-
1
-
-
0031805147
-
How optimized is the translational machinery in Escherichia coli Salmonella typhimurium and Saccharomyces cerevisiae?
-
Xia,X. (1998) How optimized is the translational machinery in Escherichia coli, Salmonella typhimurium and Saccharomyces cerevisiae? Genetics, 149, 37-44.
-
(1998)
Genetics
, vol.149
, pp. 37-44
-
-
Xia, X.1
-
2
-
-
77951734603
-
A role for codon order in translation dynamics
-
Cannarozzi,G., Schraudolph,N.N., Faty,M., von Rohr,P., Friberg,M.T., Roth,A.C., Gonnet,P., Gonnet,G. and Barral,Y. (2010) A role for codon order in translation dynamics. Cell, 141, 355-367.
-
(2010)
Cell
, vol.141
, pp. 355-367
-
-
Cannarozzi, G.1
Schraudolph, N.N.2
Faty, M.3
Von Rohr, P.4
Friberg, M.T.5
Roth, A.C.6
Gonnet, P.7
Gonnet, G.8
Barral, Y.9
-
3
-
-
33645801951
-
Comparison of characteristics and function of translation termination signals between and within prokaryotic and eukaryotic organisms
-
Cridge,A.G., Major,L.L., Mahagaonkar,A.A., Poole,E.S., Isaksson,L.A. and Tate,W.P. (2006) Comparison of characteristics and function of translation termination signals between and within prokaryotic and eukaryotic organisms. Nucleic Acids Res., 34, 1959-1973.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 1959-1973
-
-
Cridge, A.G.1
Major, L.L.2
Mahagaonkar, A.A.3
Poole, E.S.4
Isaksson, L.A.5
Tate, W.P.6
-
4
-
-
0037406116
-
A quantitative analysis of intron effects on mammalian gene expression
-
Nott,A., Meislin,S.H. and Moore,M.J. (2003) A quantitative analysis of intron effects on mammalian gene expression. RNA, 9, 607-617.
-
(2003)
RNA
, vol.9
, pp. 607-617
-
-
Nott, A.1
Meislin, S.H.2
Moore, M.J.3
-
5
-
-
34447255471
-
Post-transcriptional regulatory element boosts baculovirus-mediated gene expression in vertebrate cells
-
Mahonen,A.J., Airenne,K.J., Purola,S., Peltomaa,E., Kaikkonen,M.U., Riekkinen,M.S., Heikura,T., Kinnunen,K., Roschier,M.M.,Wirth,T. et al. (2007) Post-transcriptional regulatory element boosts baculovirus-mediated gene expression in vertebrate cells. J. Biotechnol., 131, 1-8.
-
(2007)
J. Biotechnol.
, vol.131
, pp. 1-8
-
-
Mahonen, A.J.1
Airenne, K.J.2
Purola, S.3
Peltomaa, E.4
Kaikkonen, M.U.5
Riekkinen, M.S.6
Heikura, T.7
Kinnunen, K.8
Roschier, M.M.9
Wirth, T.10
-
6
-
-
0022552131
-
Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes
-
Kozak,M. (1986) Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell, 44, 283-292.
-
(1986)
Cell
, vol.44
, pp. 283-292
-
-
Kozak, M.1
-
7
-
-
84860197135
-
Using translational enhancers to increase transgene expression in Drosophila
-
Pfeiffer,B.D., Truman,J.W. and Rubin,G.M. (2012) Using translational enhancers to increase transgene expression in Drosophila. Proc. Natl Acad. Sci. U.S.A., 109, 6626-6631.
-
(2012)
Proc. Natl Acad. Sci. U.S.A.
, vol.109
, pp. 6626-6631
-
-
Pfeiffer, B.D.1
Truman, J.W.2
Rubin, G.M.3
-
8
-
-
0025348395
-
Suppression of the negative effect of minor arginine codons on gene expression; Preferential usage of minor codons within the first 25 codons of the Escherichia coli genes
-
Chen,G.-F.T. and Inouye,M. (1990) Suppression of the negative effect of minor arginine codons on gene expression; preferential usage of minor codons within the first 25 codons of the Escherichia coli genes. Nucleic Acids Res., 18, 1465-1473.
-
(1990)
Nucleic Acids Res.
, vol.18
, pp. 1465-1473
-
-
Chen, G.-F.T.1
Inouye, M.2
-
9
-
-
0027137059
-
The effect of sequences with high AU content on mRNA stability in tobacco
-
Ohme-Takagi,M., Taylor,C.B., Newman,T.C. and Green,P.J. (1993) The effect of sequences with high AU content on mRNA stability in tobacco. Proc. Natl Acad. Sci. U.S.A., 90, 11811-11815.
-
(1993)
Proc. Natl Acad. Sci. U.S.A.
, vol.90
, pp. 11811-11815
-
-
Ohme-Takagi, M.1
Taylor, C.B.2
Newman, T.C.3
Green, P.J.4
-
10
-
-
0030989517
-
Removal of a cryptic intron and subcellular localization of green fluorescent protein are required to mark transgenic Arabidopsis plants brightly
-
Haseloff,J., Siemering,K.R., Prasher,D.C. and Hodge,S. (1997) Removal of a cryptic intron and subcellular localization of green fluorescent protein are required to mark transgenic Arabidopsis plants brightly. Proc. Natl Acad. Sci. U.S.A., 94, 2122-2127.
