-
1
-
-
85018806648
-
Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2017)
-
Adams MJ, Lefkowitz EJ, King AMQ, Harrach B, Harrison RL et al. Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2017). Arch Virol 2017;162:2505– 2538.
-
(2017)
Arch Virol
, vol.162
, pp. 2505-2538
-
-
Adams, M.J.1
Lefkowitz, E.J.2
King, A.M.Q.3
Harrach, B.4
Harrison, R.L.5
-
2
-
-
84880443496
-
Pandor-aviruses: Amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes
-
Philippe N, Legendre M, Doutre G, Coute Y, Poirot O et al. Pandor-aviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes. Science 2013;341:281–286.
-
(2013)
Science
, vol.341
, pp. 281-286
-
-
Philippe, N.1
Legendre, M.2
Doutre, G.3
Coute, Y.4
Poirot, O.5
-
4
-
-
79956105255
-
What does virus evolution tell us about virus origins?
-
Holmes EC. What does virus evolution tell us about virus origins? J Virol 2011;85:5247–5251.
-
(2011)
J Virol
, vol.85
, pp. 5247-5251
-
-
Holmes, E.C.1
-
5
-
-
0036330981
-
The phage proteomic tree: A genome-based taxonomy for phage
-
Rohwer F, Edwards R. The phage proteomic tree: a genome-based taxonomy for phage. J Bacteriol 2002;184:4529–4535.
-
(2002)
J Bacteriol
, vol.184
, pp. 4529-4535
-
-
Rohwer, F.1
Edwards, R.2
-
6
-
-
84885961394
-
Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses
-
Krupovic M. Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses. Curr Opin Virol 2013;3:578– 586.
-
(2013)
Curr Opin Virol
, vol.3
, pp. 578-586
-
-
Krupovic, M.1
-
7
-
-
0015114139
-
Expression of animal virus genomes
-
Baltimore D. Expression of animal virus genomes. Bacteriol Rev 1971;35:235–241.
-
(1971)
Bacteriol Rev
, vol.35
, pp. 235-241
-
-
Baltimore, D.1
-
8
-
-
85027877354
-
The phage nucleus and tubulin spindle are conserved among large pseudomonas phages
-
Chaikeeratisak V, Nguyen K, Egan ME, Erb ML, Vavilina A et al. The phage nucleus and tubulin spindle are conserved among large pseudomonas phages. Cell Rep 2017;20:1563–1571.
-
(2017)
Cell Rep
, vol.20
, pp. 1563-1571
-
-
Chaikeeratisak, V.1
Nguyen, K.2
Egan, M.E.3
Erb, M.L.4
Vavilina, A.5
-
9
-
-
84960849632
-
Role of bacteriophage T4 baseplate in regulating assembly and infection
-
Yap ML, Klose T, Arisaka F, Speir JA, Veesler D et al. Role of bacteriophage T4 baseplate in regulating assembly and infection. Proc Natl Acad Sci USA 2016;113:2654–2659.
-
(2016)
Proc Natl Acad Sci USA
, vol.113
, pp. 2654-2659
-
-
Yap, M.L.1
Klose, T.2
Arisaka, F.3
Speir, J.A.4
Veesler, D.5
-
10
-
-
42449112438
-
X-ray crystal structure of the polymerase domain of the bacteriophage N4 virion RNA polymerase
-
Murakami KS, Davydova EK, Rothman-Denes LB. X-ray crystal structure of the polymerase domain of the bacteriophage N4 virion RNA polymerase. Proc Natl Acad Sci USA 2008;105:5046– 5051.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 5046-5051
-
-
Murakami, K.S.1
Davydova, E.K.2
Rothman-Denes, L.B.3
-
11
-
-
84941011872
-
Structural remodeling of bacteriophage T4 and host membranes during infection initiation
-
Hu B, Margolin W, Molineux IJ, Liu J. Structural remodeling of bacteriophage T4 and host membranes during infection initiation. Proc Natl Acad Sci USA 2015;112:E4919–E4928.
