-
1
-
-
25144506135
-
Viruses in the sea
-
Suttle, C. A. Viruses in the sea. Nature 437, 356-361 (2005).
-
(2005)
Nature
, vol.437
, pp. 356-361
-
-
Suttle, C.A.1
-
2
-
-
83655191021
-
Marine viruses: Truth or dare
-
Breitbart, M. Marine viruses: truth or dare. Mar. Sci. 4, 425-448 (2012).
-
(2012)
Mar. Sci
, vol.4
, pp. 425-448
-
-
Breitbart, M.1
-
3
-
-
44849118073
-
Global-scale processes with a nanoscale drive: The role of marine viruses
-
Brussaard, C. P. D. et al. Global-scale processes with a nanoscale drive: the role of marine viruses. ISME J. 2, 575-578 (2008).
-
(2008)
ISME J
, vol.2
, pp. 575-578
-
-
Brussaard, C.P.D.1
-
4
-
-
34548792911
-
Marine viruses-major players in the global ecosystem
-
Suttle, C. A. Marine viruses-major players in the global ecosystem. Nat. Rev. Microbiol. 5, 801-812 (2007).
-
(2007)
Nat. Rev. Microbiol
, vol.5
, pp. 801-812
-
-
Suttle, C.A.1
-
5
-
-
0032858844
-
Viruses and nutrient cycles in the sea
-
Wilhelm, W. & Suttle, C. A. Viruses and nutrient cycles in the sea. Bioscience 49, 781-788 (1999).
-
(1999)
Bioscience
, vol.49
, pp. 781-788
-
-
Wilhelm, W.1
Suttle, C.A.2
-
6
-
-
70350180460
-
Explaining microbial population genomics through phage predation
-
Rodriguez-Valera, F. et al. Explaining microbial population genomics through phage predation. Nat. Rev. Microbiol. 7, 828-836 (2009).
-
(2009)
Nat. Rev. Microbiol
, vol.7
, pp. 828-836
-
-
Rodriguez-Valera, F.1
-
7
-
-
84855931244
-
Ocean time-series reveals recurring seasonal patterns of virioplankton dynamics in the northwestern Sargasso Sea
-
Parsons, R. J., Breitbart, M., Lomas, M. W. & Carlson, C. A. Ocean time-series reveals recurring seasonal patterns of virioplankton dynamics in the northwestern Sargasso Sea. ISME J. 6, 273-284 (2012).
-
(2012)
ISME J
, vol.6
, pp. 273-284
-
-
Parsons, R.J.1
Breitbart, M.2
Lomas, M.W.3
Carlson, C.A.4
-
8
-
-
0033826796
-
Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems
-
Thingstad, T. F. Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems. Limnol. Oceanogr. 45, 1320-1328 (2000).
-
(2000)
Limnol. Oceanogr
, vol.45
, pp. 1320-1328
-
-
Thingstad, T.F.1
-
9
-
-
0037398111
-
Viral influence on aquatic bacterial communities
-
Fuhrman, J. A. & Schwalbach, M. Viral influence on aquatic bacterial communities. Biol. Bull. 204, 192-195 (2003).
-
(2003)
Biol. Bull
, vol.204
, pp. 192-195
-
-
Fuhrman, J.A.1
Schwalbach, M.2
-
10
-
-
0002058563
-
Theoretical models for the control of bacterial growth rate, abundance, diversity and carbon demand
-
Thingstad, T. F. & Lignell, R. Theoretical models for the control of bacterial growth rate, abundance, diversity and carbon demand. Aquat. Microb. Ecol. 13, 19-27 (1997).
-
(1997)
Aquat. Microb. Ecol
, vol.13
, pp. 19-27
-
-
Thingstad, T.F.1
Lignell, R.2
-
11
-
-
84961583797
-
Lytic to temperate switching of viral communities
-
Knowles, B. et al. Lytic to temperate switching of viral communities. Nature 531, 466-470 (2016).