-
(1997)
Proc. Natl Acad. Sci. U.S.A.
, vol.94
, pp. 2122-2127
-
-
Haseloff, J.1
Siemering, K.R.2
Prasher, D.C.3
Hodge, S.4
-
11
-
-
64849114915
-
Coding-sequence determinants of gene expression in Escherichia coli
-
Kudla,G., Murray,A.W., Tollervey,D. and Plotkin,J.B. (2009) Coding-sequence determinants of gene expression in Escherichia coli. Science, 324, 255-258.
-
(2009)
Science
, vol.324
, pp. 255-258
-
-
Kudla, G.1
Murray, A.W.2
Tollervey, D.3
Plotkin, J.B.4
-
12
-
-
69449096142
-
Optimized Gal4 genetics for permanent gene expression mapping in zebrafish
-
Distel,M., Wullimann,M.F. and Koster,R.W. (2009) Optimized Gal4 genetics for permanent gene expression mapping in zebrafish. Proc. Natl Acad. Sci. U.S.A., 106, 13365-13370.
-
(2009)
Proc. Natl Acad. Sci. U.S.A.
, vol.106
, pp. 13365-13370
-
-
Distel, M.1
Wullimann, M.F.2
Koster, R.W.3
-
13
-
-
16644391315
-
Transgenesis and gene trap methods in zebrafish by using the Tol2 transposable element
-
Kawakami,K. (2004) Transgenesis and gene trap methods in zebrafish by using the Tol2 transposable element. Methods Cell Biol., 77, 201-222.
-
(2004)
Methods Cell Biol.
, vol.77
, pp. 201-222
-
-
Kawakami, K.1
-
14
-
-
84887466041
-
Transcript processing and export kinetics are rate-limiting steps in expressing vertebrate segmentation clock genes
-
Hoyle,N.P. and Ish-Horowicz,D. (2013) Transcript processing and export kinetics are rate-limiting steps in expressing vertebrate segmentation clock genes. Proc. Natl Acad. Sci. U.S.A., 110, E4316-E4324.
-
(2013)
Proc. Natl Acad. Sci. U.S.A.
, vol.110
, pp. 4316-4324
-
-
Hoyle, N.P.1
Ish-Horowicz, D.2
-
15
-
-
77951925182
-
The Q system: A repressible binary system for transgene expression, lineage tracing, and mosaic analysis
-
Potter,C.J., Tasic,B., Russler,E.V., Liang,L. and Luo,L. (2010) The Q system: A repressible binary system for transgene expression, lineage tracing, and mosaic analysis. Cell, 141, 536-548.
-
(2010)
Cell
, vol.141
, pp. 536-548
-
-
Potter, C.J.1
Tasic, B.2
Russler, E.V.3
Liang, L.4
Luo, L.5
-
16
-
-
84894045252
-
TAILOR: Transgene activation and inactivation using lox and rox in zebrafish
-
Park,J.T. and Leach,S.D. (2013) TAILOR: Transgene activation and inactivation using lox and rox in zebrafish. PLoS One, 8, e85218.
-
(2013)
PLoS One
, vol.8
, pp. e85218
-
-
Park, J.T.1
Leach, S.D.2
-
17
-
-
33847012504
-
Targeted ablation of beta cells in the embryonic zebrafish pancreas using E. Coli nitroreductase
-
Pisharath,H., Rhee,J.M., Swanson,M.A., Leach,S.D. and Parsons,M.J. (2007) Targeted ablation of beta cells in the embryonic zebrafish pancreas using E. coli nitroreductase. Mech. Dev., 124, 218-229.
-
(2007)
Mech. Dev.
, vol.124
, pp. 218-229
-
-
Pisharath, H.1
Rhee, J.M.2
Swanson, M.A.3
Leach, S.D.4
Parsons, M.J.5
-
18
-
-
0025360095
-
Targeted insertion of exogenous DNA into the eukaryotic genome by the Cre recombinase
-
Sauer,B. and Henderson,N. (1990) Targeted insertion of exogenous DNA into the eukaryotic genome by the Cre recombinase. New Biol., 2, 441-449.
-
(1990)
New Biol.
, vol.2
, pp. 441-449
-
-
Sauer, B.1
Henderson, N.2
-
19
-
-
39549113462
-
Genetic dissection of neural circuits by Tol2 transposon-mediated Gal4 gene and enhancer trapping in zebrafish
-
Asakawa,K., Suster,M.L., Mizusawa,K., Nagayoshi,S., Kotani,T., Urasaki,A., Kishimoto,Y., Hibi,M. and Kawakami,K. (2008) Genetic dissection of neural circuits by Tol2 transposon-mediated Gal4 gene and enhancer trapping in zebrafish. Proc. Natl Acad. Sci. U.S.A., 105, 1255-1260.
-
(2008)
Proc. Natl Acad. Sci. U.S.A.
, vol.105
, pp. 1255-1260
-
-
Asakawa, K.1
Suster, M.L.2
Mizusawa, K.3
Nagayoshi, S.4
Kotani, T.5
Urasaki, A.6
Kishimoto, Y.7
Hibi, M.8
Kawakami, K.9
-
20
-
-
51549109524
-
Germline transgenesis of zebrafish using the medaka Tol1 transposon system
-
Koga,A., Cheah,F.S., Hamaguchi,S., Yeo,G.H. and Chong,S.S. (2008) Germline transgenesis of zebrafish using the medaka Tol1 transposon system. Dev. Dyn., 237, 2466-2474.
