-
1
-
-
1942443733
-
Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons
-
Acinas, S. G., Marcelino, L. A., Klepac-Ceraj, V., and Polz, M. F. (2004). Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J. Bacteriol. 186, 2629-2635. doi: 10.1128/JB.186.9.2629-2635.2004
-
(2004)
J. Bacteriol
, vol.186
, pp. 2629-2635
-
-
Acinas, S.G.1
Marcelino, L.A.2
Klepac-Ceraj, V.3
Polz, M.F.4
-
3
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., et al. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402. doi: 10.1093/nar/25.17.3389
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
-
4
-
-
84880923991
-
Waiting for the human intestinal Eukaryotome
-
Andersen, L. O., Vedel Nielsen, H., and Stensvold, C. R. (2013). Waiting for the human intestinal Eukaryotome. ISME J. 7, 1253-1255. doi: 10.1038/ismej.2013.21
-
(2013)
ISME J
, vol.7
, pp. 1253-1255
-
-
Andersen, L.O.1
Vedel Nielsen, H.2
Stensvold, C.R.3
-
6
-
-
85040852545
-
-
Oxford: Blackwell Scientific Publications
-
Begon, M., Harper, J. L., and Townsend, C. R. (1986). Ecology: Individuals, Populations and Communities. Oxford: Blackwell Scientific Publications.
-
(1986)
Ecology: Individuals, Populations and Communities
-
-
Begon, M.1
Harper, J.L.2
Townsend, C.R.3
-
7
-
-
3142780737
-
Solexa Ltd
-
Bennett, S. (2004). Solexa Ltd. Pharmacogenomics 5, 433-438. doi: 10.1517/14622416.5.4.433
-
(2004)
Pharmacogenomics
, vol.5
, pp. 433-438
-
-
Bennett, S.1
-
8
-
-
0035182182
-
Use of Gram stain in microbiology
-
Beveridge, T. J. (2001). Use of Gram stain in microbiology. Biotech. Histochem. 76, 111-118. doi: 10.1080/bih.76.3.111.118
-
(2001)
Biotech. Histochem
, vol.76
, pp. 111-118
-
-
Beveridge, T.J.1
-
9
-
-
77956615417
-
Robert Koch and the "golden age" of bacteriology
-
Blevins, S. M., and Bronze, M. S. (2010). Robert Koch and the "golden age" of bacteriology. Inter. J. Infect. Diseases 14, e744-e751. doi: 10.1016/j.ijid.2009.12.003
-
(2010)
Inter. J. Infect. Diseases
, vol.14
, pp. e744-e751
-
-
Blevins, S.M.1
Bronze, M.S.2
-
10
-
-
84860124422
-
Variable copy number, intra-genomic heterogeneities and lateral transfers of the 16S rRNA gene in pseudomonas
-
Bodilis, J., Nsigue-Meilo, S., Besaury, L., and Quillet, L. (2012). Variable copy number, intra-genomic heterogeneities and lateral transfers of the 16S rRNA gene in pseudomonas. PLoS ONE 7:e35647. doi: 10.1371/journal.pone.0035647
-
(2012)
PLoS ONE
, vol.7
-
-
Bodilis, J.1
Nsigue-Meilo, S.2
Besaury, L.3
Quillet, L.4
-
11
-
-
84871396799
-
Ray Meta: scalable de novo metagenome assembly and profiling
-
Boisvert, S., Raymond, F., Godzaridis, é., Laviolette, F., and Corbeil, J. (2012). Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biol. 13:R122. doi: 10.1186/gb-2012-13-12-r122
-
(2012)
Genome Biol
, vol.13
-
-
Boisvert, S.1
Raymond, F.2
Godzaridis, é.3
Laviolette, F.4
Corbeil, J.5
-
12
-
-
84871979584
-
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing
-
Bokulich, N. A., Subramanian, S., Faith, J. J., Gevers, D., Gordon, J. I., Knight, R., et al. (2013). Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat. Meth. 10, 57-59. doi: 10.1038/nmeth.2276
-
(2013)
Nat. Meth
, vol.10
, pp. 57-59
-
-
Bokulich, N.A.1
Subramanian, S.2
Faith, J.J.3
Gevers, D.4
Gordon, J.I.5
Knight, R.6
-
13
-
-
84866035770
-
Understanding microbial community diversity metrics derived from metagenomes: performance evaluation using simulated data sets
-
Bonilla-Rosso, G., Eguiarte, L. E., Romero, D., Travisano, M., and Souza, V. (2012). Understanding microbial community diversity metrics derived from metagenomes: performance evaluation using simulated data sets. FEMS Microbiol. Ecol. 82, 37-49. doi: 10.1111/j.1574-6941.2012.01405.x
-
(2012)
FEMS Microbiol. Ecol
, vol.82
, pp. 37-49
-
-
Bonilla-Rosso, G.1
Eguiarte, L.E.2
Romero, D.3
Travisano, M.4
Souza, V.5
-
14
-
-
84899721102
-
The Eukaryotic Tree of Life from a Global Phylogenomic Perspective
-
Burki, F. (2014). The Eukaryotic Tree of Life from a Global Phylogenomic Perspective. Cold Spring Harb. Perspect. Biol. 6:a016147. doi: 10.1101/cshperspect.a016147
-
(2014)
Cold Spring Harb. Perspect. Biol
, vol.6
-
-
Burki, F.1
-
15
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., et al. (2010). QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335-336. doi: 10.1038/nmeth.f.303
-
(2010)
Nat. Methods
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
Kuczynski, J.2
Stombaugh, J.3
Bittinger, K.4
Bushman, F.D.5
Costello, E.K.6
-
16
-
-
84863981120
-
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
-
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Huntley, J., Fierer, N., et al. (2012). Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621-1624. doi: 10.1038/ismej.2012.8
-
(2012)
ISME J
, vol.6
, pp. 1621-1624
-
-
Caporaso, J.G.1
Lauber, C.L.2
Walters, W.A.3
Berg-Lyons, D.4
Huntley, J.5
Fierer, N.6
-
17
-
-
84922717073
-
Comparative analysis of functional metagenomic annotation and the mappability of short reads
-
Carr, R., and Borenstein, E. (2014). Comparative analysis of functional metagenomic annotation and the mappability of short reads. PLoS ONE 9:e105776. doi: 10.1371/journal.pone.0105776
-
(2014)
PLoS ONE
, vol.9
-
-
Carr, R.1
Borenstein, E.2
-
18
-
-
84891774001
-
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
-
Caspi, R., Altman, T., Billington, R., Dreher, K., Foerster, H., Fulcher, C. A., et al. (2014). The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucl. Acids Res. 42, D459-D471. doi: 10.1093/nar/gkt1103
-
(2014)
Nucl. Acids Res
, vol.42
, pp. D459-D471
-
-
Caspi, R.1
Altman, T.2
Billington, R.3
Dreher, K.4
Foerster, H.5
Fulcher, C.A.6
-
19
-
-
33745244776
-
Abundance-based similarity indices and their estimation when there are unseen species in samples
-
Chao, A., Chazdon, R. L., Colwell, R. K., and Shen, T. J. (2006). Abundance-based similarity indices and their estimation when there are unseen species in samples. Biometrics 62, 361-371. doi: 10.1111/j.1541-0420.2005.00489.x
-
(2006)
Biometrics
, vol.62
, pp. 361-371
-
-
Chao, A.1
Chazdon, R.L.2
Colwell, R.K.3
Shen, T.J.4
-
20
-
-
84928228359
-
Assessment of diversity indices for the characterization of the soil prokaryotic community by metagenomic analysis
-
Chernov, T. I., Tkhakakhova, A. K., and Kutovaya, O. V. (2015). Assessment of diversity indices for the characterization of the soil prokaryotic community by metagenomic analysis. Eurasian Soil Sc. 48, 410-415. doi: 10.1134/S1064229315040031
-
(2015)
Eurasian Soil Sc
, vol.48
, pp. 410-415
-
-
Chernov, T.I.1
Tkhakakhova, A.K.2
Kutovaya, O.V.3
-
21
-
-
33644700003
-
Toward automatic reconstruction of a highly resolved tree of life
-
