-
1
-
-
33845212250
-
Anticipating the 1,000 dollar genome
-
Mardis E, Anticipating the 1,000 dollar genome, Genome Biol 7 112, 2006.
-
(2006)
Genome Biol
, vol.7
, pp. 112
-
-
Mardis, E.1
-
2
-
-
0008048504
-
Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses
-
Lane D, Pace B, Olsen G et al., Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses, Proc Natl Acad Sci USA 82:6955-6959, 1985.
-
(1985)
Proc Natl Acad Sci USA
, vol.82
, pp. 6955-6959
-
-
Lane, D.1
Pace, B.2
Olsen, G.3
-
3
-
-
0037195156
-
Genomic analysis of uncultured marine viral communities
-
Breitbart M, Salamon P, Andresen B et al., Genomic analysis of uncultured marine viral communities, Proc Natl Acad Sci USA 99 14250-14255, 2002.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 14250-14255
-
-
Breitbart, M.1
Salamon, P.2
Andresen, B.3
-
4
-
-
2642558991
-
Metagenomics: From acid mine to shining sea
-
Galperin M, Metagenomics: From acid mine to shining sea, Environ Microbiol 6:543-545, 2004.
-
(2004)
Environ Microbiol
, vol.6
, pp. 543-545
-
-
Galperin, M.1
-
5
-
-
11244319620
-
Exploring the unmined richness of microbes to degrade xenobiotics
-
Environmental genomics
-
Eyers L, George I, Schuler L et al., Environmental genomics: Exploring the unmined richness of microbes to degrade xenobiotics, Appl Microbiol Biotechnol 66:123-130, 2004.
-
(2004)
Appl Microbiol Biotechnol
, vol.66
, pp. 123-130
-
-
Eyers, L.1
George, I.2
Schuler, L.3
-
6
-
-
4644354371
-
Metagenomics - the key to the uncultured microbes
-
Streit W, Schmitz R, Metagenomics - the key to the uncultured microbes, Curr Opin Microbiol 7:492-498, 2004.
-
(2004)
Curr Opin Microbiol
, vol.7
, pp. 492-498
-
-
Streit, W.1
Schmitz, R.2
-
7
-
-
10944226351
-
Metagenomics: Genomic analysis of microbial communities
-
Riesenfeld C, Schloss P, Handelsman J, Metagenomics: Genomic analysis of microbial communities, Annu Rev Genet 38:525-552, 2004.
-
(2004)
Annu Rev Genet
, vol.38
, pp. 525-552
-
-
Riesenfeld, C.1
Schloss, P.2
Handelsman, J.3
-
8
-
-
11144354360
-
Environmental genome shotgun sequencing of the Sargasso Sea
-
Venter J, Remington K, Heidelberg J et al., Environmental genome shotgun sequencing of the Sargasso Sea, Science 304:66-74, 2004.
-
(2004)
Science
, vol.304
, pp. 66-74
-
-
Venter, J.1
Remington, K.2
Heidelberg, J.3
-
9
-
-
1542377296
-
Community structure and metabolism through reconstruction of microbial genomes from the environment
-
Tyson G, Chapman J, Hugenholtz P et al., Community structure and metabolism through reconstruction of microbial genomes from the environment, Nature 428:37-43, 2004.
-
(2004)
Nature
, vol.428
, pp. 37-43
-
-
Tyson, G.1
Chapman, J.2
Hugenholtz, P.3
-
10
-
-
19144366814
-
Metagenomics and industrial applications
-
Lorenz P, Eck J, Metagenomics and industrial applications, Nat Rev Microbiol 3:510-516, 2005.
-
(2005)
Nat Rev Microbiol
, vol.3
, pp. 510-516
-
-
Lorenz, P.1
Eck, J.2
-
11
-
-
33845874101
-
An obesity-associated gut microbiome with increased capacity for energy harvest
-
Turnbaugh P, Ley R, Mahowald M et al., An obesity-associated gut microbiome with increased capacity for energy harvest, Nature 444:1027-1031, 2006.
-
(2006)
Nature
, vol.444
, pp. 1027-1031
-
-
Turnbaugh, P.1
Ley, R.2
Mahowald, M.3
-
12
-
-
33744804299
-
Metagenomic analysis of the human distal gut microbiome
-
Gill S, Pop M, Deboy R et al., Metagenomic analysis of the human distal gut microbiome, Science 312:1355-1359, 2006.
-
(2006)
Science
, vol.312
, pp. 1355-1359
-
-
Gill, S.1
Pop, M.2
Deboy, R.3
-
13
-
-
55449131166
-
Bioinformatics for whole-genome shotgun sequencing of microbial communities
-
Chen K, Pachter L, Bioinformatics for whole-genome shotgun sequencing of microbial communities, PLoS Comput Biol 1:106-112, 2005.
-
(2005)
PLoS Comput Biol
, vol.1
, pp. 106-112
-
-
Chen, K.1
Pachter, L.2
-
14
-
-
33646374948
-
Potential and challenges
-
Comparative analysis of environmental sequences
-
Foerstner K, von Mering C, Bork P, Comparative analysis of environmental sequences: Potential and challenges, Philos Trans R Soc Lond B Biol Sci 361:519-523, 2006.
