-
1
-
-
25144506135
-
Viruses in the sea
-
10.1038/nature04160, 16163346
-
Suttle CA. Viruses in the sea. Nature 2005, 437:356-361. 10.1038/nature04160, 16163346.
-
(2005)
Nature
, vol.437
, pp. 356-361
-
-
Suttle, C.A.1
-
2
-
-
34548792911
-
Marine viruses-major players in the global ecosystem
-
10.1038/nrmicro1750, 17853907
-
Suttle CA. Marine viruses-major players in the global ecosystem. Nat Rev Microbiol 2007, 5:801-812. 10.1038/nrmicro1750, 17853907.
-
(2007)
Nat Rev Microbiol
, vol.5
, pp. 801-812
-
-
Suttle, C.A.1
-
3
-
-
66149151286
-
Viruses manipulate the marine environment
-
10.1038/nature08060, 19444207
-
Rohwer F, Thurber RV. Viruses manipulate the marine environment. Nature 2009, 459:207-212. 10.1038/nature08060, 19444207.
-
(2009)
Nature
, vol.459
, pp. 207-212
-
-
Rohwer, F.1
Thurber, R.V.2
-
4
-
-
80053377130
-
Bacteriophages and their Genomes
-
10.1016/j.coviro.2011.06.009, 3199584, 22034588
-
Hatfull GF, Hendrix RW. Bacteriophages and their Genomes. Curr Opin Virol 2011, 1:298-303. 10.1016/j.coviro.2011.06.009, 3199584, 22034588.
-
(2011)
Curr Opin Virol
, vol.1
, pp. 298-303
-
-
Hatfull, G.F.1
Hendrix, R.W.2
-
5
-
-
84858263195
-
Assessing the diversity and specificity of two freshwater viral communities through metagenomics
-
10.1371/journal.pone.0033641, 3303852, 22432038
-
Roux S, Enault F, Robin A, Ravet V, Personnic S, Theil S, Colombet J, Sime-Ngando T, Debroas D. Assessing the diversity and specificity of two freshwater viral communities through metagenomics. PLoS One 2012, 7:e33641. 10.1371/journal.pone.0033641, 3303852, 22432038.
-
(2012)
PLoS One
, vol.7
-
-
Roux, S.1
Enault, F.2
Robin, A.3
Ravet, V.4
Personnic, S.5
Theil, S.6
Colombet, J.7
Sime-Ngando, T.8
Debroas, D.9
-
6
-
-
19144366140
-
Viral metagenomics
-
10.1038/nrmicro1163, 15886693
-
Edwards RA, Rohwer F. Viral metagenomics. Nat Rev Microbiol 2005, 3:504-510. 10.1038/nrmicro1163, 15886693.
-
(2005)
Nat Rev Microbiol
, vol.3
, pp. 504-510
-
-
Edwards, R.A.1
Rohwer, F.2
-
7
-
-
84870665503
-
Ocean viruses: rigorously evaluating the metagenomic sample-to-sequence pipeline
-
10.1016/j.virol.2012.09.036, 23084423
-
Duhaime MB, Sullivan MB. Ocean viruses: rigorously evaluating the metagenomic sample-to-sequence pipeline. Virology 2012, 434:181-186. 10.1016/j.virol.2012.09.036, 23084423.
-
(2012)
Virology
, vol.434
, pp. 181-186
-
-
Duhaime, M.B.1
Sullivan, M.B.2
-
8
-
-
64749109065
-
Laboratory procedures to generate viral metagenomes
-
10.1038/nprot.2009.10, 19300441
-
Vega Thurber R, Haynes M, Breitbart M, Wegley L, Rohwer F. Laboratory procedures to generate viral metagenomes. Nat Protoc 2009, 4:470-483. 10.1038/nprot.2009.10, 19300441.
-
(2009)
Nat Protoc
, vol.4
, pp. 470-483
-
-
Vega Thurber, R.1
Haynes, M.2
Breitbart, M.3
Wegley, L.4
Rohwer, F.5
-
9
-
-
84876330266
-
From deep sequencing to viral tagging: Recent advances in viral metagenomics
-
10.1002/bies.201200174, 23450659
-
Willner D, Hugenholtz P. From deep sequencing to viral tagging: Recent advances in viral metagenomics. BioEssays 2013, 35:436-442. 10.1002/bies.201200174, 23450659.
