-
1
-
-
51349125147
-
The virophage as a unique parasite of the giant mimivirus
-
La Scola, B. et al. The virophage as a unique parasite of the giant mimivirus. Nature 455, 100-104 (2008).
-
(2008)
Nature
, vol.455
, pp. 100-104
-
-
La Scola, B.1
-
3
-
-
84899701948
-
Zamilon, a novel virophage with mimiviridae host specificity
-
Gaia, M. et al. Zamilon, a novel virophage with mimiviridae host specificity. PLoS ONE 9, e94923 (2014).
-
(2014)
PLoS ONE
, vol.9
, pp. e94923
-
-
Gaia, M.1
-
4
-
-
84876186121
-
Broad spectrum of mimiviridae virophage allows its isolation using a mimivirus reporter
-
Gaia, M. et al. Broad spectrum of mimiviridae virophage allows its isolation using a mimivirus reporter. PLoS ONE 8, e61912 (2013).
-
(2013)
PLoS ONE
, vol.8
, pp. e61912
-
-
Gaia, M.1
-
5
-
-
79953806385
-
A virophage at the origin of large DNA transposons
-
Fischer, M. G. & Suttle, Ca. A virophage at the origin of large DNA transposons. Science 332, 231-234 (2011).
-
(2011)
Science
, vol.332
, pp. 231-234
-
-
Fischer, M.G.1
Suttle, Ca.2
-
6
-
-
84879516342
-
Genome of Phaeocystis globosa virus PgV-16 T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes
-
Santini, S. et al. Genome of Phaeocystis globosa virus PgV-16 T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes. Proc. Natl Acad. Sci. USA 110, 10800-10805 (2013).
-
(2013)
Proc. Natl Acad. Sci. USA
, vol.110
, pp. 10800-10805
-
-
Santini, S.1
-
7
-
-
84901235660
-
Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses
-
Krupovic, M., Bamford, D. H. & Koonin, E. V. Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses. Biol. Direct 9, 6 (2014).
-
(2014)
Biol. Direct
, vol.9
, pp. 6
-
-
Krupovic, M.1
Bamford, D.H.2
Koonin, E.V.3
-
8
-
-
80054809678
-
Viruses with more than 1,000 genes: Mamavirus, a new acanthamoeba polyphaga mimivirus strain, and reannotation of mimivirus genes
-
Colsonf, P. et al. Viruses with more than 1,000 genes: mamavirus, a new acanthamoeba polyphaga mimivirus strain, and reannotation of mimivirus genes. Genome Biol. Evol. 3, 737-742 (2011).
-
(2011)
Genome Biol. Evol
, vol.3
, pp. 737-742
-
-
Colsonf, P.1
-
9
-
-
84876156192
-
Related giant viruses in distant locations and different habitats: Acanthamoeba polyphaga moumouvirus represents a third lineage of the Mimiviridae that is close to the Megavirus lineage
-
Yoosuf, N. et al. Related giant viruses in distant locations and different habitats: Acanthamoeba polyphaga moumouvirus represents a third lineage of the Mimiviridae that is close to the Megavirus lineage. Genome Biol. Evol. 4, 1324-1330 (2012).
-
(2012)
Genome Biol. Evol
, vol.4
, pp. 1324-1330
-
-
Yoosuf, N.1
-
10
-
-
77953692396
-
Origin and evolution of eukaryotic large nucleo-cytoplasmic DNA viruses
-
Koonin, E. V. & Yutin, N. Origin and evolution of eukaryotic large nucleo-cytoplasmic DNA viruses. Intervirology 53, 284-292 (2010).
-
(2010)
Intervirology
, vol.53
, pp. 284-292
-
-
Koonin, E.V.1
Yutin, N.2
-
11
-
-
78650627880
-
Giant virus with a remarkable complement of genes infects marine zooplankton
-
Fischer, M. G., Allen, M. J., Wilson, W. H. & Suttle, C. A. Giant virus with a remarkable complement of genes infects marine zooplankton. Proc. Natl Acad. Sci. USA 107, 1-6 (2010).
