-
1
-
-
84897581176
-
Total synthesis of a functional designer eukaryotic chromosome
-
Annaluru N, Muller H, Mitchell LA, Ramalingam S, Stracquadanio G, Richardson SM. 2014. Total synthesis of a functional designer eukaryotic chromosome. Science 344:55-58. doi: 10.1126/science.1249252
-
(2014)
Science
, vol.344
, pp. 55-58
-
-
Annaluru, N.1
Muller, H.2
Mitchell, L.A.3
Ramalingam, S.4
Stracquadanio, G.5
Richardson, S.M.6
-
2
-
-
84898943386
-
The influence of CpG and UpA dinucleotide frequencies on RNA virus replication and characterization of the innate cellular pathways underlying virus attenuation and enhanced replication
-
Atkinson NJ, Evans DJ, Simmonds P. 2014. The influence of CpG and UpA dinucleotide frequencies on RNA virus replication and characterization of the innate cellular pathways underlying virus attenuation and enhanced replication. Nucleic Acids Research 42:4527-4545. doi: 10.1093/nar/gku075
-
(2014)
Nucleic Acids Research
, vol.42
, pp. 4527-4545
-
-
Atkinson, N.J.1
Evans, D.J.2
Simmonds, P.3
-
4
-
-
0038620436
-
Codon pairs in the genome of escherichia coli
-
Boycheva S, Chkodrov G, Ivanov I. 2003. Codon pairs in the genome of escherichia coli. Bioinformatics 19:987-998. doi: 10.1093/bioinformatics/btg082
-
(2003)
Bioinformatics
, vol.19
, pp. 987-998
-
-
Boycheva, S.1
Chkodrov, G.2
Ivanov, I.3
-
5
-
-
33644862478
-
TRNA properties help shape codon pair preferences in open reading frames
-
Buchan JR, Aucott LS, Stansfield I. 2006. TRNA properties help shape codon pair preferences in open reading frames. Nucleic Acids Research 34:1015-1027. doi: 10.1093/nar/gkj488
-
(2006)
Nucleic Acids Research
, vol.34
, pp. 1015-1027
-
-
Buchan, J.R.1
Aucott, L.S.2
Stansfield, I.3
-
6
-
-
70349272204
-
Genetic inactivation of poliovirus infectivity by increasing the frequencies of CpG and UpA dinucleotides within and across synonymous capsid region codons
-
Burns CC, Campagnoli R, Shaw J, Vincent A, Jorba J, Kew O. 2009. Genetic inactivation of poliovirus infectivity by increasing the frequencies of CpG and UpA dinucleotides within and across synonymous capsid region codons. Journal of Virology 83:9957-9969. doi: 10.1128/JVI.00508-09
-
(2009)
Journal of Virology
, vol.83
, pp. 9957-9969
-
-
Burns, C.C.1
Campagnoli, R.2
Shaw, J.3
Vincent, A.4
Jorba, J.5
Kew, O.6
-
7
-
-
33645215084
-
Modulation of poliovirus replicative fitness in HeLa cells by deoptimization of synonymous codon usage in the capsid region
-
Burns CC, Shaw J, Campagnoli R, Jorba J, Vincent A, Quay J. 2006. Modulation of poliovirus replicative fitness in HeLa cells by deoptimization of synonymous codon usage in the capsid region. Journal of Virology 80:3259-3272. doi: 10.1128/JVI.80.7.3259-3272.2006
-
(2006)
Journal of Virology
, vol.80
, pp. 3259-3272
-
-
Burns, C.C.1
Shaw, J.2
Campagnoli, R.3
Jorba, J.4
Vincent, A.5
Quay, J.6
-
8
-
-
46449120581
-
Virus attenuation by genome-scale changes in codon pair bias
-
Coleman JR, Papamichail D, Skiena S, Futcher B, Wimmer E, Mueller S. 2008. Virus attenuation by genome-scale changes in codon pair bias. Science 320:1784-1787. doi: 10.1126/science.1155761
-
(2008)
Science
, vol.320
, pp. 1784-1787
-
-
Coleman, J.R.1
Papamichail, D.2
Skiena, S.3
Futcher, B.4
Wimmer, E.5
Mueller, S.6
-
9
-
-
2442528187
-
Efficient generation and growth of influenza virus A/PR/8/34 from eight cDNA fragments