-
(2013)
BioEssays
, vol.35
, pp. 436-442
-
-
Willner, D.1
Hugenholtz, P.2
-
10
-
-
84872922002
-
Viruses in the desert: a metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara
-
10.1038/ismej.2012.101, 3554411, 23038177
-
Fancello L, Trape S, Robert C, Boyer M, Popgeorgiev N, Raoult D, Desnues C. Viruses in the desert: a metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara. ISME J 2013, 7:359-369. 10.1038/ismej.2012.101, 3554411, 23038177.
-
(2013)
ISME J
, vol.7
, pp. 359-369
-
-
Fancello, L.1
Trape, S.2
Robert, C.3
Boyer, M.4
Popgeorgiev, N.5
Raoult, D.6
Desnues, C.7
-
11
-
-
84864389184
-
Metagenomic characterization of airborne viral DNA diversity in the near-surface atmosphere
-
10.1128/JVI.00293-12, 3421691, 22623790
-
Whon TW, Kim M-S, Roh SW, Shin N-R, Lee H-W, Bae J-W. Metagenomic characterization of airborne viral DNA diversity in the near-surface atmosphere. J Virol 2012, 86:8221-8331. 10.1128/JVI.00293-12, 3421691, 22623790.
-
(2012)
J Virol
, vol.86
, pp. 8221-8331
-
-
Whon, T.W.1
Kim, M.-S.2
Roh, S.W.3
Shin, N.-R.4
Lee, H.-W.5
Bae, J.-W.6
-
12
-
-
72949103741
-
New dimensions of the virus world discovered through metagenomics
-
10.1016/j.tim.2009.11.003, 3293453, 19942437
-
Kristensen DM, Mushegian AR, Dolja VV, Koonin EV. New dimensions of the virus world discovered through metagenomics. Trends Microbiol 2010, 18:11-19. 10.1016/j.tim.2009.11.003, 3293453, 19942437.
-
(2010)
Trends Microbiol
, vol.18
, pp. 11-19
-
-
Kristensen, D.M.1
Mushegian, A.R.2
Dolja, V.V.3
Koonin, E.V.4
-
13
-
-
40449115382
-
A new arenavirus in a cluster of fatal transplant-associated diseases
-
10.1056/NEJMoa073785, 18256387
-
Palacios G, Druce J, Du L, Tran T, Birch C, Briese T, Conlan S, Quan P, Hui J, Marshall J, Simons JF, Egholm M, Paddock CD, Shieh W, Goldsmith CS, Zaki SR, Catton M, Lipkin WI. A new arenavirus in a cluster of fatal transplant-associated diseases. N Engl J Med 2008, 358:991-998. 10.1056/NEJMoa073785, 18256387.
-
(2008)
N Engl J Med
, vol.358
, pp. 991-998
-
-
Palacios, G.1
Druce, J.2
Du, L.3
Tran, T.4
Birch, C.5
Briese, T.6
Conlan, S.7
Quan, P.8
Hui, J.9
Marshall, J.10
Simons, J.F.11
Egholm, M.12
Paddock, C.D.13
Shieh, W.14
Goldsmith, C.S.15
Zaki, S.R.16
Catton, M.17
Lipkin, W.I.18
-
14
-
-
80054896129
-
Bambus 2: scaffolding metagenomes
-
10.1093/bioinformatics/btr520, 3198580, 21926123
-
Koren S, Treangen TJ, Pop M. Bambus 2: scaffolding metagenomes. Bioinformatics 2011, 27:2964-2971. 10.1093/bioinformatics/btr520, 3198580, 21926123.
-
(2011)
Bioinformatics
, vol.27
, pp. 2964-2971
-
-
Koren, S.1
Treangen, T.J.2
Pop, M.3
-
15
-
-
84861760530
-
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
-
10.1093/bioinformatics/bts174, 22495754
-
Peng Y, Leung HCM, Yiu SM, Chin FYL. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 2012, 28:1420-1428. 10.1093/bioinformatics/bts174, 22495754.
