-
1
-
-
0023126266
-
Coevolution of codon usage and transfer RNA abundance
-
Bulmer M, (1987) Coevolution of codon usage and transfer RNA abundance. Nature 325: 728-730.
-
(1987)
Nature
, vol.325
, pp. 728-730
-
-
Bulmer, M.1
-
2
-
-
0032581609
-
Codon usage in highly expressed genes of Haemophillus influenzae and Mycobacterium tuberculosis: translational selection versus mutational bias
-
Pan A, Dutta C, Das J, (1998) Codon usage in highly expressed genes of Haemophillus influenzae and Mycobacterium tuberculosis: translational selection versus mutational bias. Gene 215: 405-413.
-
(1998)
Gene
, vol.215
, pp. 405-413
-
-
Pan, A.1
Dutta, C.2
Das, J.3
-
3
-
-
0030012885
-
Preference for guanosine at first codon position in highly expressed Escherichia coli genes. A relationship with translational efficiency
-
Gutierrez G, Marquez L, Marin A, (1996) Preference for guanosine at first codon position in highly expressed Escherichia coli genes. A relationship with translational efficiency. Nucleic Acids Res 24: 2525-2527.
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 2525-2527
-
-
Gutierrez, G.1
Marquez, L.2
Marin, A.3
-
4
-
-
0020491327
-
Codon usage in bacteria: correlation with gene expressivity
-
Gouy M, Gautier C, (1982) Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res 10: 7055-7074.
-
(1982)
Nucleic Acids Res
, vol.10
, pp. 7055-7074
-
-
Gouy, M.1
Gautier, C.2
-
5
-
-
0030018101
-
Ribosome-mediated translational pause and protein domain organization
-
Thanaraj TA, Argos P, (1996) Ribosome-mediated translational pause and protein domain organization. Protein Sci 5: 1594-1612.
-
(1996)
Protein Sci
, vol.5
, pp. 1594-1612
-
-
Thanaraj, T.A.1
Argos, P.2
-
6
-
-
84860231100
-
The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
-
Li GW, Oh E, Weissman JS, (2012) The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature 484: 538-541.
-
(2012)
Nature
, vol.484
, pp. 538-541
-
-
Li, G.W.1
Oh, E.2
Weissman, J.S.3
-
7
-
-
52949137359
-
Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima
-
Tsai CJ, Sauna ZE, Kimchi-Sarfaty C, Ambudkar SV, Gottesman MM, et al. (2008) Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima. J Mol Biol 383: 281-291.
-
(2008)
J Mol Biol
, vol.383
, pp. 281-291
-
-
Tsai, C.J.1
Sauna, Z.E.2
Kimchi-Sarfaty, C.3
Ambudkar, S.V.4
Gottesman, M.M.5
-
8
-
-
0034915863
-
Evidence for translational selection in codon usage in Echinococcus spp
-
Fernandez V, Zavala A, Musto H, (2001) Evidence for translational selection in codon usage in Echinococcus spp. Parasitology 123: 203-209.
-
(2001)
Parasitology
, vol.123
, pp. 203-209
-
-
Fernandez, V.1
Zavala, A.2
Musto, H.3
-
9
-
-
2442655226
-
Similar rates but different modes of sequence evolution in introns and at exonic silent sites in rodents: evidence for selectively driven codon usage
-
Chamary JV, Hurst LD, (2004) Similar rates but different modes of sequence evolution in introns and at exonic silent sites in rodents: evidence for selectively driven codon usage. Mol Biol Evol 21: 1014-1023.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 1014-1023
-
-
Chamary, J.V.1
Hurst, L.D.2
-
11
-
-
31144465926
-
Hearing silence: non-neutral evolution at synonymous sites in mammals
-
Chamary JV, Parmley JL, Hurst LD, (2006) Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet 7: 98-108.
-
(2006)
Nat Rev Genet
, vol.7
, pp. 98-108
-
-
Chamary, J.V.1
Parmley, J.L.2
Hurst, L.D.3
-
12
-
-
1542618322
-
Codon usage between genomes is constrained by genome-wide mutational processes
-
Chen SL, Lee W, Hottes AK, Shapiro L, McAdams HH, (2004) Codon usage between genomes is constrained by genome-wide mutational processes. Proc Natl Acad Sci U S A 101: 3480-3485.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 3480-3485
-
-
Chen, S.L.1
Lee, W.2
Hottes, A.K.3
Shapiro, L.4
McAdams, H.H.5
-
13
-
-
0027715731
-
Codon usage: mutational bias, translational selection, or both?
