
55249109000
-
The genome organization of Ralstonia eutropha strain H16 and related species of the Burkholderiaceae
-
Fricke, W. F., Kusian, B., and Bowien, B. (2009). The genome organization of Ralstonia eutropha strain H16 and related species of the Burkholderiaceae. J. Mol. Microbiol. Biotechnol. 16, 124-135.
-
(2009)
J. Mol. Microbiol. Biotechnol.
, vol.16
, pp. 124-135
-
-
Fricke, W.F.1
Kusian, B.2
Bowien, B.3
-
20
-
-
78650355798
-
Functional gene analysis suggests different acetogen populations in the bovine rumen and tammar wallaby forestomach
-
Gagen, E. J., Denman, S. E., Padmanabha, J., Zadbuke, S., Al Jassim, R., Morrison, M., and McSweeney, C. S. (2010). Functional gene analysis suggests different acetogen populations in the bovine rumen and tammar wallaby forestomach. Appl. Environ. Microbiol. 76, 7785-7795.
-
(2010)
Appl. Environ. Microbiol.
, vol.76
, pp. 7785-7795
-
-
Gagen, E.J.1
Denman, S.E.2
Padmanabha, J.3
Zadbuke, S.4
Al Jassim, R.5
Morrison, M.6
McSweeney, C.S.7
-
21
-
-
70350294348
-
Systematic artifacts in metagenomes from complex microbial communities
-
Gomez-Alvarez, V., Teal, T. K., and Schmidt, T. M. (2009). Systematic artifacts in metagenomes from complex microbial communities. ISME J. 3, 1314-1317.
-
(2009)
ISME J
, vol.3
, pp. 1314-1317
-
-
Gomez-Alvarez, V.1
Teal, T.K.2
Schmidt, T.M.3
-
22
-
-
0036211208
-
Temporal changes in archaeal diversity and chemistry in a mid-ocean ridge subseafloor habitat
-
Huber, J. A., Butterfield, D. A., and Baross, J. A. (2002). Temporal changes in archaeal diversity and chemistry in a mid-ocean ridge subseafloor habitat. Appl. Environ. Microbiol. 68, 1585-1594.
-
(2002)
Appl. Environ. Microbiol.
, vol.68
, pp. 1585-1594
-
-
Huber, J.A.1
Butterfield, D.A.2
Baross, J.A.3
-
23
-
-
35148888609
-
Microbial population structures in the deep marine biosphere
-
Huber, J. A, Mark Welch, D. B., Morrison, H. G., Huse, S. M., Neal, P. R., Butterfield, D. A., and Sogin, M. L. (2007). Microbial population structures in the deep marine biosphere. Science 318, 97-100.
-
(2007)
Science
, vol.318
, pp. 97-100
-
-
Huber, J.A.1
Mark Welch, D.B.2
Morrison, H.G.3
Huse, S.M.4
Neal, P.R.5
Butterfield, D.A.6
Sogin, M.L.7
-
24
-
-
0026599072
-
The structural genes encoding CO dehydrogenase subunits (cox L, M and S) in Pseudomonas carboxydovorans OM5 reside on plasmid pHCG3 and are, with the exception of Streptomyces thermoautotrophicus, conserved in carboxydotrophic bacteria
-
Hugendieek, I., and Meyer, O. (1992). The structural genes encoding CO dehydrogenase subunits (cox L, M and S) in Pseudomonas carboxydovorans OM5 reside on plasmid pHCG3 and are, with the exception of Streptomyces thermoautotrophicus, conserved in carboxydotrophic bacteria. Arch. Microbiol. 157, 301-304.
-
(1992)
Arch. Microbiol.
, vol.157
, pp. 301-304
-
-
Hugendieek, I.1
Meyer, O.2
-
25
-
-
33644950423
-
Non-sulfate-reducing, syntrophic bacteria affiliated with Desulfotomaculum cluster I are widely distributed in methanogenic environments
-
Imachi, H., Sekiguchi, Y., Kamagata, Y., Loy, A., Qiu, Y.-L., Hugenholtz, P., Kimura, N., Wagner, M., Ohashi, A., and Harada, H. (2006). Non-sulfate-reducing, syntrophic bacteria affiliated with Desulfotomaculum cluster I are widely distributed in methanogenic environments. Appl. Environ. Microbiol. 72, 2080-2091.