-
(2012)
Bioinformatics
, vol.28
, pp. 1420-1428
-
-
Peng, Y.1
Leung, H.C.M.2
Yiu, S.M.3
Chin, F.Y.L.4
-
16
-
-
84865013146
-
Conservation of gene cassettes among diverse viruses of the human Gut
-
10.1371/journal.pone.0042342, 3416800, 22900013
-
Minot S, Wu GD, Lewis JD, Bushman FD. Conservation of gene cassettes among diverse viruses of the human Gut. PLoS One 2012, 7:e42342. 10.1371/journal.pone.0042342, 3416800, 22900013.
-
(2012)
PLoS One
, vol.7
-
-
Minot, S.1
Wu, G.D.2
Lewis, J.D.3
Bushman, F.D.4
-
17
-
-
79958145122
-
Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes
-
10.1371/journal.pone.0020579, 3108952, 21674005
-
Ng TFF, Willner DL, Lim YW, Schmieder R, Chau B, Nilsson C, Anthony S, Ruan Y, Rohwer F, Breitbart M. Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes. PLoS One 2011, 6:e20579. 10.1371/journal.pone.0020579, 3108952, 21674005.
-
(2011)
PLoS One
, vol.6
-
-
Ng, T.F.F.1
Willner, D.L.2
Lim, Y.W.3
Schmieder, R.4
Chau, B.5
Nilsson, C.6
Anthony, S.7
Ruan, Y.8
Rohwer, F.9
Breitbart, M.10
-
18
-
-
70350491059
-
Diverse circovirus-like genome architectures revealed by environmental metagenomics
-
10.1099/vir.0.012955-0, 19570956
-
Rosario K, Duffy S, Breitbart M. Diverse circovirus-like genome architectures revealed by environmental metagenomics. J Gen Virol 2009, 90:2418-2424. 10.1099/vir.0.012955-0, 19570956.
-
(2009)
J Gen Virol
, vol.90
, pp. 2418-2424
-
-
Rosario, K.1
Duffy, S.2
Breitbart, M.3
-
19
-
-
84859814245
-
A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses
-
10.1186/1745-6150-7-13, 3372434, 22515485
-
Diemer GS, Stedman KM. A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses. Biol Direct 2012, 7:13. 10.1186/1745-6150-7-13, 3372434, 22515485.
-
(2012)
Biol Direct
, vol.7
, pp. 13
-
-
Diemer, G.S.1
Stedman, K.M.2
-
20
-
-
84863838397
-
Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads
-
10.1371/journal.pone.0040418, 3394797, 22808158
-
Roux S, Krupovic M, Poulet A, Debroas D, Enault F. Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads. PLoS One 2012, 7:e40418. 10.1371/journal.pone.0040418, 3394797, 22808158.
-
(2012)
PLoS One
, vol.7
-
-
Roux, S.1
Krupovic, M.2
Poulet, A.3
Debroas, D.4
Enault, F.5
-
21
-
-
77949570473
-
Deep sequencing analysis of viruses infecting grapevines: virome of a vineyard
-
10.1016/j.virol.2010.01.023, 20172578
-
Coetzee B, Freeborough M-J, Maree HJ, Celton J-M, Rees DJG, Burger JT. Deep sequencing analysis of viruses infecting grapevines: virome of a vineyard. Virology 2010, 400:157-163. 10.1016/j.virol.2010.01.023, 20172578.
-
(2010)
Virology
, vol.400
, pp. 157-163
-
-
Coetzee, B.1
Freeborough, M.-J.2
Maree, H.J.3
Celton, J.-M.4
Rees, D.J.G.5
Burger, J.T.6
-
22
-
-
84866154398
-
Metagenomic assembly reveals dynamic viral populations in hypersaline systems
-
10.1128/AEM.01212-12, 3416638, 22773627
-
Emerson JB, Thomas BC, Andrade K, Allen EE, Heidelberg KB, Banfield JF. Metagenomic assembly reveals dynamic viral populations in hypersaline systems. Appl Environ Microbiol 2012, 78:6309-6320. 10.1128/AEM.01212-12, 3416638, 22773627.
