-
1
-
-
0034053843
-
Virioplankton: viruses in aquatic ecosystems
-
10.1128/MMBR.64.1.69-114.2000, 98987, 10704475
-
Wommack KE, Colwell RR. Virioplankton: viruses in aquatic ecosystems. Microbiol Mol Biol Rev 2000, 64:69-114. 10.1128/MMBR.64.1.69-114.2000, 98987, 10704475.
-
(2000)
Microbiol Mol Biol Rev
, vol.64
, pp. 69-114
-
-
Wommack, K.E.1
Colwell, R.R.2
-
2
-
-
78249233383
-
Exploring the vast diversity of marine viruses
-
Breitbart M, Thompson L, Suttle C, Sullivan M. Exploring the vast diversity of marine viruses. Oceanography 2007, 20:135-139.
-
(2007)
Oceanography
, vol.20
, pp. 135-139
-
-
Breitbart, M.1
Thompson, L.2
Suttle, C.3
Sullivan, M.4
-
3
-
-
55049133396
-
Bacteriophage genomics
-
10.1016/j.mib.2008.09.004, 2706577, 18824125
-
Hatfull GF. Bacteriophage genomics. Curr Opin Microbiol 2008, 11:447-453. 10.1016/j.mib.2008.09.004, 2706577, 18824125.
-
(2008)
Curr Opin Microbiol
, vol.11
, pp. 447-453
-
-
Hatfull, G.F.1
-
4
-
-
0037398111
-
Viral influence on aquatic bacterial communities
-
10.2307/1543557, 12700152
-
Fuhrman JA, Schwalbach M. Viral influence on aquatic bacterial communities. Biol Bull 2003, 204:192-195. 10.2307/1543557, 12700152.
-
(2003)
Biol Bull
, vol.204
, pp. 192-195
-
-
Fuhrman, J.A.1
Schwalbach, M.2
-
5
-
-
0842266354
-
Are viruses driving microbial diversification and diversity?
-
Weinbauer MG, Rassoulzadegan F. Are viruses driving microbial diversification and diversity?. Environ Microbiol 2004, 6:1-11.
-
(2004)
Environ Microbiol
, vol.6
, pp. 1-11
-
-
Weinbauer, M.G.1
Rassoulzadegan, F.2
-
6
-
-
0031902076
-
Gene transfer by transduction in the marine environment
-
106772, 9687430
-
Jiang S, Paul J. Gene transfer by transduction in the marine environment. Appl Environ Microbiol 1998, 64:2780-2787. 106772, 9687430.
-
(1998)
Appl Environ Microbiol
, vol.64
, pp. 2780-2787
-
-
Jiang, S.1
Paul, J.2
-
7
-
-
44849088966
-
Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas?
-
Paul J. Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas?. The ISME J 2008, 2:579-589.
-
(2008)
The ISME J
, vol.2
, pp. 579-589
-
-
Paul, J.1
-
8
-
-
0032858844
-
Viruses and nutrient cycles in the sea - viruses play critical roles in the structure and function of aquatic food webs
-
Wilhelm SW, Suttle CA. Viruses and nutrient cycles in the sea - viruses play critical roles in the structure and function of aquatic food webs. Bioscience 1999, 49:781-788.
-
(1999)
Bioscience
, vol.49
, pp. 781-788
-
-
Wilhelm, S.W.1
Suttle, C.A.2
-
9
-
-
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
-
10
-
-
1842290529
-
Bacteriophage sensitivity patterns among bacteria isolated from marine waters
-
Moebus K, Nattkemper H. Bacteriophage sensitivity patterns among bacteria isolated from marine waters. Helgolander Meeresun 1981, 34:375-385.
-
(1981)
Helgolander Meeresun
, vol.34
, pp. 375-385
-
-
Moebus, K.1
Nattkemper, H.2
-
11
-
-
35948993040
-
Large variabilities in host strain susceptibility and phage host range govern interactions between lytic marine phages and their Flavobacterium hosts
-
10.1128/AEM.01399-07, 2074958, 17766444
-
Holmfeldt K, Middelboe M, Nybroe O, Riemann L. Large variabilities in host strain susceptibility and phage host range govern interactions between lytic marine phages and their Flavobacterium hosts. Appl Environ Microbiol 2007, 73:6730-6739. 10.1128/AEM.01399-07, 2074958, 17766444.