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 1-6
-
-
Fischer, M.G.1
Allen, M.J.2
Wilson, W.H.3
Suttle, C.A.4
-
12
-
-
84923103071
-
Polintons: A hotbed of eukaryotic virus, transposon and plasmid evolution
-
Krupovic, M. & Koonin, E. V. Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution. Nat. Rev. Microbiol. 13, 105-115 (2015).
-
(2015)
Nat. Rev. Microbiol.
, vol.13
, pp. 105-115
-
-
Krupovic, M.1
Koonin, E.V.2
-
13
-
-
84878007916
-
Virophages, polintons, and transpovirons: A complex evolutionary network of diverse selfish genetic elements with different reproduction strategies
-
Yutin, N., Raoult, D. & Koonin, E. V. Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies. Virol. J. 10, 158 (2013).
-
(2013)
Virol. J.
, vol.10
, pp. 158
-
-
Yutin, N.1
Raoult, D.2
Koonin, E.V.3
-
14
-
-
84952861406
-
A classification system for virophages and satellite viruses
-
Krupovic, M., Kuhn, J. H. & Fischer, M. G. A classification system for virophages and satellite viruses. Arch. Virol. 161, 233-247 (2016).
-
(2016)
Arch. Virol.
, vol.161
, pp. 233-247
-
-
Krupovic, M.1
Kuhn, J.H.2
Fischer, M.G.3
-
15
-
-
79955006806
-
Virophage control of antarctic algal host-virus dynamics
-
Yau, S. et al. Virophage control of antarctic algal host-virus dynamics. Proc. Natl Acad. Sci. USA 108, 6163-6168 (2011).
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 6163-6168
-
-
Yau, S.1
-
16
-
-
84875777180
-
Diversity of virophages in metagenomic data sets
-
Zhou, J. et al. Diversity of virophages in metagenomic data sets. J. Virol. 87, 4225-4236 (2013).
-
(2013)
J. Virol.
, vol.87
, pp. 4225-4236
-
-
Zhou, J.1
-
17
-
-
84920842319
-
Three novel virophage genomes discovered from yellowstone lake metagenomes
-
Zhou, J. et al. Three novel virophage genomes discovered from yellowstone lake metagenomes. J. Virol. 89, 1278-1285 (2015).
-
(2015)
J. Virol.
, vol.89
, pp. 1278-1285
-
-
Zhou, J.1
-
18
-
-
84928556807
-
A new family of hybrid virophages from an animal gut metagenome
-
Yutin, N., Kapitonov, V. V. & Koonin, E. V. A new family of hybrid virophages from an animal gut metagenome. Biol. Direct 10, 19 (2015).
-
(2015)
Biol. Direct
, vol.10
, pp. 19
-
-
Yutin, N.1
Kapitonov, V.V.2
Koonin, E.V.3
-
19
-
-
84975885780
-
Metagenomics reveals a novel virophage population in a tibetan mountain lake
-
Oh, S., Yoo, D. & Liu, W.-T. Metagenomics reveals a novel virophage population in a tibetan mountain lake. Microbes Environ. 31, 163-177 (2016).
-
(2016)
Microbes Environ.
, vol.31
, pp. 163-177
-
-
Oh, S.1
Yoo, D.2
Liu, W.-T.3
-
20
-
-
84957976582
-
Novel virophages discovered in a freshwater lake in China
-
Gong, C. et al. Novel virophages discovered in a freshwater lake in China. Front. Microbiol 7, 5 (2016).
-
(2016)
Front. Microbiol
, vol.7
, pp. 5
-
-
Gong, C.1
-
21
-
-
79952369878
-
A guide to the natural history of freshwater lake bacteria
-
Newton, R. J., Jones, S. E., Eiler, A., McMahon, K. D. & Bertilsson, S. A guide to the natural history of freshwater lake bacteria. Microbiol. Mol. Biol. Rev. 75, (2011).
-
(2011)
Microbiol. Mol. Biol. Rev.