-
(2016)
Nature
, vol.531
, pp. 466-470
-
-
Knowles, B.1
-
12
-
-
85018237311
-
Re-examination of the relationship between marine virus and microbial cell abundances
-
Wigington, C. H. et al. Re-examination of the relationship between marine virus and microbial cell abundances. Nat. Microbiol. 1, 15024 (2016).
-
(2016)
Nat. Microbiol
, vol.1
, pp. 15024
-
-
Wigington, C.H.1
-
13
-
-
85021813111
-
Piggyback-the-Winner in host-associated microbial communities
-
Silveira, C. B. & Rohwer, F. L. Piggyback-the-Winner in host-associated microbial communities. npj Biofilms Microbiomes 2, 1-5 (2016).
-
(2016)
Npj Biofilms Microbiomes
, vol.2
, pp. 1-5
-
-
Silveira, C.B.1
Rohwer, F.L.2
-
14
-
-
84887380143
-
Metabolic reprogramming by viruses in the sunlit and dark ocean
-
Hurwitz, B. L., Hallam, S. J. & Sullivan, M. B. Metabolic reprogramming by viruses in the sunlit and dark ocean. Genome Biol. 14, R123 (2013).
-
(2013)
Genome Biol
, vol.14
, pp. R123
-
-
Hurwitz, B.L.1
Hallam, S.J.2
Sullivan, M.B.3
-
15
-
-
80053624997
-
Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism
-
Thompson, L. R. et al. Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism. Proc. Natl Acad. Sci. USA 108, E757-E764 (2011).
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. E757-E764
-
-
Thompson, L.R.1
-
16
-
-
79959588019
-
Comparative metagenomics of microbial traits within oceanic viral communities
-
Sharon, I. et al. Comparative metagenomics of microbial traits within oceanic viral communities. ISME J. 5, 1178-1190 (2011).
-
(2011)
ISME J
, vol.5
, pp. 1178-1190
-
-
Sharon, I.1
-
17
-
-
85000501937
-
Viruses inhibit CO2 fixation in the most abundant phototrophs on earth
-
Puxty, R. J. et al. Viruses inhibit CO2 fixation in the most abundant phototrophs on earth. Curr. Biol. 26, 1585-1589 (2016).
-
(2016)
Curr. Biol
, vol.26
, pp. 1585-1589
-
-
Puxty, R.J.1
-
18
-
-
84962854177
-
Viral metabolic reprogramming in marine ecosystems
-
Hurwitz, B. L. & U'Ren, J. M. Viral metabolic reprogramming in marine ecosystems. Curr. Opin. Microbiol. 31, 161-168 (2016).
-
(2016)
Curr. Opin. Microbiol
, vol.31
, pp. 161-168
-
-
Hurwitz, B.L.1
U'Ren, J.M.2
-
19
-
-
84867985452
-
Oxygen minimum zones harbour novel viral communities with low diversity
-
Cassman, N. et al. Oxygen minimum zones harbour novel viral communities with low diversity. Env. Microbiol. 14, 3043-3065 (2012).
-
(2012)
Env. Microbiol
, vol.14
, pp. 3043-3065
-
-
Cassman, N.1
-
20
-
-
85046025173
-
The marine viromes of four oceanic regions
-
Angly, F. E. et al. The marine viromes of four oceanic regions. PLoS Biol. 4, e368 (2006).
-
(2006)
PLoS Biol
, vol.4
, pp. e368
-
-
Angly, F.E.1
-
21
-
-
84943327698
-
Insights into the microbial and viral dynamics of a coastal downwelling-upwelling transition
-
Gregoracci, G. B., Dos Santos Soares, A. C., Miranda, M. D., Coutinho, R. & Thompson, F. L. Insights into the microbial and viral dynamics of a coastal downwelling-upwelling transition. PLoS ONE 10, 1-14 (2015).