-
(2012)
Appl Environ Microbiol
, vol.78
, pp. 6309-6320
-
-
Emerson, J.B.1
Thomas, B.C.2
Andrade, K.3
Allen, E.E.4
Heidelberg, K.B.5
Banfield, J.F.6
-
23
-
-
84863393452
-
Hypervariable loci in the human gut virome
-
10.1073/pnas.1119061109, 3309749, 22355105
-
Minot S, Grunberg S, Wu GD, Lewis JD, Bushman FD. Hypervariable loci in the human gut virome. Proc Natl Acad Sci USA 2012, 109:3962-3966. 10.1073/pnas.1119061109, 3309749, 22355105.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. 3962-3966
-
-
Minot, S.1
Grunberg, S.2
Wu, G.D.3
Lewis, J.D.4
Bushman, F.D.5
-
24
-
-
80054911634
-
Metavir: a web server dedicated to virome analysis
-
10.1093/bioinformatics/btr519, 21911332
-
Roux S, Faubladier M, Mahul A, Paulhe N, Bernard A, Debroas D, Enault F. Metavir: a web server dedicated to virome analysis. Bioinformatics 2011, 27:3074-3075. 10.1093/bioinformatics/btr519, 21911332.
-
(2011)
Bioinformatics
, vol.27
, pp. 3074-3075
-
-
Roux, S.1
Faubladier, M.2
Mahul, A.3
Paulhe, N.4
Bernard, A.5
Debroas, D.6
Enault, F.7
-
25
-
-
84865205784
-
VIROME: a standard operating procedure for analysis of viral metagenome sequences
-
10.4056/sigs.2945050, 3558967, 23407591
-
Wommack KE, Bhavsar J, Polson SW, Chen J, Dumas M, Srinivasiah S, Furman M, Jamindar S, Nasko DJ. VIROME: a standard operating procedure for analysis of viral metagenome sequences. Stand Genomic Sci 2012, 6:427-439. 10.4056/sigs.2945050, 3558967, 23407591.
-
(2012)
Stand Genomic Sci
, vol.6
, pp. 427-439
-
-
Wommack, K.E.1
Bhavsar, J.2
Polson, S.W.3
Chen, J.4
Dumas, M.5
Srinivasiah, S.6
Furman, M.7
Jamindar, S.8
Nasko, D.J.9
-
26
-
-
80053379379
-
TheViral MetaGenome Annotation Pipeline (VMGAP): an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data
-
10.4056/sigs.1694706, 3156399, 21886867
-
Lorenzi HA, Hoover J, Inman J, Safford T, Murphy S, Kagan L, Williamson SJ. TheViral MetaGenome Annotation Pipeline (VMGAP): an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data. Stand Genomic Sci 2011, 4:418-429. 10.4056/sigs.1694706, 3156399, 21886867.
-
(2011)
Stand Genomic Sci
, vol.4
, pp. 418-429
-
-
Lorenzi, H.A.1
Hoover, J.2
Inman, J.3
Safford, T.4
Murphy, S.5
Kagan, L.6
Williamson, S.J.7
-
27
-
-
84870704775
-
Computational tools for viral metagenomics and their application in clinical research
-
10.1016/j.virol.2012.09.025, 23062738
-
Fancello L, Raoult D, Desnues C. Computational tools for viral metagenomics and their application in clinical research. Virology 2012, 434:162-174. 10.1016/j.virol.2012.09.025, 23062738.
-
(2012)
Virology
, vol.434
, pp. 162-174
-
-
Fancello, L.1
Raoult, D.2
Desnues, C.3
-
28
-
-
77954627922
-
Viruses in the faecal microbiota of monozygotic twins and their mothers
-
10.1038/nature09199, 2919852, 20631792
-
Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, Rohwer F, Gordon JI. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 2010, 466:334-338. 10.1038/nature09199, 2919852, 20631792.
