-
1
-
-
84879678051
-
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
-
Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH. 2013. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotechnology 31:533-538 DOI 10.1038/nbt.2579.
-
(2013)
Nature Biotechnology
, vol.31
, pp. 533-538
-
-
Albertsen, M.1
Hugenholtz, P.2
Skarshewski, A.3
Nielsen, K.L.4
Tyson, G.W.5
Nielsen, P.H.6
-
2
-
-
84908597294
-
Binning metagenomic contigs by coverage and composition
-
Alneberg J, Bjarnason BS, De Bruijn I, Schirmer M, Quick J, Ijaz UZ, Lahti L, Loman NJ, Andersson AF, Quince C. 2014. Binning metagenomic contigs by coverage and composition. Nature Methods 11:1144-1146 DOI 10.1038/nmeth.3103.
-
(2014)
Nature Methods
, vol.11
, pp. 1144-1146
-
-
Alneberg, J.1
Bjarnason, B.S.2
De Bruijn, I.3
Schirmer, M.4
Quick, J.5
Ijaz, U.Z.6
Lahti, L.7
Loman, N.J.8
Andersson, A.F.9
Quince, C.10
-
3
-
-
84868130695
-
Role for urea in nitrification by polar marine Archaea
-
Alonso-Sáez L,Waller AS,Mende DR, Bakker K, Farnelid H, Yager PL, Lovejoy C, Tremblay J- É, Potvin M, Heinrich F, Estrada M, Riemann L, Bork P, Pedros-Alio C, Bertilsson S. 2012. Role for urea in nitrification by polar marine Archaea. Proceedings of the National Academy of Sciences of the United States of America 109:17989-17994 DOI 10.1073/pnas.1201914109.
-
(2012)
Proceedings of the National Academy of Sciences of the United States of America
, vol.109
, pp. 17989-17994
-
-
Alonso-Sáez, L.1
Waller, A.S.2
Mende, D.R.3
Bakker, K.4
Farnelid, H.5
Yager, P.L.6
Lovejoy, C.7
Tremblay, J.-É.8
Potvin, M.9
Heinrich, F.10
Estrada, M.11
Riemann, L.12
Bork, P.13
Pedros-Alio, C.14
Bertilsson, S.15
-
4
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W,Miller W,Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215:403-410 DOI 10.1016/S0022-2836(05)80360-2.
-
(1990)
Journal of Molecular Biology
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
5
-
-
33751059692
-
The marine viromes of four oceanic regions
-
Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, Carlson C, Chan AM, Haynes M, Kelley S, Liu H,Mahaffy JM,Mueller JE, Nulton J, Olson R, Parsons R, Rayhawk S, Suttle CA, Rohwer F. 2006. The marine viromes of four oceanic regions. PLoS Biology 4:e368 DOI 10.1371/journal.pbio.0040368.
-
(2006)
PLoS Biology
, vol.4
, pp. e368
-
-
Angly, F.E.1
Felts, B.2
Breitbart, M.3
Salamon, P.4
Edwards, R.A.5
Carlson, C.6
Chan, A.M.7
Haynes, M.8
Kelley, S.9
Liu, H.10
Mahaffy, J.M.11
Mueller, J.E.12
Nulton, J.13
Olson, R.14
Parsons, R.15
Rayhawk, S.16
Suttle, C.A.17
Rohwer, F.18
-
6
-
-
80051755726
-
Oil biodegradation and bioremediation: a tale of the two worst spills in US history
-
Atlas RM, Hazen TC. 2011. Oil biodegradation and bioremediation: a tale of the two worst spills in US history. Environmental Science and Technology 45:6709-6715 DOI 10.1021/es2013227.
-
(2011)
Environmental Science and Technology
, vol.45
, pp. 6709-6715
-
-
Atlas, R.M.1
Hazen, T.C.2
-
7
-
-
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..
-
8
-
-
84871396799
-
Ray Meta: scalable de novo metagenome assembly and profiling
-
Boisvert S, Raymond F, Godzaridis E, Laviolette F, Corbeil J. 2012. Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biology 13:R122 DOI 10.1186/gb-2012-13-12-r122.
-
(2012)
Genome Biology
, vol.13
, pp. R122
-
-
Boisvert, S.1
Raymond, F.2
Godzaridis, E.3
Laviolette, F.4
Corbeil, J.5
-
9
-
-
84872043258
-
A reference-free algorithm for computational normalization of shotgun sequencing data
-
ArXiv preprint. arXiv:1203.4802.
-
Brown CT, Howe A, Zhang Q, Pyrkosz AB, BromTH. 2012. A reference-free algorithm for computational normalization of shotgun sequencing data. ArXiv preprint. arXiv:1203.4802.