-
Sharp PM, Stenico M, Peden JF, Lloyd AT, (1993) Codon usage: mutational bias, translational selection, or both? Biochem Soc Trans 21: 835-841.
-
(1993)
Biochem Soc Trans
, vol.21
, pp. 835-841
-
-
Sharp, P.M.1
Stenico, M.2
Peden, J.F.3
Lloyd, A.T.4
-
14
-
-
70450217879
-
Human DNA methylomes at base resolution show widespread epigenomic differences
-
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315-322.
-
(2009)
Nature
, vol.462
, pp. 315-322
-
-
Lister, R.1
Pelizzola, M.2
Dowen, R.H.3
Hawkins, R.D.4
Hon, G.5
-
15
-
-
79959829720
-
Widespread RNA and DNA sequence differences in the human transcriptome
-
Li M, Wang IX, Li Y, Bruzel A, Richards AL, et al. (2011) Widespread RNA and DNA sequence differences in the human transcriptome. Science 333: 53-58.
-
(2011)
Science
, vol.333
, pp. 53-58
-
-
Li, M.1
Wang, I.X.2
Li, Y.3
Bruzel, A.4
Richards, A.L.5
-
16
-
-
84865149716
-
RNA editing of protein sequences: a rare event in human transcriptomes
-
Kleinman CL, Adoue V, Majewski J, (2012) RNA editing of protein sequences: a rare event in human transcriptomes. RNA 18: 1586-1596.
-
(2012)
RNA
, vol.18
, pp. 1586-1596
-
-
Kleinman, C.L.1
Adoue, V.2
Majewski, J.3
-
17
-
-
36049005257
-
Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses
-
Woo PC, Wong BH, Huang Y, Lau SK, Yuen KY, (2007) Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses. Virology 369: 431-442.
-
(2007)
Virology
, vol.369
, pp. 431-442
-
-
Woo, P.C.1
Wong, B.H.2
Huang, Y.3
Lau, S.K.4
Yuen, K.Y.5
-
18
-
-
0028931102
-
CpG motifs in bacterial DNA trigger direct B-cell activation
-
Krieg AM, Yi AK, Matson S, Waldschmidt TJ, Bishop GA, et al. (1995) CpG motifs in bacterial DNA trigger direct B-cell activation. Nature 374: 546-549.
-
(1995)
Nature
, vol.374
, pp. 546-549
-
-
Krieg, A.M.1
Yi, A.K.2
Matson, S.3
Waldschmidt, T.J.4
Bishop, G.A.5
-
19
-
-
0032079356
-
The 2-5A system: modulation of viral and cellular processes through acceleration of RNA degradation
-
Player MR, Torrence PF, (1998) The 2-5A system: modulation of viral and cellular processes through acceleration of RNA degradation. Pharmacol Ther 78: 55-113.
-
(1998)
Pharmacol Ther
, vol.78
, pp. 55-113
-
-
Player, M.R.1
Torrence, P.F.2
-
20
-
-
35748972351
-
Hepatitis C virus RNA: dinucleotide frequencies and cleavage by RNase L
-
Washenberger CL, Han JQ, Kechris KJ, Jha BK, Silverman RH, et al. (2007) Hepatitis C virus RNA: dinucleotide frequencies and cleavage by RNase L. Virus Res 130: 85-95.
-
(2007)
Virus Res
, vol.130
, pp. 85-95
-
-
Washenberger, C.L.1
Han, J.Q.2
Kechris, K.J.3
Jha, B.K.4
Silverman, R.H.5
-
21
-
-
4344619191
-
Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses: Implications for virus evolution and host persistence
-
Simmonds P, Tuplin A, Evans DJ, (2004) Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses: Implications for virus evolution and host persistence. Rna 10: 1337-1351.