-
(2007)
Appl Environ Microbiol
, vol.73
, pp. 6730-6739
-
-
Holmfeldt, K.1
Middelboe, M.2
Nybroe, O.3
Riemann, L.4
-
12
-
-
40949113443
-
-
New York: Elsevier
-
Fauquet CM, Mayo MA, Maniloff J, Desselberger U, VBall LA. Virus taxonomy VIIIth report of the international committee on taxonomy of viruses 2005, New York: Elsevier.
-
(2005)
Virus taxonomy VIIIth report of the international committee on taxonomy of viruses
-
-
Fauquet, C.M.1
Mayo, M.A.2
Maniloff, J.3
Desselberger, U.4
VBall, L.A.5
-
13
-
-
0036330981
-
The phage proteomic tree: a genome-based taxonomy for phage
-
10.1128/JB.184.16.4529-4535.2002, 135240, 12142423
-
Rohwer F, Edwards R. The phage proteomic tree: a genome-based taxonomy for phage. J Bacteriol 2002, 184:4529-4535. 10.1128/JB.184.16.4529-4535.2002, 135240, 12142423.
-
(2002)
J Bacteriol
, vol.184
, pp. 4529-4535
-
-
Rohwer, F.1
Edwards, R.2
-
14
-
-
6044228193
-
Phage taxonomy: we agree to disagree
-
10.1128/JB.186.21.7029-7031.2004, 523225, 15489416
-
Nelson D. Phage taxonomy: we agree to disagree. J Bacteriol 2004, 186:7029-7031. 10.1128/JB.186.21.7029-7031.2004, 523225, 15489416.
-
(2004)
J Bacteriol
, vol.186
, pp. 7029-7031
-
-
Nelson, D.1
-
15
-
-
49149115195
-
Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools
-
10.1016/j.resmic.2008.03.005, 18555669
-
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. 10.1016/j.resmic.2008.03.005, 18555669.
-
(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
-
16
-
-
70449380104
-
Classification of Myoviridae bacteriophages using protein sequence similarity
-
10.1186/1471-2180-9-224, 2771037, 19857251
-
Lavigne R, Darius P, Summer E, Seto D, Mahadevan P, Nilsson A, Ackermann H, Kropinski A. Classification of Myoviridae bacteriophages using protein sequence similarity. BMC Microbiol 2009, 9:224. 10.1186/1471-2180-9-224, 2771037, 19857251.
-
(2009)
BMC Microbiol
, vol.9
, pp. 224
-
-
Lavigne, R.1
Darius, P.2
Summer, E.3
Seto, D.4
Mahadevan, P.5
Nilsson, A.6
Ackermann, H.7
Kropinski, A.8
-
17
-
-
3343005637
-
Unravelling rhizosphere-microbial interactions: opportunities and limitations
-
10.1016/j.tim.2004.06.008, 15276615
-
Singh BK, Millard P, Whiteley AS, Murrell JC. Unravelling rhizosphere-microbial interactions: opportunities and limitations. Trends Microbiol 2004, 12:386-393. 10.1016/j.tim.2004.06.008, 15276615.
-
(2004)
Trends Microbiol
, vol.12
, pp. 386-393
-
-
Singh, B.K.1
Millard, P.2
Whiteley, A.S.3
Murrell, J.C.4
-
18
-
-
0028946084
-
Phylogenetic identification and in situ detection of individual microbial cells without cultivation
-
239358, 7535888
-
Amann R, Ludwig W, Schleifer K. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 1995, 59:143-169. 239358, 7535888.
-
(1995)
Microbiol Rev
, vol.59
, pp. 143-169
-
-
Amann, R.1
Ludwig, W.2
Schleifer, K.3
-
19
-
-
41649109613
-
Functional metagenomic profiling of nine biomes
-
10.1038/nature06810, 18337718
-
Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM, Furlan M, Desnues C, Haynes M, Li LL, et al. Functional metagenomic profiling of nine biomes. Nature 2008, 452:629-632. 10.1038/nature06810, 18337718.