-
de Wit E, Spronken MI, Bestebroer TM, Rimmelzwaan GF, Osterhaus AD, Fouchier RA. 2004. Efficient generation and growth of influenza virus A/PR/8/34 from eight cDNA fragments. Virus Research 103:155-161. doi: 10.1016/j.virusres.2004.02.028
-
(2004)
Virus Research
, vol.103
, pp. 155-161
-
-
De Wit, E.1
Spronken, M.I.2
Bestebroer, T.M.3
Rimmelzwaan, G.F.4
Osterhaus, A.D.5
Fouchier, R.A.6
-
10
-
-
84945231559
-
Generation of live attenuated influenza virus by using codon usage bias
-
Fan RL, Valkenburg SA, Wong CK, Li OT, Nicholls JM, Rabadan R. 2015. Generation of live attenuated influenza virus by using codon usage bias. Journal of Virology 89:10762-10773. doi: 10.1128/JVI.01443-15
-
(2015)
Journal of Virology
, vol.89
, pp. 10762-10773
-
-
Fan, R.L.1
Valkenburg, S.A.2
Wong, C.K.3
Li, O.T.4
Nicholls, J.M.5
Rabadan, R.6
-
11
-
-
77953584054
-
Creation of a bacterial cell controlled by a chemically synthesized genome
-
Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA. 2010. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329:52-56. doi: 10.1126/science.1190719
-
(2010)
Science
, vol.329
, pp. 52-56
-
-
Gibson, D.G.1
Glass, J.I.2
Lartigue, C.3
Noskov, V.N.4
Chuang, R.Y.5
Algire, M.A.6
-
12
-
-
79954456859
-
Determinants of translation efficiency and accuracy
-
Gingold H, Pilpel Y. 2011. Determinants of translation efficiency and accuracy. Molecular Systems Biology 7:481. doi: 10.1038/msb.2011.14
-
(2011)
Molecular Systems Biology
, vol.7
, pp. 481
-
-
Gingold, H.1
Pilpel, Y.2
-
13
-
-
34247869063
-
Codon conservation in the influenza a virus genome defines RNA packaging signals
-
Gog JR, Afonso ES, Dalton RM, Leclercq I, Tiley L, Elton D. 2007. Codon conservation in the influenza a virus genome defines RNA packaging signals. Nucleic Acids Research 35:1897-1907. doi: 10.1093/nar/gkm087
-
(2007)
Nucleic Acids Research
, vol.35
, pp. 1897-1907
-
-
Gog, J.R.1
Afonso, E.S.2
Dalton, R.M.3
Leclercq, I.4
Tiley, L.5
Elton, D.6
-
15
-
-
56449098772
-
Mutational analysis of cis-acting RNA signals in segment 7 of influenza a virus
-
Hutchinson EC, Curran MD, Read EK, Gog JR, Digard P. 2008. Mutational analysis of cis-acting RNA signals in segment 7 of influenza a virus. Journal of Virology 82:11869-11879. doi: 10.1128/JVI.01634-08
-
(2008)
Journal of Virology
, vol.82
, pp. 11869-11879
-
-
Hutchinson, E.C.1
Curran, M.D.2
Read, E.K.3
Gog, J.R.4
Digard, P.5
-
17
-
-
0037293142
-
Multiple amino acid residues confer temperature sensitivity to human influenza virus vaccine strains (Flumist) derived from cold-adapted a/ann arbor/6/60
-
Jin H, Lu B, Zhou H, Ma C, Zhao J, Yang CF. 2003. Multiple amino acid residues confer temperature sensitivity to human influenza virus vaccine strains (flumist) derived from cold-adapted a/ann arbor/6/60. Virology 306:18-24. doi: 10.1016/S0042-6822(02)00035-1
-
(2003)
Virology
, vol.306
, pp. 18-24
-
-
Jin, H.1
Lu, B.2
Zhou, H.3
Ma, C.4
Zhao, J.5
Yang, C.F.6
-
18
-
-
84880860622
-
Changes in codon-pair bias of human immunodeficiency virus type 1 have profound effects on virus replication in cell culture
-
Martrus G, Nevot M, Andres C, Clotet B, Martinez MA. 2013. Changes in codon-pair bias of human immunodeficiency virus type 1 have profound effects on virus replication in cell culture. Retrovirology 10:78. doi: 10.1186/1742-4690-10-78
-
