-
3
-
-
84868099390
-
PhiSpy: A novel algorithm for fnding prophages in bacterial genomes that combines similarity- and composition-based strategies
-
Akhter S, Aziz RK, Edwards RA. 2012. PhiSpy: a novel algorithm for fnding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Research 40:1–13. doi:10.1093/nar/gks406.
-
(2012)
Nucleic Acids Research
, vol.40
, pp. 1-13
-
-
Akhter, S.1
Aziz, R.K.2
Edwards, R.A.3
-
4
-
-
84881263143
-
Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses
-
Allers E, Moraru C, Duhaime MB, Beneze E, Solonenko N, Canosa JB, Amann R, Sullivan MB. 2013. Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses. Environmental Microbiology 15:2306–2318. doi: 10.1111/1462-2920.12100.
-
(2013)
Environmental Microbiology
, vol.15
, pp. 2306-2318
-
-
Allers, E.1
Moraru, C.2
Duhaime, M.B.3
Beneze, E.4
Solonenko, N.5
Canosa, J.B.6
Amann, R.7
Sullivan, M.B.8
-
5
-
-
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
-
7
-
-
84900502880
-
Sulfur oxidation genes in diverse deep-sea viruses
-
Anantharaman K, Duhaime MB, Breier JA, Wendt K, Toner BM, Dick GJ. 2014. Sulfur oxidation genes in diversedeep-sea viruses. Science 344:757–760. doi:10.1126/science.1252229.
-
(2014)
Science
, vol.344
, pp. 757-760
-
-
Anantharaman, K.1
Duhaime, M.B.2
Breier, J.A.3
Wendt, K.4
Toner, B.M.5
Dick, G.J.6
-
8
-
-
44449133775
-
Virus population dynamics and acquired virus resistance in natural microbial communities
-
Andersson AF, Banfeld J F. 2008. Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320:1047–1050. doi:10.1126/science.1157358.
-
(2008)
Science
, vol.320
, pp. 1047-1050
-
-
Andersson, A.F.1
Banfeld, J.F.2
-
9
-
-
79960468271
-
Using CRISPRs as a metagenomic tool to identify microbial hosts of a diffuse fow hydrothermal vent viral assemblage
-
Anderson RE, Brazelton WJ, Baross JA. 2011. Using CRISPRs as a metagenomic tool to identify microbial hosts of a diffuse fow hydrothermal vent viral assemblage. FEMS Microbiology Ecology 77:120–133. doi:10.1111/j.1574-6941.2011.01090.x.
-
(2011)
FEMS Microbiology Ecology
, vol.77
, pp. 120-133
-
-
Anderson, R.E.1
Brazelton, W.J.2
Baross, J.A.3
-
10
-
-
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 fouroceanic regions. PLOS Biology 4:e368. doi:10.1371/journal.pbio.0040368.
-
(2006)
PLOS Biology
, vol.4
-
-
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
-
11
-
-
74549198200
-
The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes
-
Angly FE, Willner D, Prieto-Davó A, Edwards RA, Schmieder R, Vega-Thurber R, Antonopoulos DA, Barott K, Cottrell MT, Desnues C, Dinsdale EA, Furlan M, Haynes M, Henn MR, Hu Y, Kirchman DL, McDole T, McPherson JD, Meyer F, Miller RM, Mundt E, Naviaux RK, Rodriguez-Mueller B, Stevens R, Wegley L, Zhang L, Zhu B, Rohwer F. 2009. The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLOS Computational Biology 5:e1000593. doi:10.1371/journal.pcbi.1000593.
-
(2009)
PLOS Computational Biology
, vol.5
-
-
Angly, F.E.1
Willner, D.2
Prieto-Davó, A.3
Edwards, R.A.4
Schmieder, R.5
Vega-Thurber, R.6
Antonopoulos, D.A.7
Barott, K.8
Cottrell, M.T.9
Desnues, C.10
Dinsdale, E.A.11
Furlan, M.12
Haynes, M.13
Henn, M.R.14
Hu, Y.15
Kirchman, D.L.16
McDole, T.17
McPherson, J.D.18
Meyer, F.19
Miller, R.M.20
Mundt, E.21
Naviaux, R.K.22
Rodriguez-Mueller, B.23
Stevens, R.24
Wegley, L.25
Zhang, L.26
Zhu, B.27
Rohwer, F.28
more..
-
12
-
-
34447644810
-
CRISPR recognition tool (CRT): A tool for automatic detection of clustered regularly interspaced palindromic repeats
-
Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P. 2007. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 8:209. doi:10.1186/1471-2105-8-209.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 209
-
-
Bland, C.1
Ramsey, T.L.2
Sabree, F.3
Lowe, M.4
Brown, K.5
Kyrpides, N.C.6
Hugenholtz, P.7
-
15
-
-
78649710753
-
A cryptic sulfur cycle in oxygen-minimum-zone waters off the Chilean coast
-
Canfeld DE, Stewart FJ, Thamdrup B, De Brabandere L, Dalsgaard T, Delong E F, Revsbech N P, Ulloa O. 2010. A cryptic sulfur cycle in oxygen-minimum-zone waters off the Chilean coast. Science 330:1375–1378. doi: 10.1126/science.1196889.
-
(2010)
Science
, vol.330
, pp. 1375-1378
-
-
Canfeld, D.E.1
Stewart, F.J.2
Thamdrup, B.3
De Brabandere, L.4
Dalsgaard, T.5
Delong, E.F.6
Revsbech, N.P.7
Ulloa, O.8
-
16
-
-
84867985452
-
Oxygen minimum zones harbor novel viral communities with low diversity
-
Cassman N, Prieto-Davó A, Walsh K, Silva GG, Angly F, Akhter S, Barott K, Busch J, McDole T, Haggerty JM, Willner D, Alarcón G, Ulloa O, DeLong E F, Dutilh BE, Rohwer F, Dinsdale EA. 2012. Oxygen minimum zones harbornovel viral communities with low diversity. Environmental Microbiology 14:3043–3065. doi: 10.1111/j.1462-2920.2012.02891.x.