Ciccarelli, F. D., Doerks, T., Von Mering, C., Creevey, C. J., Snel, B., and Bork, P. (2006). Toward automatic reconstruction of a highly resolved tree of life. Science 311, 1283-1287. doi: 10.1126/science.1123061
-
(2006)
Science
, vol.311
, pp. 1283-1287
-
-
Ciccarelli, F.D.1
Doerks, T.2
Von Mering, C.3
Creevey, C.J.4
Snel, B.5
Bork, P.6
-
22
-
-
0028782130
-
Estimating terrestrial biodiversity through extrapolation
-
Colwell, R. K., and Coddington, J. A. (1994). Estimating terrestrial biodiversity through extrapolation. Philos. Trans. R. Soc. Lond. B 345, 101-118. doi: 10.1098/rstb.1994.0091
-
(1994)
Philos. Trans. R. Soc. Lond. B
, vol.345
, pp. 101-118
-
-
Colwell, R.K.1
Coddington, J.A.2
-
23
-
-
0030061238
-
Viable but non-culturable Vibrio cholerae O1 revert to a cultivable state in the human intestine
-
Colwell, R. R., Brayton, P., Herrington, D., Tall, B., Huq, A., and Levine, M. M. (1996). Viable but non-culturable Vibrio cholerae O1 revert to a cultivable state in the human intestine. World J. Microbiol. Biotechnol. 12, 28-31. doi: 10.1007/BF00327795
-
(1996)
World J. Microbiol. Biotechnol
, vol.12
, pp. 28-31
-
-
Colwell, R.R.1
Brayton, P.2
Herrington, D.3
Tall, B.4
Huq, A.5
Levine, M.M.6
-
24
-
-
84871931440
-
Advances in computational analysis of metagenome sequences: In silico metagenome analysis
-
Davenport, C. F., and Tümmler, B. (2013). Advances in computational analysis of metagenome sequences: In silico metagenome analysis. Environ. Microbiol. 15, 1-5. doi: 10.1111/j.1462-2920.2012.02843.x
-
(2013)
Environ. Microbiol
, vol.15
, pp. 1-5
-
-
Davenport, C.F.1
Tümmler, B.2
-
25
-
-
84930382531
-
Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway
-
de Crécy-Lagard, V. (2014). Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway. Comput. Struct. Biotechnol. J. 10, 41-50. doi: 10.1016/j.csbj.2014.05.008
-
(2014)
Comput. Struct. Biotechnol. J
, vol.10
, pp. 41-50
-
-
de Crécy-Lagard, V.1
-
26
-
-
84870041387
-
Bioinformatic approaches for functional annotation and pathway inference in metagenomics data
-
De Filippo, C., Ramazzotti, M., Fontana, P., and Cavalieri, D. (2012). Bioinformatic approaches for functional annotation and pathway inference in metagenomics data. Brief. Bioinformatics 13, 696-710. doi: 10.1093/bib/bbs070
-
(2012)
Brief. Bioinformatics
, vol.13
, pp. 696-710
-
-
De Filippo, C.1
Ramazzotti, M.2
Fontana, P.3
Cavalieri, D.4
-
27
-
-
34248188820
-
Hidden markov models in bioinformatics
-
De Fonzo, V., Aluffi-Pentini, F., and Parisi, V. (2007). Hidden markov models in bioinformatics. Curr. Bioinform. 2, 49-61. doi: 10.2174/157489307779314348
-
(2007)
Curr. Bioinform
, vol.2
, pp. 49-61
-
-
De Fonzo, V.1
Aluffi-Pentini, F.2
Parisi, V.3
-
28
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., et al. (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069-5072. doi: 10.1128/AEM.03006-05
-
(2006)
Appl. Environ. Microbiol
, vol.72
, pp. 5069-5072
-
-
DeSantis, T.Z.1
Hugenholtz, P.2
Larsen, N.3
Rojas, M.4
Brodie, E.L.5
Keller, K.6
-
29
-
-
80055082271
-
Accelerated profile HMM searches
-
Eddy, S. R. (2011). Accelerated profile HMM searches. PLoS Comput. Biol. 7:e1002195. doi: 10.1371/journal.pcbi.1002195
-
(2011)
PLoS Comput. Biol
, vol.7
-
-
Eddy, S.R.1
-
30
-
-
84878631963
-
Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform
-
Fichot, E. B., and Norman, R. S. (2013). Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform. Microbiome 1:10. doi: 10.1186/2049-2618-1-10
-
(2013)
Microbiome
, vol.1
, pp. 10
-
-
Fichot, E.B.1
Norman, R.S.2
-
31
-
-
0026585263
-
How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity
-
Fox, G. E., Wisotzkey, J. D., and Jurtshuk, P. (1992). How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int. J. Syst. Bacteriol. 42, 166-170. doi: 10.1099/00207713-42-1-166
-
(1992)
Int. J. Syst. Bacteriol
, vol.42
, pp. 166-170
-
-
Fox, G.E.1
Wisotzkey, J.D.2
Jurtshuk, P.3
-
32
-
-
84865180134
-
ProViDE: A software tool for accurate estimation of viral diversity in metagenomic samples
-
Ghosh, T. S., Mohammed, M. H., Komanduri, D., and Mande, S. S. (2011). ProViDE: A software tool for accurate estimation of viral diversity in metagenomic samples. Bioinformation 6, 91-94. doi: 10.6026/97320630006091
-
(2011)
Bioinformation
, vol.6
, pp. 91-94
-
-
Ghosh, T.S.1
Mohammed, M.H.2
Komanduri, D.3
Mande, S.S.4
-
33
-
-
77957895590
-
DiScRIBinATE: a rapid method for accurate taxonomic classification of metagenomic sequences
-
Ghosh, T. S., Monzoorul Haque, M., and Mande, S. S. (2010). DiScRIBinATE: a rapid method for accurate taxonomic classification of metagenomic sequences. BMC Bioinformatics 11 (Suppl. 7):S14. doi: 10.1186/1471-2105-11-S7-S14
-
(2010)
BMC Bioinformatics
, vol.11
, pp. S14
-
-
Ghosh, T.S.1
Monzoorul Haque, M.2
Mande, S.S.3
-
34
-
-
84856563821
-
Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes
-
Gihring, T. M., Green, S. J., and Schadt, C. W. (2012). Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes. Environ. Microbiol. 14, 285-290. doi: 10.1111/j.1462-2920.2011.02550.x
-
(2012)
Environ. Microbiol
, vol.14
, pp. 285-290
-
-
Gihring, T.M.1
Green, S.J.2
Schadt, C.W.3
-
35
-
-
79953007909
-
Microbial metagenomics: beyond the genome
-
Gilbert, J. A., and Dupont, C. L. (2011). Microbial metagenomics: beyond the genome. Ann. Rev. Mar. Sci. 3, 347-371. doi: 10.1146/annurev-marine-120709-142811
-
(2011)
Ann. Rev. Mar. Sci
, vol.3
, pp. 347-371
-
-
Gilbert, J.A.1
Dupont, C.L.2
-
36
-
-
84904811373
-
Alignment-Annotator web server: rendering and annotating sequence alignments
-
Gille, C., Fähling, M., Weyand, B., Wieland, T., and Gille, A. (2014). Alignment-Annotator web server: rendering and annotating sequence alignments. Nucl. Acids Res. 42, W3-W6. doi: 10.1093/nar/gku400
-
(2014)
Nucl. Acids Res
, vol.42
, pp. W3-W6
-
-
Gille, C.1
Fähling, M.2
Weyand, B.3
Wieland, T.4
Gille, A.5
-
37
-
-
0036727242
-
Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA
-
Gillespie, D. E., Brady, S. F., Bettermann, A. D., Cianciotto, N. P., Liles, M. R., Rondon, M. R., et al. (2002). Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Appl. Environ. Microbiol. 68, 4301-4306. doi: 10.1128/AEM.68.9.4301-4306.2002
-
(2002)
Appl. Environ. Microbiol
, vol.68
, pp. 4301-4306
-
-
Gillespie, D.E.1
Brady, S.F.2
Bettermann, A.D.3
Cianciotto, N.P.4
Liles, M.R.5
Rondon, M.R.6
-
38
-
-
0025322547
-
Tangential flow filtration and preliminary phylogenetic analysis of marine picoplankton
-
Giovannoni, S. J., DeLong, E. F., Schmidt, T. M., and Pace, N. R. (1990). Tangential flow filtration and preliminary phylogenetic analysis of marine picoplankton. Appl. Environ. Microbiol. 56, 2572-2575.