-
(2006)
Appl. Environ. Microbiol.
, vol.72
, pp. 2080-2091
-
-
Imachi, H.1
Sekiguchi, Y.2
Kamagata, Y.3
Loy, A.4
Qiu, Y.-L.5
Hugenholtz, P.6
Kimura, N.7
Wagner, M.8
Ohashi, A.9
Harada, H.10
-
26
-
-
0032885353
-
Cloning and molecular characterization of the genes for carbon monoxide dehydrogenase and localization of molybdopterin, flavin adenine dinucleotide, and iron-sulfur centers in the enzyme of Hydrogenophaga pseudoflava
-
Kang, B. S., and Kim, Y. M. (1999). Cloning and molecular characterization of the genes for carbon monoxide dehydrogenase and localization of molybdopterin, flavin adenine dinucleotide, and iron-sulfur centers in the enzyme of Hydrogenophaga pseudoflava. J. Bacteriol. 181, 5581-5590.
-
(1999)
J. Bacteriol.
, vol.181
, pp. 5581-5590
-
-
Kang, B.S.1
Kim, Y.M.2
-
27
-
-
20044396151
-
A serpentinite-hosted ecosystem: the Lost City hydrothermal field
-
Kelley, D. S., Karson, J. A., Fruh-Green, G. L., Yoerger, D. R., Shank, T. M., Butterfield, D. A., Hayes, J. M., Schrenk, M. O., Olson, E. J., Proskurowski, G., Jakuba, M., Bradley, A., Larson, B., Ludwig, K., Glickson, D., Buckman, K., Bradley, A. S., Brazelton, W. J., Roe, K., Elend, M. J., Delacour, A., Bernasconi, S. M., Lilley, M. D., Baross, J. A., Summons, R. E., and Sylva, S. P. (2005). A serpentinite-hosted ecosystem: the Lost City hydrothermal field. Science 307, 1428-1434.
-
(2005)
Science
, vol.307
, pp. 1428-1434
-
-
Kelley, D.S.1
Karson, J.A.2
Fruh-Green, G.L.3
Yoerger, D.R.4
Shank, T.M.5
Butterfield, D.A.6
Hayes, J.M.7
Schrenk, M.O.8
Olson, E.J.9
Proskurowski, G.10
Jakuba, M.11
Bradley, A.12
Larson, B.13
Ludwig, K.14
Glickson, D.15
Buckman, K.16
Bradley, A.S.17
Brazelton, W.J.18
Roe, K.19
Elend, M.J.20
Delacour, A.21
Bernasconi, S.M.22
Lilley, M.D.23
Baross, J.A.24
Summons, R.E.25
Sylva, S.P.26
more..
-
28
-
-
0021193863
-
Effects of cultivation gas phase on hydrogenase of the acetogen Clostridium thermoaceticum
-
Kellum, R., and Drake, H. L. (1984). Effects of cultivation gas phase on hydrogenase of the acetogen Clostridium thermoaceticum. J. Bacteriol. 160, 466-469.
-
(1984)
J. Bacteriol.
, vol.160
, pp. 466-469
-
-
Kellum, R.1
Drake, H.L.2
-
29
-
-
2142693754
-
Molecular and culture-based analyses of aerobic carbon monoxide oxidizer diversity
-
King, G. M. (2003). Molecular and culture-based analyses of aerobic carbon monoxide oxidizer diversity. Appl. Environ. Microbiol. 69, 7257-7265.
-
(2003)
Appl. Environ. Microbiol.
, vol.69
, pp. 7257-7265
-
-
King, G.M.1
-
30
-
-
33645031318
-
Nitrate-dependent anaerobic carbon monoxide oxidation by aerobic CO-oxidizing bacteria
-
King, G. M. (2006). Nitrate-dependent anaerobic carbon monoxide oxidation by aerobic CO-oxidizing bacteria. FEMS Microbiol. Ecol. 56, 1-7.
-
(2006)
FEMS Microbiol. Ecol.