-
(2012)
Environmental Microbiology
, vol.14
, pp. 3043-3065
-
-
Cassman, N.1
Prieto-Davó, A.2
Walsh, K.3
Silva, G.G.4
Angly, F.5
Akhter, S.6
Barott, K.7
Busch, J.8
McDole, T.9
Haggerty, J.M.10
Willner, D.11
Alarcón, G.12
Ulloa, O.13
Delong, E.F.14
Dutilh, B.E.15
Rohwer, F.16
Dinsdale, E.A.17
-
17
-
-
33645461497
-
Transcription of a ‘photosynthetic’ T4-type phage during infection of a marine cyanobacterium
-
Clokie MR, Shan J, Bailey S, Jia Y, Krisch HM, West S, Mann NH. 2006. Transcription of a ‘photosynthetic’ T4-typephage during infection of a marine cyanobacterium. Environmental Microbiology 8:827–835. doi: 10.1111/j.1462-2920.2005.00969.x.
-
(2006)
Environmental Microbiology
, vol.8
, pp. 827-835
-
-
Clokie, M.R.1
Shan, J.2
Bailey, S.3
Jia, Y.4
Krisch, H.M.5
West, S.6
Mann, N.H.7
-
18
-
-
42049110060
-
Effcient phage-mediated pigment biosynthesis in oceanic cyanobacteria
-
Dammeyer T, Bagby SC, Sullivan MB, Chisholm SW, Frankenberg-Dinkel N. 2008. Effcient phage-mediated pigment biosynthesis in oceanic cyanobacteria. Current Biology 18:442–448. doi:10.1016/j.cub.2008.02.067.
-
(2008)
Current Biology
, vol.18
, pp. 442-448
-
-
Dammeyer, T.1
Bagby, S.C.2
Sullivan, M.B.3
Chisholm, S.W.4
Frankenberg-Dinkel, N.5
-
20
-
-
31544483932
-
Community genomics among stratifed microbial assemblages in the ocean's interior
-
DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard NU, Martinez A, Sullivan MB, Edwards R, Brito BR, Chisholm SW, Karl DM. 2006. Community genomics among stratifed microbial assemblages in the ocean's interior. Science 311:496–503. doi: 10.1126/science.1120250.
-
(2006)
Science
, vol.311
, pp. 496-503
-
-
Delong, E.F.1
Preston, C.M.2
Mincer, T.3
Rich, V.4
Hallam, S.J.5
Frigaard, N.U.6
Martinez, A.7
Sullivan, M.B.8
Edwards, R.9
Brito, B.R.10
Chisholm, S.W.11
Karl, D.M.12
-
21
-
-
84906254581
-
Viral tagging reveals discrete populations in Synechococcus viral genome sequence space
-
in press
-
Deng L, Ignacio-Espinoza JC, Gregory A, Poulos BT, Weitz JS, Hugenholtz P, Sullivan MB. 2014. Viral tagging revealsdiscrete populations in Synechococcus viral genome sequence space. Nature. in press. doi:10.1038/nature13459.
-
(2014)
Nature
-
-
Deng, L.1
Ignacio-Espinoza, J.C.2
Gregory, A.3
Poulos, B.T.4
Weitz, J.S.5
Hugenholtz, P.6
Sullivan, M.B.7
-
22
-
-
84857182032
-
Virophages question the existence of satellites
-
author reply 234
-
Desnues C, Raoult D. 2012. Virophages question the existence of satellites. Nature Reviews Microbiology 10:234.author reply 234. doi: 10.1038/nrmicro2676-c3.
-
(2012)
Nature Reviews Microbiology
, vol.10
, pp. 234
-
-
Desnues, C.1
Raoult, D.2
-
23
-
-
84859814245
-
A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses
-
Diemer GS, Stedman KM. 2012. A novel virus genome discovered in an extreme environment suggests recombinationbetween unrelated groups of RNA and DNA viruses. Biology Direct 7:13. doi: 10.1186/1745-6150-7-13.
-
(2012)
Biology Direct
, vol.7
, pp. 13
-
-
Diemer, G.S.1
Stedman, K.M.2
-
24
-
-
80055082271
-
Accelerated profle HMM searches
-
Eddy SR. 2011. Accelerated profle HMM searches. PLOS Computational Biology 7:e1002195. doi: 10.1371/journal.pcbi.1002195.
-
(2011)
PLOS Computational Biology
, vol.7
-
-
Eddy, S.R.1
-
25
-
-
13244255415
-
MUSCLE: A multiple sequence alignment method with reduced time and space complexity
-
Edgar RC. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity.BMC Bioinformatics 5:113. doi: 10.1186/1471-2105-5-113.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 113
-
-
Edgar, R.C.1
-
26
-
-
44449137093
-
The microbial engines that drive earth's biogeochemical cycles
-
Falkowski PG, Fenchel T, Delong E F. 2008. The microbial engines that drive earth's biogeochemical cycles.Science 320:1034–1039. doi: 10.1126/science.1153213.
-
(2008)
Science
, vol.320
, pp. 1034-1039
-
-
Falkowski, P.G.1
Fenchel, T.2
Delong, E.F.3
-
27
-
-
83855161526
-
Sputnik and Mavirus: More than just satellite viruses
-
author reply 78
-
Fischer MG. 2012. Sputnik and Mavirus: more than just satellite viruses. Nature Reviews Microbiology 10:78.author reply 78. doi: 10.1038/nrmicro2676-c1.
-
(2012)
Nature Reviews Microbiology
, vol.10
, pp. 78
-
-
Fischer, M.G.1
-
28
-
-
41649114407
-
Microbial community gene expression in ocean surface waters
-
Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, Chisholm SW, Delong E F. 2008. Microbial community gene expression in ocean surface waters. Proceedings of the National Academy of Sciences of USA 105:3805–3810.doi: 10.1073/pnas.0708897105.
-
(2008)
Proceedings of the National Academy of Sciences of USA
, vol.105
, pp. 3805-3810
-
-
Frias-Lopez, J.1
Shi, Y.2
Tyson, G.W.3
Coleman, M.L.4
Schuster, S.C.5
Chisholm, S.W.6
Delong, E.F.7
-
29
-
-
84891160721
-
Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone
-
Ganesh S, Parris DJ, Delong E F, Stewart FJ. 2014. Metagenomic analysis of size-fractionated picoplankton in amarine oxygen minimum zone. The ISME Journal 8:187–211. doi: 10.1038/ismej.2013.144.
-
(2014)
The ISME Journal
, vol.8
, pp. 187-211
-
-
Ganesh, S.1
Parris, D.J.2
Delong, E.F.3
Stewart, F.J.4
-
30
-
-
79952178131
-
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
-
Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea T P, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB. 2011. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proceedings of the National Academy of Sciences of USA 108:1513–1518. doi: 10.1073/pnas.1017351108.