-
(2015)
PLoS ONE
, vol.10
, pp. 1-14
-
-
Gregoracci, G.B.1
Dos Santos Soares, A.C.2
Miranda, M.D.3
Coutinho, R.4
Thompson, F.L.5
-
22
-
-
84961580368
-
Seasonal time bombs: Dominant temperate viruses affect Southern Ocean microbial dynamics
-
Brum, J. R., Hurwitz, B. L., Schofield, O., Ducklow, H. W. & Sullivan, M. B. Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics. ISME J. 10, 1-13 (2015).
-
(2015)
ISME J
, vol.10
, pp. 1-13
-
-
Brum, J.R.1
Hurwitz, B.L.2
Schofield, O.3
Ducklow, H.W.4
Sullivan, M.B.5
-
23
-
-
84903527526
-
Comparison of deep-water viromes from the Atlantic Ocean and the Mediterranean Sea
-
Winter, C., Garcia, J. A. L., Weinbauer, M. G., DuBow, M. S. & Herndl, G. J. Comparison of deep-water viromes from the Atlantic Ocean and the Mediterranean Sea. PLoS ONE 9, 1-8 (2014).
-
(2014)
PLoS ONE
, vol.9
, pp. 1-8
-
-
Winter, C.1
Garcia, J.A.L.2
Weinbauer, M.G.3
DuBow, M.S.4
Herndl, G.J.5
-
24
-
-
84929992013
-
Structure and function of the global ocean microbiome
-
Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1-10 (2015).
-
(2015)
Science
, vol.348
, pp. 1-10
-
-
Sunagawa, S.1
-
25
-
-
84927540709
-
Metagenomic ventures into outer sequence space
-
Dutilh, B. E. Metagenomic ventures into outer sequence space. Bacteriophage 7081, 3-5 (2014).
-
(2014)
Bacteriophage
, vol.7081
, pp. 3-5
-
-
Dutilh, B.E.1
-
26
-
-
84929998256
-
Patterns and ecological drivers of ocean viral communities
-
Brum, J. R. et al. Patterns and ecological drivers of ocean viral communities. Science 348, 1261498 (2015).
-
(2015)
Science
, vol.348
, pp. 1261498
-
-
Brum, J.R.1
-
27
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65 (2010).
-
(2010)
Nature
, vol.464
, pp. 59-65
-
-
Qin, J.1
-
28
-
-
84942883364
-
Gut DNA viromes of Malawian twins discordant for severe acute malnutrition
-
Reyes, A. et al. Gut DNA viromes of Malawian twins discordant for severe acute malnutrition. Proc. Natl Acad. Sci. USA 112, 11941-11946 (2015).
-
(2015)
Proc. Natl Acad. Sci. USA
, vol.112
, pp. 11941-11946
-
-
Reyes, A.1
-
29
-
-
84905041075
-
A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
-
Dutilh, B. E. et al. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat. Commun. 5, 1-11 (2014).
-
(2014)
Nat. Commun
, vol.5
, pp. 1-11
-
-
Dutilh, B.E.1
-
30
-
-
84880652104
-
Rapid evolution of the human gut virome
-
Minot, S. & Bryson, A. Rapid evolution of the human gut virome. Proc. Natl Acad. Sci. USA 110, 12450-12455 (2013).
-
(2013)
Proc. Natl Acad. Sci. USA
, vol.110
, pp. 12450-12455
-
-
Minot, S.1
Bryson, A.2
-
31
-
-
84892736640
-
Expanding the marine virosphere using metagenomics
-
Mizuno, C. M., Rodriguez-Valera, F., Kimes, N. E. & Ghai, R. Expanding the marine virosphere using metagenomics. PLoS Genet. 9, e1003987 (2013).
-
(2013)
PLoS Genet
, vol.9
, pp. e1003987
-
-
Mizuno, C.M.1
Rodriguez-Valera, F.2
Kimes, N.E.3
Ghai, R.4
-
32
-
-
84939526110
-
Viral dark matter and virus-host interactions resolved from publicly available microbial genomes
-
Roux, S., Hallam, S. J., Woyke, T. & Sullivan, M. B. Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. Elife 4, e08490 (2015).