(2013)
Retrovirology
, vol.10
, pp. 78
-
-
Martrus, G.1
Nevot, M.2
Res, C.3
Clotet, B.4
Martinez, M.A.5
-
19
-
-
79956225207
-
Identification of potential conserved RNA secondary structure throughout influenza a coding regions
-
Moss WN, Priore SF, Turner DH. 2011. Identification of potential conserved RNA secondary structure throughout influenza a coding regions. RNA 17:991-1011. doi: 10.1261/rna.2619511
-
(2011)
RNA
, vol.17
, pp. 991-1011
-
-
Moss, W.N.1
Priore, S.F.2
Turner, D.H.3
-
20
-
-
33644889434
-
Comparative context analysis of codon pairs on an ORFeome scale
-
Moura G, Pinheiro M, Silva R, Miranda I, Afreixo V, Dias G. 2005. Comparative context analysis of codon pairs on an ORFeome scale. Genome Biology 6:R28. doi: 10.1186/gb-2005-6-3-r28
-
(2005)
Genome Biology
, vol.6
, pp. 28
-
-
Moura, G.1
Pinheiro, M.2
Silva, R.3
Miranda, I.4
Afreixo, V.5
Dias, G.6
-
21
-
-
77954482089
-
Live attenuated influenza virus vaccines by computer-aided rational design
-
Mueller S, Coleman JR, Papamichail D, Ward CB, Nimnual A, Futcher B. 2010. Live attenuated influenza virus vaccines by computer-aided rational design. Nature Biotechnology 28:723-726. doi: 10.1038/nbt.1636
-
(2010)
Nature Biotechnology
, vol.28
, pp. 723-726
-
-
Mueller, S.1
Coleman, J.R.2
Papamichail, D.3
Ward, C.B.4
Nimnual, A.5
Futcher, B.6
-
22
-
-
84891460319
-
Computer-aided codon-pairs deoptimization of the major envelope GP5 gene attenuates porcine reproductive and respiratory syndrome virus
-
Ni YY, Zhao Z, Opriessnig T, Subramaniam S, Zhou L, Cao D. 2014. Computer-aided codon-pairs deoptimization of the major envelope GP5 gene attenuates porcine reproductive and respiratory syndrome virus. Virology 450-451:132-139. doi: 10.1016/j.virol.2013.12.009
-
(2014)
Virology
, vol.450-451
, pp. 132-139
-
-
Ni, Y.Y.1
Zhao, Z.2
Opriessnig, T.3
Subramaniam, S.4
Zhou, L.5
Cao, D.6
-
23
-
-
84906337251
-
Influenza a virus attenuation by codon deoptimization of the NS gene for vaccine development
-
Nogales A, Baker SF, Ortiz-Riano E, Dewhurst S, Topham DJ, Martinez-Sobrido L. 2014. Influenza a virus attenuation by codon deoptimization of the NS gene for vaccine development. Journal of Virology 88:10525-10540. doi: 10.1128/JVI.01565-14
-
(2014)
Journal of Virology
, vol.88
, pp. 10525-10540
-
-
Nogales, A.1
Baker, S.F.2
Ortiz-Riano, E.3
Dewhurst, S.4
Topham, D.J.5
Martinez-Sobrido, L.6
-
24
-
-
33845724694
-
Contributions of two nuclear localization signals of influenza a virus nucleoprotein to viral replication
-
Ozawa M, Fujii K, Muramoto Y, Yamada S, Yamayoshi S, Takada A. 2007. Contributions of two nuclear localization signals of influenza a virus nucleoprotein to viral replication. Journal of Virology 81:30-41. doi: 10.1128/JVI.01434-06
-
(2007)
Journal of Virology
, vol.81
, pp. 30-41
-
-
Ozawa, M.1
Fujii, K.2
Muramoto, Y.3
Yamada, S.4
Yamayoshi, S.5
Takada, A.6
-
25
-
-
84862012854
-
Influenza a virus coding regions exhibit host-specific global ordered RNA structure
-
Priore SF, Moss WN, Turner DH. 2012. Influenza a virus coding regions exhibit host-specific global ordered RNA structure. PLoS ONE 7:e35989. doi: 10.1371/journal.pone.0035989
-
(2012)
Plos ONE
, vol.7
-
-
Priore, S.F.1
Moss, W.N.2
Turner, D.H.3
-
26
-
-
53149111160
-
CAIcal: A combined set of tools to assess codon usage adaptation
-