-
(2011)
Proceedings of the National Academy of Sciences of USA
, vol.108
, pp. 1513-1518
-
-
Gnerre, S.1
Maccallum, I.2
Przybylski, D.3
Ribeiro, F.J.4
Burton, J.N.5
Walker, B.J.6
Sharpe, T.7
Hall, G.8
Shea, T.P.9
Sykes, S.10
Berlin, A.M.11
Aird, D.12
Costello, M.13
Daza, R.14
Williams, L.15
Nicol, R.16
Gnirke, A.17
Nusbaum, C.18
Lander, E.S.19
Jaffe, D.B.20
more..
-
31
-
-
83155178413
-
Development of phoH as a novel signature gene for assessing marine phage diversity
-
Goldsmith DB, Crosti G, Dwivedi B, McDaniel LD, Varsani A, Suttle CA, Weinbauer MG, Sandaa RA, Breitbart M. 2011. Development of phoH as a novel signature gene for assessing marine phage diversity. Applied and Environmental Microbiology 77:7730–7739. doi: 10.1128/AEM.05531-11.
-
(2011)
Applied and Environmental Microbiology
, vol.77
, pp. 7730-7739
-
-
Goldsmith, D.B.1
Crosti, G.2
Dwivedi, B.3
McDaniel, L.D.4
Varsani, A.5
Suttle, C.A.6
Weinbauer, M.G.7
Sandaa, R.A.8
Breitbart, M.9
-
32
-
-
0242578620
-
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
-
Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52:696–704. doi: 10.1080/10635150390235520.
-
(2003)
Systematic Biology
, vol.52
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
33
-
-
84905639696
-
Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes
-
Hawley AK, Brewer HM, Norbeck AD, Pasa-Tolic L, Hallam SJ. 2014. Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes. Proceedings of the National Academy of Sciences of USA 111:11395–1140. doi: 10.1073/pnas.1322132111.
-
(2014)
Proceedings of the National Academy of Sciences of USA
, vol.111
, pp. 11395-21140
-
-
Hawley, A.K.1
Brewer, H.M.2
Norbeck, A.D.3
Pasa-Tolic, L.4
Hallam, S.J.5
-
35
-
-
84887380143
-
Metabolic reprogramming by viruses in the sunlit and dark ocean
-
Hurwitz BL, Hallam SJ, Sullivan MB. 2013. Metabolic reprogramming by viruses in the sunlit and dark ocean.Genome Biology 14:R123. doi: 10.1186/gb-2013-14-11-r123.
-
(2013)
Genome Biology
, vol.14
, pp. R123
-
-
Hurwitz, B.L.1
Hallam, S.J.2
Sullivan, M.B.3
-
36
-
-
84874530236
-
The Pacifc Ocean virome (POV): A marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology
-
Hurwitz BL, Sullivan MB. 2013. The Pacifc Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLOS ONE 8:e57355. doi: 10.1371/journal.pone.0057355.
-
(2013)
PLOS ONE
, vol.8
-
-
Hurwitz, B.L.1
Sullivan, M.B.2
-
38
-
-
79954570132
-
A simple and effcient method for concentration of ocean viruses by chemical focculation
-
John SG, Mendez CB, Deng L, Poulos B, Kauffman AK, Kern S, Brum J, Polz M F, Boyle EA, Sullivan MB. 2011. A simple and effcient method for concentration of ocean viruses by chemical focculation. Environmental Microbiology Reports 3:195–202. doi: 10.1111/j.1758-2229.2010.00208.x.
-
(2011)
Environmental Microbiology Reports
, vol.3
, pp. 195-202
-
-
John, S.G.1
Mendez, C.B.2
Deng, L.3
Poulos, B.4
Kauffman, A.K.5
Kern, S.6
Brum, J.7
Polz, M.F.8
Boyle, E.A.9
Sullivan, M.B.10
-
39
-
-
83155190998
-
Amplifcation methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses
-
Kim KH, Bae JW. 2011. Amplifcation methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses. Applied and Environmental Microbiology 77:7663–7668. doi: 10.1128/AEM.00289-11.
-
(2011)
Applied and Environmental Microbiology
, vol.77
, pp. 7663-7668
-
-
Kim, K.H.1
Bae, J.W.2
-
40
-
-
84879121025
-
MetaPathways: A modular pipeline for constructing pathway/genome databases from environmental sequence information
-
Konwar KM, Hanson NW, Pagé A P, Hallam SJ. 2013. MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information. BMC Bioinformatics 14:202. doi: 10.1186/1471-2105-14-202.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 202
-
-
Konwar, K.M.1
Hanson, N.W.2
Pagé, A.P.3
Hallam, S.J.4
-
41
-
-
84857148117
-
Towards a more comprehensive classifcation of satellite viruses
-
Krupovic M, Cvirkaite-Krupovic V. 2012. Towards a more comprehensive classifcation of satellite viruses. NatureReviews Microbiology 10:234. doi: 10.1038/nrmicro2676-c4.
-
(2012)
Nature Reviews Microbiology
, vol.10
, pp. 234
-
-
Krupovic, M.1
Cvirkaite-Krupovic, V.2
-
42
-
-
51349125147
-
The virophage as a unique parasite of the giant mimivirus
-
La Scola B, Desnues C, Pagnier I, Robert C, Barrassi L, Fournous G, Merchat M, Suzan-Monti M, Forterre P, Koonin E, Raoult D. 2008. The virophage as a unique parasite of the giant mimivirus. Nature 455:100–104. doi: 10.1038/nature07218.
-
(2008)
Nature
, vol.455
, pp. 100-104
-
-
La Scola, B.1
Desnues, C.2
Pagnier, I.3
Robert, C.4
Barrassi, L.5
Fournous, G.6
Merchat, M.7
Suzan-Monti, M.8
Forterre, P.9
Koonin, E.10
Raoult, D.11
-
43
-
-
84892152977
-
Metagenomic and whole-genome analysis reveals new lineages of gokushovi-ruses and biogeographic separation in the sea
-
Labonté JM, Suttle CA. 2013a. Metagenomic and whole-genome analysis reveals new lineages of gokushovi-ruses and biogeographic separation in the sea. Frontiers in Microbiology 4:404. doi: 10.3389/fmicb.2013.00404.