, vol.75
-
-
Newton, R.J.1
Jones, S.E.2
Eiler, A.3
McMahon, K.D.4
Bertilsson, S.5
-
22
-
-
84906944762
-
Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics
-
Eiler, A. et al. Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics. Environ. Microbiol. 16, 2682-2698 (2014).
-
(2014)
Environ. Microbiol.
, vol.16
, pp. 2682-2698
-
-
Eiler, A.1
-
23
-
-
84953439697
-
Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations
-
Bendall, M. L. et al. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations. ISME J. 10, 1-13 (2016).
-
(2016)
ISME J.
, vol.10
, pp. 1-13
-
-
Bendall, M.L.1
-
24
-
-
84940387197
-
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
-
Kang, D. D., Froula, J., Egan, R. & Wang, Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. Peer J. 3, e1165 (2015).
-
(2015)
Peer J.
, vol.3
, pp. e1165
-
-
Kang, D.D.1
Froula, J.2
Egan, R.3
Wang, Z.4
-
25
-
-
40849126681
-
Reticulate representation of evolutionary and functional relationships between phage genomes
-
Lima-Mendez, G., Van Helden, J., Toussaint, A. & Leplae, R. Reticulate representation of evolutionary and functional relationships between phage genomes. Mol. Biol. Evol. 25, 762-777 (2008).
-
(2008)
Mol. Biol. Evol.
, vol.25
, pp. 762-777
-
-
Lima-Mendez, G.1
Van Helden, J.2
Toussaint, A.3
Leplae, R.4
-
26
-
-
85016129519
-
Host genome integration and giant virus-induced reactivation of the virophage mavirus
-
Fischer, M. G. & Hackl, T. Host genome integration and giant virus-induced reactivation of the virophage mavirus. Nature 540, 288-291 (2016).
-
(2016)
Nature
, vol.540
, pp. 288-291
-
-
Fischer, M.G.1
Hackl, T.2
-
27
-
-
84946729375
-
A novel group of diverse Polinton-like viruses discovered by metagenome analysis
-
Yutin, N., Shevchenko, S., Kapitonov, V., Krupovic, M. & Koonin, E. V. A novel group of diverse Polinton-like viruses discovered by metagenome analysis. BMC Biol. 13, 95 (2015).
-
(2015)
BMC Biol.
, vol.13
, pp. 95
-
-
Yutin, N.1
Shevchenko, S.2
Kapitonov, V.3
Krupovic, M.4
Koonin, E.V.5
-
28
-
-
14044262978
-
Genomic insights that advance the species definition for prokaryotes
-
Konstantinidis, K. T. & Tiedje, J. M. Genomic insights that advance the species definition for prokaryotes. Proc. Natl Acad. Sci. USA 102, 2567-2572 (2005).
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 2567-2572
-
-
Konstantinidis, K.T.1
Tiedje, J.M.2
-
29
-
-
84996629629
-
Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer
-
Gregory, A. C. et al. Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer. BMC Genomics 17, 930 (2016).
-
(2016)
BMC Genomics
, vol.17
, pp. 930
-
-
Gregory, A.C.1
-
30
-
-
0030007094
-
Large-scale search for genes on which positive selection may operate
-
Endo, T., Ikeo, K. & Gojobori, T. Large-scale search for genes on which positive selection may operate. Mol. Biol. Evol. 13, 685-690 (1996).
-
(1996)
Mol. Biol. Evol.
, vol.13
, pp. 685-690
-
-
Endo, T.1
Ikeo, K.2
Gojobori, T.3
-
31
-
-
77957959525
-
GG11CH12-Nei the neutral theory of molecular evolution in the genomic era
-
Nei, M., Suzuki, Y. & Nozawa, M. GG11CH12-Nei the neutral theory of molecular evolution in the genomic era. Annu. Rev. Genomics Hum. Genet. 11, 265-289 (2010).
-
(2010)
Annu. Rev. Genomics Hum. Genet.
, vol.11
, pp. 265-289
-
-
Nei, M.1
Suzuki, Y.2
Nozawa, M.3
-
32
-
-
84871732071
-
Genomic variation landscape of the human gut microbiome
-
Schloissnig, S. et al. Genomic variation landscape of the human gut microbiome. Nature 493, 45-50 (2013).