-
(2008)
Dev. Dyn.
, vol.237
, pp. 2466-2474
-
-
Koga, A.1
Cheah, F.S.2
Hamaguchi, S.3
Yeo, G.H.4
Chong, S.S.5
-
21
-
-
1842424983
-
An improved cyan fluorescent protein variant useful for FRET
-
Rizzo,M.A., Springer,G.H., Granada,B. and Piston,D.W. (2004) An improved cyan fluorescent protein variant useful for FRET. Nat. Biotech., 22, 445-449.
-
(2004)
Nat. Biotech.
, vol.22
, pp. 445-449
-
-
Rizzo, M.A.1
Springer, G.H.2
Granada, B.3
Piston, D.W.4
-
22
-
-
84906092822
-
Direct activation of the Mauthner cell by electric field pulses drives ultra-rapid escape responses
-
Tabor,K.M., Bergeron,S.A., Horstick,E.J., Jordan,D.C., Aho,V., Porkka-Heiskanen,T., Haspel,G. and Burgess,H.A. (2014) Direct activation of the Mauthner cell by electric field pulses drives ultra-rapid escape responses. J. Neurophysiol., 112, 834-844.
-
(2014)
J. Neurophysiol.
, vol.112
, pp. 834-844
-
-
Tabor, K.M.1
Bergeron, S.A.2
Horstick, E.J.3
Jordan, D.C.4
Aho, V.5
Porkka-Heiskanen, T.6
Haspel, G.7
Burgess, H.A.8
-
23
-
-
84867785683
-
The dorsal raphe modulates sensory responsiveness during arousal in zebrafish
-
Yokogawa,T., Hannan,M.C. and Burgess,H.A. (2012) The dorsal raphe modulates sensory responsiveness during arousal in zebrafish. J. Neurosci., 32, 15205-15215.
-
(2012)
J. Neurosci.
, vol.32
, pp. 15205-15215
-
-
Yokogawa, T.1
Hannan, M.C.2
Burgess, H.A.3
-
24
-
-
33645103149
-
Woodchuck hepatitis virus post-transcriptional regulatory element deleted from X protein and promoter sequences enhances retroviral vector titer and expression
-
Schambach,A., Bohne,J., Baum,C., Hermann,F.G., Egerer,L., von Laer,D. and Giroglou,T. (2006) Woodchuck hepatitis virus post-transcriptional regulatory element deleted from X protein and promoter sequences enhances retroviral vector titer and expression. Gene Ther., 13, 641-645.
-
(2006)
Gene Ther.
, vol.13
, pp. 641-645
-
-
Schambach, A.1
Bohne, J.2
Baum, C.3
Hermann, F.G.4
Egerer, L.5
Von Laer, D.6
Giroglou, T.7
-
25
-
-
0034084367
-
GFP as a genetic marker scorable throughout the life cycle of transgenic zebra fish
-
(NY
-
Gibbs,P.D. and Schmale,M.C. (2000) GFP as a genetic marker scorable throughout the life cycle of transgenic zebra fish. Mar. Biotechnol. (NY), 2, 107-125.
-
(2000)
Mar. Biotechnol.
, vol.2
, pp. 107-125
-
-
Gibbs, P.D.1
Schmale, M.C.2
-
26
-
-
61649086683
-
Adaptation of GAL4 activators for GAL4 enhancer trapping in zebrafish
-
Ogura,E., Okuda,Y., Kondoh,H. and Kamachi,Y. (2009) Adaptation of GAL4 activators for GAL4 enhancer trapping in zebrafish. Dev. Dyn., 238, 641-655.
-
(2009)
Dev. Dyn.
, vol.238
, pp. 641-655
-
-
Ogura, E.1
Okuda, Y.2
Kondoh, H.3
Kamachi, Y.4
-
27
-
-
33846470670
-
Controlled expression of transgenes introduced by in vivo electroporation
-
Matsuda,T. and Cepko,C.L. (2007) Controlled expression of transgenes introduced by in vivo electroporation. Proc. Natl Acad. Sci. U.S.A., 104, 1027-1032.
-
(2007)
Proc. Natl Acad. Sci. U.S.A.
, vol.104
, pp. 1027-1032
-
-
Matsuda, T.1
Cepko, C.L.2
-
28
-
-
0021770860
-
Functional messenger RNAs are produced by SP6 in vitro transcription of cloned cDNAs
-
Krieg,P.A. and Melton,D.A. (1984) Functional messenger RNAs are produced by SP6 in vitro transcription of cloned cDNAs. Nucleic Acids Res., 12, 7057-7070.
-
(1984)
Nucleic Acids Res.
, vol.12
, pp. 7057-7070
-
-
Krieg, P.A.1
Melton, D.A.2
-
29
-
-
84897934960
-
Adoption of the Q transcriptional regulatory system for zebrafish transgenesis
-
Subedi,A., Macurak,M., Gee,S.T., Monge,E., Goll,M.G., Potter,C.J., Parsons,M.J. and Halpern,M.E. (2014) Adoption of the Q transcriptional regulatory system for zebrafish transgenesis. Methods, 66, 433-440.