-
(2015)
Elife
, vol.4
, pp. e08490
-
-
Roux, S.1
Hallam, S.J.2
Woyke, T.3
Sullivan, M.B.4
-
33
-
-
84865733148
-
Inferring correlation networks from genomic survey data
-
Friedman, J. & Alm, E. J. Inferring correlation networks from genomic survey data. PLoS Comput. Biol. 8, e1002687 (2012).
-
(2012)
PLoS Comput. Biol
, vol.8
, pp. e1002687
-
-
Friedman, J.1
Alm, E.J.2
-
34
-
-
84877278609
-
Sequencing platform and library preparation choices impact viral metagenomes
-
Solonenko, S. A. et al. Sequencing platform and library preparation choices impact viral metagenomes. BMC Genomics 14, 320 (2013).
-
(2013)
BMC Genomics
, vol.14
, pp. 320
-
-
Solonenko, S.A.1
-
35
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 57, 289-300 (1995).
-
(1995)
J. R. Stat. Soc. Ser. B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
36
-
-
84857371051
-
Metagenomics and future perspectives in virus discovery
-
Mokili, J. L., Rohwer, F. & Dutilh, B. E. Metagenomics and future perspectives in virus discovery. Curr. Opin. Virol. 2, 63-77 (2012).
-
(2012)
Curr. Opin. Virol
, vol.2
, pp. 63-77
-
-
Mokili, J.L.1
Rohwer, F.2
Dutilh, B.E.3
-
37
-
-
84945491851
-
Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton
-
Labonté, J. M. et al. Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton. ISME J. 9, 2386-2399 (2015).
-
(2015)
ISME J
, vol.9
, pp. 2386-2399
-
-
Labonté, J.M.1
-
38
-
-
84945191979
-
Niche distribution and influence of environmental parameters in marine microbial communities: A systematic review
-
Coutinho, F. H. et al. Niche distribution and influence of environmental parameters in marine microbial communities: A systematic review. PeerJ 3, e1008 (2015).
-
(2015)
PeerJ
, vol.3
, pp. e1008
-
-
Coutinho, F.H.1
-
39
-
-
84864579031
-
Microbial co-occurence relationships in the human microbiome
-
Faust, K. et al. Microbial co-occurence relationships in the human microbiome. PLoS Comput. Biol. 8, e1002606 (2012).
-
(2012)
PLoS Comput. Biol
, vol.8
, pp. e1002606
-
-
Faust, K.1
-
40
-
-
78649732106
-
The taxonomic and functional diversity of microbes at a temperate coastal site: A 'multi-omic' study of seasonal and diel temporal variation
-
Gilbert, J. A. et al. The taxonomic and functional diversity of microbes at a temperate coastal site: A 'multi-omic' study of seasonal and diel temporal variation. PLoS ONE 5, e15545 (2010).
-
(2010)
PLoS ONE
, vol.5
, pp. e15545
-
-
Gilbert, J.A.1
-
41
-
-
20144389217
-
Genetic diversity of marine Synechococcus and co-occurring cyanophage communities: Evidence for viral control of phytoplankton
-
Fuller, N. J. et al. Genetic diversity of marine Synechococcus and co-occurring cyanophage communities: evidence for viral control of phytoplankton. Environ. Microbiol. 7, 499-508 (2005).
-
(2005)
Environ. Microbiol
, vol.7
, pp. 499-508
-
-
Fuller, N.J.1
-
42
-
-
33746102191
-
Seasonal variations in virus-host populations in Norwegian coastal waters: Focusing on the cyanophage community infecting marine Synechococcus spp
-
Sandaa, R. A. & Larsen, A. Seasonal variations in virus-host populations in Norwegian coastal waters: focusing on the cyanophage community infecting marine Synechococcus spp. Appl. Environ. Microbiol. 72, 4610-4618 (2006).