-
(2013)
Nature
, vol.493
, pp. 45-50
-
-
Schloissnig, S.1
-
33
-
-
84868550621
-
Structure of Sputnik, a virophage, at 3.5-A resolution
-
Zhang, X. et al. Structure of Sputnik, a virophage, at 3.5-A resolution. Proc. Natl Acad. Sci. 109, 18431-18436 (2012).
-
(2012)
Proc. Natl Acad. Sci.
, vol.109
, pp. 18431-18436
-
-
Zhang, X.1
-
34
-
-
84929223635
-
Microcystin mcyA and mcyE gene abundances are not appropriate indicators of microcystin concentrations in lakes
-
Beversdorf, L. J., Chaston, S. D., Miller, T. R. & McMahon, K. D. Microcystin mcyA and mcyE gene abundances are not appropriate indicators of microcystin concentrations in lakes. PLoS ONE 10, e0125353 (2015).
-
(2015)
PLoS ONE
, vol.10
, pp. e0125353
-
-
Beversdorf, L.J.1
Chaston, S.D.2
Miller, T.R.3
McMahon, K.D.4
-
35
-
-
84963785126
-
Invasive species triggers a massive loss of ecosystem services through a trophic cascade
-
Walsh, J. R., Carpenter, S. R. & Vander Zanden, M. J. Invasive species triggers a massive loss of ecosystem services through a trophic cascade. Proc. Natl Acad. Sci. 113, 4081-4085 (2016).
-
(2016)
Proc. Natl Acad. Sci.
, vol.113
, pp. 4081-4085
-
-
Walsh, J.R.1
Carpenter, S.R.2
Vander Zanden, M.J.3
-
36
-
-
44849106473
-
Population dynamics and diversity of viruses, bacteria and phytoplankton in a shallow eutrophic lake
-
Tijdens, M. et al. Population dynamics and diversity of viruses, bacteria and phytoplankton in a shallow eutrophic lake. Microb. Ecol. 56, 29-42 (2008).
-
(2008)
Microb. Ecol.
, vol.56
, pp. 29-42
-
-
Tijdens, M.1
-
37
-
-
43549115658
-
Temporal variation in freshwater viral and bacterial community composition
-
Lymer, D. et al. Temporal variation in freshwater viral and bacterial community composition. Freshw. Biol. 53, 1163-1175 (2008).
-
(2008)
Freshw. Biol.
, vol.53
, pp. 1163-1175
-
-
Lymer, D.1
-
38
-
-
84899409844
-
Top-down controls on bacterial community structure: Microbial network analysis of bacteria, T4-like viruses and protists
-
Chow, C.-E. T., Kim, D. Y., Sachdeva, R., Caron, D. A. & Fuhrman, J. A. Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists. ISME J. 8, 816-829 (2014).
-
(2014)
ISME J.
, vol.8
, pp. 816-829
-
-
Chow, C.-E.T.1
Kim, D.Y.2
Sachdeva, R.3
Caron, D.A.4
Fuhrman, J.A.5
-
39
-
-
84866175103
-
Temporal dynamics and decay of putatively allochthonous and autochthonous viral genotypes in contrasting freshwater lakes
-
Hewson, I. et al. Temporal dynamics and decay of putatively allochthonous and autochthonous viral genotypes in contrasting freshwater lakes. Appl. Environ. Microbiol. 78, 6583-6591 (2012).
-
(2012)
Appl. Environ. Microbiol.
, vol.78
, pp. 6583-6591
-
-
Hewson, I.1
-
40
-
-
84866154398
-
Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly
-
Emerson, J. B. et al. Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly. Appl. Environ. Microbiol. 78, 6309-6320 (2012).
-
(2012)
Appl. Environ. Microbiol.
, vol.78
, pp. 6309-6320
-
-
Emerson, J.B.1
-
41
-
-
84961057176
-
Plankton networks driving carbon export in the oligotrophic ocean
-
Guidi, L. et al. Plankton networks driving carbon export in the oligotrophic ocean. Nature 532, 465-470 (2016).