, vol.56
, pp. 1-7
-
-
King, G.M.1
-
31
-
-
33846476676
-
Distribution, diversity and ecology of aerobic CO-oxidizing bacteria
-
King, G. M., and Weber, C. F. (2007). Distribution, diversity and ecology of aerobic CO-oxidizing bacteria. Nat. Rev. Microbiol. 5, 107-118.
-
(2007)
Nat. Rev. Microbiol.
, vol.5
, pp. 107-118
-
-
King, G.M.1
Weber, C.F.2
-
32
-
-
72149118443
-
Elevated concentrations of formate, acetate and dissolved organic carbon found at the Lost City hydrothermal field
-
Lang, S. Q., Butterfield, D. A., Schulte, M., Kelley, D. S., and Lilley, M. D. (2010). Elevated concentrations of formate, acetate and dissolved organic carbon found at the Lost City hydrothermal field. Geochim. Cosmochim. Acta 74, 941-952.
-
(2010)
Geochim. Cosmochim. Acta
, vol.74
, pp. 941-952
-
-
Lang, S.Q.1
Butterfield, D.A.2
Schulte, M.3
Kelley, D.S.4
Lilley, M.D.5
-
33
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., Mc William, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., and Higgins, D. G. (2007). Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
McGettigan, P.A.5
Mc William, H.6
Valentin, F.7
Wallace, I.M.8
Wilm, A.9
Lopez, R.10
Thompson, J.D.11
Gibson, T.J.12
Higgins, D.G.13
-
34
-
-
33750332574
-
Long-term sustainability of a high-energy, low-diversity crustal biome
-
Lin, L.-H., Wang, P.-L., Rumble, D., Lippmann-Pipke, J., Boice, E., Pratt, L. M., Sherwood Lollar, B., Brodie, E. L., Hazen, T. C., Andersen, G. L., DeSantis, T. Z., Moser, D. P., Kershaw, D., and Onstott, T. C. (2006). Long-term sustainability of a high-energy, low-diversity crustal biome. Science 314, 479-482.
-
(2006)
Science
, vol.314
, pp. 479-482
-
-
Lin, L.-H.1
Wang, P.-L.2
Rumble, D.3
Lippmann-Pipke, J.4
Boice, E.5
Pratt, L.M.6
Sherwood Lollar, B.7
Brodie, E.L.8
Hazen, T.C.9
Andersen, G.L.10
DeSantis, T.Z.11
Moser, D.P.12
Kershaw, D.13
Onstott, T.C.14
-
35
-
-
2542523843
-
ARB: a software environment for sequence data
-
Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, Buchner, A., Lai, T., Steppi, S., Jobb, G., Förster, W., Brettske, I., Gerber, S., Ginhart, A. W., Gross, O., Grumann, S., Hermann, S., Jost, R., König, A., Liss, T., Lüssmann, R., May, M., Nonhoff, B., Reichel, B., Strehlow, R., Stamatakis, A., Stuckmann, N., Vilbig, A., Lenke, M., Ludwig, T., Bode, A., and Schleifer, K.-H. (2004). ARB: a software environment for sequence data. Nucleic Acids Res. 32, 1363-1371.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1363-1371
-
-
Ludwig, W.1
Strunk, O.2
Westram, R.3
Richter, L.4
Meier, H.5
Yadhukumar6
Buchner, A.7
Lai, T.8
Steppi, S.9
Jobb, G.10
Förster, W.11
Brettske, I.12
Gerber, S.13
Ginhart, A.W.14
Gross, O.15
Grumann, S.16
Hermann, S.17
Jost, R.18
König, A.19
Liss, T.20
Lüssmann, R.21
May, M.22
Nonhoff, B.23
Reichel, B.24
Strehlow, R.25
Stamatakis, A.26
Stuckmann, N.27
Vilbig, A.28
Lenke, M.29
Ludwig, T.30
Bode, A.31
Schleifer, K.-H.32
more..
-
36
-
-
33747881518
-
An experimental metagenome data management and analysis system
-
Markowitz, V. M., Ivanova, N., Palaniappan, K., Szeto, E., Korzeniewski, E, Lykidis, A., Anderson, I., Mavromatis, K., Mavrommatis, K., Kunin, V., Garcia Martin, H., Dubchak, I., Hugenholtz, P., and Kyrpides, N. C. (2006). An experimental metagenome data management and analysis system. Bioinformatics 22, e359-e367.