-
(1990)
Appl. Environ. Microbiol
, vol.56
, pp. 2572-2575
-
-
Giovannoni, S.J.1
DeLong, E.F.2
Schmidt, T.M.3
Pace, N.R.4
-
40
-
-
77955801615
-
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
-
Goecks, J., Nekrutenko, A., and Taylor, J. (2010). Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11:R86. doi: 10.1186/gb-2010-11-8-r86
-
(2010)
Genome Biol
, vol.11
-
-
Goecks, J.1
Nekrutenko, A.2
Taylor, J.3
-
41
-
-
84922662497
-
"Metagenomic mining of enzyme diversity, "
-
ed K. N. Timmis (Berlin; Heidelberg: Springer) (Accessed May 17, 2015)
-
Guazzaroni, M. E., Beloqui, A., Vieites, J. M., Al-ramahi, Y., Cortés, N. L., Ghazi, A., et al. (2010). "Metagenomic mining of enzyme diversity, " in Handbook of Hydrocarbon and Lipid Microbiology, ed K. N. Timmis (Berlin; Heidelberg: Springer), 2911-2927. Available online at: http://link.springer.com/referenceworkentry/10.1007/978-3-540-77587-4_216 (Accessed May 17, 2015).
-
(2010)
Handbook of Hydrocarbon and Lipid Microbiology
, pp. 2911-2927
-
-
Guazzaroni, M.E.1
Beloqui, A.2
Vieites, J.M.3
Al-ramahi, Y.4
Cortés, N.L.5
Ghazi, A.6
-
42
-
-
84878270728
-
Robust estimation of microbial diversity in theory and in practice
-
Haegeman, B., Hamelin, J., Moriarty, J., Neal, P., Dushoff, J., and Weitz, J. S. (2013). Robust estimation of microbial diversity in theory and in practice. ISME J. 7, 1092-1101. doi: 10.1038/ismej.2013.10
-
(2013)
ISME J
, vol.7
, pp. 1092-1101
-
-
Haegeman, B.1
Hamelin, J.2
Moriarty, J.3
Neal, P.4
Dushoff, J.5
Weitz, J.S.6
-
43
-
-
0032192790
-
Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products
-
Handelsman, J., Rondon, M. R., Brady, S. F., Clardy, J., and Goodman, R. M. (1998). Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol. 5, R245-R249. doi: 10.1016/s1074-5521(98)90108-9
-
(1998)
Chem. Biol
, vol.5
, pp. R245-R249
-
-
Handelsman, J.1
Rondon, M.R.2
Brady, S.F.3
Clardy, J.4
Goodman, R.M.5
-
44
-
-
0000917309
-
Explicit calculation of the rarefaction diversity measurement and the determination of sufficient sample size
-
Heck, K. L. Jr., Belle, G., and van Simberloff, D. (1975). Explicit calculation of the rarefaction diversity measurement and the determination of sufficient sample size. Ecology 56, 1459-1461. doi: 10.2307/1934716
-
(1975)
Ecology
, vol.56
, pp. 1459-1461
-
-
Heck, K.L.1
Belle, G.2
van Simberloff, D.3
-
45
-
-
84899679811
-
Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia
-
Hugerth, L. W., Muller, E. E. L., Hu, Y. O. O., Lebrun, L. A. M., Roume, H., Lundin, D., et al. (2014). Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia. PLoS ONE 9:e95567. doi: 10.1371/journal.pone.0095567
-
(2014)
PLoS ONE
, vol.9
-
-
Hugerth, L.W.1
Muller, E.E.L.2
Hu, Y.O.O.3
Lebrun, L.A.M.4
Roume, H.5
Lundin, D.6
-
46
-
-
84884560630
-
Microbial community analysis using MEGAN
-
Huson, D. H., and Weber, N. (2013). Microbial community analysis using MEGAN. Meth. Enzymol. 531, 465-485. doi: 10.1016/B978-0-12-407863-5.00021-6
-
(2013)
Meth. Enzymol
, vol.531
, pp. 465-485
-
-
Huson, D.H.1
Weber, N.2
-
47
-
-
84856246802
-
De novo assembly and genotyping of variants using colored de Bruijn graphs
-
Iqbal, Z., Caccamo, M., Turner, I., Flicek, P., and McVean, G. (2012). De novo assembly and genotyping of variants using colored de Bruijn graphs. Nat. Genet. 44, 226-232. doi: 10.1038/ng.1028
-
(2012)
Nat. Genet
, vol.44
, pp. 226-232
-
-
Iqbal, Z.1
Caccamo, M.2
Turner, I.3
Flicek, P.4
McVean, G.5
-
48
-
-
84864448769
-
Template-based protein structure modeling using the RaptorX web server
-
Källberg, M., Wang, H., Wang, S., Peng, J., Wang, Z., Lu, H., et al. (2012). Template-based protein structure modeling using the RaptorX web server. Nat. Protocols 7, 1511-1522. doi: 10.1038/nprot.2012.085
-
(2012)
Nat. Protocols
, vol.7
, pp. 1511-1522
-
-
Källberg, M.1
Wang, H.2
Wang, S.3
Peng, J.4
Wang, Z.5
Lu, H.6
-
49
-
-
0029060923
-
Dinucleotide relative abundance extremes: a genomic signature
-
Karlin, S., and Burge, C. (1995). Dinucleotide relative abundance extremes: a genomic signature. Trends Genet. 11, 283-290. doi: 10.1016/S0168-9525(00)89076-9
-
(1995)
Trends Genet
, vol.11
, pp. 283-290
-
-
Karlin, S.1
Burge, C.2
-
50
-
-
84954265162
-
Following Roche's Decision to Shut Down 454, Customers Make Plans to Move to Other Platforms
-
(Accessed October 29, 2015)
-
Karow, J. (2013). Following Roche's Decision to Shut Down 454, Customers Make Plans to Move to Other Platforms. GenomeWeb. Available online at: https://www.genomeweb.com/sequencing/following-roches-decision-shut-down-454-customers-make-plans-move-other-platform (Accessed October 29, 2015).
-
(2013)
GenomeWeb
-
-
Karow, J.1
-
51
-
-
33846074757
-
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation
-
Karro, J. E., Yan, Y., Zheng, D., Zhang, Z., Carriero, N., Cayting, P., et al. (2007). Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res. 35, D55-D60. doi: 10.1093/nar/gkl851
-
(2007)
Nucleic Acids Res
, vol.35
, pp. D55-D60
-
-
Karro, J.E.1
Yan, Y.2
Zheng, D.3
Zhang, Z.4
Carriero, N.5
Cayting, P.6
-
52
-
-
0030465241
-
Characterization of individual polynucleotide molecules using a membrane channel
-
Kasianowicz, J. J., Brandin, E., Branton, D., and Deamer, D. W. (1996). Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl. Acad. Sci. U.S.A. 93, 13770-13773. doi: 10.1073/pnas.93.24.13770
-
(1996)
Proc. Natl. Acad. Sci. U.S.A
, vol.93
, pp. 13770-13773
-
-
Kasianowicz, J.J.1
Brandin, E.2
Branton, D.3
Deamer, D.W.4
-
53
-
-
84903286893
-
The marine microbial eukaryote transcriptome sequencing project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing
-
Keeling, P. J., Burki, F., Wilcox, H. M., Allam, B., Allen, E. E., Amaral-Zettler, L. A., et al. (2014). The marine microbial eukaryote transcriptome sequencing project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol. 12:e1001889. doi: 10.1371/journal.pbio.1001889
-
(2014)
PLoS Biol
, vol.12
-
-
Keeling, P.J.1
Burki, F.2
Wilcox, H.M.3
Allam, B.4
Allen, E.E.5
Amaral-Zettler, L.A.6
-
54
-
-
1842560595
-
Tapping into microbial diversity
-
Keller, M., and Zengler, K. (2004). Tapping into microbial diversity. Nat. Rev. Micro. 2, 141-150. doi: 10.1038/nrmicro819
-
(2004)
Nat. Rev. Micro
, vol.2
, pp. 141-150
-
-
Keller, M.1
Zengler, K.2
-
55
-
-
84855258501
-
Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering
-
Kelley, D. R., Liu, B., Delcher, A. L., Pop, M., and Salzberg, S. L. (2012). Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering. Nucleic Acids Res. 40, e9. doi: 10.1093/nar/gkr1067
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Kelley, D.R.1
Liu, B.2
Delcher, A.L.3
Pop, M.4
Salzberg, S.L.5
-
56
-
-
12344309156
-
Estimating prokaryotic diversity: When are 16S rDNA libraries large enough?