-
(2016)
Nature
, vol.532
, pp. 465-470
-
-
Guidi, L.1
-
42
-
-
60549111634
-
WGCNA: An R package for weighted correlation network analysis
-
Langfelder, P. & Horvath, S. WGCNA: an R package for weighted correlation network analysis. BMC. Bioinformatics 9, 559 (2008).
-
(2008)
BMC. Bioinformatics
, vol.9
, pp. 559
-
-
Langfelder, P.1
Horvath, S.2
-
43
-
-
84875689946
-
Mimiviridae: Clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family
-
Yutin, N., Colson, P., Raoult, D. & Koonin, E. V. Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family. Virol. J. 10, 1 (2013).
-
(2013)
Virol. J.
, vol.10
, pp. 1
-
-
Yutin, N.1
Colson, P.2
Raoult, D.3
Koonin, E.V.4
-
44
-
-
84964907432
-
Diversity and dynamics of algal Megaviridae members during a harmful brown tide caused by the pelagophyte, Aureococcus anophagefferens
-
Moniruzzaman, M. et al. Diversity and dynamics of algal Megaviridae members during a harmful brown tide caused by the pelagophyte, Aureococcus anophagefferens. FEMS Microbiol. Ecol. 92, 1-10 (2016).
-
(2016)
FEMS Microbiol. Ecol.
, vol.92
, pp. 1-10
-
-
Moniruzzaman, M.1
-
45
-
-
84870506713
-
Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates
-
Xia, L. C. et al. Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates. BMC Syst. Biol. 5, S15 (2011).
-
(2011)
BMC Syst. Biol.
, vol.5
, pp. S15
-
-
Xia, L.C.1
-
46
-
-
84872568885
-
Efficient statistical significance approximation for local similarity analysis of high-throughput time series data
-
Xia, L. C., Ai, D., Cram, J., Fuhrman, J. A. & Sun, F. Efficient statistical significance approximation for local similarity analysis of high-throughput time series data. Bioinformatics 29, 230-237 (2013).
-
(2013)
Bioinformatics
, vol.29
, pp. 230-237
-
-
Xia, L.C.1
Ai, D.2
Cram, J.3
Fuhrman, J.A.4
Sun, F.5
-
47
-
-
77951857386
-
mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus
-
Legendre, M. et al. mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus. Genome Res. 20, 664-674 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 664-674
-
-
Legendre, M.1
-
48
-
-
84898684449
-
The virus of my virus is my friend: Ecological effects of virophage with alternative modes of coinfection
-
Taylor, B. P., Cortez, M. H. & Weitz, J. S. The virus of my virus is my friend: Ecological effects of virophage with alternative modes of coinfection. J. Theor. Biol. 354, 124-136 (2014).
-
(2014)
J. Theor. Biol.
, vol.354
, pp. 124-136
-
-
Taylor, B.P.1
Cortez, M.H.2
Weitz, J.S.3
-
49
-
-
70350459198
-
Recombination and microdiversity in coastal marine cyanophages
-
Marston, M. F. & Amrich, C. G. Recombination and microdiversity in coastal marine cyanophages. Environ. Microbiol. 11, 2893-2903 (2009).
-
(2009)
Environ. Microbiol.
, vol.11
, pp. 2893-2903
-
-
Marston, M.F.1
Amrich, C.G.2
-
50
-
-
84859499489
-
Population Genomics of Early Events in the Ecological Differentiation of Bacteria
-
Shapiro, B. J. et al. Population Genomics of Early Events in the Ecological Differentiation of Bacteria. Science 336, 48-51 (2012).
-
(2012)
Science
, vol.336
, pp. 48-51
-
-
Shapiro, B.J.1
-
51
-
-
84883147815
-
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes
-
Hingamp, P. et al. Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. ISME J. 7, 1678-1695 (2013).
-
(2013)
ISME J.