-
(2006)
Philos Trans R Soc Lond B Biol Sci
, vol.361
, pp. 519-523
-
-
Foerstner, K.1
von Mering, C.2
Bork, P.3
-
15
-
-
0036144823
-
A whole-genome shotgun assembler
-
ARACHNE
-
Batzoglou S, Jaffe D, Stanley K et al., ARACHNE: A whole-genome shotgun assembler, Genome Res 12:177-189, 2002.
-
(2002)
Genome Res
, vol.12
, pp. 177-189
-
-
Batzoglou, S.1
Jaffe, D.2
Stanley, K.3
-
16
-
-
0037267048
-
Whole-genome sequence assembly for mammalian genomes: Arachne 2
-
Jaffe D, Butler J, Gnerre S et al., Whole-genome sequence assembly for mammalian genomes: Arachne 2, Genome Res 13:91-96, 2003.
-
(2003)
Genome Res
, vol.13
, pp. 91-96
-
-
Jaffe, D.1
Butler, J.2
Gnerre, S.3
-
17
-
-
0035224746
-
Design of a compartmentalized shotgun assembler for the human genome
-
Huson D, Reinert K, Kravitz S et al., Design of a compartmentalized shotgun assembler for the human genome, Bioinformatics 17 Suppl 1:S132-139, 2001.
-
(2001)
Bioinformatics
, vol.17
, Issue.SUPPL. 1
-
-
Huson, D.1
Reinert, K.2
Kravitz, S.3
-
18
-
-
0037162885
-
Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes
-
Aparicio S, Chapman J, Stupka E et al., Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes, Science 297:1301-1310, 2002.
-
(2002)
Science
, vol.297
, pp. 1301-1310
-
-
Aparicio, S.1
Chapman, J.2
Stupka, E.3
-
19
-
-
16644401595
-
Probabilistic methods of identifying genes in prokaryotic genomes: Connections to the HMM theory
-
Azad R, Borodovsky M, Probabilistic methods of identifying genes in prokaryotic genomes: Connections to the HMM theory, Brief Bioinformatics 5:118-130, 2004.
-
(2004)
Brief Bioinformatics
, vol.5
, pp. 118-130
-
-
Azad, R.1
Borodovsky, M.2
-
20
-
-
33947235074
-
The sorcerer II global ocean sampling expedition: Expanding the universe of protein families
-
Yooseph S, Sutton G, Rusch D et al., The sorcerer II global ocean sampling expedition: Expanding the universe of protein families, PLoS Biol 5:e16, 2007.
-
(2007)
PLoS Biol
, vol.5
-
-
Yooseph, S.1
Sutton, G.2
Rusch, D.3
-
21
-
-
34249794257
-
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
-
Mavromatis K, Ivanova N, Barry K et al., Use of simulated data sets to evaluate the fidelity of metagenomic processing methods, Nat Methods 4:495-500, 2007.
-
(2007)
Nat Methods
, vol.4
, pp. 495-500
-
-
Mavromatis, K.1
Ivanova, N.2
Barry, K.3
-
22
-
-
33751059692
-
The marine viromes of four oceanic regions
-
Angly F, Felts B, Breitbart M et al., The marine viromes of four oceanic regions, PLoS Biol 4:e368, 2006.
-
(2006)
PLoS Biol
, vol.4
-
-
Angly, F.1
Felts, B.2
Breitbart, M.3
-
23
-
-
33847702910
-
MEGAN analysis of metagenomic data
-
Huson D, Auch A, Qi J et al., MEGAN analysis of metagenomic data, Genome Res 17:377-386, 2007.
-
(2007)
Genome Res
, vol.17
, pp. 377-386
-
-
Huson, D.1
Auch, A.2
Qi, J.3
-
24
-
-
40549141418
-
Metagenomics: Read length matters
-
Wommack K, Bhavsar J, Ravel J, Metagenomics: Read length matters, Appl Environ Microbiol 74:1453-1463, 2008.
-
(2008)
Appl Environ Microbiol
, vol.74
, pp. 1453-1463
-
-
Wommack, K.1
Bhavsar, J.2
Ravel, J.3
-
25
-
-
34548272144
-
Genome assembly, rearrangement, and repeats
-
Tang H, Genome assembly, rearrangement, and repeats, Chem Rev 107:3391-3406, 2007.
-
(2007)
Chem Rev
, vol.107
, pp. 3391-3406
-
-
Tang, H.1
-
26
-
-
0035859921
-
An Eulerian path approach to DNA fragment assembly
-
Pevzner P, Tang H, Waterman M, An Eulerian path approach to DNA fragment assembly, Proc Natl Acad Sci USA 98:9748-9753, 2001.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 9748-9753
-
-
Pevzner, P.1
Tang, H.2
Waterman, M.3
-
27
-
-
0029312158
-
Toward simplifying and accurately formulating fragment assembly
-
Myers E, Toward simplifying and accurately formulating fragment assembly, J Comput Biol 2:275-290, 1995.