-
(2014)
Methods
, vol.66
, pp. 433-440
-
-
Subedi, A.1
Macurak, M.2
Gee, S.T.3
Monge, E.4
Goll, M.G.5
Potter, C.J.6
Parsons, M.J.7
Halpern, M.E.8
-
30
-
-
33750433896
-
Functional dissection of the Tol2 transposable element identified the minimal cis-sequence and a highly repetitive sequence in the subterminal region essential for transposition
-
Urasaki,A., Morvan,G. and Kawakami,K. (2006) Functional dissection of the Tol2 transposable element identified the minimal cis-sequence and a highly repetitive sequence in the subterminal region essential for transposition. Genetics, 174, 639-649.
-
(2006)
Genetics
, vol.174
, pp. 639-649
-
-
Urasaki, A.1
Morvan, G.2
Kawakami, K.3
-
31
-
-
36448963734
-
The Tol2kit: A multisite gateway-based construction kit for Tol2 transposon transgenesis constructs
-
Kwan,K.M., Fujimoto,E., Grabher,C., Mangum,B.D., Hardy,M.E., Campbell,D.S., Parant,J.M., Yost,H.J., Kanki,J.P. and Chien,C.-B. (2007) The Tol2kit: A multisite gateway-based construction kit for Tol2 transposon transgenesis constructs. Dev. Dyn., 236, 3088-3099.
-
(2007)
Dev. Dyn.
, vol.236
, pp. 3088-3099
-
-
Kwan, K.M.1
Fujimoto, E.2
Grabher, C.3
Mangum, B.D.4
Hardy, M.E.5
Campbell, D.S.6
Parant, J.M.7
Yost, H.J.8
Kanki, J.P.9
Chien, C.-B.10
-
32
-
-
84937816222
-
Gsx1 expression defines neurons required for prepulse inhibition
-
Bergeron,S.A., Carrier,N., Li,G.H., Ahn,S. and Burgess,H.A. (2014) Gsx1 expression defines neurons required for prepulse inhibition. Mol. Psychiatry., doi:10.1038/mp.2014.106.
-
(2014)
Mol. Psychiatry.
-
-
Bergeron, S.A.1
Carrier, N.2
Li, G.H.3
Ahn, S.4
Burgess, H.A.5
-
33
-
-
84871303702
-
Brain selective transgene expression in zebrafish using an NRSE derived motif
-
Bergeron,S.A., Hannan,M.C., Codore,H., Fero,K., Li,G., Moak,Z.B., Yokogawa,T. and Burgess,H.A. (2012) Brain selective transgene expression in zebrafish using an NRSE derived motif. Front. Neural Circuits, 6, 110.
-
(2012)
Front. Neural Circuits
, vol.6
, pp. 110
-
-
Bergeron, S.A.1
Hannan, M.C.2
Codore, H.3
Fero, K.4
Li, G.5
Moak, Z.B.6
Yokogawa, T.7
Burgess, H.A.8
-
34
-
-
0033818956
-
Multiplex detection and quantitation of proteins on western blots using fluorescent probes
-
Gingrich,J.C., Davis,D.R. and Nguyen,Q. (2000) Multiplex detection and quantitation of proteins on western blots using fluorescent probes. BioTechniques, 29, 636-642.
-
(2000)
BioTechniques
, vol.29
, pp. 636-642
-
-
Gingrich, J.C.1
Davis, D.R.2
Nguyen, Q.3
-
35
-
-
56149092930
-
Identification of Spt5 target genes in zebrafish development reveals its dual activity in vivo
-
Krishnan,K., Salomonis,N. and Guo,S. (2008) Identification of Spt5 target genes in zebrafish development reveals its dual activity in vivo. PLoS One, 3, e3621.
-
(2008)
PLoS One
, vol.3
, pp. e3621
-
-
Krishnan, K.1
Salomonis, N.2
Guo, S.3
-
36
-
-
77953037177
-
Ovo1 links Wnt signaling with N-cadherin localization during neural crest migration
-
Piloto,S. and Schilling,T.F. (2010) Ovo1 links Wnt signaling with N-cadherin localization during neural crest migration. Development, 137, 1981-1990.
-
(2010)
Development
, vol.137
, pp. 1981-1990
-
-
Piloto, S.1
Schilling, T.F.2
-
37
-
-
0347763875
-
Dynamics of global gene expression changes during mouse preimplantation development
-
Hamatani,T., Carter,M.G., Sharov,A.A. and Ko,M.S.H. (2004) Dynamics of global gene expression changes during mouse preimplantation development. Dev. Cell, 6, 117-131.
-
(2004)
Dev. Cell
, vol.6
, pp. 117-131
-
-
Hamatani, T.1
Carter, M.G.2
Sharov, A.A.3
Ko, M.S.H.4
-
38
-
-
77952962147
-
Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species
-
Xie,D., Chen,C.-C., Ptaszek,L.M., Xiao,S., Cao,X., Fang,F., Ng,H.H., Lewin,H.A., Cowan,C. and Zhong,S. (2010) Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species. Genome Res., 20, 804-815.
-
(2010)
Genome Res.
