-
1
-
-
0030801002
-
Gapped blast and psi-blast: a new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 1997, 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.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
48749117805
-
Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment
-
Biddle JF, Fitz-Gibbon S, Schuster SC, Brenchley JE, House CH. Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. Proc Natl Acad Sci USA 2008, 105:10583-10588.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 10583-10588
-
-
Biddle, J.F.1
Fitz-Gibbon, S.2
Schuster, S.C.3
Brenchley, J.E.4
House, C.H.5
-
3
-
-
77149132167
-
Archaeal diversity in the Dead Sea: Microbial survival under increasingly harsh conditions
-
Oren A, Naftz D, Palacios P, Wurtsbaugh WA. In, eds, Logan, UT, USA, The S.J. and Jessie E. Quinney Natural Resources Research Library, College of Natural Resources, Utah State University
-
Bodaker I, Béjà O, Sharon I, Feingersch R, Rosenberg M, Oren A. Archaeal diversity in the Dead Sea: Microbial survival under increasingly harsh conditions. Saline Lakes around the World: Unique Systems with Unique Values 2009, 137-143. Oren A, Naftz D, Palacios P, Wurtsbaugh WA, In, eds, Logan, UT, USA, The S.J. and Jessie E. Quinney Natural Resources Research Library, College of Natural Resources, Utah State University, pp.
-
(2009)
Saline Lakes around the World: Unique Systems with Unique Values
, pp. 137-143
-
-
Bodaker, I.1
Béjà, O.2
Sharon, I.3
Feingersch, R.4
Rosenberg, M.5
Oren, A.6
et al7
-
4
-
-
33747334086
-
The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity
-
Bolhuis H, Palm P, Wende A, Falb M, Rampp M, Rodriguez-Valera F. The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity. BMC Genomics 2006, 7:169.
-
(2006)
BMC Genomics
, vol.7
, pp. 169
-
-
Bolhuis, H.1
Palm, P.2
Wende, A.3
Falb, M.4
Rampp, M.5
Rodriguez-Valera, F.6
et al7
-
5
-
-
33846072878
-
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data
-
Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, McGarrell DM. The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res 2007, 35:D169-D172.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Cole, J.R.1
Chai, B.2
Farris, R.J.3
Wang, Q.4
Kulam-Syed-Mohideen, A.S.5
McGarrell, D.M.6
et al7
-
6
-
-
0034830935
-
Rapid amplification of plasmid and phage DNA using Phi29 DNA polymerase and multiply-primed rolling circle amplification
-
Dean FB, Nelson JR, Giesler TL, Lasken RS. Rapid amplification of plasmid and phage DNA using Phi29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res 2001, 11:1095-1099.
-
(2001)
Genome Res
, vol.11
, pp. 1095-1099
-
-
Dean, F.B.1
Nelson, J.R.2
Giesler, T.L.3
Lasken, R.S.4
-
7
-
-
3042666256
-
Muscle: multiple sequence alignment with high accuracy and high throughput
-
Edgar RC. muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
8
-
-
0003962446
-
The Dead Sea-A terminal lake in the Dead Sea rift: a short overview
-
Oren A. In, ed., Boca Raton, USA, CRC Press
-
Gavrieli I, Beyth M, Yechieli Y. The Dead Sea-A terminal lake in the Dead Sea rift: a short overview. Microbiology and Biogeochemistry of Hypersaline Environments 1999, 121-127. Oren A, In, ed., Boca Raton, USA, CRC Press, pp.
-
(1999)
Microbiology and Biogeochemistry of Hypersaline Environments
, pp. 121-127
-
-
Gavrieli, I.1
Beyth, M.2
Yechieli, Y.3
-
9
-
-
33744804299
-
Metagenomic analysis of the human distal gut microbiome
-
Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS. Metagenomic analysis of the human distal gut microbiome. Science 2006, 312:1355-1359.
-
(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
et al7
-
10
-
-
37049026439
-
Amino acid and codon usage profiles: adaptive changes in the frequency of amino acids and codons
-
Goodarzi H, Torabi N, Najafabadi HS, Archetti M. Amino acid and codon usage profiles: adaptive changes in the frequency of amino acids and codons. Gene 2008, 407:30-41.