-
(2012)
-
-
Brown, C.T.1
Howe, A.2
Zhang, Q.3
Pyrkosz, A.B.4
Brom, T.H.5
-
10
-
-
84875828875
-
UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota
-
Campbell JH, O'Donoghue P, Campbell AG, Schwientek P, Sczyrba A,Woyke T, Söll D, Podar M. 2013. UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proceedings of the National Academy of Sciences of the United States of America 110:5540-5545 DOI 10.1073/pnas.1303090110.
-
(2013)
Proceedings of the National Academy of Sciences of the United States of America
, vol.110
, pp. 5540-5545
-
-
Campbell, J.H.1
O'Donoghue, P.2
Campbell, A.G.3
Schwientek, P.4
Sczyrba, A.5
Woyke, T.6
Söll, D.7
Podar, M.8
-
11
-
-
84930212654
-
Elviz-exploration of metagenome assemblies with an interactive visualization tool
-
Cantor M, Nordberg H, Smirnova T, Hess M, Tringe S, Dubchak I. 2015. Elviz-exploration of metagenome assemblies with an interactive visualization tool. BMC Bioinformatics 16:130 DOI 10.1186/s12859-015-0566-4.
-
(2015)
BMC Bioinformatics
, vol.16
, pp. 130
-
-
Cantor, M.1
Nordberg, H.2
Smirnova, T.3
Hess, M.4
Tringe, S.5
Dubchak, I.6
-
12
-
-
84922717073
-
Comparative analysis of functional metagenomic annotation and the mappability of short reads
-
Carr R, 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
, pp. e105776
-
-
Carr, R.1
Borenstein, E.2
-
13
-
-
84954388471
-
Arsenic cycling in hydrocarbon plumes: secondary effects of natural attenuation
-
Ground Water Epub ahead of print
-
Cozzarelli IM, Schreiber ME, Erickson ML, Ziegler BA. 2015. Arsenic cycling in hydrocarbon plumes: secondary effects of natural attenuation. Ground Water Epub ahead of print DOI 10.1111/gwat.12316.
-
(2015)
-
-
Cozzarelli, I.M.1
Schreiber, M.E.2
Erickson, M.L.3
Ziegler, B.A.4
-
14
-
-
79961144263
-
Universally distributed single-copy genes indicate a constant rate of horizontal transfer
-
Creevey CJ, Doerks T, Fitzpatrick DA, Raes J, Bork P. 2011. Universally distributed single-copy genes indicate a constant rate of horizontal transfer. PLoS ONE 6:e22099 DOI 10.1371/journal.pone.0022099.
-
(2011)
PLoS ONE
, vol.6
, pp. e22099
-
-
Creevey, C.J.1
Doerks, T.2
Fitzpatrick, D.A.3
Raes, J.4
Bork, P.5
-
15
-
-
84930943953
-
Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics
-
Delmont TO, Eren AM,Maccario L, Prestat E, Esen OC, Pelletier E, Le Paslier D, Simonet P, Vogel TM. 2015. Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics. Frontiers in Microbiology 6(358) DOI 10.3389/fmicb.2015.00358.
-
(2015)
Frontiers in Microbiology
, vol.6
, Issue.358
-
-
Delmont, T.O.1
Ecsdn, O.C.2
Pelletier, E.3
Le Paslier, D.4
Simonet, P.5
Vogel, T.M.6
-
16
-
-
84865339798
-
Describing microbial communities and performing global comparisons in the 'omic era
-
Delmont TO, Simonet P, Vogel TM. 2012. Describing microbial communities and performing global comparisons in the 'omic era. The ISME Journal 6:1625-1628 DOI 10.1038/ismej.2012.55.
-
(2012)
The ISME Journal
, vol.6
, pp. 1625-1628
-
-
Delmont, T.O.1
Simonet, P.2
Vogel, T.M.3
-
17
-
-
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..
-
18
-
-
84861342496
-
Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage
-
Dupont CL, Rusch DB, Yooseph S, Lombardo M-J, Richter RA, Valas R, Novotny M, Yee-Greenbaum J, Selengut JD, Haft DH, Halpern AL, Lasken RS, Nealson K, Friedman R, Craig Venter J. 2012. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. The ISME Journal 6:1186-1199 DOI 10.1038/ismej.2011.189.