-
(2006)
Appl. Environ. Microbiol
, vol.72
, pp. 4610-4618
-
-
Sandaa, R.A.1
Larsen, A.2
-
43
-
-
13444255983
-
Seasonal epidemics of cholera inversely correlate with the prevalence of environmental cholera phages
-
Faruque, S. M. et al. Seasonal epidemics of cholera inversely correlate with the prevalence of environmental cholera phages. Proc. Natl Acad. Sci. USA 102, 1702-1707 (2005).
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 1702-1707
-
-
Faruque, S.M.1
-
44
-
-
84880922997
-
Short-term observations of marine bacterial and viral communities: Patterns, connections and resilience
-
Needham, D. M. et al. Short-term observations of marine bacterial and viral communities: patterns, connections and resilience. ISME J. 7, 1274-1285 (2013).
-
(2013)
ISME J
, vol.7
, pp. 1274-1285
-
-
Needham, D.M.1
-
45
-
-
84963785503
-
Computational approaches to predict virus-host relationships
-
Edwards, R. A., McNair, K., Faust, K., Raes, J. & Dutilh, B. E. Computational approaches to predict virus-host relationships. FEMS Microbiol. Rev. 40, 258-272 (2015).
-
(2015)
FEMS Microbiol. Rev
, vol.40
, pp. 258-272
-
-
Edwards, R.A.1
McNair, K.2
Faust, K.3
Raes, J.4
Dutilh, B.E.5
-
46
-
-
84961711517
-
Genetic and life-history traits associated with the distribution of prophages in bacteria
-
Touchon, M., Bernheim, A. & Rocha, E. P. Genetic and life-history traits associated with the distribution of prophages in bacteria. ISME J. 10, 2744-2754 (2016).
-
(2016)
ISME J
, vol.10
, pp. 2744-2754
-
-
Touchon, M.1
Bernheim, A.2
Rocha, E.P.3
-
47
-
-
70349458100
-
The genomic basis of trophic strategy in marine bacteria
-
Lauro, F. M. et al. The genomic basis of trophic strategy in marine bacteria. Proc. Natl Acad. Sci. USA 106, 15527-15533 (2009).
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 15527-15533
-
-
Lauro, F.M.1
-
48
-
-
84906809090
-
Factors affecting virus dynamics and microbial host-virus interactions in marine environments
-
Mojica, K. D. A. & Brussaard, C. P. D. Factors affecting virus dynamics and microbial host-virus interactions in marine environments. FEMS Microbiol. Ecol. 89, 495-515 (2014).
-
(2014)
FEMS Microbiol. Ecol
, vol.89
, pp. 495-515
-
-
Mojica, K.D.A.1
Brussaard, C.P.D.2
-
49
-
-
84942645259
-
Bacterial diversity and community composition from seasurface to subseafloor
-
Walsh, E. A. et al. Bacterial diversity and community composition from seasurface to subseafloor. ISME J. 10, 979-989 (2015).
-
(2015)
ISME J
, vol.10
, pp. 979-989
-
-
Walsh, E.A.1
-
50
-
-
31544483932
-
Community genomics among stratified microbial assemblages in the ocean's interior
-
Delong, E. F. et al. Community genomics among stratified microbial assemblages in the ocean's interior. Science 311, 496-503 (2006).
-
(2006)
Science
, vol.311
, pp. 496-503
-
-
Delong, E.F.1
-
51
-
-
84925276427
-
Hadal biosphere: Insight into the microbial ecosystem in the deepest ocean on Earth
-
Nunoura, T. et al. Hadal biosphere: insight into the microbial ecosystem in the deepest ocean on Earth. Proc. Natl Acad. Sci. USA 112, E1230-E1236 (2015).
-
(2015)
Proc. Natl Acad. Sci. USA
, vol.112
, pp. E1230-E1236
-
-
Nunoura, T.1
-
52
-
-
80051800391
-
Marine viruses and global climate change
-
Danovaro, R. et al. Marine viruses and global climate change. FEMS Microbiol. Rev. 35, 993-1034 (2011).