-
(2008)
Gene
, vol.407
, pp. 30-41
-
-
Goodarzi, H.1
Torabi, N.2
Najafabadi, H.S.3
Archetti, M.4
-
11
-
-
0033616712
-
Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species
-
Haney PJ, Badger JH, Buldak GL, Reich CI, Woese CR, Olsen GJ. Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. Proc Natl Acad Sci USA 1999, 96:3578-3583.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 3578-3583
-
-
Haney, P.J.1
Badger, J.H.2
Buldak, G.L.3
Reich, C.I.4
Woese, C.R.5
Olsen, G.J.6
-
12
-
-
33847702910
-
Megan analysis of metagenomic data
-
Huson DH, Auch AF, Qi J, Schuster SC. megan analysis of metagenomic data. Genome Res 2007, 17:377-386.
-
(2007)
Genome Res
, vol.17
, pp. 377-386
-
-
Huson, D.H.1
Auch, A.F.2
Qi, J.3
Schuster, S.C.4
-
13
-
-
0030305457
-
R: a language for data analysis and graphics
-
Ihaka R, Gentleman R. R: a language for data analysis and graphics. J Comput Graph Stat 1996, 5:299-314.
-
(1996)
J Comput Graph Stat
, vol.5
, pp. 299-314
-
-
Ihaka, R.1
Gentleman, R.2
-
14
-
-
0034767491
-
Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence
-
Kennedy SP, Ng WV, Salzberg SL, Hood L, DasSarma S. Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence. Genome Res 2001, 11:1641-1650.
-
(2001)
Genome Res
, vol.11
, pp. 1641-1650
-
-
Kennedy, S.P.1
Ng, W.V.2
Salzberg, S.L.3
Hood, L.4
DasSarma, S.5
-
15
-
-
44649171625
-
Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat
-
Kunin V, Raes J, Harris JK, Spear JR, Walker JJ, Ivanova N. Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Mol Syst Biol 2008, 4:198.
-
(2008)
Mol Syst Biol
, vol.4
, pp. 198
-
-
Kunin, V.1
Raes, J.2
Harris, J.K.3
Spear, J.R.4
Walker, J.J.5
Ivanova, N.6
et al7
-
16
-
-
0001857117
-
16S/23S rRNA sequencing
-
Stackebrandt E, Goodfellow M. In, eds, Chichester, UK, Wiley
-
Lane DJ. 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics 1991, 115-175. Stackebrandt EGoodfellow M. In, eds, Chichester, UK, Wiley
-
(1991)
Nucleic Acid Techniques in Bacterial Systematics
, pp. 115-175
-
-
Lane, D.J.1
-
17
-
-
0016139829
-
Salt-dependent properties of proteins from extremely halophilic bacteria
-
Lanyi JK. Salt-dependent properties of proteins from extremely halophilic bacteria. Microbiol Rev 1974, 38:272-290.
-
(1974)
Microbiol Rev
, vol.38
, pp. 272-290
-
-
Lanyi, J.K.1
-
18
-
-
33748299286
-
Environmental genomics of 'Haloquadratum walsbyi' in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species
-
Legault B, Lopez-Lopez A, Alba-Casado J, Doolittle WF, Bolhuis H, Rodriguez-Valera F, Papke RT. Environmental genomics of 'Haloquadratum walsbyi' in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species. BMC Genomics 2006, 7:171.
-
(2006)
BMC Genomics
, vol.7
, pp. 171
-
-
Legault, B.1
Lopez-Lopez, A.2
Alba-Casado, J.3
Doolittle, W.F.4
Bolhuis, H.5
Rodriguez-Valera, F.6
Papke, R.T.7
-
19
-
-
33646584137
-
Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat
-
Ley RE, Harris JK, Wilcox J, Spear JR, Miller SR, Bebout BM. Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl Environ Microbiol 2006, 72:3685-3695.
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 3685-3695
-
-
Ley, R.E.1
Harris, J.K.2
Wilcox, J.3
Spear, J.R.4
Miller, S.R.5
Bebout, B.M.6
et al7
-
20
-
-
2542523843
-
Arb: a software environment for sequence data
-
Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar. arb: a software environment for sequence data. Nucleic Acids Res 2004, 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
et al7
-
22
-
-
0033609333
-
Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima
-
Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH. Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature 1999, 399:323-329.