-
(2006)
Bioinformatics
, vol.22
-
-
Markowitz, V.M.1
Ivanova, N.2
Palaniappan, K.3
Szeto, E.4
Korzeniewski, E.5
Lykidis, A.6
Anderson, I.7
Mavromatis, K.8
Mavrommatis, K.9
Kunin, V.10
Garcia Martin, H.11
Dubchak, I.12
Hugenholtz, P.13
Kyrpides, N.C.14
-
37
-
-
38549101119
-
The integrated microbial genomes (IMG) system in 2007 data content and analysis tool extensions
-
Markowitz, V. M., Szeto, E., Palaniappan, K., Grechkin, Y., Chu, K., Chen, I.-M., Dubchak, I., Anderson, I., Lykidis, A., Mavromatis, K., Ivanova, N. N., and Kyrpides, N. C. (2008). The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res. 36, D528-D533.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Markowitz, V.M.1
Szeto, E.2
Palaniappan, K.3
Grechkin, Y.4
Chu, K.5
Chen, I.-M.6
Dubchak, I.7
Anderson, I.8
Lykidis, A.9
Mavromatis, K.10
Ivanova, N.N.11
Kyrpides, N.C.12
-
38
-
-
33847746181
-
Abiotic synthesis of organic compounds in deep-sea hydrothermal environments
-
McCollom, T. M., and Seewald, J. S. (2007). Abiotic synthesis of organic compounds in deep-sea hydrothermal environments. Chem. Rev. 107, 382-401.
-
(2007)
Chem. Rev.
, vol.107
, pp. 382-401
-
-
McCollom, T.M.1
Seewald, J.S.2
-
39
-
-
53549118607
-
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
-
doi:10.1186/1471-2105-9-386
-
Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E. M., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R., Wilke, A., Wilkening, J., and Edwards, R. A. (2008). The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9, 386. doi:10.1186/1471-2105-9-386.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 386
-
-
Meyer, F.1
Paarmann, D.2
D'Souza, M.3
Olson, R.4
Glass, E.M.5
Kubal, M.6
Paczian, T.7
Rodriguez, A.8
Stevens, R.9
Wilke, A.10
Wilkening, J.11
Edwards, R.A.12
-
40
-
-
29144452882
-
Desulfotomaculum and Methanobacterium spp. Dominate 4- to 5-kilometer-deep fault
-
Moser, D. P., Gihring, T. M., Brockman, F. J., Fredrickson, J. K., Balkwill, D. L., Dollhopf, M. E., Lollar, B. S., Pratt, L. M., Boice, E., Southam, G., Wanger, G., Baker, B. J., Pfiffner, S. M., Lin, L.-H., and Onstott, T. C. (2005). Desulfotomaculum and Methanobacterium spp. Dominate 4- to 5-kilometer-deep fault. Appl. Environ. Microbiol. 71, 8773-8783.
-
(2005)
Appl. Environ. Microbiol.
, vol.71
, pp. 8773-8783
-
-
Moser, D.P.1
Gihring, T.M.2
Brockman, F.J.3
Fredrickson, J.K.4
Balkwill, D.L.5
Dollhopf, M.E.6
Lollar, B.S.7
Pratt, L.M.8
Boice, E.9
Southam, G.10
Wanger, G.11
Baker, B.J.12
Pfiffner, S.M.13
Lin, L.-H.14
Onstott, T.C.15
-
41
-
-
44949239735
-
Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment
-
Norton, J. M., Klotz, M. G., Stein, L. Y., Arp, D. J., Bottomley, P. J., Chain, P. S., Hauser, L. J., Land, M. L., Larimer, F. W., Shin, M. W., and Starkenburg, S. R. (2008). Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment. Appl. Environ. Microbiol. 74, 3559-3572.
-
(2008)
Appl. Environ. Microbiol.