-
(2008)
Nature
, vol.452
, pp. 629-632
-
-
Dinsdale, E.A.1
Edwards, R.A.2
Hall, D.3
Angly, F.4
Breitbart, M.5
Brulc, J.M.6
Furlan, M.7
Desnues, C.8
Haynes, M.9
Li, L.L.10
-
20
-
-
66249128247
-
Phylogenetic analysis indicates evolutionary diversity and environmental segregation of marine podovirus DNA polymerase gene sequences
-
10.1128/AEM.02317-08, 2687296, 19363063
-
Labonte JM, Reid KE, Suttle CA. Phylogenetic analysis indicates evolutionary diversity and environmental segregation of marine podovirus DNA polymerase gene sequences. Appl Environ Microbiol 2009, 75:3634-3640. 10.1128/AEM.02317-08, 2687296, 19363063.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 3634-3640
-
-
Labonte, J.M.1
Reid, K.E.2
Suttle, C.A.3
-
21
-
-
3142570537
-
Global distribution of nearly identical phage-encoded DNA sequences
-
10.1111/j.1574-6968.2004.tb09654.x, 15251204
-
Breitbart M, Miyake JH, Rohwer F. Global distribution of nearly identical phage-encoded DNA sequences. FEMS Microbiol Lett 2004, 236:249-256. 10.1111/j.1574-6968.2004.tb09654.x, 15251204.
-
(2004)
FEMS Microbiol Lett
, vol.236
, pp. 249-256
-
-
Breitbart, M.1
Miyake, J.H.2
Rohwer, F.3
-
22
-
-
51649084501
-
Portal protein diversity and phage ecology
-
10.1111/j.1462-2920.2008.01702.x, 2657995, 18673386
-
Sullivan MB, Coleman ML, Quinlivan V, Rosenkrantz JE, DeFrancesco AS, Tan G, Fu R, Lee JA, Waterbury JB, Bielawski JP, et al. Portal protein diversity and phage ecology. Environ Microbiol 2008, 10:2810-2823. 10.1111/j.1462-2920.2008.01702.x, 2657995, 18673386.
-
(2008)
Environ Microbiol
, vol.10
, pp. 2810-2823
-
-
Sullivan, M.B.1
Coleman, M.L.2
Quinlivan, V.3
Rosenkrantz, J.E.4
DeFrancesco, A.S.5
Tan, G.6
Fu, R.7
Lee, J.A.8
Waterbury, J.B.9
Bielawski, J.P.10
-
23
-
-
77956987118
-
Ubiquitous cyanobacterial podoviruses in the global oceans unveiled through viral DNA polymerase gene sequences
-
10.1038/ismej.2010.56, 20463765
-
Huang SJ, Wilhelm SW, Jiao NAZ, Chen F. Ubiquitous cyanobacterial podoviruses in the global oceans unveiled through viral DNA polymerase gene sequences. ISME J 2010, 4:1243-1251. 10.1038/ismej.2010.56, 20463765.
-
(2010)
ISME J
, vol.4
, pp. 1243-1251
-
-
Huang, S.J.1
Wilhelm, S.W.2
Jiao, N.A.Z.3
Chen, F.4
-
24
-
-
33747073504
-
Microbial diversity in the deep sea and the underexplored "rare biosphere"
-
10.1073/pnas.0605127103, 1524930, 16880384
-
Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, Arrieta JM, Herndl GJ. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci USA 2006, 103:12115-12120. 10.1073/pnas.0605127103, 1524930, 16880384.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 12115-12120
-
-
Sogin, M.L.1
Morrison, H.G.2
Huber, J.A.3
Mark Welch, D.4
Huse, S.M.5
Neal, P.R.6
Arrieta, J.M.7
Herndl, G.J.8
-
25
-
-
0030982247
-
A molecular view of microbial diversity and the biosphere
-
10.1126/science.276.5313.734, 9115194
-
Pace N. A molecular view of microbial diversity and the biosphere. Science 1997, 276:734-740. 10.1126/science.276.5313.734, 9115194.