-
(2013)
Frontiers in Microbiology
, vol.4
, pp. 404
-
-
Labonté, J.M.1
Suttle, C.A.2
-
44
-
-
84886729050
-
Previously unknown and highly divergent ssDNA viruses populate the oceans
-
Labonté JM, Suttle CA. 2013b. Previously unknown and highly divergent ssDNA viruses populate the oceans.The ISME Journal 7:2169–2177. doi: 10.1038/ismej.2013.110.
-
(2013)
The ISME Journal
, vol.7
, pp. 2169-2177
-
-
Labonté, J.M.1
Suttle, C.A.2
-
45
-
-
63849329587
-
Revising the nitrogen cycle in the Peruvian oxygen minimum zone
-
Lam P, Lavik G, Jensen MM, van de Vossenberg J, Schmid M, Woebken D, Gutiérrez D, Amann R, Jetten MS, Kuypers MM. 2009. Revising the nitrogen cycle in the Peruvian oxygen minimum zone. Proceedings of the National Academy of Sciences of USA 106:4752–4757. doi: 10.1073/pnas.0812444106.
-
(2009)
Proceedings of the National Academy of Sciences of USA
, vol.106
, pp. 4752-4757
-
-
Lam, P.1
Lavik, G.2
Jensen, M.M.3
Van De Vossenberg, J.4
Schmid, M.5
Woebken, D.6
Gutiérrez, D.7
Amann, R.8
Jetten, M.S.9
Kuypers, M.M.10
-
46
-
-
49149115195
-
Unifying classical and molecular taxonomic classifcation: Analysis of the Podoviridae using BLASTP-based tools
-
Lavigne R, Seto D, Mahadevan P, Ackermann HW, Kropinski AM. 2008. Unifying classical and molecular taxonomic classifcation: analysis of the Podoviridae using BLASTP-based tools. Research in Microbiology 159:406–414. doi: 10.1016/j.resmic.2008.03.005.
-
(2008)
Research in Microbiology
, vol.159
, pp. 406-414
-
-
Lavigne, R.1
Seto, D.2
Mahadevan, P.3
Ackermann, H.W.4
Kropinski, A.M.5
-
47
-
-
33845873289
-
Interactive Tree Of Life (iTOL): An online tool for phylogenetic tree display and annotation
-
Letunic I, Bork P. 2007.Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.Bioinformatics 23:127–128. doi: 10.1093/bioinformatics/btl529.
-
(2007)
Bioinformatics
, vol.23
, pp. 127-128
-
-
Letunic, I.1
Bork, P.2
-
48
-
-
27744480467
-
Photosynthesis genes in marine viruses yield proteins during host infection
-
Lindell D, Jaffe JD, Johnson ZI, Church GM, Chisholm SW. 2005. Photosynthesis genes in marine viruses yieldproteins during host infection. Nature 438:86–89. doi: 10.1038/nature04111.
-
(2005)
Nature
, vol.438
, pp. 86-89
-
-
Lindell, D.1
Jaffe, J.D.2
Johnson, Z.I.3
Church, G.M.4
Chisholm, S.W.5
-
49
-
-
24044531934
-
X-ray structure of the gamma-subunit of a dissimilatory sulfte reductase: Fxed and fexible C-terminal arms
-
Mander GJ, Weiss MS, Hedderich R, Kahnt J, Ermler U, Warkentin E. 2005. X-ray structure of the gamma-subunit of a dissimilatory sulfte reductase: fxed and fexible C-terminal arms. FEBS Letters 579:4600–4604. doi: 10.1016/j.febslet.2005.07.029.
-
(2005)
FEBS Letters
, vol.579
, pp. 4600-4604
-
-
Mander, G.J.1
Weiss, M.S.2
Hedderich, R.3
Kahnt, J.4
Ermler, U.5
Warkentin, E.6
-
50
-
-
0041736065
-
Bacterial photosynthesis genes in a virus
-
Mann NH, Cook A, Millard A, Bailey S, Clokie M. 2003. Bacterial photosynthesis genes in a virus. Nature 424:741. doi: 10.1038/424741a.
-
(2003)
Nature
, vol.424
, pp. 741
-
-
Mann, N.H.1
Cook, A.2
Millard, A.3
Bailey, S.4
Clokie, M.5
-
51
-
-
84891800783
-
IMG/M 4 version of the integrated metagenome comparative analysis system
-
Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Pillay M, Ratner A, Huang J, Pagani I, Tringe S, Huntemann M, Billis K, Varghese N, Tennessen K, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC. 2014. IMG/M 4 version of the integrated metagenome comparative analysis system. Nucleic Acids Research42:D568–D573. doi: 10.1093/nar/gkt919.
-
(2014)
Nucleic Acids Research
, vol.4-2
, pp. D568-D573
-
-
Markowitz, V.M.1
Chen, I.M.2
Chu, K.3
Szeto, E.4
Palaniappan, K.5
Pillay, M.6
Ratner, A.7
Huang, J.8
Pagani, I.9
Tringe, S.10
Huntemann, M.11
Billis, K.12
Varghese, N.13
Tennessen, K.14
Mavromatis, K.15
Pati, A.16
Ivanova, N.N.17
Kyrpides, N.C.18
-
52
-
-
84857121184
-
Unveiling in situ interactions between marine protists and bacteria through single cell sequencing
-
Martinez-Garcia M, Brazel D, Poulton NJ, Swan BK, Gomez ML, Masland D, Sieracki ME, Stepanauskas R. 2012. Unveiling in situ interactions between marine protists and bacteria through single cell sequencing. The ISME Journal 6:703–707. doi: 10.1038/ismej.2011.126.
-
(2012)
The Ismejournal
, vol.6
, pp. 703-707
-
-
Martinez-Garcia, M.1
Brazel, D.2
Poulton, N.J.3
Swan, B.K.4
Gomez, M.L.5
Masland, D.6
Sieracki, M.E.7
Stepanauskas, R.8
-
53
-
-
84888198483
-
Sulfur oxidizers dominate carbon fxation at a biogeochemical hot spot in the dark ocean
-
Mattes TE, Nunn BL, Marshall KT, Proskurowski G, Kelley DS, Kawka OE, Goodlett DR, Hansell DA, Morris RM. 2013. Sulfur oxidizers dominate carbon fxation at a biogeochemical hot spot in the dark ocean. The ISME Journal 7:2349–2360. doi: 10.1038/ismej.2013.113.