, vol.74
, pp. 3559-3572
-
-
Norton, J.M.1
Klotz, M.G.2
Stein, L.Y.3
Arp, D.J.4
Bottomley, P.J.5
Chain, P.S.6
Hauser, L.J.7
Land, M.L.8
Larimer, F.W.9
Shin, M.W.10
Starkenburg, S.R.11
-
42
-
-
51649124894
-
The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum)
-
Pierce, E., Xie, G., Barabote, R. D., Saunders, E., Han, C. S., Detter, J. C., Richardson, P., Brettin, T. S., Das, A., Ljungdahl, L. G., and Ragsdale, S. W. (2008). The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). Environ. Microbiol. 10, 2550-2573.
-
(2008)
Environ. Microbiol.
, vol.10
, pp. 2550-2573
-
-
Pierce, E.1
Xie, G.2
Barabote, R.D.3
Saunders, E.4
Han, C.S.5
Detter, J.C.6
Richardson, P.7
Brettin, T.S.8
Das, A.9
Ljungdahl, L.G.10
Ragsdale, S.W.11
-
43
-
-
38849138652
-
Abiogenic hydrocarbon production at lost city hydrothermal field
-
Proskurowski, G., Lilley, M. D., Seewald, J. S., Fruh-Green, G. L., Olson, E. J., Lupton, J. E., Sylva, S. P., and Kelley, D. S. (2008). Abiogenic hydrocarbon production at lost city hydrothermal field. Science 319, 604-607.
-
(2008)
Science
, vol.319
, pp. 604-607
-
-
Proskurowski, G.1
Lilley, M.D.2
Seewald, J.S.3
Fruh-Green, G.L.4
Olson, E.J.5
Lupton, J.E.6
Sylva, S.P.7
Kelley, D.S.8
-
44
-
-
37549027613
-
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
-
Pruesse, E., Quast, C., Knittel, K., Fuchs, B. M., Ludwig, W., Peplies, J., and Glöckner, F. O. (2007). SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188-7196.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 7188-7196
-
-
Pruesse, E.1
Quast, C.2
Knittel, K.3
Fuchs, B.M.4
Ludwig, W.5
Peplies, J.6
Glöckner, F.O.7
-
46
-
-
54949153045
-
Acetogenesis and the Wood-Ljungdahl pathway of CO2 fixation
-
Ragsdale, S. W., and Pierce, E. (2008). Acetogenesis and the Wood-Ljungdahl pathway of CO2 fixation. Biochim. Biophys. Acta 1784, 1873-1898.
-
(2008)
Biochim. Biophys. Acta
, vol.1784
, pp. 1873-1898
-
-
Ragsdale, S.W.1
Pierce, E.2
-
47
-
-
44449094057
-
Abundance and diversity of microbial life in ocean crust
-
Santelli, C. M., Orcutt, B. N., Banning, E., Bach, W., Moyer, C. L., Sogin, M. L., Staudigel, H., and Edwards, K. J. (2008). Abundance and diversity of microbial life in ocean crust. Nature 453, 653-656.
-
(2008)
Nature
, vol.453
, pp. 653-656
-
-
Santelli, C.M.1
Orcutt, B.N.2
Banning, E.3
Bach, W.4
Moyer, C.L.5
Sogin, M.L.6
Staudigel, H.7
Edwards, K.J.8
-
48
-
-
77749245784
-
Hitherto unknown [Fe-Fe]-hydrogenase gene diversity in anaerobes and anoxic enrichments from a moderately acidic fen
-
Schmidt, O., Drake, H. L., and Horn, M. A. (2010). Hitherto unknown [Fe-Fe]-hydrogenase gene diversity in anaerobes and anoxic enrichments from a moderately acidic fen. Appl. Environ. Microbiol. 76, 2027-2031.
-
(2010)
Appl. Environ. Microbiol.
, vol.76
, pp. 2027-2031
-
-
Schmidt, O.1
Drake, H.L.2
Horn, M.A.3
-
49
-
-
80052762929
-
Novel [NiFe]- and [FeFe]-hydrogenase gene transcripts indicative of active facultative aerobes and obligate anaerobes in earthworm gut contents
-
Schmidt, O., Wüst, P. K., Hellmuth, S., Borst, K., Horn, M. A., and Drake, H. L. (2011). Novel [NiFe]- and [FeFe]-hydrogenase gene transcripts indicative of active facultative aerobes and obligate anaerobes in earthworm gut contents. Appl. Environ. Microbiol. 77, 5842-5850.