-
Kemp, P. F., and Aller, J. Y. (2004). Estimating prokaryotic diversity: When are 16S rDNA libraries large enough? Limnol. Oceanogr. Methods 2, 114-125. doi: 10.4319/lom.2004.2.114
-
(2004)
Limnol. Oceanogr. Methods
, vol.2
, pp. 114-125
-
-
Kemp, P.F.1
Aller, J.Y.2
-
57
-
-
42449162998
-
Phylogenetic classification of short environmental DNA fragments
-
Krause, L., Diaz, N. N., Goesmann, A., Kelley, S., Nattkemper, T. W., Rohwer, F., et al. (2008). Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res. 36, 2230-2239. doi: 10.1093/nar/gkn038
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 2230-2239
-
-
Krause, L.1
Diaz, N.N.2
Goesmann, A.3
Kelley, S.4
Nattkemper, T.W.5
Rohwer, F.6
-
58
-
-
0342896170
-
"CHAPTER 12-species diversity measures, "
-
(Boston: Addison-Wesley Educational Publishers, Inc.) (Accessed August 3, 2015)
-
Krebs, C. (2014). "CHAPTER 12-species diversity measures, " in Ecological Methodology (Boston: Addison-Wesley Educational Publishers, Inc.). Available online at: http://www.zoology.ubc.ca/~krebs/downloads/krebs_chapter_13_2014.pdf (Accessed August 3, 2015).
-
(2014)
Ecological Methodology
-
-
Krebs, C.1
-
59
-
-
70349993601
-
ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes
-
Kristiansson, E., Hugenholtz, P., and Dalevi, D. (2009). ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes. Bioinformatics 25, 2737-2738. doi: 10.1093/bioinformatics/btp508
-
(2009)
Bioinformatics
, vol.25
, pp. 2737-2738
-
-
Kristiansson, E.1
Hugenholtz, P.2
Dalevi, D.3
-
60
-
-
84867634981
-
MOCAT: a metagenomics assembly and gene prediction toolkit
-
Kultima, J. R., Sunagawa, S., Li, J., Chen, W., Chen, H., Mende, D. R., et al. (2012). MOCAT: a metagenomics assembly and gene prediction toolkit. PLoS ONE 7:e47656. doi: 10.1371/journal.pone.0047656
-
(2012)
PLoS ONE
, vol.7
-
-
Kultima, J.R.1
Sunagawa, S.2
Li, J.3
Chen, W.4
Chen, H.5
Mende, D.R.6
-
61
-
-
84884127512
-
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
-
Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., et al. (2013). Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 31, 814-821. doi: 10.1038/nbt.2676
-
(2013)
Nat. Biotechnol
, vol.31
, pp. 814-821
-
-
Langille, M.G.I.1
Zaneveld, J.2
Caporaso, J.G.3
McDonald, D.4
Knights, D.5
Reyes, J.A.6
-
62
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B., and Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Meth. 9, 357-359. doi: 10.1038/nmeth.1923
-
(2012)
Nat. Meth
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
63
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li, H., and Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760. doi: 10.1093/bioinformatics/btp324
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
64
-
-
84862197046
-
Analyses of the microbial diversity across the human microbiome
-
Li, K., Bihan, M., Yooseph, S., and Methé, B. A. (2012). Analyses of the microbial diversity across the human microbiome. PLoS ONE 7:e32118. doi: 10.1371/journal.pone.0032118
-
(2012)
PLoS ONE
, vol.7
-
-
Li, K.1
Bihan, M.2
Yooseph, S.3
Methé, B.A.4
-
65
-
-
71749111168
-
Analysis and comparison of very large metagenomes with fast clustering and functional annotation
-
Li, W. (2009). Analysis and comparison of very large metagenomes with fast clustering and functional annotation. BMC Bioinformatics 10:359. doi: 10.1186/1471-2105-10-359
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 359
-
-
Li, W.1
-
66
-
-
33745634395
-
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li, W., and Godzik, A. (2006). Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658-1659. doi: 10.1093/bioinformatics/btl158
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
67
-
-
85016968027
-
"Metagenomics for study of fungal ecology, "
-
ed Francisrtin (John Wiley & Sons, Inc) (Accessed May 28, 2015)
-
Lindahl, B. D., and Kuske, C. R. (2013). "Metagenomics for study of fungal ecology, " in The Ecological Genomics of Fungi, ed Francisrtin (John Wiley & Sons, Inc), 279-303. Available online at: http://onlinelibrary.wiley.com/doi/10.1002/9781118735893.ch13/summary (Accessed May 28, 2015).
-
(2013)
The Ecological Genomics of Fungi
, pp. 279-303
-
-
Lindahl, B.D.1
Kuske, C.R.2
-
68
-
-
77953734944
-
"Identifying differentially abundant metabolic pathways in metagenomic datasets, "
-
eds M. Borodovsky, J. P. Gogarten, T. M. Przytycka, and S. Rajasekaran (Berlin; Heidelberg: Springer) (Accessed May 17, 2015)
-
Liu, B., and Pop, M. (2010). "Identifying differentially abundant metabolic pathways in metagenomic datasets, " in Bioinformatics Research and Applications Lecture Notes in Computer Science, eds M. Borodovsky, J. P. Gogarten, T. M. Przytycka, and S. Rajasekaran (Berlin; Heidelberg: Springer), 101-112. Available online at: http://link.springer.com/chapter/10.1007/978-3-642-13078-6_12 (Accessed May 17, 2015).
-
(2010)
Bioinformatics Research and Applications Lecture Notes in Computer Science
, pp. 101-112
-
-
Liu, B.1
Pop, M.2
-
69
-
-
83755166448
-
MetaPath: identifying differentially abundant metabolic pathways in metagenomic datasets
-
Liu, B., and Pop, M. (2011). MetaPath: identifying differentially abundant metabolic pathways in metagenomic datasets. BMC Proc. 5:S9. doi: 10.1186/1753-6561-5-S2-S9
-
(2011)
BMC Proc
, vol.5
, pp. S9
-
-
Liu, B.1
Pop, M.2
-
70
-
-
84876113075
-
Gene prediction in metagenomic fragments based on the SVM algorithm
-
Liu, Y., Guo, J., Hu, G., and Zhu, H. (2013). Gene prediction in metagenomic fragments based on the SVM algorithm. BMC Bioinformatics 14:S12. doi: 10.1186/1471-2105-14-S5-S12
-
(2013)
BMC Bioinformatics
, vol.14
, pp. S12
-
-
Liu, Y.1
Guo, J.2
Hu, G.3
Zhu, H.4
-
71
-
-
11144239489
-
Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes
-
Liu, Y., Harrison, P. M., Kunin, V., and Gerstein, M. (2004). Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes. Genome Biol. 5:R64. doi: 10.1186/gb-2004-5-9-r64
-
(2004)
Genome Biol
, vol.5
-
-
Liu, Y.1
Harrison, P.M.2
Kunin, V.3
Gerstein, M.4
-
72
-
-
84865285541
-
Environmental microbiology through the lens of high-throughput DNA sequencing: synopsis of current platforms and bioinformatics approaches
-
Logares, R., Haverkamp, T. H. A., Kumar, S., Lanzén, A., Nederbragt, A. J., Quince, C., et al. (2012). Environmental microbiology through the lens of high-throughput DNA sequencing: synopsis of current platforms and bioinformatics approaches. J. Microbiol. Methods 91, 106-113. doi: 10.1016/j.mimet.2012.07.017
-
(2012)
J. Microbiol. Methods
, vol.91
, pp. 106-113
-
-
Logares, R.1
Haverkamp, T.H.A.2
Kumar, S.3
Lanzén, A.4
Nederbragt, A.J.5
Quince, C.6
-
73
-
-
29144464937
-
UniFrac: a new phylogenetic method for comparing microbial communities
-
Lozupone, C., and Knight, R. (2005). UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71, 8228-8235. doi: 10.1128/AEM.71.12.8228-8235.2005
-
(2005)
Appl. Environ. Microbiol
, vol.71
, pp. 8228-8235
-
-
Lozupone, C.1
Knight, R.2
-
74
-
-
84884557900
-
"Chapter twenty-three-a user's guide to quantitative and comparative analysis of metagenomic datasets, "
-
ed E. F. DeLong (Academic Press) (Accessed February 17, 2015)
-
Luo, C., Rodriguez, -R. L. M., and Konstantinidis, K. T. (2013). "Chapter twenty-three-a user's guide to quantitative and comparative analysis of metagenomic datasets, " in Methods in Enzymology Microbial Metagenomics, Metatranscriptomics, and Metaproteomics, ed E. F. DeLong (Academic Press), 525-547. Available online at: http://www.sciencedirect.com/science/article/pii/B978012407863500023X (Accessed February 17, 2015).