-
(2012)
The ISME Journal
, vol.6
, pp. 1186-1199
-
-
Dupont, C.L.1
Rusch, D.B.2
Yooseph, S.3
Lombardo, M.-J.4
Richter, R.A.5
Valas, R.6
Novotny, M.7
Yee-Greenbaum, J.8
Selengut, J.D.9
Haft, D.H.10
Halpern, A.L.11
Lasken, R.S.12
Nealson, K.13
Friedman, R.14
Craig Venter, J.15
-
19
-
-
33745595097
-
Using pyrosequencing to shed light on deep mine microbial ecology
-
Edwards RA, Rodriguez-Brito B,Wegley L, Haynes M, Breitbart M, Peterson DM, Saar MO, Alexander S, Alexander EC, Rohwer F. 2006. Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 7:57 DOI 10.1186/1471-2164-7-57.
-
(2006)
BMC Genomics
, vol.7
, pp. 57
-
-
Edwards, R.A.1
Rodriguez-Brito, B.2
Wegley, L.3
Haynes, M.4
Breitbart, M.5
Peterson, D.M.6
Saar, M.O.7
Alexander, S.8
Alexander, E.C.9
Rohwer, F.10
-
20
-
-
84879138105
-
A filtering method to generate high quality short reads using illumina paired-end technology
-
Eren AM, Vineis JH,Morrison HG, Sogin ML. 2013. A filtering method to generate high quality short reads using illumina paired-end technology. PLoS ONE 8:e66643 DOI 10.1371/journal.pone.0066643.
-
(2013)
PLoS ONE
, vol.8
, pp. e66643
-
-
Eren, A.M.1
Vineis, J.H.2
Morrison, H.G.3
Sogin, M.L.4
-
21
-
-
84908641515
-
ggplot2: elegant graphics for data analysis
-
Ginestet C. 2011. ggplot2: elegant graphics for data analysis. Journal of the Royal Statistical Society: Series A 174:245-246 DOI 10.1111/j.1467-985X.2010.00676 9.x.
-
(2011)
Journal of the Royal Statistical Society: Series A
, vol.174
, pp. 245-246
-
-
Ginestet, C.1
-
22
-
-
0032192790
-
Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products
-
Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. 1998. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chemistry and Biology 5:R245-R249 DOI 10.1016/S1074-5521(98)90108-9.
-
(1998)
Chemistry and Biology
, vol.5
, pp. R245-R249
-
-
Handelsman, J.1
Rondon, M.R.2
Brady, S.F.3
Clardy, J.4
Goodman, R.M.5
-
23
-
-
77956299931
-
Deep-sea oil plume enriches indigenous oil-degrading bacteria
-
Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, Piceno YM, Singh N, Jansson JK, Probst A, Borglin SE, For++tney JL, StringfellowWT, Bill M, Conrad ME, TomLM, Chavarria KL, Alusi TR, Lamendella R, Joyner DC, Spier C, Baelum J, Auer M, Zemla ML, Chakraborty R, Sonnenthal EL, D'haeseleer P, Holman H-YN, Osman S, Lu Z, Van Nostrand JD, Deng Y, Zhou J,Mason OU. 2010. Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 330:204-208 DOI 10.1126/science.1195979.
-
(2010)
Science
, vol.330
, pp. 204-208
-
-
Hazen, T.C.1
Dubinsky, E.A.2
DeSantis, T.Z.3
Andersen, G.L.4
Piceno, Y.M.5
Singh, N.6
Jansson, J.K.7
Probst, A.8
Borglin, S.E.9
Fortney, J.L.10
Stringfellow, W.T.11
Bill, M.12
Conrad, M.E.13
Tom, L.M.14
Chavarria, K.L.15
Alusi, T.R.16
Lamendella, R.17
Joyner, D.C.18
Spier, C.19
Baelum, J.20
Auer, M.21
Zemla, M.L.22
Chakraborty, R.23
Sonnenthal, E.L.24
D'haeseleer, P.25
Holman, H.-Y.N.26
Osman, S.27
Lu, Z.28
van Nostrand, J.D.29
Deng, Y.30
Zhou, J.31
Mason, O.U.32
more..
-
24
-
-
84949039377
-
-
Hess M, Sczyrba A, Egan R, Kim T-W, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T,Mackie RI, Pennacchio LA, Tringe SG, Visel A,Woyke T,Wang Z, Rubin EM. 2011.
-
(2011)
-
-
Hess, M.1
Sczyrba, A.2
Egan, R.3
Kim, T.-W.4
Chokhawala, H.5
Schroth, G.6
Luo, S.7
Clark, D.S.8
Chen, F.9
Zhang, T.10
Mackie, R.I.11
Pennacchio, L.A.12
Tringe, S.G.13
Visel, A.14
Woyke, T.15
Wang, Z.16
Rubin, E.M.17
-
25
-
-
79251587455
-
Metagenomic discovery of biomass-degrading genes and genomes from cow rumen
-
Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331:463-467 DOI 10.1126/science.1200387.
