-
1
-
-
84879060146
-
Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus
-
Flombaum, P. et al. Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus. Proc Natl Acad Sci USA 110, 9824–9829 (2013).
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, pp. 9824-9829
-
-
Flombaum, P.1
-
2
-
-
0032805444
-
Sea of Change: Biogeochemical Variability in the North Pacific Subtropical Gyre
-
Karl, D. M. A Sea of Change: Biogeochemical Variability in the North Pacific Subtropical Gyre. Ecosystems 2, 181–214 (1999).
-
(1999)
Ecosystems
, vol.2
, pp. 181-214
-
-
Karl, D.M.A.1
-
3
-
-
0033009854
-
Prochlorococcus, a marine photosynthetic prokaryote of global significance
-
Partensky, F., Hess, W. R. & Vaulot, D. Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbiol Mol Biol Rev 63, 106–127 (1999).
-
(1999)
Microbiol Mol Biol Rev
, vol.63
, pp. 106-127
-
-
Partensky, F.1
Hess, W.R.2
Vaulot, D.3
-
4
-
-
84862195254
-
Prochlorococcus: Advantages and limits of minimalism
-
Partensky, F. & Garczarek, L. Prochlorococcus: advantages and limits of minimalism. Ann Rev Mar Sci 2, 305–331 (2010).
-
(2010)
Ann Rev Mar Sci
, vol.2
, pp. 305-331
-
-
Partensky, F.1
Garczarek, L.2
-
5
-
-
84885221140
-
Effect of temperature on photosynthesis and growth in marine Synechococcus spp
-
Mackey, K. R. et al. Effect of temperature on photosynthesis and growth in marine Synechococcus spp. Plant Physiol 163, 815–829 (2013).
-
(2013)
Plant Physiol
, vol.163
, pp. 815-829
-
-
Mackey, K.R.1
-
6
-
-
84927050723
-
Prochlorococcus: The structure and function of collective diversity
-
Biller, S. J., Berube, P. M., Lindell, D. & Chisholm, S. W. Prochlorococcus: the structure and function of collective diversity. Nat Rev Microbiol 13, 13–27 (2015).
-
(2015)
Nat Rev Microbiol
, vol.13
, pp. 13-27
-
-
Biller, S.J.1
Berube, P.M.2
Lindell, D.3
Chisholm, S.W.4
-
7
-
-
84864083035
-
The infinitely many genes model for the distributed genome of bacteria
-
Baumdicker, F., Hess, W. R. & Pfaffelhuber, P. The infinitely many genes model for the distributed genome of bacteria. Genome Biol Evol 4, 443–456 (2012).
-
(2012)
Genome Biol Evol
, vol.4
, pp. 443-456
-
-
Baumdicker, F.1
Hess, W.R.2
Pfaffelhuber, P.3
-
8
-
-
80052318679
-
Dependence of the cyanobacterium Prochlorococcus on hydrogen peroxide scavenging microbes for growth at the ocean's surface
-
Morris, J. J., Johnson, Z. I., Szul, M. J., Keller, M. & Zinser, E. R. Dependence of the cyanobacterium Prochlorococcus on hydrogen peroxide scavenging microbes for growth at the ocean's surface. PLoS ONE 6, e16805 (2011).
-
(2011)
Plos ONE
, vol.6
-
-
Morris, J.J.1
Johnson, Z.I.2
Szul, M.J.3
Keller, M.4
Zinser, E.R.5
-
9
-
-
77953981581
-
Complete genome sequence of "Candidatus Puniceispirillum marinum" IMCC1322, a representative of the SAR116 clade in the Alphaproteobacteria
-
Oh, H. M. et al. Complete genome sequence of "Candidatus Puniceispirillum marinum" IMCC1322, a representative of the SAR116 clade in the Alphaproteobacteria. J Bacteriol 192, 3240–3241 (2010).
-
(2010)
J Bacteriol
, vol.192
, pp. 3240-3241
-
-
Oh, H.M.1
-
10
-
-
84863155147
-
Draft genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria
-
Grote, J. et al. Draft genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria. Stand Genomic Sci 5, 269–278 (2011).
-
(2011)
Stand Genomic Sci
, vol.5
, pp. 269-278
-
-
Grote, J.1
-
11
-
-
85028313974
-
Metabolic evolution and the self-organization of ecosystems
-
Braakman, R., Follows, M. J. & Chisholm, S. W. Metabolic evolution and the self-organization of ecosystems. Proc Natl Acad Sci USA 114, E3091–E3100 (2017).
-
(2017)
Proc Natl Acad Sci USA
, vol.114
, pp. E3091-E3100
-
-
Braakman, R.1
Follows, M.J.2
Chisholm, S.W.3
-
12
-
-
84887622857
-
Stabilizing the foundation of the house that ‘omics builds: The evolving value of cultured isolates to marine microbiology
-
Rappé, M. S. Stabilizing the foundation of the house that ‘omics builds: the evolving value of cultured isolates to marine microbiology. Current Opinion in Microbiology 16, 618–624 (2013).