-
(1997)
Science
, vol.276
, pp. 734-740
-
-
Pace, N.1
-
26
-
-
0031662188
-
Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity
-
107498, 9733676
-
Hugenholtz P, Goebel B, Pace N. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 1998, 180:4765-4774. 107498, 9733676.
-
(1998)
J Bacteriol
, vol.180
, pp. 4765-4774
-
-
Hugenholtz, P.1
Goebel, B.2
Pace, N.3
-
27
-
-
0036211846
-
Phylogenetic diversity of marine cyanophage isolates and natural virus communities as revealed by sequences of viral capsid assembly protein gene g2
-
10.1128/AEM.68.4.1576-1584.2002, 123904, 11916671
-
Zhong Y, Chen F, Wilhelm SW, Poorvin L, Hodson RE. Phylogenetic diversity of marine cyanophage isolates and natural virus communities as revealed by sequences of viral capsid assembly protein gene g2. Appl Environ Microbiol 2002, 68:1576-1584. 10.1128/AEM.68.4.1576-1584.2002, 123904, 11916671.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 1576-1584
-
-
Zhong, Y.1
Chen, F.2
Wilhelm, S.W.3
Poorvin, L.4
Hodson, R.E.5
-
28
-
-
12244252269
-
Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments
-
10.1128/AEM.71.1.480-486.2005, 544240, 15640224
-
Short CM, Suttle CA. Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments. Appl Environ Microbiol 2005, 71:480-486. 10.1128/AEM.71.1.480-486.2005, 544240, 15640224.
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 480-486
-
-
Short, C.M.1
Suttle, C.A.2
-
29
-
-
24644448794
-
Marine T4-type bacteriophages, a ubiquitous component of the dark matter of the biosphere
-
10.1073/pnas.0503404102, 1194919, 16116082
-
Filee J, Tetart F, Suttle CA, Krisch HM. Marine T4-type bacteriophages, a ubiquitous component of the dark matter of the biosphere. Proc Natl Acad Sci USA 2005, 102:12471-12476. 10.1073/pnas.0503404102, 1194919, 16116082.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 12471-12476
-
-
Filee, J.1
Tetart, F.2
Suttle, C.A.3
Krisch, H.M.4
-
30
-
-
50949084124
-
Phylogenetic diversity of sequences of cyanophage photosynthetic gene psbA in marine and freshwaters
-
10.1128/AEM.02480-07, 2546643, 18586962
-
Chenard C, Suttle CA. Phylogenetic diversity of sequences of cyanophage photosynthetic gene psbA in marine and freshwaters. Appl Environ Microbiol 2008, 74:5317-5324. 10.1128/AEM.02480-07, 2546643, 18586962.
-
(2008)
Appl Environ Microbiol
, vol.74
, pp. 5317-5324
-
-
Chenard, C.1
Suttle, C.A.2
-
31
-
-
79952575963
-
Molecular analysis of the major capsid genes (g2) of T4-type bacteriophages in an upland black soil in Northeast China
-
Wang GH, Yu ZH, Liu JJ, Jin JA, Liu XB, Kimura M. Molecular analysis of the major capsid genes (g2) of T4-type bacteriophages in an upland black soil in Northeast China. Biol Fert Soils 2011, 47:273-282.
-
(2011)
Biol Fert Soils
, vol.47
, pp. 273-282
-
-
Wang, G.H.1
Yu, Z.H.2
Liu, J.J.3
Jin, J.A.4
Liu, X.B.5
Kimura, M.6
-
32
-
-
78650061156
-
Low diversity of T4-type bacteriophages in applied rice straw, plant residues and rice roots in Japanese rice soils: Estimation from major capsid gene (g2) composition
-
Fujihara S, Murase J, Tun CC, Matsuyama T, Ikenaga M, Asakawa S, Kimura M. Low diversity of T4-type bacteriophages in applied rice straw, plant residues and rice roots in Japanese rice soils: Estimation from major capsid gene (g2) composition. Soil Sci Plant Nutr 2010, 56:800-812.