-
(2013)
Methods in Enzymology Microbial Metagenomics, Metatranscriptomics, and Metaproteomics
, pp. 525-547
-
-
Luo, C.1
Rodriguez, -R.L.M.2
Konstantinidis, K.T.3
-
75
-
-
84856770811
-
Direct comparisons of illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample
-
Luo, C., Tsementzi, D., Kyrpides, N., Read, T., and Konstantinidis, K. T. (2012). Direct comparisons of illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS ONE 7:e30087. doi: 10.1371/journal.pone.0030087
-
(2012)
PLoS ONE
, vol.7
-
-
Luo, C.1
Tsementzi, D.2
Kyrpides, N.3
Read, T.4
Konstantinidis, K.T.5
-
76
-
-
0030456630
-
3. Biodiversity, biogeography and conservation of diatoms
-
Mann, D. G., and Droop, S. J. M. (1996). 3. Biodiversity, biogeography and conservation of diatoms. Hydrobiologia 336, 19-32. doi: 10.1007/BF00010816
-
(1996)
Hydrobiologia
, vol.336
, pp. 19-32
-
-
Mann, D.G.1
Droop, S.J.M.2
-
77
-
-
24044455869
-
Genome sequencing in open microfabricated high density picoliter reactors
-
Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., et al. (2005). Genome sequencing in open microfabricated high density picoliter reactors. Nature 437, 376-380. doi: 10.1038/nature03959
-
(2005)
Nature
, vol.437
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Altman, W.E.3
Attiya, S.4
Bader, J.S.5
Bemben, L.A.6
-
78
-
-
84862024797
-
IMG/M: the integrated metagenome data management and comparative analysis system
-
Markowitz, V. M., Chen, I. M. A., Chu, K., Szeto, E., Palaniappan, K., Grechkin, Y., et al. (2012). IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res. 40, D123-D129. doi: 10.1093/nar/gkr975
-
(2012)
Nucleic Acids Res
, vol.40
, pp. D123-D129
-
-
Markowitz, V.M.1
Chen, I.M.A.2
Chu, K.3
Szeto, E.4
Palaniappan, K.5
Grechkin, Y.6
-
79
-
-
52049102283
-
Are biologists in "future shock"? Symbiosis integrates biology across domains
-
McFall-Ngai, M. (2008). Are biologists in "future shock"? Symbiosis integrates biology across domains. Nat. Rev. Micro. 6, 789-792. doi: 10.1038/nrmicro1982
-
(2008)
Nat. Rev. Micro
, vol.6
, pp. 789-792
-
-
McFall-Ngai, M.1
-
80
-
-
33845957530
-
Accurate phylogenetic classification of variable-length DNA fragments
-
McHardy, A. C., Martín, H. G., Tsirigos, A., Hugenholtz, P., and Rigoutsos, I. (2007). Accurate phylogenetic classification of variable-length DNA fragments. Nat. Methods 4, 63-72. doi: 10.1038/nmeth976
-
(2007)
Nat. Methods
, vol.4
, pp. 63-72
-
-
McHardy, A.C.1
Martín, H.G.2
Tsirigos, A.3
Hugenholtz, P.4
Rigoutsos, I.5
-
81
-
-
84876427223
-
Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data
-
McMurdie, P. J., and Holmes, S. (2013). Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8:e61217. doi: 10.1371/journal.pone.0061217
-
(2013)
PLoS ONE
, vol.8
-
-
McMurdie, P.J.1
Holmes, S.2
-
82
-
-
84928987348
-
Shiny-phyloseq: web application for interactive microbiome analysis with provenance tracking
-
McMurdie, P. J., and Holmes, S. (2014) Shiny-phyloseq: web application for interactive microbiome analysis with provenance tracking. Bioinformatics 31, 282-283. doi: 10.1093/bioinformatics/btu616
-
(2014)
Bioinformatics
, vol.31
, pp. 282-283
-
-
McMurdie, P.J.1
Holmes, S.2
-
83
-
-
53549118607
-
The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes
-
Meyer, F., Paarmann, D., D'souza, M., Olson, R., Glass, E. M., Kubal, M., et al. (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
-
84
-
-
67649887316
-
SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences
-
Monzoorul Haque, M., Ghosh, T. S., Komanduri, D., and Mande, S. S. (2009). SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences. Bioinformatics 25, 1722-1730. doi: 10.1093/bioinformatics/btp317
-
(2009)
Bioinformatics
, vol.25
, pp. 1722-1730
-
-
Monzoorul Haque, M.1
Ghosh, T.S.2
Komanduri, D.3
Mande, S.S.4
-
85
-
-
77956095453
-
Metagenomic sequencing of an in vitro-simulated microbial community
-
Morgan, J. L., Darling, A. E., and Eisen, J. A. (2010). Metagenomic sequencing of an in vitro-simulated microbial community. PLoS ONE 5:e10209. doi: 10.1371/journal.pone.0010209
-
(2010)
PLoS ONE
, vol.5
-
-
Morgan, J.L.1
Darling, A.E.2
Eisen, J.A.3
-
86
-
-
84894135682
-
Metagenomic analysis of the microbial community in kefir grains
-
Nalbantoglu, U., Cakar, A., Dogan, H., Abaci, N., Ustek, D., Sayood, K., et al. (2014). Metagenomic analysis of the microbial community in kefir grains. Food Microbiol. 41, 42-51. doi: 10.1016/j.fm.2014.01.014
-
(2014)
Food Microbiol
, vol.41
, pp. 42-51
-
-
Nalbantoglu, U.1
Cakar, A.2
Dogan, H.3
Abaci, N.4
Ustek, D.5
Sayood, K.6
-
87
-
-
84867397631
-
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
-
Namiki, T., Hachiya, T., Tanaka, H., and Sakakibara, Y. (2012). MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res. 40, e155. doi: 10.1093/nar/gks678
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Namiki, T.1
Hachiya, T.2
Tanaka, H.3
Sakakibara, Y.4
-
88
-
-
0001075725
-
Algal biodiversity
-
Norton, T. A., Melkonian, M., and Andersen, R. (1996). Algal biodiversity. Phycologia 35, 308-326. doi: 10.2216/i0031-8884-35-4-308.1
-
(1996)
Phycologia
, vol.35
, pp. 308-326
-
-
Norton, T.A.1
Melkonian, M.2
Andersen, R.3
-
89
-
-
0032919364
-
KEGG: kyoto encyclopedia of genes and genomes
-
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., and Kanehisa, M. (1999). KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 27, 29-34. doi: 10.1093/nar/27.1.29
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 29-34
-
-
Ogata, H.1
Goto, S.2
Sato, K.3
Fujibuchi, W.4
Bono, H.5
Kanehisa, M.6
-
90
-
-
0025856532
-
Formation of nonculturable Vibrio vulnificus cells and its relationship to the starvation state
-
Oliver, J. D., Nilsson, L., and Kjelleberg, S. (1991). Formation of nonculturable Vibrio vulnificus cells and its relationship to the starvation state. Appl. Environ. Microbiol. 57, 2640-2644.