-
(2010)
Nature
, vol.466
, pp. 334-338
-
-
Reyes, A.1
Haynes, M.2
Hanson, N.3
Angly, F.E.4
Heath, A.C.5
Rohwer, F.6
Gordon, J.I.7
-
29
-
-
84859582922
-
Finding a needle in the virus metagenome haystack-micro-metagenome analysis captures a snapshot of the diversity of a bacteriophage armoire
-
10.1371/journal.pone.0034238, 3324506, 22509283
-
Ray J, Dondrup M, Modha S, Steen IH, Sandaa R-A, Clokie M. Finding a needle in the virus metagenome haystack-micro-metagenome analysis captures a snapshot of the diversity of a bacteriophage armoire. PLoS One 2012, 7:e34238. 10.1371/journal.pone.0034238, 3324506, 22509283.
-
(2012)
PLoS One
, vol.7
-
-
Ray, J.1
Dondrup, M.2
Modha, S.3
Steen, I.H.4
Sandaa, R.-A.5
Clokie, M.6
-
30
-
-
40049104732
-
SOAP: short oligonucleotide alignment program
-
10.1093/bioinformatics/btn025, 18227114
-
Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008, 24:713-714. 10.1093/bioinformatics/btn025, 18227114.
-
(2008)
Bioinformatics
, vol.24
, pp. 713-714
-
-
Li, R.1
Li, Y.2
Kristiansen, K.3
Wang, J.4
-
31
-
-
84867397631
-
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
-
10.1093/nar/gks678, 3488206, 22821567
-
Namiki T, Hachiya T, Tanaka H, Sakakibara Y. MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res 2012, 40:e155. 10.1093/nar/gks678, 3488206, 22821567.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Namiki, T.1
Hachiya, T.2
Tanaka, H.3
Sakakibara, Y.4
-
32
-
-
74549198200
-
The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes
-
10.1371/journal.pcbi.1000593, 2781106, 20011103
-
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. The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput Biol 2009, 5:e1000593. 10.1371/journal.pcbi.1000593, 2781106, 20011103.
-
(2009)
PLoS Comput Biol
, 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..
-
33
-
-
80053366291
-
Interactive metagenomic visualization in a Web browser
-
10.1186/1471-2105-12-385, 3190407, 21961884
-
Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics 2011, 12:385. 10.1186/1471-2105-12-385, 3190407, 21961884.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 385
-
-
Ondov, B.D.1
Bergman, N.H.2
Phillippy, A.M.3
-
34
-
-
67649911268
-
Metagenomic signatures of 86 microbial and viral metagenomes
-
10.1111/j.1462-2920.2009.01901.x, 19302541
-
Willner D, Thurber RV, Rohwer F. Metagenomic signatures of 86 microbial and viral metagenomes. Environ Microbiol 2009, 11:1752-1756. 10.1111/j.1462-2920.2009.01901.x, 19302541.
-
(2009)
Environ Microbiol
, vol.11
, pp. 1752-1756
-
-
Willner, D.1
Thurber, R.V.2
Rohwer, F.3
-
35
-
-
84863304598
-
-
Vienna, Austria: R Foundation for Statistical Computing, R Core Team
-
R Core Team R: A Language and Environment for Statistical Computing 2013, Vienna, Austria: R Foundation for Statistical Computing, R Core Team.
-
(2013)
R: A Language and Environment for Statistical Computing
-
-
-
36
-
-
33745612095
-
Pvclust: an R package for assessing the uncertainty in hierarchical clustering
-
10.1093/bioinformatics/btl117, 16595560
-
Suzuki R, Shimodaira H. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 2006, 22:1540-1542. 10.1093/bioinformatics/btl117, 16595560.
-
(2006)
Bioinformatics
, vol.22
, pp. 1540-1542
-
-
Suzuki, R.1
Shimodaira, H.2
-
37
-
-
84872617153
-
-
Oksanen J, Kindt R, Legendre P, O'Hara B, Simpson GL, Solymos P, Stevens MHH, Wagner H. The vegan Package 2008
-
(2008)
The vegan Package
-
-
Oksanen, J.1
Kindt, R.2
Legendre, P.3
O'Hara, B.4
Simpson, G.L.5
Solymos, P.6
Stevens, M.H.H.7
Wagner, H.8
-
38
-
-
77949718257
-
FastTree 2-approximately maximum-likelihood trees for large alignments
-
10.1371/journal.pone.0009490, 2835736, 20224823
-
Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 2010, 5:e9490. 10.1371/journal.pone.0009490, 2835736, 20224823.