, vol.7
, pp. 1678-1695
-
-
Hingamp, P.1
-
52
-
-
80054913451
-
FLASH: Fast length adjustment of short reads to improve genome assemblies
-
Magoč, T. & Salzberg, S. L. FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957-2963 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 2957-2963
-
-
Magoč, T.1
Salzberg, S.L.2
-
53
-
-
84942887758
-
SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler
-
Luo, R. et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1, 18 (2012).
-
(2012)
Gigascience
, vol.1
, pp. 18
-
-
Luo, R.1
-
54
-
-
33947398002
-
Minimus: A fast, lightweight genome assembler
-
Sommer, D. D., Delcher, A. L., Salzberg, S. L. & Pop, M. Minimus: a fast, lightweight genome assembler. BMC Bioinformatics 8, 64 (2007).
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 64
-
-
Sommer, D.D.1
Delcher, A.L.2
Salzberg, S.L.3
Pop, M.4
-
55
-
-
84871396799
-
Ray Meta: Scalable de novo metagenome assembly and profiling
-
Boisvert, S., Raymond, F., Godzaridis, E., Laviolette, F. & Corbeil, J. Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biol. 13, (R122 (2012).
-
(2012)
Genome Biol.
, vol.13
, pp. R122
-
-
Boisvert, S.1
Raymond, F.2
Godzaridis, E.3
Laviolette, F.4
Corbeil, J.5
-
56
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012).
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
57
-
-
84976491899
-
The Enveomics Collection: A Toolbox for Specialized Analyses of Microbial Genomes and Metagenomes
-
Rodriguez-R, L. M. & Konstantinidis, K. T. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. Peer J. Prepr. 4, e1900v1. Preprint at https://doi.org/10.7287/peerj.preprints.1900v1 (2016).
-
(2016)
Peer J. Prepr.
, vol.4
, pp. e1900v1
-
-
Rodriguez-R, L.M.1
Konstantinidis, K.T.2
-
58
-
-
79953306448
-
Easyfig: A genome comparison visualizer
-
Sullivan, M. J., Petty, N. K. & Beatson, S. A. Easyfig: a genome comparison visualizer. Bioinformatics. 27, 1009-1010 (2011).
-
(2011)
Bioinformatics.
, vol.27
, pp. 1009-1010
-
-
Sullivan, M.J.1
Petty, N.K.2
Beatson, S.A.3
-
59
-
-
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 Res. 30, 1575-1584 (2002).
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
60
-
-
16344373015
-
Protein homology detection by HMM-HMM comparison
-
Söding, J. Protein homology detection by HMM-HMM comparison. Bioinformatics 21, 951-960 (2005).
-
(2005)
Bioinformatics
, vol.21
, pp. 951-960
-
-
Söding, J.1
-
61
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
-
62
-
-
4444221565
-
UCSF Chimera-a visualization system for exploratory research and analysis
-
Pettersen, E., Goddard, T. & Huang, C. UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605-1612 (2004).
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.1
Goddard, T.2
Huang, C.3
-
63
-
-
84899518211
-
InterProScan 5: Genome-scale protein function classification
-
Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236-1240 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 1236-1240
-
-
Jones, P.1
-
64
-
-
13244255415
-
MUSCLE: A multiple sequence alignment method with reduced time and space complexity
-
Edgar, R. C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5, 113 (2004).
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 113
-
-
Edgar, R.C.1
-
65
-
-
77949718257
-
FastTree 2-approximately maximum-likelihood trees for large alignments
-
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).
-
(2010)
PLoS ONE
, vol.5
, pp. e9490
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
66
-
-
85014768147
-
Interactive tree of life (iTOL) v3: An online tool for the display and annotation of phylogenetic and other trees
-
Letunic, I. & Bork, P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 44, W242-W245 (2016).
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. W242-W245
-
-
Letunic, I.1
Bork, P.2
-
67
-
-
0034849408
-
MRBAYES: Bayesian inference of phylogenetic trees
-
Huelsenbeck, J. P. & Ronquist, F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755 (2001).