-
(2015)
Proc Natl Acad Sci USA
, vol.112
, pp. E4919-E4928
-
-
Hu, B.1
Margolin, W.2
Molineux, I.J.3
Liu, J.4
-
12
-
-
84895198685
-
Phage lysis: Three steps, three choices, one outcome
-
Young R. Phage lysis: three steps, three choices, one outcome. J Microbiol 2014;52:243–258.
-
(2014)
J Microbiol
, vol.52
, pp. 243-258
-
-
Young, R.1
-
13
-
-
84984985848
-
Uncovering earth’s virome
-
Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M et al. Uncovering earth’s virome. Nature 2016;536: 425–430.
-
(2016)
Nature
, vol.536
, pp. 425-430
-
-
Paez-Espino, D.1
Eloe-Fadrosh, E.A.2
Pavlopoulos, G.A.3
Thomas, A.D.4
Huntemann, M.5
-
14
-
-
85019307757
-
Environmental viral genomes shed new light on virus-host interactions in the ocean
-
Nishimura Y, Watai H, Honda T, Mihara T, Omae K et al. Environmental viral genomes shed new light on virus-host interactions in the ocean. mSphere 2017;2:e00359-16.
-
(2017)
Msphere
, vol.2
, pp. 9-16
-
-
Nishimura, Y.1
Watai, H.2
Honda, T.3
Mihara, T.4
Omae, K.5
-
15
-
-
84867142028
-
Prokaryote viruses studied by electron microscopy
-
Ackermann HW, Prangishvili D. Prokaryote viruses studied by electron microscopy. Arch Virol 2012;157:1843–1849.
-
(2012)
Arch Virol
, vol.157
, pp. 1843-1849
-
-
Ackermann, H.W.1
Prangishvili, D.2
-
16
-
-
85035327063
-
Viruses of archaea: Structural, functional, environmental and evolutionary genomics
-
Krupovic M, Cvirkaite-Krupovic V, Iranzo J, Prangishvili D, Koonin EV. Viruses of archaea: structural, functional, environmental and evolutionary genomics. Virus Res 2018;244:181–193.
-
(2018)
Virus Res
, vol.244
, pp. 181-193
-
-
Krupovic, M.1
Cvirkaite-Krupovic, V.2
Iranzo, J.3
Prangishvili, D.4
Koonin, E.V.5
-
17
-
-
6044228193
-
Phage taxonomy: We agree to disagree
-
Nelson D. Phage taxonomy: we agree to disagree. J Bacteriol 2004;186:7029–7031.
-
(2004)
J Bacteriol
, vol.186
, pp. 7029-7031
-
-
Nelson, D.1
-
18
-
-
49149115195
-
Unifying classical and molecular taxonomic classification: Analysis of the Podoviridae using BLASTP-based tools
-
Lavigne R, Seto D, Mahadevan P, Ackermann HW, Kropinski AM. Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools. Res Microbiol 2008; 159:406–414.
-
(2008)
Res Microbiol
, vol.159
, pp. 406-414
-
-
Lavigne, R.1
Seto, D.2
Mahadevan, P.3
Ackermann, H.W.4
Kropinski, A.M.5
-
19
-
-
70449380104
-
Classification of Myoviridae bacteriophages using protein sequence similarity
-
Lavigne R, Darius P, Summer EJ, Seto D, Mahadevan P et al. Classification of Myoviridae bacteriophages using protein sequence similarity. BMC Microbiol 2009;9:224.
-
(2009)
BMC Microbiol
, vol.9
, pp. 224
-
-
Lavigne, R.1
Darius, P.2
Summer, E.J.3
Seto, D.4
Mahadevan, P.5
-
20
-
-
84929999962
-
Integration of genomic and proteomic analyses in the classification of the Siphoviridae family
-
Adriaenssens EM, Edwards R, Nash JHE, Mahadevan P, Seto D et al. Integration of genomic and proteomic analyses in the classification of the Siphoviridae family. Virology 2015;477:144–154.