, vol.20
, pp. 804-815
-
-
Xie, D.1
Chen, C.-C.2
Ptaszek, L.M.3
Xiao, S.4
Cao, X.5
Fang, F.6
Ng, H.H.7
Lewin, H.A.8
Cowan, C.9
Zhong, S.10
-
39
-
-
41549113766
-
Transcriptome and proteome analysis of early embryonic mouse brain development
-
Hartl,D., Irmler,M., Römer,I., Mader,M.T., Mao,L., Zabel,C., De Angelis,M.H., Beckers,J. and Klose,J. (2008) Transcriptome and proteome analysis of early embryonic mouse brain development. Proteomics, 8, 1257-1265.
-
(2008)
Proteomics
, vol.8
, pp. 1257-1265
-
-
Hartl, D.1
Irmler, M.2
Römer, I.3
Mader, M.T.4
Mao, L.5
Zabel, C.6
De Angelis, M.H.7
Beckers, J.8
Klose, J.9
-
40
-
-
67949097345
-
Maternal diabetes alters transcriptional programs in the developing embryo
-
Pavlinkova,G., Salbaum,J.M. and Kappen,C. (2009) Maternal diabetes alters transcriptional programs in the developing embryo. BMC Genomics, 10, 274.
-
(2009)
BMC Genomics
, vol.10
, pp. 274
-
-
Pavlinkova, G.1
Salbaum, J.M.2
Kappen, C.3
-
41
-
-
0345346377
-
Codon usage tabulated from international DNA sequence databases: Status for the year 2000
-
Nakamura,Y., Gojobori,T. and Ikemura,T. (2000) Codon usage tabulated from international DNA sequence databases: Status for the year 2000. Nucleic Acids Res., 28, 292.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 292
-
-
Nakamura, Y.1
Gojobori, T.2
Ikemura, T.3
-
42
-
-
0030854739
-
TRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
-
Lowe,T.M. and Eddy,S.R. (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
43
-
-
2142738304
-
WebLogo: A sequence logo generator
-
Crooks,G.E., Hon,G., Chandonia,J.-M. and Brenner,S.E. (2004) WebLogo: A sequence logo generator. Genome Res., 14, 1188-1190.
-
(2004)
Genome Res.
, vol.14
, pp. 1188-1190
-
-
Crooks, G.E.1
Hon, G.2
Chandonia, J.-M.3
Brenner, S.E.4
-
44
-
-
84934438960
-
UNAFold: Software for nucleic acid folding and hybridization
-
Markham,N.R. and Zuker,M. (2008) UNAFold: Software for nucleic acid folding and hybridization. Methods Mol. Biol., 453, 3-31.
-
(2008)
Methods Mol. Biol.
, vol.453
, pp. 3-31
-
-
Markham, N.R.1
Zuker, M.2
-
45
-
-
80053442983
-
A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes
-
Csuros,M., Rogozin,I.B. and Koonin,E.V. (2011) A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes. PLoS Comput. Biol., 7, e1002150.
-
(2011)
PLoS Comput. Biol.
, vol.7
, pp. e1002150
-
-
Csuros, M.1
Rogozin, I.B.2
Koonin, E.V.3
-
46
-
-
0036699596
-
Selection for short introns in highly expressed genes
-
Castillo-Davis,C.I., Mekhedov,S.L., Hartl,D.L., Koonin,E.V. and Kondrashov,F.A. (2002) Selection for short introns in highly expressed genes. Nat. Genet., 31, 415-418.
-
(2002)
Nat. Genet.
, vol.31
, pp. 415-418
-
-
Castillo-Davis, C.I.1
Mekhedov, S.L.2
Hartl, D.L.3
Koonin, E.V.4
Kondrashov, F.A.5
-
47
-
-
0023650543
-
The codon adaptation index-A measure of directional synonymous codon usage bias, and its potential applications
-
Sharp,P.M. and Li,W.H. (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
-
48
-
-
84055220321
-
On finding poorly translated codons based on their usage frequency
-
Ponnala,L. (2009) On finding poorly translated codons based on their usage frequency. Bioinformation, 4, 63-65.
-
(2009)
Bioinformation
, vol.4
, pp. 63-65
-
-
Ponnala, L.1
-
49
-
-
84862529706
-
TRNAomics: TRNA gene copy number variation and codon use provide bioinformatic evidence of a new anticodon:codon wobble pair in a eukaryote
-
Iben,J.R. and Maraia,R.J. (2012) tRNAomics: TRNA gene copy number variation and codon use provide bioinformatic evidence of a new anticodon:codon wobble pair in a eukaryote. RNA, 18, 1358-1372.
-
(2012)
RNA
, vol.18
, pp. 1358-1372
-
-
Iben, J.R.1
Maraia, R.J.2
-
50
-
-
0013936167
-
Codon-anticodon pairing: The wobble hypothesis
-
Crick,F.H. (1966) Codon-anticodon pairing: The wobble hypothesis. J. Mol. Biol., 19, 548-555.
-
(1966)
J. Mol. Biol.
, vol.19
, pp. 548-555
-
-
Crick, F.H.1
-
51
-
-
33846269602
-
TRNA's wobble decoding of the genome: 40 years of modification
-
Agris,P.F., Vendeix,F.A. and Graham,W.D. (2007) tRNA's wobble decoding of the genome: 40 years of modification. J. Mol. Biol., 366, 1-13.