Puigbo P, Bravo IG, CAIcal G-VS. 2008. CAIcal: a combined set of tools to assess codon usage adaptation. Biology Direct 3:38. doi: 10.1186/1745-6150-3-38
-
(2008)
Biology Direct
, vol.3
, pp. 38
-
-
Puigbo, P.1
Bravo, I.G.2
Caical, G.-V.S.3
-
27
-
-
37549015223
-
Influenza virus-specific cytotoxic t lymphocytes: A correlate of protection and a basis for vaccine development
-
Rimmelzwaan GF, Fouchier RA, Osterhaus AD. 2007. Influenza virus-specific cytotoxic t lymphocytes: a correlate of protection and a basis for vaccine development. Current Opinion in Biotechnology 18:529-536. doi: 10.1016/j.copbio.2007.11.002
-
(2007)
Current Opinion in Biotechnology
, vol.18
, pp. 529-536
-
-
Rimmelzwaan, G.F.1
Fouchier, R.A.2
Osterhaus, A.D.3
-
28
-
-
14544277543
-
Variation in the strength of selected codon usage bias among bacteria
-
Sharp PM, Bailes E, Grocock RJ, Peden JF, Sockett RE. 2005. Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Research 33:1141-1153. doi: 10.1093/nar/gki242
-
(2005)
Nucleic Acids Research
, vol.33
, pp. 1141-1153
-
-
Sharp, P.M.1
Bailes, E.2
Grocock, R.J.3
Peden, J.F.4
Sockett, R.E.5
-
29
-
-
84928152193
-
Large-scale recoding of an arbovirus genome to rebalance its insect versus mammalian preference
-
Shen SH, Stauft CB, Gorbatsevych O, Song Y, Ward CB, Yurovsky A. 2015. Large-scale recoding of an arbovirus genome to rebalance its insect versus mammalian preference. Proceedings of the National Academy of Sciences of the United States of America 112:4749-4754. doi: 10.1073/pnas.1502864112
-
(2015)
Proceedings of the National Academy of Sciences of the United States of America
, vol.112
, pp. 4749-4754
-
-
Shen, S.H.1
Stauft, C.B.2
Gorbatsevych, O.3
Song, Y.4
Ward, C.B.5
Yurovsky, A.6
-
30
-
-
84937113784
-
Dengue Attenuation of. 2015. Attenuation of dengue and other RNA viruses with codon pair recoding can be explained by increased CpG/UpA dinucleotide frequencies: Table 1
-
Simmonds P, Tulloch F, Evans DJ, Ryan MD, dengue Attenuation of. 2015. Attenuation of dengue (and other RNA viruses) with codon pair recoding can be explained by increased CpG/UpA dinucleotide frequencies: table 1. Proceedings of the National Academy of Sciences of the United States of America 112:E3633-E3634. doi: 10.1073/pnas.1507339112
-
Proceedings of the National Academy of Sciences of the United States of America
, vol.112
, pp. E3633-E3634
-
-
Simmonds, P.1
Tulloch, F.2
Evans, D.J.3
Ryan, M.D.4
-
31
-
-
84856017600
-
SSE: A nucleotide and amino acid sequence analysis platform
-
Simmonds P. SSE. 2012. SSE: a nucleotide and amino acid sequence analysis platform. BMC Research Notes 5: 50. doi: 10.1186/1756-0500-5-50
-
(2012)
BMC Research Notes
, vol.5
, pp. 50
-
-
Simmonds, P.S.S.E.1
-
32
-
-
13444267330
-
Impact of influenza vaccination on seasonal mortality in the US elderly population
-
Simonsen L, Reichert TA, Viboud C, Blackwelder WC, Taylor RJ, Miller MA. 2005. Impact of influenza vaccination on seasonal mortality in the US elderly population. Archives of Internal Medicine 165:265-272. doi: 10.1001/archinte.165.3.265
-
(2005)
Archives of Internal Medicine
, vol.165
, pp. 265-272
-
-
Simonsen, L.1
Reichert, T.A.2
Viboud, C.3
Blackwelder, W.C.4
Taylor, R.J.5
Miller, M.A.6
-
33
-
-
84887473368
-
Cellular immune correlates of protection against symptomatic pandemic influenza
-