-
(2013)
The Ismejournal
, vol.7
, pp. 2349-2360
-
-
Mattes, T.E.1
Nunn, B.L.2
Marshall, K.T.3
Proskurowski, G.4
Kelley, D.S.5
Kawka, O.E.6
Goodlett, D.R.7
Hansell, D.A.8
Morris, R.M.9
-
56
-
-
59149090570
-
MetaGeneAnnotator: Detecting species-specifc patterns of ribosomalbinding site for precise gene prediction in anonymous prokaryotic and phage genomes
-
Noguchi H, Taniguchi T, Itoh T. 2008. MetaGeneAnnotator: detecting species-specifc patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Research 15:387–396. doi: 10.1093/dnares/dsn027.
-
(2008)
DNA Research
, vol.1-5
, pp. 387-396
-
-
Noguchi, H.1
Taniguchi, T.2
Itoh, T.3
-
57
-
-
57749097713
-
The crystal structure ofDesulfovibrio vulgaris dissimilatory sulfte reductase bound to DsrC provides novel insights into themechanism of sulfate respiration
-
Oliveira TF, Vonrhein C, Matias PM, Venceslau SS, Pereira IA, Archer M. 2008. The crystal structure of Desulfovibrio vulgaris dissimilatory sulfte reductase bound to DsrC provides novel insights into the mechanism of sulfate respiration. The Journal of Biological Chemistry 283:34141–34149. doi: 10.1074/jbc.M805643200.
-
(2008)
The Journal of Biological Chemistry
, vol.283
, pp. 34141-34149
-
-
Oliveira, T.F.1
Vonrhein, C.2
Matias, P.M.3
Venceslau, S.S.4
Pereira, I.A.5
Archer, M.6
-
58
-
-
84861760530
-
IDBA-UD: A de novo assembler for single-cell and metagenomicsequencing data with highly uneven depth
-
Peng Y, Leung HC, Yiu SM, 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
-
59
-
-
84858077472
-
The Pfam protein families database
-
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD. 2012. The Pfam protein families database. Nucleic Acids Research 40:D290–D301. doi: 10.1093/nar/gkr1065.
-
(2012)
Nucleicacids Research
, vol.40
, pp. D290-D301
-
-
Punta, M.1
Coggill, P.C.2
Eberhardt, R.Y.3
Mistry, J.4
Tate, J.5
Boursnell, C.6
Pang, N.7
Forslund, K.8
Ceric, G.9
Clements, J.10
Heger, A.11
Holm, L.12
Sonnhammer, E.L.13
Eddy, S.R.14
Bateman, A.15
Finn, R.D.16
-
61
-
-
84881138595
-
Insights into the phylogeny and coding potential of microbial darkmatter
-
Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng J F, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund B P, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499:431–437. doi: 10.1038/nature12352.
-
(2013)
Nature
, vol.499
, pp. 431-437
-
-
Rinke, C.1
Schwientek, P.2
Sczyrba, A.3
Ivanova, N.N.4
Erson, I.J.5
Cheng, J.F.6
Darling, A.7
Malfatti, S.8
Swan, B.K.9
Gies, E.A.10
Dodsworth, J.A.11
Hedlund, B.P.12
Tsiamis, G.13
Sievert, S.M.14
Liu, W.T.15
Eisen, J.A.16
Hallam, S.J.17
Kyrpides, N.C.18
Stepanauskas, R.19
Rubin, E.M.20
Hugenholtz, P.21
Woyke, T.22
more..
-
62
-
-
70350180460
-
Explaining microbial population genomics through phage predation
-
Rodriguez-Valera F, Martin-Cuadrado AB, Rodriguez-Brito B, Pasić L, Thingstad T F, Rohwer F, Mira A. 2009. Explaining microbial population genomics through phage predation. Nature Reviews Microbiology 7:828–836. doi: 10.1038/nrmicro2235.
-
(2009)
Nature Reviews Microbiology
, vol.7
, pp. 828-836
-
-
Rodriguez-Valera, F.1
Martin-Cuadrado, A.B.2
Rodriguez-Brito, B.3
Pasić, L.4
Thingstad, T.F.5
Rohwer, F.6
Mira, A.7
-
63
-
-
84889253615
-
Chimeric viruses blur the borders betweenthe major groups of eukaryotic single-stranded DNA viruses
-
Roux S, Enault F, Bronner G, Vaulot D, Forterre P, Krupovic M. 2013. Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses. Nature Communications 4:2700. doi: 10.1038/ncomms3700.
-
(2013)
Nature Communications
, vol.4
, pp. 2700
-
-
Roux, S.1
Enault, F.2
Bronner, G.3
Vaulot, D.4
Forterre, P.5
Krupovic, M.6
-
64
-
-
84863838397
-
Evolution and diversity of the Microviridae viral familythrough a collection of 81 new complete genomes assembled from virome reads
-
Roux S, Krupovic M, Poulet A, Debroas D, Enault F. 2012. Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads. PLOS ONE 7:e40418. doi: 10.1371/journal.pone.0040418.
-
(2012)
PLOS ONE
, vol.7
-
-
Roux, S.1
Krupovic, M.2
Poulet, A.3
Debroas, D.4
Enault, F.5
-
65
-
-
84899552918
-
Metavir 2: Virome comparative analysis and annotationof assembled genomic fragments
-
Roux S, Tournayre J, Mahul A, Debroas D, Enault F. 2014. Metavir 2: virome comparative analysis and annotation of assembled genomic fragments. BMC Bioinformatics 15:76. doi: 10.1186/1471-2105-15-76.
-
(2014)
BMC Bioinformatics
, vol.15
, pp. 76
-
-
Roux, S.1
Tournayre, J.2
Mahul, A.3
Debroas, D.4
Enault, F.5
-
66
-
-
72949107142
-
Introducing mothur: Open-source,platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 75:7537–7541. doi: 10.1128/AEM.01541-09.
-
(2009)
Applied and Environmental Microbiology
, 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
Lesniewski, R.A.7
Oakley, B.B.8
Parks, D.H.9
Robinson, C.J.10
Sahl, J.W.11
Stres, B.12
Thallinger, G.G.13
Van Horn, D.J.14
Weber, C.F.15
-
67
-
-
70249108768
-
Photosystem I Gene cassettes are present in marine virus genomes
-
Sharon I, Alperovitch A, Rohwer F, Haynes M, Glaser F, Atamna-Ismaeel N, Pinter RY, Partensky F, Koonin E V, Wolf YI, Nelson N, Béjà O. 2009. Photosystem I Gene cassettes are present in marine virus genomes. Nature 461:258–262. doi: 10.1038/nature08284.