-
(1991)
Appl. Environ. Microbiol
, vol.57
, pp. 2640-2644
-
-
Oliver, J.D.1
Nilsson, L.2
Kjelleberg, S.3
-
91
-
-
84891479561
-
The function of our microbiota: who is out there and what do they do?
-
Ottman, N., Smidt, H., de Vos, W. M., and Belzer, C. (2012). The function of our microbiota: who is out there and what do they do? Front. Cell. Infect. Microbiol. 2:104. doi: 10.3389/fcimb.2012.00104
-
(2012)
Front. Cell. Infect. Microbiol
, vol.2
, pp. 104
-
-
Ottman, N.1
Smidt, H.2
de Vos, W.M.3
Belzer, C.4
-
92
-
-
84856468953
-
NGS QC toolkit: a toolkit for quality control of next generation sequencing data
-
Patel, R. K., and Jain, M. (2012). NGS QC toolkit: a toolkit for quality control of next generation sequencing data. PLoS ONE 7:e30619. doi: 10.1371/journal.pone.0030619
-
(2012)
PLoS ONE
, vol.7
-
-
Patel, R.K.1
Jain, M.2
-
93
-
-
84888865593
-
Differential abundance analysis for microbial marker-gene surveys
-
Paulson, J. N., Stine, O. C., Bravo, H. C., and Pop, M. (2013). Differential abundance analysis for microbial marker-gene surveys. Nat. Meth. 10, 1200-1202. doi: 10.1038/nmeth.2658
-
(2013)
Nat. Meth
, vol.10
, pp. 1200-1202
-
-
Paulson, J.N.1
Stine, O.C.2
Bravo, H.C.3
Pop, M.4
-
94
-
-
84861760530
-
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
-
Peng, Y., Leung, H. C., Yiu, S. M., and Chin, F. Y. (2012). IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28, 1420-1428. doi: 10.1093/bioinformatics/bts174
-
(2012)
Bioinformatics
, vol.28
, pp. 1420-1428
-
-
Peng, Y.1
Leung, H.C.2
Yiu, S.M.3
Chin, F.Y.4
-
95
-
-
65949108590
-
Metagenomic Pyrosequencing and Microbial Identification
-
Petrosino, J. F., Highlander, S., Luna, R. A., Gibbs, R. A., and Versalovic, J. (2009). Metagenomic Pyrosequencing and Microbial Identification. Clin. Chem. 55, 856-866. doi: 10.1373/clinchem.2008.107565
-
(2009)
Clin. Chem
, vol.55
, pp. 856-866
-
-
Petrosino, J.F.1
Highlander, S.2
Luna, R.A.3
Gibbs, R.A.4
Versalovic, J.5
-
96
-
-
84928989683
-
A two-stage statistical procedure for feature selection and comparison in functional analysis of metagenomes
-
Pookhao, N., Sohn, M. B., Li, Q., Jenkins, I., Du, R., Jiang, H., et al. (2015). A two-stage statistical procedure for feature selection and comparison in functional analysis of metagenomes. Bioinformatics 31, 158-165. doi: 10.1093/bioinformatics/btu635
-
(2015)
Bioinformatics
, vol.31
, pp. 158-165
-
-
Pookhao, N.1
Sohn, M.B.2
Li, Q.3
Jenkins, I.4
Du, R.5
Jiang, H.6
-
97
-
-
84899535363
-
Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics
-
Poretsky, R., Rodriguez, -R. L. M., Luo, C., Tsementzi, D., and Konstantinidis, K. T. (2014). Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics. PLoS ONE 9:e93827. doi: 10.1371/journal.pone.0093827
-
(2014)
PLoS ONE
, vol.9
-
-
Poretsky, R.1
Rodriguez, -R.L.M.2
Luo, C.3
Tsementzi, D.4
Konstantinidis, K.T.5
-
98
-
-
79957841562
-
Snapshot of the eukaryotic gene expression in muskoxen rumen-a metatranscriptomic approach
-
Qi, M., Wang, P., O'Toole, N., Barboza, P. S., Ungerfeld, E., Leigh, M. B., et al. (2011). Snapshot of the eukaryotic gene expression in muskoxen rumen-a metatranscriptomic approach. PLoS ONE 6:e20521. doi: 10.1371/journal.pone.0020521
-
(2011)
PLoS ONE
, vol.6
-
-
Qi, M.1
Wang, P.2
O'Toole, N.3
Barboza, P.S.4
Ungerfeld, E.5
Leigh, M.B.6
-
99
-
-
84873739311
-
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
-
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., et al. (2013). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590-D596. doi: 10.1093/nar/gks1219
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D590-D596
-
-
Quast, C.1
Pruesse, E.2
Yilmaz, P.3
Gerken, J.4
Schweer, T.5
Yarza, P.6
-
100
-
-
84925545767
-
BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes
-
Rey, J., Deschavanne, P., and Tuffery, P. (2014). BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes. Database (Oxford). 2014:bau106. doi: 10.1093/database/bau106
-
(2014)
Database (Oxford)
, vol.2014
-
-
Rey, J.1
Deschavanne, P.2
Tuffery, P.3
-
101
-
-
78651326786
-
FragGeneScan: predicting genes in short and error-prone reads
-
Rho, M., Tang, H., and Ye, Y. (2010). FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res. 38, e191. doi: 10.1093/nar/gkq747
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Rho, M.1
Tang, H.2
Ye, Y.3
-
102
-
-
84865182842
-
The automatic annotation of bacterial genomes
-
Richardson, E. J., and Watson, M. (2013). The automatic annotation of bacterial genomes. Brief. Bioinformatics 14, 1-12. doi: 10.1093/bib/bbs007
-
(2013)
Brief. Bioinformatics
, vol.14
, pp. 1-12
-
-
Richardson, E.J.1
Watson, M.2
-
103
-
-
33744784298
-
An application of statistics to comparative metagenomics
-
Rodriguez-Brito, B., Rohwer, F., and Edwards, R. A. (2006). An application of statistics to comparative metagenomics. BMC Bioinformatics 7:162. doi: 10.1186/1471-2105-7-162
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 162
-
-
Rodriguez-Brito, B.1
Rohwer, F.2
Edwards, R.A.3
-
104
-
-
0021280886
-
Viable but nonrecoverable stage of Salmonella enteritidis in aquatic systems
-
Roszak, D. B., Grimes, D. J., and Colwell, R. R. (1984). Viable but nonrecoverable stage of Salmonella enteritidis in aquatic systems. Can. J. Microbiol. 30, 334-338. doi: 10.1139/m84-049
-
(1984)
Can. J. Microbiol
, vol.30
, pp. 334-338
-
-
Roszak, D.B.1
Grimes, D.J.2
Colwell, R.R.3
-
105
-
-
79960597679
-
An integrated semiconductor device enabling non-optical genome sequencing
-
Rothberg, J. M., Hinz, W., Rearick, T. M., Schultz, J., Mileski, W., Davey, M., et al. (2011). An integrated semiconductor device enabling non-optical genome sequencing. Nature 475, 348-352. doi: 10.1038/nature10242
-
(2011)
Nature
, vol.475
, pp. 348-352
-
-
Rothberg, J.M.1
Hinz, W.2
Rearick, T.M.3
Schultz, J.4
Mileski, W.5
Davey, M.6
-
106
-
-
84894092867
-
A practical guide to sequencing genomes and transcriptomes
-
Sanchez-Flores, A., and Abreu-Goodger, C. (2014). A practical guide to sequencing genomes and transcriptomes. Curr. Top. Med. Chem. 14, 398-406. doi: 10.2174/1568026613666131204142353
-
(2014)
Curr. Top. Med. Chem
, vol.14
, pp. 398-406
-
-
Sanchez-Flores, A.1
Abreu-Goodger, C.2
-
107
-
-
0000755588
-
Marine benthic diversity: a comparative study
-
Sanders, H. L. (1968). Marine benthic diversity: a comparative study. Am. Nat. 102, 243-282. doi: 10.1086/282541
-
(1968)
Am. Nat
, vol.102
, pp. 243-282
-
-