-
Science
, vol.331
, pp. 463-467
-
-
-
26
-
-
84856659328
-
Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota
-
Iverson V,Morris RM, Frazar CD, Berthiaume CT,Morales RL, Armbrust EV. 2012. Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science 335:587-590 DOI 10.1126/science.1212665.
-
(2012)
Science
, vol.335
, pp. 587-590
-
-
Iverson, V.1
Morris, R.M.2
Frazar, C.D.3
Berthiaume, C.T.4
Morales, R.L.5
Armbrust, E.V.6
-
27
-
-
84940387197
-
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
-
Kang DD, Froula J, Egan R,Wang Z. 2015.MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3:e1165 DOI 10.7717/peerj.1165.
-
(2015)
PeerJ
, vol.3
, pp. e1165
-
-
Kang, D.D.1
Froula, J.2
Egan, R.3
Wang, Z.4
-
28
-
-
84955628366
-
Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics
-
Kantor RS, Van Zyl AW, Van Hille RP, Thomas BC, Harrison STL, Banfield JF. 2015. Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics. Environmental Microbiology DOI 10.1111/1462-2920.12936.
-
(2015)
Environmental Microbiology
-
-
Kantor, R.S.1
Van Zyl, A.W.2
Van Hille, R.P.3
Thomas, B.C.4
Harrison, S.T.L.5
Banfield, J.F.6
-
29
-
-
84875939754
-
Metagenomic analysis and metabolite profiling of deep-sea sediments from the Gulf of Mexico following the Deepwater Horizon oil spill
-
Kimes NE, Callaghan AV, Aktas DF, Smith WL, Sunner J, Golding B, Drozdowska M, Hazen TC, Suflita JM,Morris PJ. 2013. Metagenomic analysis and metabolite profiling of deep-sea sediments from the Gulf of Mexico following the Deepwater Horizon oil spill. Frontiers in Microbiology 4:50 DOI 10.3389/fmicb.2013.00050.
-
(2013)
Frontiers in Microbiology
, vol.4
, pp. 50
-
-
Kimes, N.E.1
Callaghan, A.V.2
Aktas, D.F.3
Smith, W.L.4
Sunner, J.5
Golding, B.6
Drozdowska, M.7
Hazen, T.C.8
Suflita, J.M.9
Morris, P.J.10
-
30
-
-
83055184882
-
Hydrocarbon-degrading bacteria and the bacterial community response in gulf of Mexico beach sands impacted by the Deepwater Horizon oil spill
-
Kostka JE, Prakash O, OverholtWA, Green SJ, Freyer G, Canion A, Delgardio J, Norton N, Hazen TC, Huettel M. 2011. Hydrocarbon-degrading bacteria and the bacterial community response in gulf of Mexico beach sands impacted by the Deepwater Horizon oil spill. Applied and Environmental Microbiology 77:7962-7974 DOI 10.1128/AEM.05402-11.
-
(2011)
Applied and Environmental Microbiology
, vol.77
, pp. 7962-7974
-
-
Kostka, J.E.1
Prakash, O.2
Overholt, W.A.3
Green, S.J.4
Freyer, G.5
Canion, A.6
Delgardio, J.7
Norton, N.8
Hazen, T.C.9
Huettel, M.10
-
31
-
-
84938483160
-
VizBin-an application for reference-independent visualization and human-augmented binning of metagenomic data
-
Laczny CC, Sternal T, Plugaru V, Gawron P, Atashpendar A,Margossian HH, Coronado S, Der Maaten L van, Vlassis N,Wilmes P. 2015. VizBin-an application for reference-independent visualization and human-augmented binning of metagenomic data. Microbiome 3:1 DOI 10.1186/s40168-014-0066-1.
-
(2015)
Microbiome
, vol.3
, pp. 1
-
-
Laczny, C.C.1
Sternal, T.2
Plugaru, V.3
Gawron, P.4
Atashpendar, A.5
Margossian, H.H.6
Coronado, S.7
Der Maaten, L.V.8
Vlassis, N.9
Wilmes, P.10
-
32
-
-
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
-
33
-
-
0030994798
-
Amelioration of bacterial genomes: rates of change and exchange
-
Lawrence JG, Ochman H. 1997. Amelioration of bacterial genomes: rates of change and exchange. Journal of Molecular Evolution 44:383-397 DOI 10.1007/PL00006158.
-
(1997)
Journal of Molecular Evolution
, vol.44
, pp. 383-397
-
-
Lawrence, J.G.1
Ochman, H.2
-
34
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H, 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
-
35
-
-
68549104404
-
The sequence alignment/map format and samtools
-
Li H, Handsaker B,Wysoker A, Fennell T, Ruan J, Homer N,Marth G, Abecasis G, Durbin R. 2009. The sequence alignment/map format and samtools. Bioinformatics 25:2078-2079 DOI 10.1093/bioinformatics/btp352.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
36
-
-
19144366814
-
Metagenomics and industrial applications
-
Lorenz P, Eck J. 2005. Metagenomics and industrial applications. Nature Reviews Microbiology 3:510-516 DOI 10.1038/nrmicro1161.