-
(2011)
FEMS Microbiol. Rev
, vol.35
, pp. 993-1034
-
-
Danovaro, R.1
-
53
-
-
34249107281
-
Effects of increased temperature and CO2 on photosynthesis, growth, and elemental ratios in marine Synechococcus and Prochlorococcus (Cyanobacteria
-
Fu, F.-X., Warner, M. E., Zhang, Y., Feng, Y. & Hutchins, D. A. Effects of increased temperature and CO2 on photosynthesis, growth, and elemental ratios in marine Synechococcus and Prochlorococcus (Cyanobacteria). J. Phycol. 43, 485-496 (2007).
-
(2007)
J. Phycol
, vol.43
, pp. 485-496
-
-
Fu, F.-X.1
Warner, M.E.2
Zhang, Y.3
Feng, Y.4
Hutchins, D.A.5
-
54
-
-
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
-
55
-
-
84921568760
-
Depth-stratified functional and taxonomic niche specialization in the 'core' and 'flexible' Pacific Ocean Virome
-
Hurwitz, B. L., Brum, J. R. & Sullivan, M. B. Depth-stratified functional and taxonomic niche specialization in the 'core' and 'flexible' Pacific Ocean Virome. ISME J. 9, 472-484 (2015).
-
(2015)
ISME J
, vol.9
, pp. 472-484
-
-
Hurwitz, B.L.1
Brum, J.R.2
Sullivan, M.B.3
-
56
-
-
84904624132
-
Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses
-
Hurwitz, B. L.,Westveld, A. H., Brum, J. R. & Sullivan, M. B. Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses. Proc. Natl Acad. Sci. USA 111, 10714-10719 (2014).
-
(2014)
Proc. Natl Acad. Sci. USA
, vol.111
, pp. 10714-10719
-
-
Hurwitz, B.L.1
Westveld, A.H.2
Brum, J.R.3
Sullivan, M.B.4
-
57
-
-
84979655916
-
Virocell metabolism: Metabolic innovations during host-virus interactions in the ocean
-
Rosenwasser, S., Ziv, C., Creveld, S. G., van & Vardi, A. Virocell metabolism: metabolic innovations during host-virus interactions in the ocean. Trends Microbiol. 24, 821-832 (2016).
-
(2016)
Trends Microbiol
, vol.24
, pp. 821-832
-
-
Rosenwasser, S.1
Ziv, C.2
Creveld, S.G.3
Van4
Vardi, A.5
-
58
-
-
84984985848
-
Uncovering Earth's virome
-
Paez-Espino, D. et al. Uncovering Earth's virome. Nature 536, 425-430 (2016).
-
(2016)
Nature
, vol.536
, pp. 425-430
-
-
Paez-Espino, D.1
-
59
-
-
85021815678
-
Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses
-
Roux, S. et al. Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses. Nature 537, 589-693 (2016).
-
(2016)
Nature
, vol.537
, pp. 589-693
-
-
Roux, S.1
-
60
-
-
80054911634
-
Metavir: A web server dedicated to virome analysis
-
Roux, S. et al. Metavir: A web server dedicated to virome analysis. Bioinformatics 27, 3074-3075 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 3074-3075
-
-
Roux, S.1
-
61
-
-
84924091005
-
Evaluation of viral genome assembly and diversity estimation in deep metagenomes
-
Aguirre de Cárcer, D. et al. Evaluation of viral genome assembly and diversity estimation in deep metagenomes. BMC Genomics 15, 989 (2014).
-
(2014)
BMC Genomics
, vol.15
, pp. 989
-
-
Aguirre De Cárcer, D.1
-
62
-
-
84874194145
-
Sequence assembly demystified
-
Nagarajan, N. & Pop, M. Sequence assembly demystified. Nat. Rev. Genet. 14, 157-167 (2013).