-
(2009)
Nature
, vol.4-61
, pp. 258-262
-
-
Sharon, I.1
Alperovitch, A.2
Rohwer, F.3
Haynes, M.4
Glaser, F.5
Atamna-Ismaeel, N.6
Pinter, R.Y.7
Partensky, F.8
Koonin, E.V.9
Wolf, Y.I.10
Nelson, N.11
Béjà, O.12
-
68
-
-
79959588019
-
Comparative metagenomics of microbial traits within oceanic viral communities
-
Sharon I, Battchikova N, Aro EM, Giglione C, Meinnel T, Glaser F, Pinter RY, Breitbart M, Rohwer F, Béjà O. 2011. Comparative metagenomics of microbial traits within oceanic viral communities. The ISME Journal 5:1178–1190. doi: 10.1038/ismej.2011.2.
-
(2011)
The ISME Journal
, vol.5
, pp. 1178-1190
-
-
Sharon, I.1
Battchikova, N.2
Aro, E.M.3
Giglione, C.4
Meinnel, T.5
Glaser, F.6
Pinter, R.Y.7
Breitbart, M.8
Rohwer, F.9
Béjà, O.10
-
69
-
-
39149142575
-
CRISPR–a widespread system that provides acquired resistance againstphages in bacteria and archaea
-
Sorek R, Kunin V, Hugenholtz P. 2008. CRISPR–a widespread system that provides acquired resistance against phages in bacteria and archaea. Nature Reviews Microbiology 6:181–186. doi: 10.1038/nrmicro1793.
-
(2008)
Nature Reviews Microbiology
, vol.6
, pp. 181-186
-
-
Sorek, R.1
Kunin, V.2
Hugenholtz, P.3
-
70
-
-
34547492897
-
Matching phylogeny and metabolism in the uncultured marine bacteria, onecell at a time
-
Stepanauskas R, Sieracki ME. 2007. Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. Proceedings of the National Academy of Sciences of USA 104:9052–9057. doi: 10.1073/pnas.0700496104.
-
(2007)
Proceedings of the National Academy of Sciences of USA
, vol.104
, pp. 9052-9057
-
-
Stepanauskas, R.1
Sieracki, M.E.2
-
71
-
-
84855287323
-
Microbial metatranscriptomics in a permanent marine oxygen minimumzone
-
Stewart FJ, Ulloa O, DeLong EF. 2012. Microbial metatranscriptomics in a permanent marine oxygen minimum zone. Environmental Microbiology 14:23–40. doi: 10.1111/j.1462-2920.2010.02400.x.
-
(2012)
Environmental Microbiology
, vol.14
, pp. 23-40
-
-
Stewart, F.J.1
Ulloa, O.2
Delong, E.F.3
-
72
-
-
46449104196
-
Expanding oxygen-minimum zones in the tropical oceans
-
Stramma L, Johnson GC, Sprintall J, Mohrholz V. 2008. Expanding oxygen-minimum zones in the tropical oceans. Science 320:655–658. doi: 10.1126/science.1153847.
-
(2008)
Science
, vol.320
, pp. 655-658
-
-
Stramma, L.1
Johnson, G.C.2
Sprintall, J.3
Mohrholz, V.4
-
73
-
-
21344461027
-
Three Prochlorococcus cyanophage genomes:Signature features and ecological interpretations
-
Sullivan MB, Coleman ML, Weigele P, Rohwer F, Chisholm SW. 2005. Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations. PLOS Biology 3:e144. doi: 10.1371/journal.pbio.0030144.
-
(2005)
PLOS Biology
, vol.3
-
-
Sullivan, M.B.1
Coleman, M.L.2
Weigele, P.3
Rohwer, F.4
Chisholm, S.W.5
-
74
-
-
78249280297
-
Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses fromdiverse hosts and environments
-
Sullivan MB, Huang KH, Ignacio-Espinoza JC, Berlin AM, Kelly L, Weigele PR, DeFrancesco AS, Kern SE, Thompson LR, Young S, Yandava C, Fu R, Krastins B, Chase M, Sarracino D, Osburne MS, Henn MR, Chisholm SW. 2010. Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments. Environmental Microbiology 12:3035–3056. doi: 10.1111/j.1462-2920.2010.02280.x.
-
(2010)
Environmental Microbiology
, vol.12
, pp. 3035-3056
-
-
Sullivan, M.B.1
Huang, K.H.2
Ignacio-Espinoza, J.C.3
Berlin, A.M.4
Kelly, L.5
Weigele, P.R.6
Defrancesco, A.S.7
Kern, S.E.8
Thompson, L.R.9
Young, S.10
Yandava, C.11
Fu, R.12
Krastins, B.13
Chase, M.14
Sarracino, D.15
Osburne, M.S.16
Henn, M.R.17
Chisholm, S.W.18
-
75
-
-
33747369803
-
Prevalence and evolution of corephotosystem II genes in marine cyanobacterial viruses and their hosts
-
Sullivan MB, Lindell D, Lee JA, Thompson LR, Bielawski J P, Chisholm SW. 2006. Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. PLOS Biology 4:e234. doi: 10.1371/journal.pbio.0040234.
-
(2006)
PLOS Biology
, vol.4
-
-
Sullivan, M.B.1
Lindell, D.2
Lee, J.A.3
Thompson, L.R.4
Bielawski, J.P.5
Chisholm, S.W.6
-
76
-
-
79953306448
-
Easyfg: A genome comparison visualizer
-
Sullivan MJ, Petty NK, Beatson SA. 2011. Easyfg: a genome comparison visualizer. Bioinformatics 27:1009–1010. doi: 10.1093/bioinformatics/btr039.
-
(2011)
Bioinformatics
, vol.27
, pp. 1009-1010
-
-
Sullivan, M.J.1
Petty, N.K.2
Beatson, S.A.3
-
77
-
-
25144506135
-
Viruses in the sea
-
Suttle CA. 2005. Viruses in the sea. Nature 437:356–361. doi: 10.1038/nature04160.