-
(2015)
Virology
, vol.477
, pp. 144-154
-
-
Adriaenssens, E.M.1
Edwards, R.2
Nash, J.H.E.3
Mahadevan, P.4
Seto, D.5
-
21
-
-
84904894989
-
Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein
-
Hopkins M, Kailasan S, Cohen A, Roux S, Tucker KP et al. Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein. ISME J 2014;8:2093–2103.
-
(2014)
ISME J
, vol.8
, pp. 2093-2103
-
-
Hopkins, M.1
Kailasan, S.2
Cohen, A.3
Roux, S.4
Tucker, K.P.5
-
22
-
-
84939526110
-
Viral dark matter and virus-host interactions resolved from publicly available microbial genomes
-
Roux S, Hallam SJ, Woyke T, Sullivan MB. Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. Elife 2015;4.
-
(2015)
Elife
, vol.4
-
-
Roux, S.1
Hallam, S.J.2
Woyke, T.3
Sullivan, M.B.4
-
23
-
-
84907450951
-
Understanding the enormous diversity of bacteriophages: The tailed phages that infect the bacterial family Enterobacteriaceae
-
Grose JH, Casjens SR. Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae. Virology 2014;468-470:421–443.
-
(2014)
Virology
, vol.468-470
, pp. 421-443
-
-
Grose, J.H.1
Casjens, S.R.2
-
24
-
-
75549086985
-
ACLAME: A classification of mobile genetic elements, update 2010
-
Leplae R, Lima-Mendez G, Toussaint A. ACLAME: a classification of mobile genetic elements, update 2010. Nucleic Acids Res 2010; 38:D57–D61.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. D57-D61
-
-
Leplae, R.1
Lima-Mendez, G.2
Toussaint, A.3
-
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 2008;25:762–777.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 762-777
-
-
Lima-Mendez, G.1
van Helden, J.2
Toussaint, A.3
Leplae, R.4
-
26
-
-
84986587931
-
The double-stranded DNA virosphere as a modular hierarchical network of gene sharing
-
Iranzo J, Krupovic M, Koonin EV. The double-stranded DNA virosphere as a modular hierarchical network of gene sharing. MBio 2016;7:e00978-16.
-
(2016)
Mbio
, vol.7
, pp. 8-16
-
-
Iranzo, J.1
Krupovic, M.2
Koonin, E.V.3
-
27
-
-
85018974675
-
VConTACT: An iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria
-
Bolduc B, Jang HB, Doulcier G, You ZQ, Roux S et al. vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria. PeerJ 2017;5:e3243.
-
(2017)
Peerj
, vol.5
-
-
Bolduc, B.1
Jang, H.B.2
Doulcier, G.3
You, Z.Q.4
Roux, S.5
-
28
-
-
0036719291
-
Imbroglios of viral taxonomy: Genetic exchange and failings of phenetic approaches
-
Lawrence JG, Hatfull GF, Hendrix RW. Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. J Bacteriol 2002;184:4891–4905.
-
(2002)
J Bacteriol
, vol.184
, pp. 4891-4905
-
-
Lawrence, J.G.1
Hatfull, G.F.2
Hendrix, R.W.3
-
29
-
-
85023738635
-
Bacteriophage evolution differs by host, lifestyle and genome
-
Mavrich TN, Hatfull GF. Bacteriophage evolution differs by host, lifestyle and genome. Nat Microbiol 2017;2:17112.
-
(2017)
Nat Microbiol
, vol.2
-
-
Mavrich, T.N.1
Hatfull, G.F.2
-
30
-
-
85042872875
-
The genomic underpinnings of eukaryotic virus taxonomy: Creating a sequence-based framework for family-level virus classification
-
Aiewsakun P, Simmonds P. The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification. Microbiome 2018;6:38.
-
(2018)
Microbiome
, vol.6
, pp. 38
-
-
Aiewsakun, P.1
Simmonds, P.2
-
31
-
-
84885304918
-
The Picornavir-ales
-
King AMQ, Adams MJ, Carstens EB and Lefkowitz EJ (editors), Elsevier
-
Sanfacon H, Gorbalenya AE, Knowles NJ, Chen YP. The Picornavir-ales. In: King AMQ, Adams MJ, Carstens EB and Lefkowitz EJ (editors). Virus Taxonomy: Classification and Nomenclature of Viruses. San Diego: Elsevier; 2012. pp. 835–839.