-
(2010)
Soil Sci Plant Nutr
, vol.56
, pp. 800-812
-
-
Fujihara, S.1
Murase, J.2
Tun, C.C.3
Matsuyama, T.4
Ikenaga, M.5
Asakawa, S.6
Kimura, M.7
-
33
-
-
41449088355
-
Novel capsid genes (g2) of T4-type bacteriophages in a Japanese paddy field
-
Fujii T, Nakayama N, Nishida M, Sekiya H, Kato N, Asakawa S, Kimura M. Novel capsid genes (g2) of T4-type bacteriophages in a Japanese paddy field. Soil Biol Biochem 2008, 40:1049-1058.
-
(2008)
Soil Biol Biochem
, vol.40
, pp. 1049-1058
-
-
Fujii, T.1
Nakayama, N.2
Nishida, M.3
Sekiya, H.4
Kato, N.5
Asakawa, S.6
Kimura, M.7
-
34
-
-
70350439595
-
Diverse and dynamic populations of cyanobacterial podoviruses in the Chesapeake Bay unveiled through DNA polymerase gene sequences
-
10.1111/j.1462-2920.2009.02033.x, 19703219
-
Chen F, Wang K, Huang SJ, Cai HY, Zhao MR, Jiao NZ, Wommack KE. Diverse and dynamic populations of cyanobacterial podoviruses in the Chesapeake Bay unveiled through DNA polymerase gene sequences. Environ Microbiol 2009, 11:2884-2892. 10.1111/j.1462-2920.2009.02033.x, 19703219.
-
(2009)
Environ Microbiol
, vol.11
, pp. 2884-2892
-
-
Chen, F.1
Wang, K.2
Huang, S.J.3
Cai, H.Y.4
Zhao, M.R.5
Jiao, N.Z.6
Wommack, K.E.7
-
35
-
-
3342915398
-
Transfer of photosynthesis genes to and from Prochlorococcus viruses
-
10.1073/pnas.0401526101, 503735, 15256601
-
Lindell D, Sullivan MB, Johnson ZI, Tolonen AC, Rohwer F, Chisholm SW. Transfer of photosynthesis genes to and from Prochlorococcus viruses. Proc Natl Acad Sci USA 2004, 101:11013-11018. 10.1073/pnas.0401526101, 503735, 15256601.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 11013-11018
-
-
Lindell, D.1
Sullivan, M.B.2
Johnson, Z.I.3
Tolonen, A.C.4
Rohwer, F.5
Chisholm, S.W.6
-
36
-
-
69949104491
-
Comparative genomics of marine cyanomyoviruses reveals the widespread occurrence of Synechococcus host genes localized to a hyperplastic region: implications for mechanisms of cyanophage evolution
-
10.1111/j.1462-2920.2009.01966.x, 19508343
-
Millard AD, Zwirglmaier K, Downey MJ, Mann NH, Scanlan DJ. Comparative genomics of marine cyanomyoviruses reveals the widespread occurrence of Synechococcus host genes localized to a hyperplastic region: implications for mechanisms of cyanophage evolution. Environ Microbiol 2009, 11:2370-2387. 10.1111/j.1462-2920.2009.01966.x, 19508343.
-
(2009)
Environ Microbiol
, vol.11
, pp. 2370-2387
-
-
Millard, A.D.1
Zwirglmaier, K.2
Downey, M.J.3
Mann, N.H.4
Scanlan, D.J.5
-
37
-
-
33747369803
-
Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts
-
Sullivan MB, Lindell D, Lee JA, Thompson LR, Bielawski JP, Chisholm SW. Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. PLoS Biol 2006, 4:1344-1357.