Sridhar S, Begom S, Bermingham A, Hoschler K, Adamson W, Carman W. 2013. Cellular immune correlates of protection against symptomatic pandemic influenza. Nature Medicine 19:1305-1312. doi: 10.1038/nm.3350
-
(2013)
Nature Medicine
, vol.19
, pp. 1305-1312
-
-
Sridhar, S.1
Begom, S.2
Bermingham, A.3
Hoschler, K.4
Adamson, W.5
Carman, W.6
-
34
-
-
56749163584
-
Preferred and avoided codon pairs in three domains of life
-
Tats A, Tenson T, Remm M. 2008. Preferred and avoided codon pairs in three domains of life. BMC Genomics 9: 463-469. doi: 10.1186/1471-2164-9-463
-
(2008)
BMC Genomics
, vol.9
, pp. 463-469
-
-
Tats, A.1
Tenson, T.2
Remm, M.3
-
35
-
-
85003348904
-
RNA virus attenuation by codon pair deoptimisation is an artefact of increases in CpG/UpA dinucleotide frequencies
-
Tulloch F, Atkinson NJ, Evans DJ, Ryan MD, Simmonds P. 2014. RNA virus attenuation by codon pair deoptimisation is an artefact of increases in CpG/UpA dinucleotide frequencies. eLife 3:e04531. doi: 10.7554/eLife.04531
-
(2014)
Elife
, vol.3
, pp. 04531
-
-
Tulloch, F.1
Atkinson, N.J.2
Evans, D.J.3
Ryan, M.D.4
Simmonds, P.5
-
36
-
-
61549102424
-
Live attenuated or inactivated influenza vaccines and medical encounters for respiratory illnesses among US military personnel
-
Wang Z, Tobler S, Roayaei J, Eick A. 2009. Live attenuated or inactivated influenza vaccines and medical encounters for respiratory illnesses among US military personnel. JAMA 301:945-953. doi: 10.1001/jama.2009.265
-
(2009)
JAMA
, vol.301
, pp. 945-953
-
-
Wang, Z.1
Tobler, S.2
Roayaei, J.3
Eick, A.4
-
37
-
-
71849083415
-
Synthetic viruses: A new opportunity to understand and prevent viral disease
-
Wimmer E, Mueller S, Tumpey TM, Taubenberger JK. 2009. Synthetic viruses: a new opportunity to understand and prevent viral disease. Nature Biotechnology 27:1163-1172. doi: 10.1038/nbt.1593
-
(2009)
Nature Biotechnology
, vol.27
, pp. 1163-1172
-
-
Wimmer, E.1
Mueller, S.2
Tumpey, T.M.3
Taubenberger, J.K.4
-
38
-
-
77649168784
-
Computational identification of rare codons of escherichia coli based on codon pairs preference
-
Wu X, Wu S, Li D, Zhang J, Hou L, Ma J. 2010. Computational identification of rare codons of escherichia coli based on codon pairs preference. BMC Bioinformatics 11:61. doi: 10.1186/1471-2105-11-61
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 61
-
-
Wu, X.1
Wu, S.2
Li, D.3
Zhang, J.4
Hou, L.5
Ma, J.6
-
39
-
-
84878743809
-
Deliberate reduction of hemagglutinin and neuraminidase expression of influenza virus leads to an ultraprotective live vaccine in mice
-
Yang C, Skiena S, Futcher B, Mueller S, Wimmer E. 2013. Deliberate reduction of hemagglutinin and neuraminidase expression of influenza virus leads to an ultraprotective live vaccine in mice. Proceedings of the National Academy of Sciences of the United States of America 110:9481-9486. doi: 10.1073/pnas.1307473110
-
(2013)
Proceedings of the National Academy of Sciences of the United States of America
, vol.110
, pp. 9481-9486
-
-
Yang, C.1
Skiena, S.2
Futcher, B.3
Mueller, S.4
Wimmer, E.5
-
40
-
-
0022405085
-
Sense codons are found in specific contexts
-
Yarus M, Folley LS. 1985. Sense codons are found in specific contexts. Journal of Molecular Biology 182:529-540. doi: 10.1016/0022-2836(85)90239-6
-
(1985)
Journal of Molecular Biology
, vol.182
, pp. 529-540
-
-
Yarus, M.1
Folley, L.S.2
|