-
(2012)
Virus Taxonomy: Classification and Nomenclature of Viruses. San Diego
, pp. 835-839
-
-
Sanfacon, H.1
Gorbalenya, A.E.2
Knowles, N.J.3
Chen, Y.P.4
-
32
-
-
85008394347
-
Consensus statement: Virus taxonomy in the age of metagenom-ics
-
Simmonds P, Adams MJ, Benko} M, Breitbart M, Brister JR et al. Consensus statement: virus taxonomy in the age of metagenom-ics. Nat Rev Microbiol 2017;15:161–168.
-
(2017)
Nat Rev Microbiol
, vol.15
, pp. 161-168
-
-
Simmonds, P.1
Adams, M.J.2
Benko, M.3
Breitbart, M.4
Brister, J.R.5
-
33
-
-
85040781306
-
Taxonomy of prokaryotic viruses: 2017 update from the ICTV bacterial and archaeal viruses subcommittee
-
Adriaenssens EM, Wittmann J, Kuhn JH, Turner D, Sullivan MB et al. Taxonomy of prokaryotic viruses: 2017 update from the ICTV bacterial and archaeal viruses subcommittee. Arch Virol 2018; 163:1125–1129.
-
(2018)
Arch Virol
, vol.163
, pp. 1125-1129
-
-
Adriaenssens, E.M.1
Wittmann, J.2
Kuhn, J.H.3
Turner, D.4
Sullivan, M.B.5
-
34
-
-
85007415695
-
Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee
-
Adriaenssens EM, Krupovic M, Knezevic P, Ackermann HW, Barylski J et al. Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee. Arch Virol 2017;162:1153–1157.
-
(2017)
Arch Virol
, vol.162
, pp. 1153-1157
-
-
Adriaenssens, E.M.1
Krupovic, M.2
Knezevic, P.3
Ackermann, H.W.4
Barylski, J.5
-
35
-
-
84953298206
-
Taxonomy of prokaryotic viruses: Update from the ICTV bacterial and archaeal viruses subcommittee
-
Krupovic M, Dutilh BE, Adriaenssens EM, Wittmann J, Vogensen FK et al. Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee. Arch Virol 2016; 161:1095–1099.
-
(2016)
Arch Virol
, vol.161
, pp. 1095-1099
-
-
Krupovic, M.1
Dutilh, B.E.2
Adriaenssens, E.M.3
Wittmann, J.4
Vogensen, F.K.5
-
36
-
-
85050567626
-
Analysis of spounaviruses as a case study for the overdue reclas-sification of tailed bacteriophages
-
Barylski J, Enault F, Dutilh BE, Schuller MB, Edwards RA et al. Analysis of spounaviruses as a case study for the overdue reclas-sification of tailed bacteriophages. bioRxiv 2018.
-
(2018)
Biorxiv
-
-
Barylski, J.1
Enault, F.2
Dutilh, B.E.3
Schuller, M.B.4
Edwards, R.A.5
-
37
-
-
85001104742
-
Bipartite network analysis of the archaeal virosphere: Evolutionary connections between viruses and capsidless mobile elements
-
Iranzo J, Koonin EV, Prangishvili D, Krupovic M. Bipartite network analysis of the archaeal virosphere: evolutionary connections between viruses and capsidless mobile elements. J Virol 2016;90: 11043–11055.
-
(2016)
J Virol
, vol.90
, pp. 11043-11055
-
-
Iranzo, J.1
Koonin, E.V.2
Prangishvili, D.3
Krupovic, M.4
-
38
-
-
84858217519
-
A new proposed taxon for double-stranded DNA viruses, the order "Ligamenvirales"
-
Prangishvili D, Krupovic M. A new proposed taxon for double-stranded DNA viruses, the order "Ligamenvirales". Arch Virol 2012;157:791–795.