-
(2011)
Appl. Environ. Microbiol.
, vol.77
, pp. 5842-5850
-
-
Schmidt, O.1
Wüst, P.K.2
Hellmuth, S.3
Borst, K.4
Horn, M.A.5
Drake, H.L.6
-
50
-
-
77952957390
-
Microbial provinces in the subseafloor
-
Schrenk, M. O., Huber, J. A., and Edwards, K. J. (2010). Microbial provinces in the subseafloor. Annu. Rev. Mar. Sci. 2, 279-306.
-
(2010)
Annu. Rev. Mar. Sci.
, vol.2
, pp. 279-306
-
-
Schrenk, M.O.1
Huber, J.A.2
Edwards, K.J.3
-
51
-
-
4644245661
-
Low archaeal diversity linked to subseafloor geochemical processes at the Lost City Hydrothermal Field, Mid-Atlantic Ridge
-
Schrenk, M. O., Kelley, D. S., Bolton, S. A., and Baross, J. A. (2004). Low archaeal diversity linked to subseafloor geochemical processes at the Lost City Hydrothermal Field, Mid-Atlantic Ridge. Environ. Microbiol. 6, 1086-1095.
-
(2004)
Environ. Microbiol.
, vol.6
, pp. 1086-1095
-
-
Schrenk, M.O.1
Kelley, D.S.2
Bolton, S.A.3
Baross, J.A.4
-
52
-
-
70949088269
-
A proteomic view of the facultatively chemolithoautotrophic lifestyle of Ralstonia eutropha H16
-
Schwartz, E., Voigt, B., Zühlke, D., Pohlmann, A., Lenz, O., Albrecht, D., Schwarze, A., Kohlmann, Y., Krause, C., Hecker, M., and Friedrich, B. (2009). A proteomic view of the facultatively chemolithoautotrophic lifestyle of Ralstonia eutropha H16. Proteomics 9, 5132-5142.
-
(2009)
Proteomics
, vol.9
, pp. 5132-5142
-
-
Schwartz, E.1
Voigt, B.2
Zühlke, D.3
Pohlmann, A.4
Lenz, O.5
Albrecht, D.6
Schwarze, A.7
Kohlmann, Y.8
Krause, C.9
Hecker, M.10
Friedrich, B.11
-
53
-
-
33845505324
-
The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2
-
doi:10.1371/journal.pbio.0040383
-
Scott, K. M., Sievert, S. M., Abril, F. N., Ball, L. A., Barrett, C. J., Blake, R. A., Boller, A. J., Chain, P. S., Clark, J. A., Davis, C. R., Detter, C., Do, K. F., Dobrinski, K. P., Faza, B. I., Fitzpatrick, K. A., Freyermuth, S. K., Harmer, T. L., Hauser, L. J., Hugler, M., Kerfeld, C. A., Klotz, M. G., Kong, W. W., Land, M., Lapidus, A., Larimer, F. W., Longo, D. L., Lucas, S., Malfatti, S. A., Massey, S. E., Martin, D. D., McCuddin, Z., Meyer, E, Moore, J. L., Ocampo, L. H. Jr., Paul, J. H., Paulsen, I. T., Reep, D. K., Ren, Q., Ross, R. L., Sato, P. Y., Thomas, P., Tinkham, L. E., and Zeruth, G. T. (2006). The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2. PLoSBiol. 4, e383. doi:10.1371/journal.pbio.0040383.
-
(2006)
PLoSBiol
, vol.4
-
-
Scott, K.M.1
Sievert, S.M.2
Abril, F.N.3
Ball, L.A.4
Barrett, C.J.5
Blake, R.A.6
Boller, A.J.7
Chain, P.S.8
Clark, J.A.9
Davis, C.R.10
Detter, C.11
Do, K.F.12
Dobrinski, K.P.13
Faza, B.I.14
Fitzpatrick, K.A.15
Freyermuth, S.K.16
Harmer, T.L.17
Hauser, L.J.18
Hugler, M.19
Kerfeld, C.A.20
Klotz, M.G.21
Kong, W.W.22
Land, M.23
Lapidus, A.24
Larimer, F.W.25
Longo, D.L.26
Lucas, S.27
Malfatti, S.A.28
Massey, S.E.29
Martin, D.D.30
McCuddin, Z.31
Meyer, E.32
Moore, J.L.33
Ocampo Jr, L.H.34
Paul, J.H.35
Paulsen, I.T.36
Reep, D.K.37
Ren, Q.38
Ross, R.L.39
Sato, P.Y.40
Thomas, P.41
Tinkham, L.E.42
Zeruth, G.T.43
more..