-
(2006)
PLoS Biol
, vol.4
, pp. 1344-1357
-
-
Sullivan, M.B.1
Lindell, D.2
Lee, J.A.3
Thompson, L.R.4
Bielawski, J.P.5
Chisholm, S.W.6
-
38
-
-
44349124497
-
Evidence for the intense exchange of MazG in marine cyanophages by horizontal gene transfer
-
10.1371/journal.pone.0002048, 2297514, 18431505
-
Bryan M, Burroughs N, Spence E, Clokie M, Mann N, Bryan S. Evidence for the intense exchange of MazG in marine cyanophages by horizontal gene transfer. PLoS ONE 2008, 3:e2048. 10.1371/journal.pone.0002048, 2297514, 18431505.
-
(2008)
PLoS ONE
, vol.3
-
-
Bryan, M.1
Burroughs, N.2
Spence, E.3
Clokie, M.4
Mann, N.5
Bryan, S.6
-
39
-
-
83155178413
-
Pho regulon genes in phage: development of pho as a novel signature gene for assessing marine phage diversity
-
10.1128/AEM.05531-11, 21926220
-
Goldsmith D, Crosti G, Dwivedi B, McDaniel L, Varsani A, Suttle C, Weinbauer M, Sandaa R-A, Breitbart M. Pho regulon genes in phage: development of pho as a novel signature gene for assessing marine phage diversity. Appl Environ Microbiol 2011, 77:7730-7739. 10.1128/AEM.05531-11, 21926220.
-
(2011)
Appl Environ Microbiol
, vol.77
, pp. 7730-7739
-
-
Goldsmith, D.1
Crosti, G.2
Dwivedi, B.3
McDaniel, L.4
Varsani, A.5
Suttle, C.6
Weinbauer, M.7
Sandaa, R.-A.8
Breitbart, M.9
-
40
-
-
33745698561
-
Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform
-
Hatfull GF, Pedulla ML, Jacobs-Sera D, Cichon PM, Foley A, Ford ME, Gonda RM, Houtz JM, Hryckowian AJ, Kelchner VA, et al. Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. PLoS Genet 2006, 2:835-847.
-
(2006)
PLoS Genet
, vol.2
, pp. 835-847
-
-
Hatfull, G.F.1
Pedulla, M.L.2
Jacobs-Sera, D.3
Cichon, P.M.4
Foley, A.5
Ford, M.E.6
Gonda, R.M.7
Houtz, J.M.8
Hryckowian, A.J.9
Kelchner, V.A.10
-
41
-
-
84888278330
-
PhAnToMe: Phage Annotation Tools and Methods
-
PhAnToMe: Phage Annotation Tools and Methods. , http://www.phantome.org/
-
-
-
-
42
-
-
0030660581
-
A genomic perspective on protein families
-
10.1126/science.278.5338.631, 9381173
-
Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science 1997, 278:631-637. 10.1126/science.278.5338.631, 9381173.
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
43
-
-
0141519279
-
OrthoMCL: identification of ortholog groups for eukaryotic genomes
-
10.1101/gr.1224503, 403725, 12952885
-
Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003, 13:2178-2189. 10.1101/gr.1224503, 403725, 12952885.
-
(2003)
Genome Res
, vol.13
, pp. 2178-2189
-
-
Li, L.1
Stoeckert, C.J.2
Roos, D.S.3
-
44
-
-
79959931985
-
HMMER web server: interactive sequence similarity searching
-
10.1093/nar/gkr367, 3125773, 21593126
-
Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 2011, 39:W29-W37. 10.1093/nar/gkr367, 3125773, 21593126.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Finn, R.D.1
Clements, J.2
Eddy, S.R.3
-
45
-
-
0642342573
-
CoreGenes: a computational tool for identifying and cataloging "core" genes in a set of small genomes
-
10.1186/1471-2105-3-12, 111185, 11972896
-
Zafar N, Mazumder R, Seto D. CoreGenes: a computational tool for identifying and cataloging "core" genes in a set of small genomes. BMC Bioinformatics 2002, 3:12. 10.1186/1471-2105-3-12, 111185, 11972896.