-
(2005)
Nature
, vol.437
, pp. 356-361
-
-
Suttle, C.A.1
-
78
-
-
34548792911
-
Marine viruses–major players in the global ecosystem
-
Suttle CA. 2007. Marine viruses–major players in the global ecosystem. Nature Reviews Microbiology 5:801–812. doi: 10.1038/nrmicro1750.
-
(2007)
Nature Reviews Microbiology
, vol.5
, pp. 801-812
-
-
Suttle, C.A.1
-
79
-
-
80052479893
-
Potential for chemolithoautotrophyamong ubiquitous bacteria lineages in the dark ocean
-
Swan BK, Martinez-Garcia M, Preston CM, Sczyrba A, Woyke T, Lamy D, Reinthaler T, Poulton NJ, Masland ED, Gomez ML, Sieracki ME, DeLong EF, Herndl GJ, Stepanauskas R. 2011. Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 333:1296–1300. doi: 10.1126/science.1203690.
-
(2011)
Science
, vol.333
, pp. 1296-1300
-
-
Swan, B.K.1
Martinez-Garcia, M.2
Preston, C.M.3
Sczyrba, A.4
Woyke, T.5
Lamy, D.6
Reinthaler, T.7
Poulton, N.J.8
Masland, E.D.9
Gomez, M.L.10
Sieracki, M.E.11
Delong, E.F.12
Herndl, G.J.13
Stepanauskas, R.14
-
80
-
-
84879932140
-
Prevalent genome streamlining and latitudinal divergence of planktonicbacteria in the surface ocean
-
Swan BK, Tupper B, Sczyrba A, Lauro FM, Martinez-Garcia M, González JM, Luo H, Wright JJ, Landry ZC, Hanson NW, Thompson B P, Poulton NJ, Schwientek P, Acinas SG, Giovannoni SJ, Moran MA, Hallam SJ, Cavicchioli R, Woyke T, Stepanauskas R. 2013. Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proceedings of the National Academy of Sciences of USA 110:11463–11468. doi: 10.1073/pnas.1304246110.
-
(2013)
Proceedings of the National Academy of Sciences of USA
, vol.110
, pp. 11463-11468
-
-
Swan, B.K.1
Tupper, B.2
Sczyrba, A.3
Lauro, F.M.4
Martinez-Garcia, M.5
González, J.M.6
Luo, H.7
Wright, J.J.8
Landry, Z.C.9
Hanson, N.W.10
Thompson, B.P.11
Poulton, N.J.12
Schwientek, P.13
Acinas, S.G.14
Giovannoni, S.J.15
Moran, M.A.16
Hallam, S.J.17
Cavicchioli, R.18
Woyke, T.19
Stepanauskas, R.20
more..
-
81
-
-
79959855149
-
Probing individual environmental bacteria for viruses byusing microfuidic digital PCR
-
Tadmor AD, Ottesen EA, Leadbetter JR, Phillips R. 2011. Probing individual environmental bacteria for viruses by using microfuidic digital PCR. Science 333:58–62. doi: 10.1126/science.1200758.
-
(2011)
Science
, vol.333
, pp. 58-62
-
-
Tadmor, A.D.1
Ottesen, E.A.2
Leadbetter, J.R.3
Phillips, R.4
-
82
-
-
80053624997
-
Phage auxiliary metabolicgenes and the rRedirection of cyanobacterial host carbon metabolism
-
Thompson LR, Zeng Q, Kelly L, Huang KH, Singer AU, Stubbe J, Chisholm SW. 2011. Phage auxiliary metabolic genes and the rRedirection of cyanobacterial host carbon metabolism. Proceedings of the National Academy of Sciences of USA 108:E757–E764. doi: 10.1073/pnas.1102164108.
-
(2011)
Proceedings of the National Academy Ofsciences of USA
, vol.108
, pp. E757-E764
-
-
Thompson, L.R.1
Zeng, Q.2
Kelly, L.3
Huang, K.H.4
Singer, A.U.5
Stubbe, J.6
Chisholm, S.W.7
-
83
-
-
84888199517
-
Microbial and viral metagenomes of a subtropical freshwater reservoir subject to climatic disturbances
-
Tseng, C.-H., Chiang, P.-W., Shiah, F.-K., Chen, Y.-L., Liou, J.-R., Hsu, T.-C., Maheswararajah, S., Saeed, I., Halgamuge, S., Tang, S.-L. "Microbial and viral metagenomes of a subtropical freshwater reservoir subject to climatic disturbances" in ISME Journal,Volume 7, Issue 12, 2013, Pages 2374-2386
-
(2013)
ISME Journal
, vol.7
, Issue.12
, pp. 2374-2386
-
-
Tseng, C.H.1
Chiang, P.-W.2
Shiah, F.-K.3
Chen, Y.-L.4
Liou, J.-R.5
Hsu, T.-C.6
Maheswararajah, S.7
Saeed, I.8
Halgamuge, S.9
Tang, S.-L.10
-
84
-
-
79955068424
-
Diversity and distribution of single-stranded DNA phagesin the North Atlantic Ocean
-
Tucker KP, Parsons R, Symonds EM, Breitbart M. 2011. Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean. The ISME Journal 5:822–830. doi: 10.1038/ismej.2010.188.
-
(2011)
The ISME Journal
, vol.5
, pp. 822-830
-
-
Tucker, K.P.1
Parsons, R.2
Symonds, E.M.3
Breitbart, M.4
-
85
-
-
84867090645
-
Microbial oceanography of anoxic oxygenminimum zones
-
Ulloa O, Canfeld DE, DeLong EF, Letelier RM, Stewart FJ. 2012. Microbial oceanography of anoxic oxygen minimum zones. Proceedings of the National Academy of Sciences of USA 109:15996–16003. doi: 10.1073/pnas.1205009109.
-
(2012)
Proceedings of the National Academy of Sciences of USA
, vol.109
, pp. 15996-16003
-
-
Ulloa, O.1
Canfeld, D.E.2
Delong, E.F.3
Letelier, R.M.4
Stewart, F.J.5
-
86
-
-
11144354360
-
Environmental genome shotgun sequencing of the Sargasso sea
-
Venter JC, Remington K, Heidelberg JF, 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 YH, 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
Rusch, D.4
Eisen, J.A.5
Wu, D.6
Paulsen, I.7
Nelson, K.E.8
Nelson, W.9
Fouts, D.E.10
Levy, S.11
Knap, A.H.12
Lomas, M.W.13
Nealson, K.14
White, O.15
Peterson, J.16
Hoffman, J.17
Parsons, R.18
Baden-Tillson, H.19
Pfannkoch, C.20
Rogers, Y.H.21
Smith, H.O.22
more..