-
(2007)
J. Mol. Biol.
, vol.366
, pp. 1-13
-
-
Agris, P.F.1
Vendeix, F.A.2
Graham, W.D.3
-
52
-
-
40849137678
-
Codon optimization can improve expression of human genes in Escherichia coli: A multi-gene study
-
Burgess-Brown,N.A., Sharma,S., Sobott,F., Loenarz,C., Oppermann,U. and Gileadi,O. (2008) Codon optimization can improve expression of human genes in Escherichia coli: A multi-gene study. Protein Expr. Purif., 59, 94-102.
-
(2008)
Protein Expr. Purif.
, vol.59
, pp. 94-102
-
-
Burgess-Brown, N.A.1
Sharma, S.2
Sobott, F.3
Loenarz, C.4
Oppermann, U.5
Gileadi, O.6
-
53
-
-
77951715627
-
An evolutionarily conserved mechanism for controlling the efficiency of protein translation
-
Tuller,T., Carmi,A., Vestsigian,K., Navon,S., Dorfan,Y., Zaborske,J., Pan,T., Dahan,O., Furman,I. and Pilpel,Y. (2010) An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell, 141, 344-354.
-
(2010)
Cell
, vol.141
, pp. 344-354
-
-
Tuller, T.1
Carmi, A.2
Vestsigian, K.3
Navon, S.4
Dorfan, Y.5
Zaborske, J.6
Pan, T.7
Dahan, O.8
Furman, I.9
Pilpel, Y.10
-
54
-
-
0030569016
-
What drives codon choices in human genes?
-
Karlin,S. and Mrázek,J. (1996) What drives codon choices in human genes? J. Mol. Biol., 262, 459-472.
-
(1996)
J. Mol. Biol.
, vol.262
, pp. 459-472
-
-
Karlin, S.1
Mrázek, J.2
-
55
-
-
0026502711
-
Over-and under-representation of short oligonucleotides in DNA sequences
-
Burge,C., Campbell,A.M. and Karlin,S. (1992) Over-and under-representation of short oligonucleotides in DNA sequences. Proc. Natl Acad. Sci. U.S.A., 89, 1358-1362.
-
(1992)
Proc. Natl Acad. Sci. U.S.A.
, vol.89
, pp. 1358-1362
-
-
Burge, C.1
Campbell, A.M.2
Karlin, S.3
-
56
-
-
0025106975
-
Sequence analysis suggests that tetra-nucleotides signal the termination of protein synthesis in eukaryotes
-
Brown,C.M., Stockwell,P.A., Trotman,C.N.A. and Tate,W.P. (1990) Sequence analysis suggests that tetra-nucleotides signal the termination of protein synthesis in eukaryotes. Nucleic Acids Res., 18, 6339-6345.
-
(1990)
Nucleic Acids Res.
, vol.18
, pp. 6339-6345
-
-
Brown, C.M.1
Stockwell, P.A.2
Trotman, C.N.A.3
Tate, W.P.4
-
57
-
-
0028821311
-
The identity of the base following the stop codon determines the efficiency of in vivo translational termination in Escherichia coli
-
Poole,E.S., Brown,C.M. and Tate,W.P. (1995) The identity of the base following the stop codon determines the efficiency of in vivo translational termination in Escherichia coli. EMBO J., 14, 151-158.
-
(1995)
EMBO J.
, vol.14
, pp. 151-158
-
-
Poole, E.S.1
Brown, C.M.2
Tate, W.P.3
-
58
-
-
0037102410
-
Cis control of gene expression in E.Coli by ribosome queuing at an inefficient translational stop signal
-
Jin,H., Bjornsson,A. and Isaksson,L.A. (2002) Cis control of gene expression in E.coli by ribosome queuing at an inefficient translational stop signal. EMBO J., 21, 4357-4367.
-
(2002)
EMBO J.
, vol.21
, pp. 4357-4367
-
-
Jin, H.1
Bjornsson, A.2
Isaksson, L.A.3
-
59
-
-
0348013051
-
Hierarchy of sequence-dependent features associated with prokaryotic translation
-
Lithwick,G. and Margalit,H. (2003) Hierarchy of sequence-dependent features associated with prokaryotic translation. Genome Res., 13, 2665-2673.
-
(2003)
Genome Res.
, vol.13
, pp. 2665-2673
-
-
Lithwick, G.1
Margalit, H.2
-
60
-
-
35348842498
-
The +4G site in Kozak consensus is not related to the efficiency of translation initiation
-
Xia,X. (2007) The +4G site in Kozak consensus is not related to the efficiency of translation initiation. PLoS One, 2, e188.
-
(2007)
PLoS One
, vol.2
, pp. e188
-
-
Xia, X.1
-
61
-
-
84886302057
-
Causes and effects of N-terminal codon bias in bacterial genes
-
Goodman,D.B., Church,G.M. and Kosuri,S. (2013) Causes and effects of N-terminal codon bias in bacterial genes. Science, 342, 475-479.
-
(2013)
Science
, vol.342
, pp. 475-479
-
-
Goodman, D.B.1
Church, G.M.2
Kosuri, S.3
-
62
-
-
0033559035
-
An RNA thermometer
-
Storz,G. (1999) An RNA thermometer. Genes Dev., 13, 633-636.
-
(1999)
Genes Dev.