-
(1999)
Nature
, vol.399
, pp. 323-329
-
-
Nelson, K.E.1
Clayton, R.A.2
Gill, S.R.3
Gwinn, M.L.4
Dodson, R.J.5
Haft, D.H.6
et al7
-
23
-
-
12944270421
-
Genome sequence of Halobacterium species NRC-1
-
Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD. Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci USA 2000, 97:12176-12181.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 12176-12181
-
-
Ng, W.V.1
Kennedy, S.P.2
Mahairas, G.G.3
Berquist, B.4
Pan, M.5
Shukla, H.D.6
et al7
-
24
-
-
0022590625
-
Intracellular salt concentrations of the anaerobic halophilic eubacteria Haloanaerobium praevalens and Halobacteroides halobius
-
Oren A. Intracellular salt concentrations of the anaerobic halophilic eubacteria Haloanaerobium praevalens and Halobacteroides halobius. Can J Microbiol 1986, 32:4-9.
-
(1986)
Can J Microbiol
, vol.32
, pp. 4-9
-
-
Oren, A.1
-
25
-
-
0033022073
-
Bioenergetic aspects of halophilism
-
Oren A. Bioenergetic aspects of halophilism. Microbiol Mol Biol Rev 1999, 63:334-348.
-
(1999)
Microbiol Mol Biol Rev
, vol.63
, pp. 334-348
-
-
Oren, A.1
-
27
-
-
0029509114
-
Dynamics of a bloom of halophilic archaea in the Dead Sea
-
Oren A, Gurevich P. Dynamics of a bloom of halophilic archaea in the Dead Sea. Hydrobiologia 1995, 315:149-158.
-
(1995)
Hydrobiologia
, vol.315
, pp. 149-158
-
-
Oren, A.1
Gurevich, P.2
-
28
-
-
23944462637
-
How to be moderately halophilic with broad salt tolerance: clues from the genome of Chromohalobacter salexigens
-
Oren A, Larimer F, Richardson P, Lapidus A, Csonka LN. How to be moderately halophilic with broad salt tolerance: clues from the genome of Chromohalobacter salexigens. Extremophiles 2005, 9:275-279.
-
(2005)
Extremophiles
, vol.9
, pp. 275-279
-
-
Oren, A.1
Larimer, F.2
Richardson, P.3
Lapidus, A.4
Csonka, L.N.5
-
29
-
-
47149088683
-
Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes
-
Paul S, Bag S, Das S, Harvill E, Dutta C. Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes. Genome Biol 2008, 9:R70.
-
(2008)
Genome Biol
, vol.9
-
-
Paul, S.1
Bag, S.2
Das, S.3
Harvill, E.4
Dutta, C.5
-
30
-
-
0014716593
-
On the composition and nature of the bulk protein of extremely halophilic bacteria
-
Reistad R. On the composition and nature of the bulk protein of extremely halophilic bacteria. Arch Microbiol 1970, 71:353-360.
-
(1970)
Arch Microbiol
, vol.71
, pp. 353-360
-
-
Reistad, R.1
-
31
-
-
0032568587
-
Genomic evidence for two functionally distinct gene classes
-
Rivera MC, Jain R, Moore JE, Lake JA. Genomic evidence for two functionally distinct gene classes. Proc Natl Acad Sci USA 1998, 95:6239-6244.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 6239-6244
-
-
Rivera, M.C.1
Jain, R.2
Moore, J.E.3
Lake, J.A.4
-
32
-
-
63849295689
-
Diversity and stratification of Archaea in a hypersaline microbial mat
-
Robertson CE, Spear JR, Harris JK, Pace NR. Diversity and stratification of Archaea in a hypersaline microbial mat. Appl Environ Microbiol 2009, 75:1801-1810.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 1801-1810
-
-
Robertson, C.E.1
Spear, J.R.2
Harris, J.K.3
Pace, N.R.4
-
33
-
-
0036742110
-
Compatible solutes of organisms that live in hot saline environments
-
Santos H, da Costa MS. Compatible solutes of organisms that live in hot saline environments. Environ Microbiol 2002, 4:501-509.
-
(2002)
Environ Microbiol
, vol.4
, pp. 501-509
-
-
Santos, H.1
da Costa, M.S.2
-
34
-
-
33747073504
-
Microbial diversity in the deep sea and the underexplored 'rare biosphere'
-
Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR. Microbial diversity in the deep sea and the underexplored 'rare biosphere'. Proc Natl Acad Sci USA 2006, 103:12115-12120.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 12115-12120
-
-
Sogin, M.L.1
Morrison, H.G.2
Huber, J.A.3
Welch, D.M.4
Huse, S.M.5
Neal, P.R.6
et al7
-
35
-
-
33645103946
-
From genomes to function: haloarchaea as model organisms
-
Soppa J. From genomes to function: haloarchaea as model organisms. Microbiology 2006, 152:585-590.
