-
1
-
-
9744231340
-
Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, recA and rpoB gene sequencing
-
Adékambi T, Drancourt M. 2004. Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, recA and rpoB gene sequencing. International Journal of Systematic and Evolutionary Microbiology 54:2095-2105 DOI 10.1099/ijs.0.63094-0.
-
(2004)
International Journal of Systematic and Evolutionary Microbiology
, vol.54
, pp. 2095-2105
-
-
Adékambi, T.1
Drancourt, M.2
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25:3389-3402 DOI 10.1093/nar/25.17.3389.
-
(1997)
Nucleic Acids Research
, 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
Lipman, D.J.7
-
3
-
-
84905661514
-
CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction
-
Angly FE, Dennis PG, Skarshewski A, VanwonterghemI, Hugenholtz P, Tyson GW. 2014. CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction. Microbiome 2:11 DOI 10.1186/2049-2618-2-11.
-
(2014)
Microbiome
, vol.2
, pp. 11
-
-
Angly, F.E.1
Dennis, P.G.2
Skarshewski, A.3
Vanwonterghem, I.4
Hugenholtz, P.5
Tyson, G.W.6
-
4
-
-
84863190624
-
Grinder: a versatile amplicon and shotgun sequence simulator
-
Angly FE, Willner D, Rohwer F, Hugenholtz P, Tyson GW. 2012. Grinder: a versatile amplicon and shotgun sequence simulator. Nucleic Acids Research 40:e94 DOI 10.1093/nar/gks251.
-
(2012)
Nucleic Acids Research
, vol.40
-
-
Angly, F.E.1
Willner, D.2
Rohwer, F.3
Hugenholtz, P.4
Tyson, G.W.5
-
5
-
-
9144232912
-
UniProt: the Universal Protein knowledgebase
-
Apweiler R, Bairoch A, Wu CH, BarkerWC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh L-SL. 2004. UniProt: the Universal Protein knowledgebase. Nucleic Acids Research 32:D115-D119 DOI 10.1093/nar/gkh131.
-
(2004)
Nucleic Acids Research
, vol.32
-
-
Apweiler, R.1
Bairoch, A.2
Wu, C.H.3
Barker, W.C.4
Boeckmann, B.5
Ferro, S.6
Gasteiger, E.7
Huang, H.8
Lopez, R.9
Magrane, M.10
Martin, M.J.11
Natale, D.A.12
O'Donovan, C.13
Redaschi, N.14
Yeh, L.-S.L.15
-
6
-
-
40549120596
-
The RAST server: rapid annotations using subsystems technology
-
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, 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.A.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..
-
7
-
-
84355161776
-
The oral metagenome in health and disease
-
Belda-Ferre P, Alcaraz LD, Cabrera-Rubio R, Romero H, Simón-Soro A, Pignatelli M, Mira A. 2012. The oral metagenome in health and disease. The ISME Journal 6:46-56 DOI 10.1038/ismej.2011.85.
-
(2012)
The ISME Journal
, vol.6
, pp. 46-56
-
-
Belda-Ferre, P.1
Alcaraz, L.D.2
Cabrera-Rubio, R.3
Romero, H.4
Simón-Soro, A.5
Pignatelli, M.6
Mira, A.7
-
8
-
-
58149185141
-
GenBank
-
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. 2009. GenBank. Nucleic Acids Research 37:D26-D31 DOI 10.1093/nar/gkn723.
-
(2009)
Nucleic Acids Research
, vol.37
-
-
Benson, D.A.1
Karsch-Mizrachi, I.2
Lipman, D.J.3
Ostell, J.4
Sayers, E.W.5
-
9
-
-
20444453307
-
Protein length in eukaryotic and prokaryotic proteomes
-
Brocchieri L, Karlin S. 2005. Protein length in eukaryotic and prokaryotic proteomes. Nucleic Acids Research 33:3390-3400 DOI 10.1093/nar/gki615.
-
(2005)
Nucleic Acids Research
, vol.33
, pp. 3390-3400
-
-
Brocchieri, L.1
Karlin, S.2
-
11
-
-
74049108922
-
BLAST+: architecture and applications
-
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10:421 DOI 10.1186/1471-2105-10-421.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 421
-
-
Camacho, C.1
Coulouris, G.2
Avagyan, V.3
Ma, N.4
Papadopoulos, J.5
Bealer, K.6
Madden, T.L.7
-
12
-
-
84887265124
-
Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution
-
Carr R, Shen-Orr SS, Borenstein E. 2013. Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution. PLoS Computational Biology 9:e1003292 DOI 10.1371/journal.pcbi.1003292.