, vol.13
, pp. 633-636
-
-
Storz, G.1
-
63
-
-
33845899137
-
Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure
-
Nackley,A.G., Shabalina,S.A., Tchivileva,I.E., Satterfield,K., Korchynskyi,O., Makarov,S.S., Maixner,W. and Diatchenko,L. (2006) Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. Science, 314, 1930-1933.
-
(2006)
Science
, vol.314
, pp. 1930-1933
-
-
Nackley, A.G.1
Shabalina, S.A.2
Tchivileva, I.E.3
Satterfield, K.4
Korchynskyi, O.5
Makarov, S.S.6
Maixner, W.7
Diatchenko, L.8
-
64
-
-
33750598481
-
The distribution and habitat preferences of the zebrafish in Bangladesh
-
Spence,R., Fatema,M.K., Reichard,M., Huq,K.A., Wahab,M.A., Ahmed,Z.F. and Smith,C. (2006) The distribution and habitat preferences of the zebrafish in Bangladesh. J. Fish Biol., 69, 1435-1448.
-
(2006)
J. Fish Biol.
, vol.69
, pp. 1435-1448
-
-
Spence, R.1
Fatema, M.K.2
Reichard, M.3
Huq, K.A.4
Wahab, M.A.5
Ahmed, Z.F.6
Smith, C.7
-
65
-
-
84867868500
-
Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements
-
Barrett,L., Fletcher,S. and Wilton,S. (2012) Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements. Cell. Mol. Life Sci., 69, 3613-3634.
-
(2012)
Cell. Mol. Life Sci.
, vol.69
, pp. 3613-3634
-
-
Barrett, L.1
Fletcher, S.2
Wilton, S.3
-
66
-
-
46249092601
-
Proliferating cells express mRNAs with shortened 3- untranslated regions and fewer microRNA target sites
-
Sandberg,R., Neilson,J.R., Sarma,A., Sharp,P.A. and Burge,C.B. (2008) Proliferating cells express mRNAs with shortened 3- untranslated regions and fewer microRNA target sites. Science, 320, 1643-1647.
-
(2008)
Science
, vol.320
, pp. 1643-1647
-
-
Sandberg, R.1
Neilson, J.R.2
Sarma, A.3
Sharp, P.A.4
Burge, C.B.5
-
67
-
-
0025906388
-
A generic intron increases gene expression in transgenic mice
-
Choi,T., Huang,M., Gorman,C. and Jaenisch,R. (1991) A generic intron increases gene expression in transgenic mice. Mol. Cell. Biol., 11, 3070-3074.
-
(1991)
Mol. Cell. Biol.
, vol.11
, pp. 3070-3074
-
-
Choi, T.1
Huang, M.2
Gorman, C.3
Jaenisch, R.4
-
68
-
-
78951477322
-
Refinement of tools for targeted gene expression in Drosophila
-
Pfeiffer,B.D., Ngo,T.T., Hibbard,K.L., Murphy,C., Jenett,A., Truman,J.W. and Rubin,G.M. (2010) Refinement of tools for targeted gene expression in Drosophila. Genetics, 186, 735-755.
-
(2010)
Genetics
, vol.186
, pp. 735-755
-
-
Pfeiffer, B.D.1
Ngo, T.T.2
Hibbard, K.L.3
Murphy, C.4
Jenett, A.5
Truman, J.W.6
Rubin, G.M.7
-
69
-
-
84859136419
-
Comparative analysis of teleost genome sequences reveals an ancient intron size expansion in the zebrafish lineage
-
Moss,S.P., Joyce,D.A., Humphries,S., Tindall,K.J. and Lunt,D.H. (2011) Comparative analysis of teleost genome sequences reveals an ancient intron size expansion in the zebrafish lineage. Genome Biol. Evol., 3, 1187-1196.
-
(2011)
Genome Biol. Evol.
, vol.3
, pp. 1187-1196
-
-
Moss, S.P.1
Joyce, D.A.2
Humphries, S.3
Tindall, K.J.4
Lunt, D.H.5
-
70
-
-
80053384136
-
IGD: A resource for intronless genes in the human genome
-
Louhichi,A., Fourati,A. and Rebä?,A. (2011) IGD: A resource for intronless genes in the human genome. Gene, 488, 35-40.
-
(2011)
Gene
, vol.488
, pp. 35-40
-
-
Louhichi, A.1
Fourati, A.2
Rebä, A.3
-
71
-
-
0028788194
-
AU-rich elements: Characterization and importance in mRNA degradation
-
Chen,C.-Y.A. and Shyu,A.-B. (1995) AU-rich elements: Characterization and importance in mRNA degradation. Trends Biochem. Sci., 20, 465-470.
-
(1995)
Trends Biochem. Sci.
, vol.20
, pp. 465-470
-
-
Chen, C.-Y.A.1
Shyu, A.-B.2
-
72
-
-
0030989517
-
Removal of a cryptic intron and subcellular localization of green fluorescent protein are required to mark transgenic Arabidopsis plants brightly
-
Haseloff,J., Siemering,K.R., Prasher,D.C. and Hodge,S. (1997) Removal of a cryptic intron and subcellular localization of green fluorescent protein are required to mark transgenic Arabidopsis plants brightly. Proc. Natl Acad. Sci. U.S.A., 94, 2122-2127.