-
54
-
-
70350455960
-
Identification of the [FeFe]-hydrogenase responsible for hydrogen generation in Thermoanaerobacterium saccharolyticum and demonstration of increased ethanol yield via hydrogenase knockout
-
Shaw, A. J., Hogsett, D. A., and Lynd, L. R. (2009). Identification of the [FeFe]-hydrogenase responsible for hydrogen generation in Thermoanaerobacterium saccharolyticum and demonstration of increased ethanol yield via hydrogenase knockout. J. Bacteriol. 191, 6457-6464.
-
(2009)
J. Bacteriol.
, vol.191
, pp. 6457-6464
-
-
Shaw, A.J.1
Hogsett, D.A.2
Lynd, L.R.3
-
55
-
-
33747073504
-
Microbial diversity in the deep sea and the underexplored "rare biosphere"
-
Sogin, M. L., Morrison, H. G., Huber, J. A., Mark Welch, D., Huse, S. M., Neal, P. R., Arrieta, J. M., and Herndl, G. J. (2006). Microbial diversity in the deep sea and the underexplored "rare biosphere." Proc. Natl. Acad. Sci U.S.A. 103, 12115-12120.
-
(2006)
Proc. Natl. Acad. Sci U. S. A.
, vol.103
, pp. 12115-12120
-
-
Sogin, M.L.1
Morrison, H.G.2
Huber, J.A.3
Mark Welch, D.4
Huse, S.M.5
Neal, P.R.6
Arrieta, J.M.7
Herndl, G.J.8
-
56
-
-
43049156579
-
Dethiobacter alkaliphilus gen. nov. sp. nov., and Desulfurivibrio alkaliphilus gen. nov. sp. nov.: two novel representatives of reductive sulfur cycle from soda lakes
-
Sorokin, D. Y., Tourova, T. P., Mussmann, M., and Muyzer, G. (2008). Dethiobacter alkaliphilus gen. nov. sp. nov., and Desulfurivibrio alkaliphilus gen. nov. sp. nov.: two novel representatives of reductive sulfur cycle from soda lakes. Extremophiles 12, 431-439.
-
(2008)
Extremophiles
, vol.12
, pp. 431-439
-
-
Sorokin, D.Y.1
Tourova, T.P.2
Mussmann, M.3
Muyzer, G.4
-
57
-
-
33750403801
-
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690.
-
(2006)
Bioinformatics
, vol.22
, pp. 2688-2690
-
-
Stamatakis, A.1
-
58
-
-
33644903802
-
Ralstonia pickettii-innocent bystander or a potential threat?
-
Stelzmueller, I., Biebl, M., Wiesmayr, S., Eller, M., Hoeller, E., Fille, M., Weiss, G., Lass-Floerl, C., and Bonatti, H. (2006). Ralstonia pickettii-innocent bystander or a potential threat? Clin. Microbiol. Infect. 12, 99-101.
-
(2006)
Clin Microbiol. Infect.
, vol.12
, pp. 99-101
-
-
Stelzmueller, I.1
Biebl, M.2
Wiesmayr, S.3
Eller, M.4
Hoeller, E.5
Fille, M.6
Weiss, G.7
Lass-Floerl, C.8
Bonatti, H.9
-
59
-
-
35748974830
-
Occurrence, classification, and biological function of hydrogenases: an overview
-
Vignais, P. M., and Billoud, B. (2007). Occurrence, classification, and biological function of hydrogenases: an overview. Chem. Rev. 107, 4206-4272.
-
(2007)
Chem. Rev.