-
(2012)
Arch Virol
, vol.157
, pp. 791-795
-
-
Prangishvili, D.1
Krupovic, M.2
-
41
-
-
56349116764
-
Virus evolution: How far does the double beta-barrel viral lineage extend?
-
Krupovic M, Bamford DH. Virus evolution: how far does the double beta-barrel viral lineage extend? Nat Rev Microbiol 2008;6:941– 948.
-
(2008)
Nat Rev Microbiol
, vol.6
, pp. 941-948
-
-
Krupovic, M.1
Bamford, D.H.2
-
43
-
-
81555221014
-
Ninth report of the International Committee on Taxonomy of Viruses
-
King AMQ, Adams MJ, Carstens EB and Lefkowitz EJ (editors), Elsevier
-
Lavigne R, Podoviridae KAM. Ninth report of the International Committee on Taxonomy of Viruses. In: King AMQ, Adams MJ, Carstens EB and Lefkowitz EJ (editors). Virus Taxonomy: Classification and Nomenclature of Viruses. San Diego: Elsevier; 2012. pp. 63–85.
-
(2012)
Virus Taxonomy: Classification and Nomenclature of Viruses. San Diego
, pp. 63-85
-
-
Lavigne, R.1
Podoviridae, K.A.M.2
-
44
-
-
84930008169
-
A structured annotation frame for the transposable phages: A new proposed family "Saltoviridae" within the Caudovirales
-
Hulo C, Masson P, Le Mercier P, Toussaint A. A structured annotation frame for the transposable phages: a new proposed family "Saltoviridae" within the Caudovirales. Virology 2015;477:155–163.
-
(2015)
Virology
, vol.477
, pp. 155-163
-
-
Hulo, C.1
Masson, P.2
Le Mercier, P.3
Toussaint, A.4
-
45
-
-
80053386018
-
A modular view of the bacteriophage genomic space: identification of host and lifestyle marker modules
-
Lima-Mendez G, Toussaint A, Leplae R. A modular view of the bacteriophage genomic space: identification of host and lifestyle marker modules. Res Microbiol 2011;162:737–746.
-
(2011)
Res Microbiol
, vol.162
, pp. 737-746
-
-
Lima-Mendez, G.1
Toussaint, A.2
Leplae, R.3
-
46
-
-
84964313653
-
Automated classification of tailed bacteriophages according to their neck organization
-
Lopes A, Tavares P, Petit MA, Guerois R, Zinn-Justin S. Automated classification of tailed bacteriophages according to their neck organization. BMC Genomics 2014;15:1027.
-
(2014)
BMC Genomics
, vol.15
, pp. 1027
-
-
Lopes, A.1
Tavares, P.2
Petit, M.A.3
Guerois, R.4
Zinn-Justin, S.5
-
47
-
-
85009278960
-
50 years of the international committee on taxonomy of viruses: Progress and prospects
-
Adams MJ, Lefkowitz EJ, King AM, Harrach B, Harrison RL et al. 50 years of the international committee on taxonomy of viruses: progress and prospects. Arch Virol 2017;162:1441–1446.
-
(2017)
Arch Virol
, vol.162
, pp. 1441-1446
-
-
Adams, M.J.1
Lefkowitz, E.J.2
King, A.M.3
Harrach, B.4
Harrison, R.L.5
-
48
-
-
84958697849
-
Network-thinking: Graphs to analyze microbial complexity and evolution
-
Corel E, Lopez P, Meheust R, Bapteste E. Network-thinking: graphs to analyze microbial complexity and evolution. Trends Microbiol 2016;24:224–237.
-
(2016)
Trends Microbiol
, vol.24
, pp. 224-237
-
-
Corel, E.1
Lopez, P.2
Meheust, R.3
Bapteste, E.4
-
49
-
-
61849113253
-
Graph clustering via a discrete uncoupling process
-
van Dongen S. Graph clustering via a discrete uncoupling process. SIAM J Matrix Anal Appl 2008;30:121–141.
-
(2008)
SIAM J Matrix Anal Appl
, vol.30
, pp. 121-141
-
-
van Dongen, S.1
|