-
(2004)
Rna
, vol.10
, pp. 1337-1351
-
-
Simmonds, P.1
Tuplin, A.2
Evans, D.J.3
-
22
-
-
0029866750
-
cis-acting elements within an RNA coliphage genome: fold as you please, but fold you must!!
-
Arora R, Priano C, Jacobson AB, Mills DR, (1996) cis-acting elements within an RNA coliphage genome: fold as you please, but fold you must!!. J Mol Biol 258: 433-446.
-
(1996)
J Mol Biol
, vol.258
, pp. 433-446
-
-
Arora, R.1
Priano, C.2
Jacobson, A.B.3
Mills, D.R.4
-
23
-
-
59749104648
-
Cis-active RNA elements (CREs) and picornavirus RNA replication
-
Steil BP, Barton DJ, (2009) Cis-active RNA elements (CREs) and picornavirus RNA replication. Virus Res 139: 240-252.
-
(2009)
Virus Res
, vol.139
, pp. 240-252
-
-
Steil, B.P.1
Barton, D.J.2
-
24
-
-
77950363191
-
A new type of IRES within gag coding region recruits three initiation complexes on HIV-2 genomic RNA
-
Weill L, James L, Ulryck N, Chamond N, Herbreteau CH, et al. (2010) A new type of IRES within gag coding region recruits three initiation complexes on HIV-2 genomic RNA. Nucleic Acids Res 38: 1367-1381.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 1367-1381
-
-
Weill, L.1
James, L.2
Ulryck, N.3
Chamond, N.4
Herbreteau, C.H.5
-
25
-
-
0023650543
-
The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications
-
Sharp PM, Li WH, (1987) The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15: 1281-1295.
-
(1987)
Nucleic Acids Res
, vol.15
, pp. 1281-1295
-
-
Sharp, P.M.1
Li, W.H.2
-
26
-
-
0021958933
-
Codon usage and tRNA content in unicellular and multicellular organisms
-
Ikemura T, (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 2: 13-34.
-
(1985)
Mol Biol Evol
, vol.2
, pp. 13-34
-
-
Ikemura, T.1
-
27
-
-
4644280499
-
Solving the riddle of codon usage preferences: a test for translational selection
-
dos Reis M, Savva R, Wernisch L, (2004) Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res 32: 5036-5044.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 5036-5044
-
-
dos Reis, M.1
Savva, R.2
Wernisch, L.3
-
28
-
-
0345188623
-
Papillomavirus capsid protein expression level depends on the match between codon usage and tRNA availability
-
Zhou J, Liu WJ, Peng SW, Sun XY, Frazer I, (1999) Papillomavirus capsid protein expression level depends on the match between codon usage and tRNA availability. J Virol 73: 4972-4982.
-
(1999)
J Virol
, vol.73
, pp. 4972-4982
-
-
Zhou, J.1
Liu, W.J.2
Peng, S.W.3
Sun, X.Y.4
Frazer, I.5
-
29
-
-
0022363196
-
Enhancement of RNA polymerase III transcription by the E1A gene product of adenovirus
-
Hoeffler WK, Roeder RG, (1985) Enhancement of RNA polymerase III transcription by the E1A gene product of adenovirus. Cell 41: 955-963.
-
(1985)
Cell
, vol.41
, pp. 955-963
-
-
Hoeffler, W.K.1
Roeder, R.G.2
-
30
-
-
0023442679
-
Inhibition of host cell RNA polymerase III-mediated transcription by poliovirus: inactivation of specific transcription factors
-
Fradkin LG, Yoshinaga SK, Berk AJ, Dasgupta A, (1987) Inhibition of host cell RNA polymerase III-mediated transcription by poliovirus: inactivation of specific transcription factors. Mol Cell Biol 7: 3880-3887.
-
(1987)
Mol Cell Biol
, vol.7
, pp. 3880-3887
-
-
Fradkin, L.G.1
Yoshinaga, S.K.2
Berk, A.J.3
Dasgupta, A.4
-
31
-
-
0025318864
-
The 'effective number of codons' used in a gene
-
Wright F, (1990) The 'effective number of codons' used in a gene. Gene 87: 23-29.
-
(1990)
Gene
, vol.87
, pp. 23-29
-
-
Wright, F.1
-
32
-
-
0036667702
-
Accounting for background nucleotide composition when measuring codon usage bias
-
Novembre JA, (2002) Accounting for background nucleotide composition when measuring codon usage bias. Mol Biol Evol 19: 1390-1394.