-
(1995)
J Comput Biol
, vol.2
, pp. 275-290
-
-
Myers, E.1
-
28
-
-
4544263565
-
Fragment assembly with short reads
-
Chaisson M, Pevzner P, Tang H, Fragment assembly with short reads, Bioinformatics 20:2067-2074, 2004.
-
(2004)
Bioinformatics
, vol.20
, pp. 2067-2074
-
-
Chaisson, M.1
Pevzner, P.2
Tang, H.3
-
29
-
-
0034708758
-
A whole-genome assembly of Drosophila
-
Myers E, Sutton G, Delcher A et al., A whole-genome assembly of Drosophila, Science 287:2196-2204, 2000.
-
(2000)
Science
, vol.287
, pp. 2196-2204
-
-
Myers, E.1
Sutton, G.2
Delcher, A.3
-
30
-
-
0035895505
-
The sequence of the human genome
-
Venter J, Adams M, Myers E et al., The sequence of the human genome, Science 291:1304-1351, 2001.
-
(2001)
Science
, vol.291
, pp. 1304-1351
-
-
Venter, J.1
Adams, M.2
Myers, E.3
-
31
-
-
33745617710
-
A fast and symmetric DUST implementation to mask low-complexity DNA sequences
-
Morgulis A, Gertz E, Scher A et al., A fast and symmetric DUST implementation to mask low-complexity DNA sequences, J Comput Biol 13:1028-1040, 2006.
-
(2006)
J Comput Biol
, vol.13
, pp. 1028-1040
-
-
Morgulis, A.1
Gertz, E.2
Scher, A.3
-
32
-
-
0033555906
-
Tandem repeats finder: A program to analyze DNA sequences
-
Benson G, Tandem repeats finder: A program to analyze DNA sequences, Nucleic Acids Res 27:573-580, 1999.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 573-580
-
-
Benson, G.1
-
33
-
-
4644275238
-
De novo repeat classification and fragment assembly
-
Pevzner PA, Tang H, Tesler G, De novo repeat classification and fragment assembly, Genome Res 14(9):1786-1796, 2004.
-
(2004)
Genome Res
, vol.14
, Issue.9
, pp. 1786-1796
-
-
Pevzner, P.A.1
Tang, H.2
Tesler, G.3
-
34
-
-
8744312854
-
A novel method for multiple alignment of sequences with repeated and shuffled elements
-
Raphael B, Zhi D, Tang H et al., A novel method for multiple alignment of sequences with repeated and shuffled elements, Genome Res 14:2336-2346, 2004.
-
(2004)
Genome Res
, vol.14
, pp. 2336-2346
-
-
Raphael, B.1
Zhi, D.2
Tang, H.3
-
35
-
-
0036203448
-
Multiple sequence alignment using partial order graphs
-
Lee C, Grasso C, SharlowMF, Multiple sequence alignment using partial order graphs, Bioinformatics 18(3):452-64, 2002.
-
(2002)
Bioinformatics
, vol.18
, Issue.3
, pp. 452-464
-
-
Lee, C.1
Grasso, C.2
SharlowMF3
-
36
-
-
0037433758
-
A segment alignment approach to protein comparison
-
Ye Y, Jaroszewski L, Li W et al., A segment alignment approach to protein comparison, Bioinformatics 19:742-749, 2003.
-
(2003)
Bioinformatics
, vol.19
, pp. 742-749
-
-
Ye, Y.1
Jaroszewski, L.2
Li, W.3
-
37
-
-
33744784298
-
An application of statistics to comparative metagenomics
-
Rodriguez-Brito B, Rohwer F, Edwards R, An application of statistics to comparative metagenomics, BMC Bioinformatics 7:162, 2006.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 162
-
-
Rodriguez-Brito, B.1
Rohwer, F.2
Edwards, R.3
-
38
-
-
0141742293
-
A library of protein families and subfamilies indexed by function
-
PANTHER
-
Thomas P, Campbell M, Kejariwal A et al., PANTHER: A library of protein families and subfamilies indexed by function, Genome Res 13:2129-2141, 2003.
-
(2003)
Genome Res
, vol.13
, pp. 2129-2141
-
-
Thomas, P.1
Campbell, M.2
Kejariwal, A.3
-
39
-
-
33947215475
-
A community resource for metagenomics
-
CAMERA
-
Seshadri R, Kravitz S, Smarr L et al., CAMERA: A community resource for metagenomics, PLoS Biol 5:e75, 2007.
-
(2007)
PLoS Biol
, vol.5
-
-
Seshadri, R.1
Kravitz, S.2
Smarr, L.3
-
40
-
-
38549101119
-
-
The integrated microbial genomes (IMG) system in, Data content and analysis tool extensions, Database issue):D528-533
-
Markowitz V, Szeto E, Palaniappan K et al., The integrated microbial genomes (IMG) system in 2007: Data content and analysis tool extensions, Nucleic Acids Res 36(Database issue):D528-533, 2008.
-
(2007)
Nucleic Acids Res
, vol.36
-
-
Markowitz, V.1
Szeto, E.2
Palaniappan, K.3
|