-
(2005)
Nature Reviews Microbiology
, vol.3
, pp. 510-516
-
-
Lorenz, P.1
Eck, J.2
-
37
-
-
84858863014
-
Individual genome assembly from complex community short-read metagenomic datasets
-
Luo C, Tsementzi D, Kyrpides NC, Konstantinidis KT. 2012. Individual genome assembly from complex community short-read metagenomic datasets. The ISME Journal 6:898-901 DOI 10.1038/ismej.2011.147.
-
(2012)
The ISME Journal
, vol.6
, pp. 898-901
-
-
Luo, C.1
Tsementzi, D.2
Kyrpides, N.C.3
Konstantinidis, K.T.4
-
38
-
-
84905374149
-
Single-cell genomics reveals features of a Colwellia species that was dominant during the Deepwater Horizon oil spill
-
Mason OU, Han J,Woyke T, Jansson JK. 2014. Single-cell genomics reveals features of a Colwellia species that was dominant during the Deepwater Horizon oil spill. Frontiers in Microbiology 5:332 DOI 10.3389/fmicb.2014.00332.
-
(2014)
Frontiers in Microbiology
, vol.5
, pp. 332
-
-
Mason, O.U.1
Han, J.2
Woyke, T.3
Jansson, J.K.4
-
39
-
-
84865318505
-
Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill
-
Mason OU, Hazen TC, Borglin S, Chain PSG, Dubinsky EA, Fortney JL, Han J, Holman H-YN, Hultman J, Lamendella R,Mackelprang R,Malfatti S, TomLM, Tringe SG,Woyke T, Zhou J, Rubin EM, Jansson JK. 2012. Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. The ISME Journal 6:1715-1727 DOI 10.1038/ismej.2012.59.
-
(2012)
The ISME Journal
, vol.6
, pp. 1715-1727
-
-
Mason, O.U.1
Hazen, T.C.2
Borglin, S.3
Chain, P.S.G.4
Dubinsky, E.A.5
Fortney, J.L.6
Han, J.7
Holman, H.-Y.N.8
Hultman, J.9
Lamendella, R.10
Mackelprang, R.11
Malfatti, S.12
Tom, L.M.13
Tringe, S.G.14
Woyke, T.15
Zhou, J.16
Rubin, E.M.17
Jansson, J.K.18
-
40
-
-
84949039379
-
-
Mende DR,Waller AS, Sunagawa S, Järvelin AI, Chan MM, Arumugam M, Raes J, Bork P. 2012.
-
(2012)
-
-
Mende, D.R.1
Waller, A.S.2
Sunagawa, S.3
Järvelin, A.I.4
Chan, M.M.5
Arumugam, M.6
Raes, J.7
Bork, P.8
-
41
-
-
84857524013
-
Assessment of metagenomic assembly using simulated next generation sequencing data
-
Assessment of metagenomic assembly using simulated next generation sequencing data. PLoS ONE 7:e31386 DOI 10.1371/journal.pone.0031386.
-
PLoS ONE
, vol.7
, pp. e31386
-
-
-
42
-
-
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
-
43
-
-
80455126001
-
Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems
-
Minoche AE, Dohm JC, Himmelbauer H. 2011. Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems. Genome Biology 12:R112 DOI 10.1186/gb-2011-12-11-r112.
-
(2011)
Genome Biology
, vol.12
, pp. R112
-
-
Minoche, A.E.1
Dohm, J.C.2
Himmelbauer, H.3
-
44
-
-
78649470145
-
Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity
-
Morelli G, Song Y,Mazzoni CJ, Eppinger M, Roumagnac P,Wagner DM, Feldkamp M, Kusecek B, Vogler AJ, Li Y, Cui Y, Thomson NR, Jombart T, Leblois R, Lichtner P, Rahalison L, Petersen JM, Balloux F, Keim P,Wirth T, Ravel J, Yang R, Carniel E, Achtman M. 2010. Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nature Genetics 42:1140-1143 DOI 10.1038/ng.705.
-
(2010)
Nature Genetics
, vol.42
, pp. 1140-1143
-
-
Morelli, G.1
Song, Y.2
Mazzoni, C.J.3
Eppinger, M.4
Roumagnac, P.5
Wagner, D.M.6
Feldkamp, M.7
Kusecek, B.8
Vogler, A.J.9
Li, Y.10
Cui, Y.11
Thomson, N.R.12
Jombart, T.13
Leblois, R.14
Lichtner, P.15
Rahalison, L.16
Petersen, J.M.17
Balloux, F.18
Keim, P.19
Wirth, T.20
Ravel, J.21
Yang, R.22
Carniel, E.23
Achtman, M.24
more..