-
(2006)
Microbiology
, vol.152
, pp. 585-590
-
-
Soppa, J.1
-
36
-
-
0037399106
-
Complexity in natural microbial ecosystems: the Guerrero Negro experience
-
Spear JR, Ley RE, Berger AB, Pace NR. Complexity in natural microbial ecosystems: the Guerrero Negro experience. Biol Bull 2003, 204:168-173.
-
(2003)
Biol Bull
, vol.204
, pp. 168-173
-
-
Spear, J.R.1
Ley, R.E.2
Berger, A.B.3
Pace, N.R.4
-
37
-
-
14644397888
-
Raxml-iii: a fast program for maximum likelihood-based inference of large phylogenetic trees
-
Stamatakis A, Ludwig T, Meier H. Raxml-iii: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 2005, 21:456-463.
-
(2005)
Bioinformatics
, vol.21
, pp. 456-463
-
-
Stamatakis, A.1
Ludwig, T.2
Meier, H.3
-
38
-
-
20244376755
-
Comparative metagenomics of microbial communities
-
Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW. Comparative metagenomics of microbial communities. Science 2005, 308:554-557.
-
(2005)
Science
, vol.308
, pp. 554-557
-
-
Tringe, S.G.1
von Mering, C.2
Kobayashi, A.3
Salamov, A.A.4
Chen, K.5
Chang, H.W.6
et al7
-
39
-
-
33845874101
-
An obesity-associated gut microbiome with increased capacity for energy harvest
-
Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006, 444:1027-1131.
-
(2006)
Nature
, vol.444
, pp. 1027-1131
-
-
Turnbaugh, P.J.1
Ley, R.E.2
Mahowald, M.A.3
Magrini, V.4
Mardis, E.R.5
Gordon, J.I.6
-
40
-
-
1542377296
-
Community structure and metabolism through reconstruction of microbial genomes from the environment
-
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 2004, 428:37-43.
-
(2004)
Nature
, vol.428
, pp. 37-43
-
-
Tyson, G.W.1
Chapman, J.2
Hugenholtz, P.3
Allen, E.E.4
Ram, R.J.5
Richardson, P.M.6
et al7
-
41
-
-
40349083715
-
Phylogenetic analysis of the archaeal community in an alkaline-saline soil of the former lake Texcoco (Mexico)
-
Valenzuela-Encinas C, Neria-González I, Alcántara-Hernández R, Enríquez-Aragón J, Estrada-Alvarado I, Hernández-Rodríguez C. Phylogenetic analysis of the archaeal community in an alkaline-saline soil of the former lake Texcoco (Mexico). Extremophiles 2008, 12:247-254.
-
(2008)
Extremophiles
, vol.12
, pp. 247-254
-
-
Valenzuela-Encinas, C.1
Neria-González, I.2
Alcántara-Hernández, R.3
Enríquez-Aragón, J.4
Estrada-Alvarado, I.5
Hernández-Rodríguez, C.6
et al7
-
42
-
-
11144354360
-
Environmental genome shotgun sequencing of the Sargasso Sea
-
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA. Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004, 304:66-74.
-
(2004)
Science
, vol.304
, pp. 66-74
-
-
Venter, J.C.1
Remington, K.2
Heidelberg, J.F.3
Halpern, A.L.4
Rusch, D.5
Eisen, J.A.6
et al7
-
43
-
-
0004597758
-
The microorganisms of the Dead Sea
-
In, Collective Volume, Rehovoth, Israel, Daniel Sieff Research Institute
-
Volcani BE. The microorganisms of the Dead Sea. Papers Collected to Commemorate the 70th Anniversary of Dr Chaim Weizmann 1944, 77-85. In, Collective Volume, Rehovoth, Israel, Daniel Sieff Research Institute, pp.
-
(1944)
Papers Collected to Commemorate the 70th Anniversary of Dr Chaim Weizmann
, pp. 77-85
-
-
Volcani, B.E.1
-
44
-
-
84944178665
-
Hierarchical grouping to optimize an objective function
-
Ward JH. Hierarchical grouping to optimize an objective function. J Am Stat Assoc 1963, 58:236-244.
-
(1963)
J Am Stat Assoc
, vol.58
, pp. 236-244
-
-
Ward, J.H.1
|