-
(2013)
Nat. Rev. Genet
, vol.14
, pp. 157-167
-
-
Nagarajan, N.1
Pop, M.2
-
63
-
-
84861760530
-
IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
-
Peng, Y., Leung, H. C. M., Yiu, S. M. & Chin, F. Y. L. IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28, 1420-1428 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 1420-1428
-
-
Peng, Y.1
Leung, H.C.M.2
Yiu, S.M.3
Chin, F.Y.L.4
-
64
-
-
77952299957
-
Prodigal: Prokaryotic gene recognition and translation initiation site identification
-
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 119
-
-
Hyatt, D.1
-
65
-
-
84901417347
-
Prokka: Rapid prokaryotic genome annotation
-
Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068-2069 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 2068-2069
-
-
Seemann, T.1
-
66
-
-
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
-
67
-
-
84953298206
-
Taxonomy of prokaryotic viruses: Update from the ICTV bacterial and archaeal viruses subcommittee
-
Krupovic, M. et al. Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee. Arch. Virol. 161, 1095-1099 (2016).
-
(2016)
Arch. Virol
, vol.161
, pp. 1095-1099
-
-
Krupovic, M.1
-
68
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990).
-
(1990)
J. Mol. Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
69
-
-
0030807655
-
BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data
-
Gascuel, O. BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14, 685-695 (1997).
-
(1997)
Mol. Biol. Evol
, vol.14
, pp. 685-695
-
-
Gascuel, O.1
-
70
-
-
33845873289
-
Interactive Tree of Life (iTOL): An online tool for phylogenetic tree display and annotation
-
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL): An online tool for phylogenetic tree display and annotation. Bioinformatics 23, 127-128 (2007).
-
(2007)
Bioinformatics
, vol.23
, pp. 127-128
-
-
Letunic, I.1
Bork, P.2
-
71
-
-
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
-
72
-
-
84856659328
-
Untangling genomes from metagenomes: Revealing an uncultured class of marine Euryarchaeota
-
Iverson, V. et al. Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science 335, 587-590 (2012).
-
(2012)
Science
, vol.335
, pp. 587-590
-
-
Iverson, V.1
-
73
-
-
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, 1669-1681 (2016).
-
(2016)
ISME J
, vol.10
, pp. 1669-1681
-
-
Weiss, S.1
-
74
-
-
84869054051
-
A travel guide to Cytoscape plugins
-
Saito, R. et al. A travel guide to Cytoscape plugins. Nat. Methods 9, 1069-1076 (2012).
-
(2012)
Nat. Methods
, vol.9
, pp. 1069-1076
-
-
Saito, R.1
-
75
-
-
84879014174
-
CRISPRTarget
-
Biswas, A., Gagnon, J. N., Brouns, S. J. J., Fineran, P. C. & Brown, C. M. CRISPRTarget. RNA Biol. 10, 817-827 (2013).
-
(2013)
RNA Biol
, vol.10
, pp. 817-827
-
-
Biswas, A.1
Gagnon, J.N.2
Brouns, S.J.J.3
Fineran, P.C.4
Brown, C.M.5
-
76
-
-
84922643947
-
Microbial community diversity and physical-chemical features of the Southwestern Atlantic Ocean
-
Alves Junior, N. et al. Microbial community diversity and physical-chemical features of the Southwestern Atlantic Ocean. Arch. Microbiol. 197, 165-179 (2014).
-
(2014)
Arch. Microbiol
, vol.197
, pp. 165-179
-
-
Alves, Jr.N.1
-
77
-
-
84903837939
-
FOCUS: An alignment-free model to identify organisms in metagenomes using nonnegative least squares
-
Silva, G. G. Z., Cuevas, D. a, Dutilh, B. E. & Edwards, R. A. FOCUS: An alignment-free model to identify organisms in metagenomes using nonnegative least squares. PeerJ 2, e425 (2014).
-
(2014)
PeerJ
, vol.2
, pp. e425
-
-
Silva, G.G.Z.1
Cuevas, D.2
Dutilh, B.E.3
Edwards, R.A.4
|