, vol.107
, pp. 4206-4272
-
-
Vignais, P.M.1
Billoud, B.2
-
60
-
-
0034886919
-
Classification and phylogeny of hydrogenases
-
Vignais, P. M., Billoud, B., and Meyer, J. (2001). Classification and phylogeny of hydrogenases. FEMS Microbiol. Rev. 25, 455-501.
-
(2001)
FEMS Microbiol. Rev.
, vol.25
, pp. 455-501
-
-
Vignais, P.M.1
Billoud, B.2
Meyer, J.3
-
61
-
-
33847192507
-
Physiological, ecological, and phylogenetic characterization of Stappia, a marine CO-oxidizing bacterial genus
-
Weber, C. F., and King, G. M. (2007). Physiological, ecological, and phylogenetic characterization of Stappia, a marine CO-oxidizing bacterial genus. Appl. Environ. Microbiol. 73, 1266-1276.
-
(2007)
Appl. Environ. Microbiol.
, vol.73
, pp. 1266-1276
-
-
Weber, C.F.1
King, G.M.2
-
62
-
-
79955071957
-
Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics
-
Weber, M., Teeling, H., Huang, S., Waldmann, J., Kassabgy, M., Fuchs, B. M., Klindworth, A., Klockow, C., Wichels, A., Gerdts, G., Amann, R., and Glockner, E O. (2010). Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics. ISME J. 918-928.
-
(2010)
ISME J
, pp. 918-928
-
-
Weber, M.1
Teeling, H.2
Huang, S.3
Waldmann, J.4
Kassabgy, M.5
Fuchs, B.M.6
Klindworth, A.7
Klockow, C.8
Wichels, A.9
Gerdts, G.10
Amann, R.11
Glockner, E.O.12
-
63
-
-
0032499758
-
Prokaryotes:the unseen majority
-
Whitman, W. B., Coleman, D. C., and Wiebe, W. J. (1998).Prokaryotes:the unseen majority. Proc. Natl. Acad. Sci. U.S.A. 95, 6578-6583.
-
(1998)
Proc. Natl. Acad. Sci. U. S. A.
, vol.95
, pp. 6578-6583
-
-
Whitman, W.B.1
Coleman, D.C.2
Wiebe, W.J.3
-
64
-
-
0024333565
-
Hydrogenophaga, a new genus of hydrogen-oxidizing bacteria that includes Hydrogenophaga flava comb. nov. (Formerly Pseudomonas flava), Hydrogenophaga palleronii (Formerly Pseudomonas palleronii), Hydrogenophaga pseudoflava (Formerly Pseudomonaspseudoflava and "Pseudomonas carboxydoflava"), and Hydrogenophaga taeniospiralis (Formerly Pseudomonas taeniospiralis)
-
Willems, A., Busse, J., Goor, M., Pot, B., Falsen, E., Jantzen, E., Hoste, B., Gillis, M., Kersters, K., Auling, G., and De Ley, J. (1989). Hydrogenophaga, a new genus of hydrogen-oxidizing bacteria that includes Hydrogenophaga flava comb. nov. (Formerly Pseudomonas flava), Hydrogenophaga palleronii (Formerly Pseudomonas palleronii), Hydrogenophaga pseudoflava (Formerly Pseudomonaspseudoflava and "Pseudomonas carboxydoflava"), and Hydrogenophaga taeniospiralis (Formerly Pseudomonas taeniospiralis). Int. J. Syst. Bacteriol. 39, 319-333.
-
(1989)
Int. J. Syst. Bacteriol.
, vol.39
, pp. 319-333
-
-
Willems, A.1
Busse, J.2
Goor, M.3
Pot, B.4
Falsen, E.5
Jantzen, E.6
Hoste, B.7
Gillis, M.8
Kersters, K.9
Auling, G.10
De Ley, J.11
-
65
-
-
0027167618
-
Microbial hydrogenases: primary structure, classification, signatures and phylogeny
-
Wu, L. F., and Mandrand, M. A. (1993). Microbial hydrogenases: primary structure, classification, signatures and phylogeny. FEMS Microbiol. Rev. 10, 243-269.
-
(1993)
FEMS Microbiol. Rev.
, vol.10
, pp. 243-269
-
-
Wu, L.F.1
Mandrand, M.A.2
|