-
87
-
-
70350502063
-
Metagenome of aversatile chemolithoautotroph from expanding oceanic dead zones
-
Walsh DA, Zaikova E, Howes CG, Song YC, Wright JJ, Tringe SG, Tortell PD, Hallam SJ. 2009. Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones. Science 326:578–582. doi: 10.1126/science.1175309.
-
(2009)
Science
, vol.326
, pp. 578-582
-
-
Walsh, D.A.1
Zaikova, E.2
Howes, C.G.3
Song, Y.C.4
Wright, J.J.5
Tringe, S.G.6
Tortell, P.D.7
Hallam, S.J.8
-
88
-
-
69949108471
-
Denitrifcation as thedominant nitrogen loss process in the Arabian sea
-
Ward BB, Devol AH, Rich JJ, Chang BX, Bulow SE, Naik H, Pratihary A, Jayakumar A. 2009. Denitrifcation as the dominant nitrogen loss process in the Arabian sea. Nature 461:78–81. doi: 10.1038/nature08276.
-
(2009)
Nature
, vol.461
, pp. 78-81
-
-
Ward, B.B.1
Devol, A.H.2
Rich, J.J.3
Chang, B.X.4
Bulow, S.E.5
Naik, H.6
Pratihary, A.7
Jayakumar, A.8
-
89
-
-
0027329223
-
Resistance to co-occurring phages enables marine synechococcus communitiesto coexist with cyanophages abundant in seawater
-
Waterbury JB, Valois FW. 1993. Resistance to co-occurring phages enables marine synechococcus communities to coexist with cyanophages abundant in seawater. Applied and Environmental Microbiology 59:3393–3399.
-
(1993)
Applied and Environmental Microbiology
, vol.59
, pp. 3393-3399
-
-
Waterbury, J.B.1
Valois, F.W.2
-
90
-
-
65449188232
-
Jalview version 2–a multiple sequencealignment editor and analysis workbench
-
Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ. 2009. Jalview version 2–a multiple sequence alignment editor and analysis workbench. Bioinformatics 25:1189–1191. doi: 10.1093/bioinformatics/btp033.
-
(2009)
Bioinformatics
, vol.25
, pp. 1189-1191
-
-
Waterhouse, A.M.1
Procter, J.B.2
Martin, D.M.3
Clamp, M.4
Barton, G.J.5
-
91
-
-
0042572533
-
Lysogeny and virus-induced mortality of bacterioplankton in surface,deep, and anoxic marine waters
-
Weinbauer MG, Brettar I, Ho MG. 2003. Lysogeny and virus-induced mortality of bacterioplankton in surface, deep, and anoxic marine waters. Limnology and Oceanography 48:1457–1465. doi: 10.4319/lo.2003.48.4.1457.
-
(2003)
Limnology and Oceanography
, vol.48
, pp. 1457-1465
-
-
Weinbauer, M.G.1
Brettar, I.2
Ho, M.G.3
-
92
-
-
35348861013
-
Persistently declining oxygen levels in the interior waters of theeastern subarctic Pacifc
-
Whitney FA, Freeland HJ, Robert M. 2007. Persistently declining oxygen levels in the interior waters of the eastern subarctic Pacifc. Progress in Oceanography 75:179–199. doi: 10.1016/j.pocean.2007.08.007.
-
(2007)
Progress in Oceanography
, vol.75
, pp. 179-199
-
-
Whitney, F.A.1
Freeland, H.J.2
Robert, M.3
-
94
-
-
84867645584
-
Metagenomic Exploration of Viruses throughout the Indian Ocean
-
Williamson SJ, Allen LZ, Lorenzi HA, Fadrosh DW, Brami D, Thiagarajan M, McCrow J P, Tovchigrechko A, Yooseph S, Venter JC. 2012. Metagenomic Exploration of Viruses throughout the Indian Ocean. PLOS ONE 7:e42047. doi: 10.1371/journal.pone.0042047.
-
(2012)
PLOS ONE
, vol.7
-
-
Williamson, S.J.1
Allen, L.Z.2
Lorenzi, H.A.3
Fadrosh, D.W.4
Brami, D.5
Thiagarajan, M.6
McCrow, J.P.7
Tovchigrechko, A.8
Yooseph, S.9
Venter, J.C.10
-
96
-
-
79955787125
-
Single-cell genomics reveals organismal interactions in uncultivated marine protists
-
Yoon HS, Price DC, Stepanauskas R, Rajah VD, Sieracki ME, Wilson WH, Yang EC, Duffy S, Bhattacharya D. 2011. Single-cell genomics reveals organismal interactions in uncultivated marine protists. Science 332:714–717. doi: 10.1126/science.1203163.
-
(2011)
Science
, vol.332
, pp. 714-717
-
-
Yoon, H.S.1
Price, D.C.2
Stepanauskas, R.3
Rajah, V.D.4
Sieracki, M.E.5
Wilson, W.H.6
Yang, E.C.7
Duffy, S.8
Bhattacharya, D.9
-
97
-
-
84874520341
-
Metagenomic analysis of viral communities in (hado)pelagic sediments
-
Yoshida M, Takaki Y, Eitoku M, Nunoura T, Takai K. 2013. Metagenomic analysis of viral communities in (hado) pelagic sediments. PLOS ONE 8:e57271. doi: 10.1371/journal.pone.0057271.
-
(2013)
PLOS ONE
, vol.8
-
-
Yoshida, M.1
Takaki, Y.2
Eitoku, M.3
Nunoura, T.4
Takai, K.5
-
98
-
-
73349133709
-
Microbial community dynamics in aseasonally anoxic fjord: Saanich Inlet, British Columbia
-
Zaikova E, Walsh DA, Stilwell C P, Mohn WW, Tortell PD, Hallam SJ. 2010. Microbial community dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia. Environmental Microbiology 12:172–191. doi: 10.1111/j.1462-2920.2009.02058.x.
-
(2010)
Environmental Microbiology
, vol.12
, pp. 172-191
-
-
Zaikova, E.1
Walsh, D.A.2
Stilwell, C.P.3
Mohn, W.W.4
Tortell, P.D.5
Hallam, S.J.6
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