-
(2010)
PLoS One
, vol.5
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
39
-
-
77957931761
-
JsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web
-
10.1371/journal.pone.0012267, 2923619, 20805892
-
Smits SA, Ouverney CC. jsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web. PLoS One 2010, 5:e12267. 10.1371/journal.pone.0012267, 2923619, 20805892.
-
(2010)
PLoS One
, vol.5
-
-
Smits, S.A.1
Ouverney, C.C.2
-
41
-
-
59149090570
-
MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes
-
10.1093/dnares/dsn027, 2608843, 18940874
-
Noguchi H, Taniguchi T, Itoh T. MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res 2008, 15:387-396. 10.1093/dnares/dsn027, 2608843, 18940874.
-
(2008)
DNA Res
, vol.15
, pp. 387-396
-
-
Noguchi, H.1
Taniguchi, T.2
Itoh, T.3
-
42
-
-
0025183708
-
Basic local alignment search tool
-
10.1016/S0022-2836(05)80360-2, 2231712
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-410. 10.1016/S0022-2836(05)80360-2, 2231712.
-
(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
-
43
-
-
84858077472
-
The Pfam protein families database
-
10.1093/nar/gkr1065, 3245129, 22127870
-
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 ELL, Eddy SR, Bateman A, Finn RD. The Pfam protein families database. Nucleic Acids Res 2012, 40:D290-D301. 10.1093/nar/gkr1065, 3245129, 22127870.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
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.L.13
Eddy, S.R.14
Bateman, A.15
Finn, R.D.16
-
44
-
-
80055082271
-
Accelerated profile HMM searches
-
10.1371/journal.pcbi.1002195, 3197634, 22039361
-
Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol 2011, 7:e1002195. 10.1371/journal.pcbi.1002195, 3197634, 22039361.
-
(2011)
PLoS Comput Biol
, vol.7
-
-
Eddy, S.R.1
-
45
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
10.1093/bioinformatics/btq461, 20709691
-
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26:2460-2461. 10.1093/bioinformatics/btq461, 20709691.
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
46
-
-
77956548953
-
Cytoscape Web: an interactive web-based network browser
-
10.1093/bioinformatics/btq430, 2935447, 20656902
-
Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD. Cytoscape Web: an interactive web-based network browser. Bioinformatics 2010, 26:2347-2348. 10.1093/bioinformatics/btq430, 2935447, 20656902.
-
(2010)
Bioinformatics
, vol.26
, pp. 2347-2348
-
-
Lopes, C.T.1
Franz, M.2
Kazi, F.3
Donaldson, S.L.4
Morris, Q.5
Bader, G.D.6
-
47
-
-
0033635022
-
Artemis: sequence visualization and annotation
-
10.1093/bioinformatics/16.10.944, 11120685
-
Rutherford K, Parkhill J, Crook J, Horsnell T, Barrell B, Rice P. Artemis: sequence visualization and annotation. Bioinformatics 2000, 16:944-945. 10.1093/bioinformatics/16.10.944, 11120685.
-
(2000)
Bioinformatics
, vol.16
, pp. 944-945
-
-
Rutherford, K.1
Parkhill, J.2
Crook, J.3
Horsnell, T.4
Barrell, B.5
Rice, P.6
-
48
-
-
79953306448
-
Easyfig: a genome comparison visualizer
-
10.1093/bioinformatics/btr039, 3065679, 21278367
-
Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics 2011, 27:1009-1010. 10.1093/bioinformatics/btr039, 3065679, 21278367.
-
(2011)
Bioinformatics
, vol.27
, pp. 1009-1010
-
-
Sullivan, M.J.1
Petty, N.K.2
Beatson, S.A.3
-
49
-
-
80053528043
-
The human gut virome: inter-individual variation and dynamic response to diet
-
10.1101/gr.122705.111, 3202279, 21880779
-
Minot S, Sinha R, Chen J, Li H, Keilbaugh SA, Wu GD, Lewis JD, Bushman FD. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res 2011, 21:1616-1625. 10.1101/gr.122705.111, 3202279, 21880779.