-
(2013)
PLoS Computational Biology
, vol.9
-
-
Carr, R.1
Shen-Orr, S.S.2
Borenstein, E.3
-
13
-
-
41649109613
-
Functional metagenomic profiling of nine biomes
-
Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM, Furlan M, Desnues C, Haynes M, Li L, McDaniel L, Moran MA, Nelson KE, Nilsson C, Olson R, Paul J, Brito BR, Ruan Y, Swan BK, Stevens R, Valentine DL, Thurber RV, Wegley L, White BA, Rohwer F. 2008. Functional metagenomic profiling of nine biomes. Nature 452:629-632 DOI 10.1038/nature06810.
-
(2008)
Nature
, vol.452
, pp. 629-632
-
-
Dinsdale, E.A.1
Edwards, R.A.2
Hall, D.3
Angly, F.4
Breitbart, M.5
Brulc, J.M.6
Furlan, M.7
Desnues, C.8
Haynes, M.9
Li, L.10
McDaniel, L.11
Moran, M.A.12
Nelson, K.E.13
Nilsson, C.14
Olson, R.15
Paul, J.16
Brito, B.R.17
Ruan, Y.18
Swan, B.K.19
Stevens, R.20
Valentine, D.L.21
Thurber, R.V.22
Wegley, L.23
White, B.A.24
Rohwer, F.25
more..
-
14
-
-
40749108545
-
Genetic classification and distinguishing of staphylococcus species based on different partial gap, 16S rRNA, hsp60, rpoB, sodA, and tuf gene sequences
-
Ghebremedhin B, Layer F, König W, König B. 2008. Genetic classification and distinguishing of staphylococcus species based on different partial gap, 16S rRNA, hsp60, rpoB, sodA, and tuf gene sequences. Journal of Clinical Microbiology 46:1019-1025 DOI 10.1128/JCM.02058-07.
-
(2008)
Journal of Clinical Microbiology
, vol.46
, pp. 1019-1025
-
-
Ghebremedhin, B.1
Layer, F.2
König, W.3
König, B.4
-
15
-
-
5444244948
-
Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam
-
Holmes DE, Nevin KP, Lovley DR. 2004. Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam. nov. International Journal of Systematic and Evolutionary Microbiology 54:1591-1599 DOI 10.1099/ijs.0.02958-0.
-
(2004)
nov. International Journal of Systematic and Evolutionary Microbiology
, vol.54
, pp. 1591-1599
-
-
Holmes, D.E.1
Nevin, K.P.2
Lovley, D.R.3
-
16
-
-
0032849859
-
CAP3: a DNA sequence assembly program
-
Huang X, Madan A. 1999. CAP3: a DNA sequence assembly program. Genome Research 9:868-877 DOI 10.1101/gr.9.9.868.
-
(1999)
Genome Research
, vol.9
, pp. 868-877
-
-
Huang, X.1
Madan, A.2
-
17
-
-
0036226603
-
BLAT-the BLAST-like alignment tool
-
Kent WJ. 2002. BLAT-the BLAST-like alignment tool. Genome Research 12:656-664 DOI 10.1101/gr.229202.
-
(2002)
Genome Research
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
18
-
-
0008048504
-
Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses
-
Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR. 1985. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proceedings of the National Academy of Sciences of the United States of America 82:6955-6959 DOI 10.1073/pnas.82.20.6955.
-
(1985)
Proceedings of the National Academy of Sciences of the United States of America
, vol.82
, pp. 6955-6959
-
-
Lane, D.J.1
Pace, B.2
Olsen, G.J.3
Stahl, D.A.4
Sogin, M.L.5
Pace, N.R.6
-
19
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9:357-359 DOI 10.1038/nmeth.1923.
-
(2012)
Nature Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
20
-
-
78651317925
-
The European nucleotide archive
-
Leinonen R, Akhtar R, Birney E, Bower L, Cerdeno-Tárraga A, Cheng Y, Cleland I, Faruque N, Goodgame N, Gibson R, Hoad G, Jang M, Pakseresht N, Plaister S, Radhakrishnan R, Reddy K, Sobhany S, Hoopen PT, Vaughan R, Zalunin V, Cochrane G. 2010. The European nucleotide archive. Nucleic Acids Research 39:D28-D31 DOI 10.1093.nar/gkq967.