-
(2013)
Current Opinion in Microbiology
, vol.16
, pp. 618-624
-
-
Rappé, M.S.1
-
13
-
-
84881138595
-
Insights into the phylogeny and coding potential of microbial dark matter
-
Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431–437 (2013).
-
(2013)
Nature
, vol.499
, pp. 431-437
-
-
Rinke, C.1
-
14
-
-
84879932140
-
Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean
-
Swan, B. K. et al. Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proc Natl Acad Sci USA 110, 11463–11468 (2013).
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, pp. 11463-11468
-
-
Swan, B.K.1
-
15
-
-
84871375552
-
Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis
-
Malmstrom, R. R. et al. Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis. ISME J 7, 184–198 (2013).
-
(2013)
ISME J
, vol.7
, pp. 184-198
-
-
Malmstrom, R.R.1
-
16
-
-
84899559579
-
Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus
-
Kashtan, N. et al. Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science 344, 416–420 (2014).
-
(2014)
Science
, vol.344
, pp. 416-420
-
-
Kashtan, N.1
-
17
-
-
85030660298
-
Fundamental differences in diversity and genomic population structure between Atlantic and Pacific Prochlorococcus
-
Kashtan, N. et al. Fundamental differences in diversity and genomic population structure between Atlantic and Pacific Prochlorococcus. ISME J 11, 1997–2011 (2017).
-
(2017)
ISME J
, vol.11
, pp. 1997-2011
-
-
Kashtan, N.1
-
18
-
-
0028981011
-
An estimate of global primary production in the ocean from satellite radiometer data
-
Longhurst, A., Sathyendranath, S., Platt, T. & Caverhill, C. An estimate of global primary production in the ocean from satellite radiometer data. Journal of Plankton Research 17, 1245–1271 (1995).
-
(1995)
Journal of Plankton Research
, vol.17
, pp. 1245-1271
-
-
Longhurst, A.1
Sathyendranath, S.2
Platt, T.3
Caverhill, C.4
-
19
-
-
84887033322
-
Dynamic biogeochemical provinces in the global ocean
-
Reygondeau, G. et al. Dynamic biogeochemical provinces in the global ocean. Global Biogeochemical Cycles 27, 1046–1058 (2013).
-
(2013)
Global Biogeochemical Cycles
, vol.27
, pp. 1046-1058
-
-
Reygondeau, G.1
-
20
-
-
84894048844
-
GEOTRACES: Changing the Way We Explore Ocean Chemistry
-
Anderson, R. F., Mawji, E., Cutter, G. A., Measures, C. I. & Jeandel, C. GEOTRACES: Changing the Way We Explore Ocean Chemistry. Oceanography 27, 50–61 (2014).
-
(2014)
Oceanography
, vol.27
, pp. 50-61
-
-
Anderson, R.F.1
Mawji, E.2
Cutter, G.A.3
Measures, C.I.4
Jeandel, C.5
-
21
-
-
85025449710
-
Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles
-
Stepanauskas, R. et al. Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles. Nat Commun 8, 84 (2017).
-
(2017)
Nat Commun
, vol.8
, pp. 84
-
-
Stepanauskas, R.1
-
22
-
-
84856186358
-
DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences
-
Wright, E. S., Yilmaz, L. S. & Noguera, D. R. DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences. Appl Environ Microbiol 78, 717–725 (2012).
-
(2012)
Appl Environ Microbiol
, vol.78
, pp. 717-725
-
-
Wright, E.S.1
Yilmaz, L.S.2
Noguera, D.R.3
-
23
-
-
84891787231
-
Ribosomal Database Project: Data and tools for high throughput rRNA analysis
-
Cole, J. R. et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 42, D633–D642 (2014).
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D633-D642
-
-
Cole, J.R.1
-
24
-
-
84891820094
-
IMG 4 version of the integrated microbial genomes comparative analysis system
-
Markowitz, V. M. et al. IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res 42, D560–D567 (2014).
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D560-D567
-
-
Markowitz, V.M.1
-
25
-
-
85016101571
-
IMG/M: Integrated genome and metagenome comparative data analysis system
-
Chen, I. A. et al. IMG/M: integrated genome and metagenome comparative data analysis system. Nucleic Acids Res 45, D507–D516 (2017).
-
(2017)
Nucleic Acids Res
, vol.45
, pp. D507-D516
-
-
Chen, I.A.1
-
26
-
-
84895751645
-
PhyloSift: Phylogenetic analysis of genomes and metagenomes
-
Darling, A. E. et al. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2, e243 (2014).
-
(2014)
Peerj
, vol.2
-
-
Darling, A.E.1
-
27
-
-
79952256999
-
Adaptive seeds tame genomic sequence comparison
-
Kiełbasa, S. M., Wan, R., Sato, K., Horton, P. & Frith, M. C. Adaptive seeds tame genomic sequence comparison. Genome Res 21, 487–493 (2011).
-
(2011)
Genome Res
, vol.21
, pp. 487-493
-
-
Kiełbasa, S.M.1
Wan, R.2
Sato, K.3
Horton, P.4
Frith, M.C.5
-
28
-
-
84885819796
-
Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups
-
Wu, D., Jospin, G. & Eisen, J. A. Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups. PLoS ONE 8, e77033 (2013).