-
(2002)
Mol Biol Evol
, vol.19
, pp. 1390-1394
-
-
Novembre, J.A.1
-
33
-
-
33745601642
-
Accounting for background nucleotide composition when measuring codon usage bias: brilliant idea, difficult in practice
-
Fuglsang A, (2006) Accounting for background nucleotide composition when measuring codon usage bias: brilliant idea, difficult in practice. Mol Biol Evol 23: 1345-1347.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 1345-1347
-
-
Fuglsang, A.1
-
34
-
-
0037372775
-
The extent of codon usage bias in human RNA viruses and its evolutionary origin
-
Jenkins GM, Holmes EC, (2003) The extent of codon usage bias in human RNA viruses and its evolutionary origin. Virus Res 92: 1-7.
-
(2003)
Virus Res
, vol.92
, pp. 1-7
-
-
Jenkins, G.M.1
Holmes, E.C.2
-
35
-
-
76549201264
-
Comparison of the base composition of nucleic acids of nuclei and cytoplasm of different mammalian tissues
-
Marshak A, (1950) Comparison of the base composition of nucleic acids of nuclei and cytoplasm of different mammalian tissues. Biol Bull 99: 332-333.
-
(1950)
Biol Bull
, vol.99
, pp. 332-333
-
-
Marshak, A.1
-
36
-
-
0028221062
-
Why is CpG suppressed in the genomes of virtually all small eukaryotic viruses but not in those of large eukaryotic viruses?
-
Karlin S, Doerfler W, Cardon LR, (1994) Why is CpG suppressed in the genomes of virtually all small eukaryotic viruses but not in those of large eukaryotic viruses? J Virol 68: 2889-2897.
-
(1994)
J Virol
, vol.68
, pp. 2889-2897
-
-
Karlin, S.1
Doerfler, W.2
Cardon, L.R.3
-
37
-
-
46449083518
-
Patterns of evolution and host gene mimicry in influenza and other RNA viruses
-
Greenbaum BD, Levine AJ, Bhanot G, Rabadan R, (2008) Patterns of evolution and host gene mimicry in influenza and other RNA viruses. PLoS Pathog 4: e1000079.
-
(2008)
PLoS Pathog
, vol.4
-
-
Greenbaum, B.D.1
Levine, A.J.2
Bhanot, G.3
Rabadan, R.4
-
38
-
-
67650169079
-
Patterns of oligonucleotide sequences in viral and host cell RNA identify mediators of the host innate immune system
-
Greenbaum BD, Rabadan R, Levine AJ, (2009) Patterns of oligonucleotide sequences in viral and host cell RNA identify mediators of the host innate immune system. PLoS One 4: e5969.
-
(2009)
PLoS One
, vol.4
-
-
Greenbaum, B.D.1
Rabadan, R.2
Levine, A.J.3
-
39
-
-
84861118756
-
Genetic variation and recombination in Aichi virus
-
Lukashev A, Drexler JF, Belalov I, Eschbach-Bludau M, Baumgarte S, et al. (2012) Genetic variation and recombination in Aichi virus. J Gen Virol.
-
(2012)
J Gen Virol
-
-
Lukashev, A.1
Drexler, J.F.2
Belalov, I.3
Eschbach-Bludau, M.4
Baumgarte, S.5
-
40
-
-
0347135951
-
Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids
-
Rispe C, Delmotte F, van Ham RC, Moya A, (2004) Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids. Genome Res 14: 44-53.
-
(2004)
Genome Res
, vol.14
, pp. 44-53
-
-
Rispe, C.1
Delmotte, F.2
van Ham, R.C.3
Moya, A.4
-
41
-
-
0842330869
-
Codon usage bias amongst plant viruses
-
Adams MJ, Antoniw JF, (2004) Codon usage bias amongst plant viruses. Arch Virol 149: 113-135.