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 12
-
-
Zafar, N.1
Mazumder, R.2
Seto, D.3
-
46
-
-
0043122986
-
CODEHOP (COnsensus-DEgenerate hybrid oligonucleotide primer) PCR primer design
-
10.1093/nar/gkg524, 168931, 12824413
-
Rose TM, Henikoff JG, Henikoff S. CODEHOP (COnsensus-DEgenerate hybrid oligonucleotide primer) PCR primer design. Nucleic Acids Res 2003, 31:3763-3766. 10.1093/nar/gkg524, 168931, 12824413.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3763-3766
-
-
Rose, T.M.1
Henikoff, J.G.2
Henikoff, S.3
-
47
-
-
84874658574
-
Integrated DNA Technologies, OligoAnalyzer 3.1
-
Integrated DNA Technologies, OligoAnalyzer 3.1. , http://www.idtdna.com/analyzer/applications/oligoanalyzer/
-
-
-
-
48
-
-
0033990048
-
Primer3 on the WWW for general users and for biologist programmers
-
Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 2000, 132:365-386.
-
(2000)
Methods Mol Biol
, vol.132
, pp. 365-386
-
-
Rozen, S.1
Skaletsky, H.2
-
49
-
-
84888278954
-
Perl.com
-
Perl.com. , http://www.perl.com/
-
-
-
-
50
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
-
(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
-
51
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
10.1093/nar/25.17.3389, 146917, 9254694
-
Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.H.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
52
-
-
0027968068
-
Clustal-W - improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
10.1093/nar/22.22.4673, 308517, 7984417
-
Thompson JD, Higgins DG, Gibson TJ. Clustal-W - improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680. 10.1093/nar/22.22.4673, 308517, 7984417.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
53
-
-
64749109065
-
Laboratory procedures to generate viral metagenomes
-
10.1038/nprot.2009.10, 19300441
-
Thurber RV, 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
-
-
Thurber, R.V.1
Haynes, M.2
Breitbart, M.3
Wegley, L.4
Rohwer, F.5
-
54
-
-
33644606606
-
FastGroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries
-
10.1186/1471-2105-7-57, 1386709, 16464253
-
Yu YN, Breitbart M, McNairnie P, Rohwer F. FastGroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries. BMC Bioinformatics 2006, 7:57. 10.1186/1471-2105-7-57, 1386709, 16464253.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 57
-
-
Yu, Y.N.1
Breitbart, M.2
McNairnie, P.3
Rohwer, F.4
-
55
-
-
79957613599
-
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
-
10.1093/molbev/msr121, 21546353
-
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28:2731-2739. 10.1093/molbev/msr121, 21546353.
-
(2011)
Mol Biol Evol
, vol.28
, pp. 2731-2739
-
-
Tamura, K.1
Peterson, D.2
Peterson, N.3
Stecher, G.4
Nei, M.5
Kumar, S.6
-
56
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
-
10.1093/sysbio/syq010, 20525638
-
Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010, 59:307-321. 10.1093/sysbio/syq010, 20525638.
-
(2010)
Syst Biol
, vol.59
, pp. 307-321
-
-
Guindon, S.1
Dufayard, J.F.2
Lefort, V.3
Anisimova, M.4
Hordijk, W.5
Gascuel, O.6
-
57
-
-
25644458211
-
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
-
10.1093/nar/gki866, 1251668, 16214803
-
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 2005, 33:5691-5702. 10.1093/nar/gki866, 1251668, 16214803.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 5691-5702
-
-
Overbeek, R.1
Begley, T.2
Butler, R.M.3
Choudhuri, J.V.4
Chuang, H.Y.5
Cohoon, M.6
de Crecy-Lagard, V.7
Diaz, N.8
Disz, T.9
Edwards, R.10
-
58
-
-
84888280860
-
The SEED
-
The SEED. , http://www.theseed.org/wiki/Home_of_the_SEED
-
-
-
-
59
-
-
84888285334
-
BLAST stand-alone package
-
BLAST stand-alone package. , ftp://ftp.ncbi.nih.gov/blast/
-
-
-
-
60
-
-
73649209034
-
Determination of base composition of deoxyribonucleic acid from its thermal denaturation temperature
-
10.1016/S0022-2836(62)80066-7, 14470099
-
Marmur J, Doty P. Determination of base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 1962, 5:109-118. 10.1016/S0022-2836(62)80066-7, 14470099.