-
(2010)
Nucleic Acids Research
, vol.39
-
-
Leinonen, R.1
Akhtar, R.2
Birney, E.3
Bower, L.4
Cerdeno-Tárraga, A.5
Cheng, Y.6
Cleland, I.7
Faruque, N.8
Goodgame, N.9
Gibson, R.10
Hoad, G.11
Jang, M.12
Pakseresht, N.13
Plaister, S.14
Radhakrishnan, R.15
Reddy, K.16
Sobhany, S.17
Hoopen, P.T.18
Vaughan, R.19
Zalunin, V.20
Cochrane, G.21
more..
-
21
-
-
33745634395
-
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li W, 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
-
22
-
-
79951881661
-
Abundant human DNA contamination identified in non-primate genome databases
-
Longo MS, O'Neill MJ, O'Neill RJ. 2011. Abundant human DNA contamination identified in non-primate genome databases. PLoS ONE 6:e16410 DOI 10.1371/journal.pone.0016410.
-
(2011)
PLoS ONE
, vol.6
-
-
Longo, M.S.1
O'Neill, M.J.2
O'Neill, R.J.3
-
23
-
-
84870020971
-
Classification of metagenomic sequences: methods and challenges
-
Mande SS, Mohammed MH, Ghosh TS. 2012. Classification of metagenomic sequences: methods and challenges. Briefings in Bioinformatics 13:669-681 DOI 10.1093/bib/bbs054.
-
(2012)
Briefings in Bioinformatics
, vol.13
, pp. 669-681
-
-
Mande, S.S.1
Mohammed, M.H.2
Ghosh, T.S.3
-
24
-
-
34249794257
-
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
-
Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy AC, Rigoutsos I, Salamov A, Korzeniewski F, Land M, Lapidus A, Grigoriev I, Richardson P, Hugenholtz P, Kyrpides NC. 2007. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nature Methods 4:495-500 DOI 10.1038/nmeth1043.
-
(2007)
Nature Methods
, vol.4
, pp. 495-500
-
-
Mavromatis, K.1
Ivanova, N.2
Barry, K.3
Shapiro, H.4
Goltsman, E.5
McHardy, A.C.6
Rigoutsos, I.7
Salamov, A.8
Korzeniewski, F.9
Land, M.10
Lapidus, A.11
Grigoriev, I.12
Richardson, P.13
Hugenholtz, P.14
Kyrpides, N.C.15
-
25
-
-
79958167222
-
Mixture models for analysis of the taxonomic composition of metagenomes
-
Meinicke P, Aßhauer KP, Lingner T. 2011. Mixture models for analysis of the taxonomic composition of metagenomes. Bioinformatics 27:1618-1624 DOI 10.1093/bioinformatics/btr266.
-
(2011)
Bioinformatics
, vol.27
, pp. 1618-1624
-
-
Meinicke, P.1
Aßhauer, K.P.2
Lingner, T.3
-
26
-
-
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 EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA. 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
-
27
-
-
11844306574
-
The SEED: a Peer-to-peer environment for genome annotation
-
Overbeek R, Disz T, Stevens R. 2004. The SEED: a Peer-to-peer environment for genome annotation. Communications of the ACM 47:46-51 DOI 10.1145/1029496.1029525.
-
(2004)
Communications of the ACM
, vol.47
, pp. 46-51
-
-
Overbeek, R.1
Disz, T.2
Stevens, R.3
-
28
-
-
84891804612
-
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
-
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R. 2013. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Research 42:D206-D214 DOI 10.1093/nar/gkt1226.
-
(2013)
Nucleic Acids Research
, vol.42
-
-
Overbeek, R.1
Olson, R.2
Pusch, G.D.3
Olsen, G.J.4
Davis, J.J.5
Disz, T.6
Edwards, R.A.7
Gerdes, S.8
Parrello, B.9
Shukla, M.10
Vonstein, V.11
Wattam, A.R.12
Xia, F.13
Stevens, R.14
-
29
-
-
13444306641
-
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
-
Pruitt KD, Tatusova T, Maglott DR. 2005. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Research 33:D501-D504 DOI 10.1093/nar/gki025.
-
(2005)
Nucleic Acids Research
, vol.33
-
-
Pruitt, K.D.1
Tatusova, T.2
Maglott, D.R.3
-
30
-
-
58149200954
-
Database resources of the national center for biotechnology information
-
Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, Ye J. 2009. Database resources of the national center for biotechnology information. Nucleic Acids Research 37:D5-D15 DOI 10.1093/nar/gkn741.