-
(2004)
Arch Virol
, vol.149
, pp. 113-135
-
-
Adams, M.J.1
Antoniw, J.F.2
-
42
-
-
0036176330
-
Codon and amino acid usage in retroviral genomes is consistent with virus-specific nucleotide pressure
-
Berkhout B, Grigoriev A, Bakker M, Lukashov VV, (2002) Codon and amino acid usage in retroviral genomes is consistent with virus-specific nucleotide pressure. AIDS Res Hum Retroviruses 18: 133-141.
-
(2002)
AIDS Res Hum Retroviruses
, vol.18
, pp. 133-141
-
-
Berkhout, B.1
Grigoriev, A.2
Bakker, M.3
Lukashov, V.V.4
-
43
-
-
33745654553
-
Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses
-
Shackelton LA, Parrish CR, Holmes EC, (2006) Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses. J Mol Evol 62: 551-563.
-
(2006)
J Mol Evol
, vol.62
, pp. 551-563
-
-
Shackelton, L.A.1
Parrish, C.R.2
Holmes, E.C.3
-
44
-
-
0033214628
-
Heuristic approach to deriving models for gene finding
-
Besemer J, Borodovsky M, (1999) Heuristic approach to deriving models for gene finding. Nucleic Acids Res 27: 3911-3920.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 3911-3920
-
-
Besemer, J.1
Borodovsky, M.2
-
45
-
-
0031020582
-
Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria
-
Foster PG, Jermiin LS, Hickey DA, (1997) Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria. J Mol Evol 44: 282-288.
-
(1997)
J Mol Evol
, vol.44
, pp. 282-288
-
-
Foster, P.G.1
Jermiin, L.S.2
Hickey, D.A.3
-
46
-
-
0033745103
-
Nucleotide bias causes a genomewide bias in the amino acid composition of proteins
-
Singer GA, Hickey DA, (2000) Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Mol Biol Evol 17: 1581-1588.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 1581-1588
-
-
Singer, G.A.1
Hickey, D.A.2
-
47
-
-
0342614926
-
Codon usage tabulated from the international DNA sequence databases: status for the year 2000
-
Nakamura Y, Gojobori T, Ikemura T, (2000) Codon usage tabulated from the international DNA sequence databases: status for the year 2000. Nucleic Acids Research pp. 292.
-
(2000)
Nucleic Acids Research
, pp. 292
-
-
Nakamura, Y.1
Gojobori, T.2
Ikemura, T.3
-
48
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
Lander, E.S.1
Linton, L.M.2
Birren, B.3
Nusbaum, C.4
Zody, M.C.5
-
49
-
-
0034818948
-
Skew of mononucleotide frequencies, relative abundance of dinucleotides, and DNA strand asymmetry
-
Shioiri C, Takahata N, (2001) Skew of mononucleotide frequencies, relative abundance of dinucleotides, and DNA strand asymmetry. J Mol Evol 53: 364-376.
-
(2001)
J Mol Evol
, vol.53
, pp. 364-376
-
-
Shioiri, C.1
Takahata, N.2
-
50
-
-
84874517150
-
-
St.Andrews, Scotland
-
Burns CC, Campagnoli R, Shaw J, Vincent A, Jorba J, et al. Introduction of CpG and UpA dinucleotides within and across synonymous capsid region codons differentially decreases replicative fitness.; 2010; St.Andrews, Scotland. pp. 68.
-
(2010)
Introduction of CpG and UpA dinucleotides within and across synonymous capsid region codons differentially decreases replicative fitness
, pp. 68
-
-
Burns, C.C.1
Campagnoli, R.2
Shaw, J.3
Vincent, A.4
Jorba, J.5
-
51
-
-
33645277360
-
Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation
-
Doma MK, Parker R, (2006) Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation. Nature 440: 561-564.
-
(2006)
Nature
, vol.440
, pp. 561-564
-
-
Doma, M.K.1
Parker, R.2
-
52
-
-
4143071549
-
APOBEC3F properties and hypermutation preferences indicate activity against HIV-1 in vivo
-
Liddament MT, Brown WL, Schumacher AJ, Harris RS, (2004) APOBEC3F properties and hypermutation preferences indicate activity against HIV-1 in vivo. Curr Biol 14: 1385-1391.
-
(2004)
Curr Biol
, vol.14
, pp. 1385-1391
-
-
Liddament, M.T.1
Brown, W.L.2
Schumacher, A.J.3
Harris, R.S.4
|