-
(2013)
Plos ONE
, vol.8
-
-
Wu, D.1
Jospin, G.2
Eisen, J.A.3
-
29
-
-
80055082271
-
Accelerated Profile HMM Searches
-
Eddy, S. R. Accelerated Profile HMM Searches. PLoS Comput Biol 7, e1002195 (2011).
-
(2011)
Plos Comput Biol
, vol.7
-
-
Eddy, S.R.1
-
30
-
-
67650757433
-
TrimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses
-
Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1972-1973
-
-
Capella-Gutiérrez, S.1
Silla-Martínez, J.M.2
Gabaldón, T.3
-
31
-
-
33750403801
-
RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688–2690 (2006).
-
(2006)
Bioinformatics
, vol.22
, pp. 2688-2690
-
-
Stamatakis, A.1
-
32
-
-
50249100595
-
A rapid bootstrap algorithm for the RAxML Web servers
-
Stamatakis, A., Hoover, P. & Rougemont, J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 57, 758–771 (2008).
-
(2008)
Syst Biol
, vol.57
, pp. 758-771
-
-
Stamatakis, A.1
Hoover, P.2
Rougemont, J.3
-
33
-
-
77950820827
-
How many bootstrap replicates are necessary?
-
Pattengale, N. D., Alipour, M., Bininda-Emonds, O. R., Moret, B. M. & Stamatakis, A. How many bootstrap replicates are necessary? J Comput Biol 17, 337–354 (2010).
-
(2010)
J Comput Biol
, vol.17
, pp. 337-354
-
-
Pattengale, N.D.1
Alipour, M.2
Bininda-Emonds, O.R.3
Moret, B.M.4
Stamatakis, A.5
-
35
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
Enright, A. J., Van Dongen, S. & Ouzounis, C. A. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Research 30, 1575–1584 (2002).
-
(2002)
Nucleic Acids Research
, vol.30
, pp. 1575-1584
-
-
Enright, A.J.1
van Dongen, S.2
Ouzounis, C.A.3
-
36
-
-
84925021592
-
Fast and sensitive protein alignment using DIAMOND
-
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat Methods 12, 59–60 (2015).
-
(2015)
Nat Methods
, vol.12
, pp. 59-60
-
-
Buchfink, B.1
Xie, C.2
Huson, D.H.3
-
37
-
-
37749041470
-
Patterns and implications of gene gain and loss in the evolution of Prochlorococcus
-
Kettler, G. C. et al. Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet 3, e231 (2007).
-
(2007)
Plos Genet
, vol.3
-
-
Kettler, G.C.1
-
38
-
-
84883197576
-
Genetic diversity in cultured and wild marine cyano-myoviruses reveals phosphorus stress as a strong selective agent
-
Kelly, L., Ding, H., Huang, K. H., Osburne, M. S. & Chisholm, S. W. Genetic diversity in cultured and wild marine cyano-myoviruses reveals phosphorus stress as a strong selective agent. ISME J 7, 1827–1841 (2013).
-
(2013)
ISME J
, vol.7
, pp. 1827-1841
-
-
Kelly, L.1
Ding, H.2
Huang, K.H.3
Osburne, M.S.4
Chisholm, S.W.5
-
39
-
-
84927076433
-
Genomes of diverse isolates of the marine cyanobacterium. Prochlorococcus
-
Biller, S. J. et al. Genomes of diverse isolates of the marine cyanobacterium. Prochlorococcus. Sci Data 1, 140034 (2014).
-
(2014)
Sci Data
, vol.1
-
-
Biller, S.J.1
-
40
-
-
84965053766
-
Global genetic capacity for mixotrophy in marine picocyanobacteria
-
Yelton, A. P. et al. Global genetic capacity for mixotrophy in marine picocyanobacteria. ISME J 10, 2946–2957 (2016).
-
(2016)
ISME J
, vol.10
, pp. 2946-2957
-
-
Yelton, A.P.1
-
41
-
-
84905049901
-
Trimmomatic: A flexible trimmer for Illumina sequence data
-
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 2114-2120
-
-
Bolger, A.M.1
Lohse, M.2
Usadel, B.3
-
42
-
-
84860771820
-
SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing
-
Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).
-
(2012)
J. Comput. Biol.
, vol.19
, pp. 455-477
-
-
Bankevich, A.1
-
43
-
-
84937040910
-
CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
-
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25, 1043–1055 (2015).
-
(2015)
Genome Res
, vol.25
, pp. 1043-1055
-
-
Parks, D.H.1
Imelfort, M.2
Skennerton, C.T.3
Hugenholtz, P.4
Tyson, G.W.5
-
44
-
-
84872972322
-
The virocell concept and environmental microbiology
-
Forterre, P. The virocell concept and environmental microbiology. ISME J 7, 233–236 (2013).
-
(2013)
ISME J
, vol.7
, pp. 233-236
-
-
Forterre, P.1
|