Sanders, H.L.1
-
108
-
-
0017681196
-
DNA sequencing with chain-terminating inhibitors
-
Sanger, F., Nicklen, S., and Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. U.S.A. 74, 5463-5467. doi: 10.1073/pnas.74.12.5463
-
(1977)
Proc. Natl. Acad. Sci. U.S.A
, vol.74
, pp. 5463-5467
-
-
Sanger, F.1
Nicklen, S.2
Coulson, A.R.3
-
110
-
-
72949107142
-
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., et al. (2009). Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537-7541. doi: 10.1128/AEM.01541-09
-
(2009)
Appl. Environ. Microbiol
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
Westcott, S.L.2
Ryabin, T.3
Hall, J.R.4
Hartmann, M.5
Hollister, E.B.6
-
111
-
-
79952422304
-
Quality control and preprocessing of metagenomic datasets
-
Schmieder, R., and Edwards, R. (2011). Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863-864. doi: 10.1093/bioinformatics/btr026
-
(2011)
Bioinformatics
, vol.27
, pp. 863-864
-
-
Schmieder, R.1
Edwards, R.2
-
112
-
-
84859972408
-
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
-
Schoch, C. L., Seifert, K. A., Huhndorf, S., Robert, V., Spouge, J. L., Levesque, C. A., et al. (2012). Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc. Natl. Acad. Sci. U.S.A. 109, 6241-6246. doi: 10.1073/pnas.1117018109
-
(2012)
Proc. Natl. Acad. Sci. U.S.A
, vol.109
, pp. 6241-6246
-
-
Schoch, C.L.1
Seifert, K.A.2
Huhndorf, S.3
Robert, V.4
Spouge, J.L.5
Levesque, C.A.6
-
113
-
-
84856496549
-
Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis
-
Scholz, M. B., Lo, C. C., and Chain, P. S. (2012). Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr. Opin. Biotechnol. 23, 9-15. doi: 10.1016/j.copbio.2011.11.013
-
(2012)
Curr. Opin. Biotechnol
, vol.23
, pp. 9-15
-
-
Scholz, M.B.1
Lo, C.C.2
Chain, P.S.3
-
114
-
-
0344666688
-
Horizontal transfer of segments of the 16S rRNA genes between species of the Streptococcus anginosus group
-
Schouls, L. M., Schot, C. S., and Jacobs, J. A. (2003). Horizontal transfer of segments of the 16S rRNA genes between species of the Streptococcus anginosus group. J. Bacteriol. 185, 7241-7246. doi: 10.1128/JB.185.24.7241-7246.2003
-
(2003)
J. Bacteriol
, vol.185
, pp. 7241-7246
-
-
Schouls, L.M.1
Schot, C.S.2
Jacobs, J.A.3
-
115
-
-
84881548286
-
Computational meta'omics for microbial community studies
-
Segata, N., Boernigen, D., Tickle, T. L., Morgan, X. C., Garrett, W. S., and Huttenhower, C. (2013). Computational meta'omics for microbial community studies. Mol. Syst. Biol. 9, 666. doi: 10.1038/msb.2013.22
-
(2013)
Mol. Syst. Biol
, vol.9
, pp. 666
-
-
Segata, N.1
Boernigen, D.2
Tickle, T.L.3
Morgan, X.C.4
Garrett, W.S.5
Huttenhower, C.6
-
116
-
-
84856043672
-
A mathematical theory of communication
-
Shannon, C. E. (1948). A mathematical theory of communication. Bell Syst. Tech. J. 27, 379-423. doi: 10.1002/j.1538-7305.1948.tb01338.x
-
(1948)
Bell Syst. Tech. J
, vol.27
, pp. 379-423
-
-
Shannon, C.E.1
-
117
-
-
84979608055
-
An introduction to the analysis of shotgun metagenomic data
-
Sharpton, T. J. (2014). An introduction to the analysis of shotgun metagenomic data. Front. Plant Sci. 5:209. doi: 10.3389/fpls.2014.00209
-
(2014)
Front. Plant Sci
, vol.5
, pp. 209
-
-
Sharpton, T.J.1
-
118
-
-
33344464667
-
Measurement of diversity
-
Simpson, E. (1949). Measurement of diversity. Nature 163:688. doi: 10.1038/163688a0
-
(1949)
Nature
, vol.163
, pp. 688
-
-
Simpson, E.1
-
119
-
-
0021779934
-
Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats
-
Staley, J. T., and Konopka, A. (1985). Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu. Rev. Microbiol. 39, 321-346. doi: 10.1146/annurev.mi.39.100185.001541
-
(1985)
Annu. Rev. Microbiol
, vol.39
, pp. 321-346
-
-
Staley, J.T.1
Konopka, A.2
-
120
-
-
84897077380
-
Parallel-META 2.0: enhanced metagenomic data analysis with functional annotation, high performance computing and advanced visualization
-
Su, X., Pan, W., Song, B., Xu, J., and Ning, K. (2014). Parallel-META 2.0: enhanced metagenomic data analysis with functional annotation, high performance computing and advanced visualization. PLoS ONE 9:e89323. doi: 10.1371/journal.pone.0089323
-
(2014)
PLoS ONE
, vol.9
-
-
Su, X.1
Pan, W.2
Song, B.3
Xu, J.4
Ning, K.5
-
121
-
-
84869998312
-
Current opportunities and challenges in microbial metagenome analysis-a bioinformatic perspective
-
Teeling, H., and Glöckner, F. O. (2012). Current opportunities and challenges in microbial metagenome analysis-a bioinformatic perspective. Brief. Bioinformatics 13, 728-742. doi: 10.1093/bib/bbs039
-
(2012)
Brief. Bioinformatics
, vol.13
, pp. 728-742
-
-
Teeling, H.1
Glöckner, F.O.2
-
122
-
-
13244253777
-
TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences
-
Teeling, H., Waldmann, J., Lombardot, T., Bauer, M., and Glöckner, F. O. (2004). TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences. BMC Bioinformatics 5:163. doi: 10.1186/1471-2105-5-163
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 163
-
-
Teeling, H.1
Waldmann, J.2
Lombardot, T.3
Bauer, M.4
Glöckner, F.O.5
-
123
-
-
84862989346
-
Metagenomics-a guide from sampling to data analysis
-
Thomas, T., Gilbert, J., and Meyer, F. (2012). Metagenomics-a guide from sampling to data analysis. Microb. Inform. Exp. 2:3. doi: 10.1186/2042-5783-2-3
-
(2012)
Microb. Inform. Exp
, vol.2
, pp. 3
-
-
Thomas, T.1
Gilbert, J.2
Meyer, F.3
-
124
-
-
84899618891
-
Amplicon-based metagenomic analysis of mixed fungal samples using proton release amplicon sequencing
-
Tonge, D. P., Pashley, C. H., and Gant, T. W. (2014). Amplicon-based metagenomic analysis of mixed fungal samples using proton release amplicon sequencing. PLoS ONE 9:e93849. doi: 10.1371/journal.pone.0093849
-
(2014)
PLoS ONE
, vol.9
-
-
Tonge, D.P.1
Pashley, C.H.2
Gant, T.W.3
-
125
-
-
77953953850
-
A diversity of beta diversities: straightening up a concept gone awry. Part 1. Defining beta diversity as a function of alpha and gamma diversity
-
Tuomisto, H. (2010). A diversity of beta diversities: straightening up a concept gone awry. Part 1. Defining beta diversity as a function of alpha and gamma diversity. Ecography 33, 2-22. doi: 10.1111/j.1600-0587.2009.05880.x
-
(2010)
Ecography
, vol.33
, pp. 2-22
-
-
Tuomisto, H.1
-
126
-
-
0034632413
-
Novel Natural Products from Soil DNA Libraries in a Streptomycete Host
-
Wang, G. Y., Graziani, E., Waters, B., Pan, W., Li, X., McDermott, J., et al. (2000). Novel Natural Products from Soil DNA Libraries in a Streptomycete Host. Org. Lett. 2, 2401-2404. doi: 10.1021/ol005860z