-
(2009)
Nucleic Acids Research
, vol.37
-
-
Sayers, E.W.1
Barrett, T.2
Benson, D.A.3
Bryant, S.H.4
Canese, K.5
Chetvernin, V.6
Church, D.M.7
DiCuccio, M.8
Edgar, R.9
Federhen, S.10
Feolo, M.11
Geer, L.Y.12
Helmberg, W.13
Kapustin, Y.14
Landsman, D.15
Lipman, D.J.16
Madden, T.L.17
Maglott, D.R.18
Miller, V.19
Mizrachi, I.20
Ostell, J.21
Pruitt, K.D.22
Schuler, G.D.23
Sequeira, E.24
Sherry, S.T.25
Shumway, M.26
Sirotkin, K.27
Souvorov, A.28
Starchenko, G.29
Tatusova, T.A.30
Wagner, L.31
Yaschenko, E.32
Ye, J.33
more..
-
31
-
-
79952390994
-
Fast identification and removal of sequence contamination from genomic and metagenomic datasets
-
Schmieder R, Edwards R. 2011. Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS ONE 6:e17288 DOI 10.1371/journal.pone.0017288.
-
(2011)
PLoS ONE
, vol.6
-
-
Schmieder, R.1
Edwards, R.2
-
32
-
-
0015767054
-
Ribosomal RNA cistrons in Euglena gracilis
-
Scott NS. 1973. Ribosomal RNA cistrons in Euglena gracilis. Journal of Molecular Biology 81:327-336 DOI 10.1016/0022-2836(73)90144-7.
-
(1973)
Journal of Molecular Biology
, vol.81
, pp. 327-336
-
-
Scott, N.S.1
-
33
-
-
84864440400
-
Metagenomic microbial community profiling using unique clade-specific marker genes
-
Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C. 2012. Metagenomic microbial community profiling using unique clade-specific marker genes. Nature Methods 9:811-814 DOI 10.1038/nmeth.2066.
-
(2012)
Nature Methods
, vol.9
, pp. 811-814
-
-
Segata, N.1
Waldron, L.2
Ballarini, A.3
Narasimhan, V.4
Jousson, O.5
Huttenhower, C.6
-
35
-
-
84903837939
-
FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares
-
Silva GGZ, Cuevas DA, Dutilh BE, Edwards RA. 2014. FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares. PeerJ 2:e425 DOI 10.7717/peerj.425.
-
(2014)
PeerJ
, vol.2
-
-
Silva, G.G.Z.1
Cuevas, D.A.2
Dutilh, B.E.3
Edwards, R.A.4
-
37
-
-
84891938742
-
Evaluating the impact of different sequence databases on metaproteome analysis: insights from a lab-assembled microbial mixture
-
Tanca A, Palomba A, Deligios M, Cubeddu T, Fraumene C, Biosa G, Pagnozzi D, Addis MF, Uzzau S. 2013. Evaluating the impact of different sequence databases on metaproteome analysis: insights from a lab-assembled microbial mixture. PLoS ONE 8:e82981 DOI 10.1371/journal.pone.0082981.
-
(2013)
PLoS ONE
, vol.8
-
-
Tanca, A.1
Palomba, A.2
Deligios, M.3
Cubeddu, T.4
Fraumene, C.5
Biosa, G.6
Pagnozzi, D.7
Addis, M.F.8
Uzzau, S.9
-
38
-
-
84862286169
-
A framework for human microbiome research
-
The HumanMicrobiome Project Consortium. 2012. A framework for human microbiome research. Nature 486:215-221 DOI 10.1038/nature11209.
-
(2012)
Nature
, vol.486
, pp. 215-221
-
-
-
40
-
-
68149160400
-
Application of recA and rpoB sequence analysis on phylogeny and molecular identification of Geobacillus species
-
Weng FY, Chiou CS, Lin PHP, Yang SS. 2009. Application of recA and rpoB sequence analysis on phylogeny and molecular identification of Geobacillus species. Journal of Applied Microbiology 107:452-464 DOI 10.1111/j.1365-2672.2009.04235.x.
-
(2009)
Journal of Applied Microbiology
, vol.107
, pp. 452-464
-
-
Weng, F.Y.1
Chiou, C.S.2
Lin, P.H.P.3
Yang, S.S.4
|