-
45
-
-
79551622954
-
Strain-resolved community genomic analysis of gut microbial colonization in a premature infant
-
Morowitz MJ, Denef VJ, Costello EK, Thomas BC, Poroyko V, Relman DA, Banfield JF. 2011. Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. Proceedings of the National Academy of Sciences of the United States of America 108:1128-1133 DOI 10.1073/pnas.1010992108.
-
(2011)
Proceedings of the National Academy of Sciences of the United States of America
, vol.108
, pp. 1128-1133
-
-
Morowitz, M.J.1
Denef, V.J.2
Costello, E.K.3
Thomas, B.C.4
Poroyko, V.5
Relman, D.A.6
Banfield, J.F.7
-
46
-
-
77349091080
-
Hydrocarbon hydroxylation by cytochrome P450 enzymes
-
Ortiz deMontellano PR. 2010. Hydrocarbon hydroxylation by cytochrome P450 enzymes. Chemical Reviews 110:932-948 DOI 10.1021/cr9002193.
-
(2010)
Chemical Reviews
, vol.110
, pp. 932-948
-
-
Ortiz deMontellano, P.R.1
-
47
-
-
84999652094
-
Draft genome sequences for oil-degrading bacterial strains from beach sands impacted by the Deepwater Horizon oil spill
-
OverholtWA, Green SJ,Marks KP, Venkatraman R, Prakash O, Kostka JE. 2013. Draft genome sequences for oil-degrading bacterial strains from beach sands impacted by the Deepwater Horizon oil spill. Genome Announcements 1:e01015-13 DOI 10.1128/genomeA.01015-13.
-
(2013)
Genome Announcements
, vol.1
, pp. e01015-13
-
-
Overholt, W.A.1
Green, S.J.2
Marks, K.P.3
Venkatraman, R.4
Prakash, O.5
Kostka, J.E.6
-
48
-
-
84861760530
-
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
-
Peng Y, Leung HCM, Yiu SM, Chin FYL. 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.M.2
Yiu, S.M.3
Chin, F.Y.L.4
-
49
-
-
67449095888
-
Genome assembly reborn: recent computational challenges
-
Pop M. 2009. Genome assembly reborn: recent computational challenges. Briefings in Bioinformatics 10:354-366 DOI 10.1093/bib/bbp026.
-
(2009)
Briefings in Bioinformatics
, vol.10
, pp. 354-366
-
-
Pop, M.1
-
50
-
-
85006276920
-
Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development
-
Raveh-Sadka T, Thomas BC, Singh A, Firek B, Brooks B, Castelle CJ, Sharon I, Baker R, Good M,Morowitz MJ et al. 2015. Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development. Elife 4:e05477 DOI 10.7554/eLife.05477.
-
(2015)
Elife
, vol.4
, pp. e05477
-
-
Raveh-Sadka, T.1
Thomas, B.C.2
Singh, A.3
Firek, B.4
Brooks, B.5
Castelle, C.J.6
Sharon, I.7
Baker, R.8
Good, M.9
Morowitz, M.J.10
-
51
-
-
5344244656
-
R: a language and environment for statistical computing
-
Vienna: R Foundation for Statistical Computing.
-
R Development Core Team. 2008. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing. Available at http://www.R-project.org.
-
(2008)
-
-
-
53
-
-
84949039381
-
-
Rodriguez-R LM, OverholtWA, Hagan C, Huettel M, Kostka JE, Konstantinidis KT. 2015.
-
(2015)
-
-
Rodriguez, R.L.M.1
Overholt, W.A.2
Hagan, C.3
Huettel, M.4
Kostka, J.E.5
Konstantinidis, K.T.6
-
54
-
-
84939570914
-
Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill
-
Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill. The ISME Journal 9:1928-1940 DOI 10.1038/ismej.2015.5.
-
The ISME Journal
, vol.9
, pp. 1928-1940
-
-
-
55
-
-
0036624819
-
Biosurfactants and oil bioremediation
-
Ron EZ, Rosenberg E. 2002. Biosurfactants and oil bioremediation. Current Opinion in Biotechnology 13:249-252 DOI 10.1016/S0958-1669(02)00316-6.