-
(2011)
Genome Res
, vol.21
, pp. 1616-1625
-
-
Minot, S.1
Sinha, R.2
Chen, J.3
Li, H.4
Keilbaugh, S.A.5
Wu, G.D.6
Lewis, J.D.7
Bushman, F.D.8
-
50
-
-
33751059692
-
The marine viromes of four oceanic regions
-
10.1371/journal.pbio.0040368, 1634881, 17090214
-
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. The marine viromes of four oceanic regions. PLoS biology 2006, 4:e368. 10.1371/journal.pbio.0040368, 1634881, 17090214.
-
(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
-
51
-
-
70350482684
-
Metagenomic analysis of viruses in reclaimed water
-
10.1111/j.1462-2920.2009.01964.x, 19555373
-
Rosario K, Nilsson C, Lim YW, Ruan Y, Breitbart M. Metagenomic analysis of viruses in reclaimed water. Environ Microbiol 2009, 11:2806-2820. 10.1111/j.1462-2920.2009.01964.x, 19555373.
-
(2009)
Environ Microbiol
, vol.11
, pp. 2806-2820
-
-
Rosario, K.1
Nilsson, C.2
Lim, Y.W.3
Ruan, Y.4
Breitbart, M.5
-
52
-
-
84874520341
-
Metagenomic analysis of viral communities in (hado) pelagic sediments
-
10.1371/journal.pone.0057271, 3584133, 23468952
-
Yoshida M, Takaki Y, Eitoku M, Nunoura T, Takai K. Metagenomic analysis of viral communities in (hado) pelagic sediments. PLoS One 2013, 8:e57271. 10.1371/journal.pone.0057271, 3584133, 23468952.
-
(2013)
PLoS One
, vol.8
-
-
Yoshida, M.1
Takaki, Y.2
Eitoku, M.3
Nunoura, T.4
Takai, K.5
-
53
-
-
77956095592
-
Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing
-
10.1038/ismej.2010.44, 20393571
-
Ghai R, Martin-Cuadrado A-B, Molto AG, Heredia IG, Cabrera R, Martin J, Verdú M, Deschamps P, Moreira D, López-García P, Mira A, Rodriguez-Valera F. Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing. ISME J 2010, 4:1154-1166. 10.1038/ismej.2010.44, 20393571.
-
(2010)
ISME J
, vol.4
, pp. 1154-1166
-
-
Ghai, R.1
Martin-Cuadrado, A.-B.2
Molto, A.G.3
Heredia, I.G.4
Cabrera, R.5
Martin, J.6
Verdú, M.7
Deschamps, P.8
Moreira, D.9
López-García, P.10
Mira, A.11
Rodriguez-Valera, F.12
-
54
-
-
40849140745
-
Characterization of 1706, a virulent phage from Lactococcus lactis with similarities to prophages from other Firmicutes
-
10.1016/j.virol.2007.12.002, 18191977
-
Garneau JE, Tremblay DM, Moineau S. Characterization of 1706, a virulent phage from Lactococcus lactis with similarities to prophages from other Firmicutes. Virology 2008, 373:298-309. 10.1016/j.virol.2007.12.002, 18191977.
-
(2008)
Virology
, vol.373
, pp. 298-309
-
-
Garneau, J.E.1
Tremblay, D.M.2
Moineau, S.3
-
55
-
-
40549141418
-
Metagenomics: read length matters
-
10.1128/AEM.02181-07, 2258652, 18192407
-
Wommack KE, Bhavsar J, Ravel J. Metagenomics: read length matters. Appl Environ Microbiol 2008, 74:1453-1463. 10.1128/AEM.02181-07, 2258652, 18192407.
-
(2008)
Appl Environ Microbiol
, vol.74
, pp. 1453-1463
-
-
Wommack, K.E.1
Bhavsar, J.2
Ravel, J.3
-
56
-
-
84874530236
-
The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology
-
10.1371/journal.pone.0057355, 3585363, 23468974
-
Hurwitz BL, Sullivan MB. The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One 2013, 8:e57355. 10.1371/journal.pone.0057355, 3585363, 23468974.
-
(2013)
PLoS One
, vol.8
-
-
Hurwitz, B.L.1
Sullivan, M.B.2
|