-
(1962)
J Mol Biol
, vol.5
, pp. 109-118
-
-
Marmur, J.1
Doty, P.2
-
61
-
-
0018787038
-
Hybridization of synthetic oligodeoxyribonucleotides to Phi X174 DNA - effect of single base pair mismatch
-
10.1093/nar/6.11.3543, 327955, 158748
-
Wallace RB, Shaffer J, Murphy RF, Bonner J, Hirose T, Itakura K. Hybridization of synthetic oligodeoxyribonucleotides to Phi X174 DNA - effect of single base pair mismatch. Nucleic Acids Res 1979, 6:3543-3557. 10.1093/nar/6.11.3543, 327955, 158748.
-
(1979)
Nucleic Acids Res
, vol.6
, pp. 3543-3557
-
-
Wallace, R.B.1
Shaffer, J.2
Murphy, R.F.3
Bonner, J.4
Hirose, T.5
Itakura, K.6
-
62
-
-
0033565267
-
Nucleic acid duplex stability: influence of base composition on cation effects
-
10.1093/nar/27.14.2957, 148512, 10390539
-
Nakano S, Fujimoto M, Hara H, Sugimoto N. Nucleic acid duplex stability: influence of base composition on cation effects. Nucleic Acids Res 1999, 27:2957-2965. 10.1093/nar/27.14.2957, 148512, 10390539.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 2957-2965
-
-
Nakano, S.1
Fujimoto, M.2
Hara, H.3
Sugimoto, N.4
-
63
-
-
0018416989
-
Rapid method for detecting and mapping homology between heterologous DNAs - evaluation of polyomavirus genomes
-
Howley PM, Israel MA, Law MF, Martin MA. Rapid method for detecting and mapping homology between heterologous DNAs - evaluation of polyomavirus genomes. J Biol Chem 1979, 254:4876-4883.
-
(1979)
J Biol Chem
, vol.254
, pp. 4876-4883
-
-
Howley, P.M.1
Israel, M.A.2
Law, M.F.3
Martin, M.A.4
-
64
-
-
0032539693
-
A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
-
10.1073/pnas.95.4.1460, 19045, 9465037
-
SantaLucia J. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA 1998, 95:1460-1465. 10.1073/pnas.95.4.1460, 19045, 9465037.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 1460-1465
-
-
SantaLucia, J.1
-
65
-
-
0036255283
-
Genomic sequence and evolution of marine cyanophage P60: a new insight on lytic and lysogenic phages
-
10.1128/AEM.68.5.2589-2594.2002, 127578, 11976141
-
Chen F, Lu JR. Genomic sequence and evolution of marine cyanophage P60: a new insight on lytic and lysogenic phages. Appl Environ Microbiol 2002, 68:2589-2594. 10.1128/AEM.68.5.2589-2594.2002, 127578, 11976141.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 2589-2594
-
-
Chen, F.1
Lu, J.R.2
-
66
-
-
16344379864
-
Primaclade - a flexible tool to find conserved PCR primers across multiple species
-
10.1093/bioinformatics/bti134, 15539448
-
Gadberry MD, Malcomber ST, Doust AN, Kellogg EA. Primaclade - a flexible tool to find conserved PCR primers across multiple species. Bioinformatics 2005, 21:1263-1264. 10.1093/bioinformatics/bti134, 15539448.
-
(2005)
Bioinformatics
, vol.21
, pp. 1263-1264
-
-
Gadberry, M.D.1
Malcomber, S.T.2
Doust, A.N.3
Kellogg, E.A.4
-
67
-
-
23144467843
-
PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs
-
10.1093/nar/gki425, 1160186, 15980525
-
Fredslund J, Schauser L, Madsen LH, Sandal N, Stougaard J. PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs. Nucleic Acids Res 2005, 33:W516-W520. 10.1093/nar/gki425, 1160186, 15980525.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Fredslund, J.1
Schauser, L.2
Madsen, L.H.3
Sandal, N.4
Stougaard, J.5
|