-
(2002)
Current Opinion in Biotechnology
, vol.13
, pp. 249-252
-
-
Ron, E.Z.1
Rosenberg, E.2
-
56
-
-
84927744062
-
Accurate, multi-kb reads resolve complex populations and detect rare microorganisms
-
Genome Research
-
Sharon I, Kertesz M, Hug LA, Pushkarev D, Blauwkamp TA, Castelle CJ, Amirebrahimi M, Thomas BC, Burstein D, Tringe SG,Williams KH, Banfield J. 2015. Accurate, multi-kb reads resolve complex populations and detect rare microorganisms. Genome Research DOI 10.1101/gr.183012.114.
-
(2015)
-
-
Sharon, I.1
Kertesz, M.2
Hug, L.A.3
Pushkarev, D.4
Blauwkamp, T.A.5
Castelle, C.J.6
Amirebrahimi, M.7
Thomas, B.C.8
Burstein, D.9
Tringe, S.G.10
Williams, K.H.11
Banfield, J.12
-
57
-
-
84871956840
-
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
-
Sharon I,Morowitz MJ, Thomas BC, Costello EK, Relman DA, Banfield JF. 2013. Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Research 23:111-120 DOI 10.1101/gr.142315.112.
-
(2013)
Genome Research
, vol.23
, pp. 111-120
-
-
Sharon, I.1
Morowitz, M.J.2
Thomas, B.C.3
Costello, E.K.4
Relman, D.A.5
Banfield, J.F.6
-
58
-
-
48349103531
-
Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation
-
Simmons SL, Dibartolo G, Denef VJ, Goltsman DSA, Thelen MP, Banfield JF. 2008. Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation. PLoS Biology 6:e177 DOI 10.1371/journal.pbio.0060177.
-
(2008)
PLoS Biology
, vol.6
, pp. e177
-
-
Simmons, S.L.1
Dibartolo, G.2
Denef, V.J.3
Goltsman, D.S.A.4
Thelen, M.P.5
Banfield, J.F.6
-
59
-
-
33747073504
-
Microbial diversity in the deep sea and the underexplored 'rare biosphere'
-
Sogin ML,Morrison HG, Huber JA,MarkWelch D, Huse SM, Neal PR, Arrieta JM, Herndl GJ. 2006. Microbial diversity in the deep sea and the underexplored 'rare biosphere'. Proceedings of the National Academy of Sciences of the United States of America 103:12115-12120 DOI 10.1073/pnas.0605127103.
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, pp. 12115-12120
-
-
Sogin, M.L.1
Morrison, H.G.2
Huber, J.A.3
MarkWelch, D.4
Huse, S.M.5
Neal, P.R.6
Arrieta, J.M.7
Herndl, G.J.8
-
60
-
-
77954263259
-
Role of urea in microbial metabolism in aquatic systems: A biochemical and molecular review
-
Solomon CM, Collier JL, Berg GM, Glibert PM. 2010. Role of urea in microbial metabolism in aquatic systems: A biochemical and molecular review. Aquatic Microbial Ecology 59:67-88 DOI 10.3354/ame01390.
-
(2010)
Aquatic Microbial Ecology
, vol.59
, pp. 67-88
-
-
Solomon, C.M.1
Collier, J.L.2
Berg, G.M.3
Glibert, P.M.4
-
61
-
-
0030023659
-
Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon
-
Stein JL,Marsh TL,Wu KY, Shizuya H, DeLong EF. 1996. Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. Journal of Bacteriology 178:591-599.
-
(1996)
Journal of Bacteriology
, vol.178
, pp. 591-599
-
-
Stein, J.L.1
Marsh, T.L.2
Wu, K.Y.3
Shizuya, H.4
DeLong, E.F.5
-
62
-
-
84872152255
-
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
-
Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M. 2013. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biology 14:R2 DOI 10.1186/gb-2013-14-1-r2.
-
(2013)
Genome Biology
, vol.14
, pp. R2
-
-
Treangen, T.J.1
Koren, S.2
Sommer, D.D.3
Liu, B.4
Astrovskaya, I.5
Ondov, B.6
Darling, A.E.7
Phillippy, A.M.8
Pop, M.9
-
63
-
-
20244376755
-
Comparative metagenomics of microbial communities
-
Tringe SG, VonMering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM. 2005. Comparative metagenomics of microbial communities. Science 308:554-557 DOI 10.1126/science.1107851.
-
(2005)
Science
, vol.308
, pp. 554-557
-
-
Tringe, S.G.1
VonMering, C.2
Kobayashi, A.3
Salamov, A.A.4
Chen, K.5
Chang, H.W.6
Podar, M.7
Short, J.M.8
Mathur, E.J.9
Detter, J.C.10
Bork, P.11
Hugenholtz, P.12
Rubin, E.M.13
-
64
-
-
33845874101
-
An obesity-associated gut microbiome with increased capacity for energy harvest
-
Turnbaugh PJ, Ley RE,Mahowald MA,Magrini V,Mardis ER, Gordon JI. 2006. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027-1031 DOI 10.1038/nature05414.