-
(2001)
Bioinformatics
, vol.17
, pp. 754-755
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
-
68
-
-
65549160988
-
Identification of ribosomal RNA genes in metagenomic fragments
-
Huang, Y., Gilna, P. & Li, W. Identification of ribosomal RNA genes in metagenomic fragments. Bioinformatics 25, 1338-1340 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1338-1340
-
-
Huang, Y.1
Gilna, P.2
Li, W.3
-
69
-
-
84873739311
-
The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools
-
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590-D596 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D590-D596
-
-
Quast, C.1
-
70
-
-
84959106176
-
Correlation detection strategies in microbial data sets vary widely in sensitivity and precision
-
Weiss, S. et al. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. ISME J. 10, 1-13 (2016).
-
(2016)
ISME J.
, vol.10
, pp. 1-13
-
-
Weiss, S.1
-
71
-
-
0000286531
-
An ordination of upland forest communities of southern Wisconsin
-
Bray, J. & Crutis, J. An ordination of upland forest communities of southern Wisconsin. Ecol. Monogr. 27, 325-349 (1957).
-
(1957)
Ecol. Monogr.
, vol.27
, pp. 325-349
-
-
Bray, J.1
Crutis, J.2
-
72
-
-
23944458138
-
A general framework for weighted gene co-expression network analysis
-
Zhang, B. & Horvath, S. A general framework for weighted gene co-expression network analysis. Stat. Appl. Genet. Mol. Biol. 4, 1-43 (2005).
-
(2005)
Stat. Appl. Genet. Mol. Biol.
, vol.4
, pp. 1-43
-
-
Zhang, B.1
Horvath, S.2
-
73
-
-
0742305866
-
Network biology: Understanding the cell's functional organization
-
Barabasi, A.-L., Oltvai, Z. N. Z. N. & Barabási, A. Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5, 101-113 (2004).
-
(2004)
Nat. Rev. Genet.
, vol.5
, pp. 101-113
-
-
Barabasi, A.-L.1
Oltvai, Z.N.Z.N.2
Barabási, A.3
-
74
-
-
84867139755
-
Topological properties of Co-occurrence networks in published gene expression signatures
-
Muller, H. & Acquati, F. Topological properties of Co-occurrence networks in published gene expression signatures. Bioinform. Biol. Insights. 2, 203-213 (2008).
-
(2008)
Bioinform. Biol. Insights.
, vol.2
, pp. 203-213
-
-
Muller, H.1
Acquati, F.2
-
75
-
-
0034887573
-
Scale-free behavior in protein domain networks
-
Wuchty, S. Scale-free behavior in protein domain networks. Mol. Biol. Evol. 18, 1694-1702 (2001).
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 1694-1702
-
-
Wuchty, S.1
-
76
-
-
84861557467
-
Molecular ecological network analyses
-
Deng, Y. et al. Molecular ecological network analyses. BMC Bioinformatics 13, 1-20 (2012).
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 1-20
-
-
Deng, Y.1
-
77
-
-
84864579031
-
Microbial co-occurrence relationships in the human microbiome
-
Faust, K. et al. Microbial co-occurrence relationships in the human microbiome. PLoS Comput. Biol. 8, e1002606 (2012).
-
(2012)
PLoS Comput. Biol.
, vol.8
, pp. e1002606
-
-
Faust, K.1
-
78
-
-
84954459052
-
Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China
-
Ma, B. et al. Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China. ISME J. 10, 1891-1901 (2016).
-
(2016)
ISME J.
, vol.10
, pp. 1891-1901
-
-
Ma, B.1
-
79
-
-
67849122320
-
MEME Suite: Tools for motif discovery and searching
-
Bailey, T. L. et al. MEME Suite: tools for motif discovery and searching. Nucleic Acids Res. 37, 202-208 (2009).
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 202-208
-
-
Bailey, T.L.1
-
80
-
-
0034201441
-
The european molecular biology open software suite EMBOSS: The european molecular biology open software suite
-
Rice, P., Longden, I. & Bleasby, A. The european molecular biology open software suite EMBOSS: the european molecular biology open software suite. Trends Genet. 16, 2-3 (2000).
-
(2000)
Trends Genet.
, vol.16
, pp. 2-3
-
-
Rice, P.1
Longden, I.2
Bleasby, A.3
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