-
(2000)
Org. Lett
, vol.2
, pp. 2401-2404
-
-
Wang, G.Y.1
Graziani, E.2
Waters, B.3
Pan, W.4
Li, X.5
McDermott, J.6
-
127
-
-
34548293679
-
Naïve bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
Wang, Q., Garrity, G. M., Tiedje, J. M., and Cole, J. R. (2007). Naïve bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261-5267. doi: 10.1128/AEM.00062-07
-
(2007)
Appl. Environ. Microbiol
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
-
128
-
-
84961616051
-
MetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning
-
Wang, Y., Leung, H., Yiu, S., and Chin, F. (2014). MetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning. BMC Genomics 15(Suppl. 1):S12. doi: 10.1186/1471-2164-15-S1-S12
-
(2014)
BMC Genomics
, vol.15
, pp. S12
-
-
Wang, Y.1
Leung, H.2
Yiu, S.3
Chin, F.4
-
129
-
-
84867613923
-
Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform
-
Whiteley, A. S., Jenkins, S., Waite, I., Kresoje, N., Payne, H., Mullan, B., et al. (2012). Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform. J. Microbiol. Methods 91, 80-88. doi: 10.1016/j.mimet.2012.07.008
-
(2012)
J. Microbiol. Methods
, vol.91
, pp. 80-88
-
-
Whiteley, A.S.1
Jenkins, S.2
Waite, I.3
Kresoje, N.4
Payne, H.5
Mullan, B.6
-
130
-
-
0001271789
-
Phylogenetic structure of the prokaryotic domain: the primary kingdoms
-
Woese, C. R., and Fox, G. E. (1977). Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. U.S.A. 74, 5088-5090. doi: 10.1073/pnas.74.11.5088
-
(1977)
Proc. Natl. Acad. Sci. U.S.A
, vol.74
, pp. 5088-5090
-
-
Woese, C.R.1
Fox, G.E.2
-
131
-
-
40549141418
-
Metagenomics: read length matters
-
Wommack, K. E., Bhavsar, J., and Ravel, J. (2008). Metagenomics: read length matters. Appl. Environ. Microbiol. 74, 1453-1463. doi: 10.1128/AEM.02181-07
-
(2008)
Appl. Environ. Microbiol
, vol.74
, pp. 1453-1463
-
-
Wommack, K.E.1
Bhavsar, J.2
Ravel, J.3
-
132
-
-
55649110049
-
A simple, fast, and accurate method of phylogenomic inference
-
Wu, M., and Eisen, J. A. (2008). A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 9:R151. doi: 10.1186/gb-2008-9-10-r151
-
(2008)
Genome Biol
, vol.9
-
-
Wu, M.1
Eisen, J.A.2
-
133
-
-
84859242353
-
Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2
-
Wu, M., and Scott, A. J. (2012). Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 28, 1033-1034. doi: 10.1093/bioinformatics/bts079
-
(2012)
Bioinformatics
, vol.28
, pp. 1033-1034
-
-
Wu, M.1
Scott, A.J.2
-
134
-
-
84925636192
-
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm
-
Wu, Y. W., Tang, Y. H., Tringe, S. G., Simmons, B. A., and Singer, S. W. (2014). MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome 2:26. doi: 10.1186/2049-2618-2-26
-
(2014)
Microbiome
, vol.2
, pp. 26
-
-
Wu, Y.W.1
Tang, Y.H.2
Tringe, S.G.3
Simmons, B.A.4
Singer, S.W.5
-
135
-
-
84862225232
-
Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field
-
Xu, D., and Zhang, Y. (2012). Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins 80, 1715-1735. doi: 10.1002/prot.24065
-
(2012)
Proteins
, vol.80
, pp. 1715-1735
-
-
Xu, D.1
Zhang, Y.2
-
136
-
-
84859898660
-
A beginner's guide to eukaryotic genome annotation
-
Yandell, M., and Ence, D. (2012). A beginner's guide to eukaryotic genome annotation. Nat. Rev. Genet. 13, 329-342. doi: 10.1038/nrg3174
-
(2012)
Nat. Rev. Genet
, vol.13
, pp. 329-342
-
-
Yandell, M.1
Ence, D.2
-
137
-
-
84925156346
-
The I-TASSER Suite: protein structure and function prediction
-
Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., and Zhang, Y. (2015). The I-TASSER Suite: protein structure and function prediction. Nat. Meth. 12, 7-8. doi: 10.1038/nmeth.3213
-
(2015)
Nat. Meth
, vol.12
, pp. 7-8
-
-
Yang, J.1
Yan, R.2
Roy, A.3
Xu, D.4
Poisson, J.5
Zhang, Y.6
-
138
-
-
84908577899
-
Evaluation of a hybrid approach using UBLAST and BLASTX for metagenomic sequences annotation of specific functional genes
-
Yang, Y., Jiang, X. T., and Zhang, T. (2014). Evaluation of a hybrid approach using UBLAST and BLASTX for metagenomic sequences annotation of specific functional genes. PLoS ONE 9:e110947. doi: 10.1371/journal.pone.0110947
-
(2014)
PLoS ONE
, vol.9
-
-
Yang, Y.1
Jiang, X.T.2
Zhang, T.3
-
139
-
-
84906272014
-
Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences
-
Yarza, P., Yilmaz, P., Pruesse, E., Glöckner, F. O., Ludwig, W., Schleifer, K. H., et al. (2014). Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat. Rev. Micro. 12, 635-645. doi: 10.1038/nrmicro3330
-
(2014)
Nat. Rev. Micro
, vol.12
, pp. 635-645
-
-
Yarza, P.1
Yilmaz, P.2
Pruesse, E.3
Glöckner, F.O.4
Ludwig, W.5
Schleifer, K.H.6
-
140
-
-
70049085269
-
A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes
-
Ye, Y., and Doak, T. G. (2009). A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. PLoS Comput. Biol. 5:e1000465. doi: 10.1371/journal.pcbi.1000465
-
(2009)
PLoS Comput. Biol
, vol.5
-
-
Ye, Y.1
Doak, T.G.2
-
141
-
-
69249234730
-
An ORFome assembly approach to metagenomics sequences analysis
-
Ye, Y., and Tang, H. (2008). An ORFome assembly approach to metagenomics sequences analysis. Comput. Syst. Bioinformatics Conf. 7, 3-13. doi: 10.1142/9781848162648_0001
-
(2008)
Comput. Syst. Bioinformatics Conf
, vol.7
, pp. 3-13
-
-
Ye, Y.1
Tang, H.2
-
142
-
-
42949114833
-
Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering
-
Yooseph, S., Li, W., and Sutton, G. (2008). Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering. BMC Bioinformatics 9:182. doi: 10.1186/1471-2105-9-182
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 182
-
-
Yooseph, S.1
Li, W.2
Sutton, G.3
-
143
-
-
84894254948
-
Meta-QC-chain: comprehensive and fast quality control method for metagenomic data
-
Zhou, Q., Su, X., Jing, G., and Ning, K. (2014). Meta-QC-chain: comprehensive and fast quality control method for metagenomic data. Genomics Proteomics Bioinformatics 12, 52-56. doi: 10.1016/j.gpb.2014.01.002
-
(2014)
Genomics Proteomics Bioinformatics
, vol.12
, pp. 52-56
-
-
Zhou, Q.1
Su, X.2
Jing, G.3
Ning, K.4
-
144
-
-
77955902981
-
Ab initio gene identification in metagenomic sequences
-
Zhu, W., Lomsadze, A., and Borodovsky, M. (2010). Ab initio gene identification in metagenomic sequences. Nucl. Acids Res. 38, e132-e132. doi: 10.1093/nar/gkq275
-
(2010)
Nucl. Acids Res
, vol.38
-
-
Zhu, W.1
Lomsadze, A.2
Borodovsky, M.3
|