-
(2006)
Nature
, vol.444
, pp. 1027-1031
-
-
Turnbaugh, P.J.1
Ley, R.E.2
Mahowald, M.A.3
Magrini, V.4
Mardis, E.R.5
Gordon, J.I.6
-
65
-
-
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, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37-43 DOI 10.1038/nature02340.
-
(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
Solovyev, V.V.7
Rubin, E.M.8
Rokhsar, D.S.9
Banfield, J.F.10
-
66
-
-
11144354360
-
Environmental genome shotgun sequencing of the Sargasso Sea
-
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA,Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K,White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers Y-H, Smith HO. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74 DOI 10.1126/science.1093857.
-
(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
Wu, D.7
Paulsen, I.8
Nelson, K.E.9
Nelson, W.10
Fouts, D.E.11
Levy, S.12
Knap, A.H.13
Lomas, M.W.14
Nealson, K.15
White, O.16
Peterson, J.17
Hoffman, J.18
Parsons, R.19
Baden-Tillson, H.20
Pfannkoch, C.21
Rogers, Y.-H.22
Smith, H.O.23
more..
-
69
-
-
33750431080
-
Symbiosis insights through metagenomic analysis of a microbial consortium
-
Woyke T, Teeling H, Ivanova NN, Huntemann M, Richter M, Gloeckner FO, Boffelli D, Anderson IJ, Barry KW, Shapiro HJ, Szeto E, Kyrpides NC,Mussmann M, Amann R, Bergin C, Ruehland C, Rubin EM, Dubilier N. 2006. Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443:950-955 DOI 10.1038/nature05192.
-
(2006)
Nature
, vol.443
, pp. 950-955
-
-
Woyke, T.1
Teeling, H.2
Ivanova, N.N.3
Huntemann, M.4
Richter, M.5
Gloeckner, F.O.6
Boffelli, D.7
Anderson, I.J.8
Barry, K.W.9
Shapiro, H.J.10
Szeto, E.11
Kyrpides, N.C.12
Mussmann, M.13
Amann, R.14
Bergin, C.15
Ruehland, C.16
Rubin, E.M.17
Dubilier, N.18
-
70
-
-
84925636192
-
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm
-
Wu Y-W, Tang Y-H, Tringe SG, Simmons BA, Singer SW. 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
-
71
-
-
84949039384
-
-
Yergeau E,Maynard C, Sanschagrin S, Champagne J, Juck D, Lee K, Greer CW. 2015.
-
(2015)
-
-
Yergeau, E.1
Maynard, C.2
Sanschagrin, S.3
Champagne, J.4
Juck, D.5
Lee, K.6
Greer, C.W.7
-
72
-
-
84938782955
-
Microbial community composition, functions and activities in the Gulf of Mexico, one year after the Deepwater Horizon accident
-
Microbial community composition, functions and activities in the Gulf of Mexico, one year after the Deepwater Horizon accident. Applied and Environmental Microbiology DOI 10.1128/AEM.01470-15.
-
Applied and Environmental Microbiology
-
-
-
73
-
-
84949039386
-
-
Zakrzewski M, Bekel T, Ander C, Pühler A, Rupp O, Stoye J, Schlüter A, Goesmann A. 2013.
-
(2013)
-
-
Zakrzewski, M.1
Bekel, T.2
Ander, C.3
Pühler, A.4
Rupp, O.5
Stoye, J.6
Schlüter, A.7
Goesmann, A.8
-
74
-
-
84881663626
-
MetaSAMS-a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets
-
MetaSAMS-a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets. Journal of Biotechnology 167:156-165 DOI 10.1016/j.jbiotec.2012.09.013.
-
Journal of Biotechnology
, vol.167
, pp. 156-165
-
-
-
75
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18:821-829 DOI 10.1101/gr.074492.107.
-
(2008)
Genome Research
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
76
-
-
33744826256
-
Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms
-
Zhang W, Qi W, Albert TJ,Motiwala AS, Alland D, Hyytia-Trees EK, Ribot EM, Fields PI, Whittam TS, Swaminathan B. 2006. Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms. Genome Research 16:757-767 DOI 10.1101/gr.4759706.
-
(2006)
Genome Research
, vol.16
, pp. 757-767
-
-
Zhang, W.1
Qi, W.2
Albert, T.J.3
Motiwala, A.S.4
Alland, D.5
Hyytia-Trees, E.K.6
Ribot, E.M.7
Fields, P.I.8
Whittam, T.S.9
Swaminathan, B.10
|