-
(1997)
Proc. Natl Acad. Sci. U.S.A.
, vol.94
, pp. 2122-2127
-
-
Haseloff, J.1
Siemering, K.R.2
Prasher, D.C.3
Hodge, S.4
-
73
-
-
33846504706
-
A 'silent' polymorphism in the MDR1 gene changes substrate specificity
-
Kimchi-Sarfaty,C., Oh,J.M., Kim,I.W., Sauna,Z.E., Calcagno,A.M., Ambudkar,S.V. and Gottesman,M.M. (2007) A 'silent' polymorphism in the MDR1 gene changes substrate specificity. Science, 315, 525-528.
-
(2007)
Science
, vol.315
, pp. 525-528
-
-
Kimchi-Sarfaty, C.1
Oh, J.M.2
Kim, I.W.3
Sauna, Z.E.4
Calcagno, A.M.5
Ambudkar, S.V.6
Gottesman, M.M.7
-
74
-
-
44449109239
-
Improving the photostability of bright monomeric orange and red fluorescent proteins
-
Shaner,N.C., Lin,M.Z., McKeown,M.R., Steinbach,P.A., Hazelwood,K.L., Davidson,M.W. and Tsien,R.Y. (2008) Improving the photostability of bright monomeric orange and red fluorescent proteins. Nat. Methods, 5, 545-551.
-
(2008)
Nat. Methods
, vol.5
, pp. 545-551
-
-
Shaner, N.C.1
Lin, M.Z.2
McKeown, M.R.3
Steinbach, P.A.4
Hazelwood, K.L.5
Davidson, M.W.6
Tsien, R.Y.7
-
75
-
-
34247359602
-
Conditional targeted cell ablation in zebrafish: A new tool for regeneration studies
-
Curado,S., Anderson,R.M., Jungblut,B.,Mumm,J., Schroeter,E. and Stainier,D.Y. (2007) Conditional targeted cell ablation in zebrafish: A new tool for regeneration studies. Dev. Dyn., 236, 1025-1035.
-
(2007)
Dev. Dyn.
, vol.236
, pp. 1025-1035
-
-
Curado, S.1
Anderson, R.M.2
Jungblut, B.3
Mumm, J.4
Schroeter, E.5
Stainier, D.Y.6
-
76
-
-
0942268832
-
Splicing enhances translation in mammalian cells: An additional function of the exon junction complex
-
Nott,A., Le Hir,H. and Moore,M.J. (2004) Splicing enhances translation in mammalian cells: An additional function of the exon junction complex. Genes Dev., 18, 210-222.
-
(2004)
Genes Dev.
, vol.18
, pp. 210-222
-
-
Nott, A.1
Le Hir, H.2
Moore, M.J.3
-
77
-
-
77952304317
-
The role of post-transcriptional RNA processing and plasmid vector sequences on transient transgene expression in zebrafish
-
Chatterjee,S., Min,L., Karuturi,R.K. and Lufkin,T. (2010) The role of post-transcriptional RNA processing and plasmid vector sequences on transient transgene expression in zebrafish. Transgenic Res.19, 299-304.
-
(2010)
Transgenic Res.
, vol.19
, pp. 299-304
-
-
Chatterjee, S.1
Min, L.2
Karuturi, R.K.3
Lufkin, T.4
-
78
-
-
0034779875
-
Impact of the six nucleotides downstream of the stop codon on translation termination
-
Namy,O., Hatin,I. and Rousset,J.P. (2001) Impact of the six nucleotides downstream of the stop codon on translation termination. EMBO Rep., 2, 787-793.
-
(2001)
EMBO Rep.
, vol.2
, pp. 787-793
-
-
Namy, O.1
Hatin, I.2
Rousset, J.P.3
-
79
-
-
0025884056
-
Efficient selection for high-expression transfectants with a novel eukaryotic vector
-
Hitoshi,N., Ken-ichi,Y. and Jun-ichi,M. (1991) Efficient selection for high-expression transfectants with a novel eukaryotic vector. Gene, 108, 193-199.
-
(1991)
Gene
, vol.108
, pp. 193-199
-
-
Hitoshi, N.1
Ken-Ichi, Y.2
Jun-Ichi, M.3
-
80
-
-
0025153740
-
Translational control by cytoplasmic polyadenylation during Xenopus oocyte maturation: Characterization of cis and trans elements and regulation by cyclin/MPF
-
McGrew,L.L. and Richter,J.D. (1990) Translational control by cytoplasmic polyadenylation during Xenopus oocyte maturation: Characterization of cis and trans elements and regulation by cyclin/MPF. EMBO J., 9, 3743-3751.
-
(1990)
EMBO J.
, vol.9
, pp. 3743-3751
-
-
McGrew, L.L.1
Richter, J.D.2
-
81
-
-
67349202780
-
Validation of a mutated PRE sequence allowing high and sustained transgene expression while abrogating WHV-X protein synthesis application to the gene therapy of WAS
-
Zanta-Boussif,M.A., Charrier,S., Brice-Ouzet,A., Martin,S., Opolon,P., Thrasher,A.J., Hope,T.J. and Galy,A. (2009) Validation of a mutated PRE sequence allowing high and sustained transgene expression while abrogating WHV-X protein synthesis: Application to the gene therapy of WAS. Gene Ther, 16, 605-619.
-
(2009)
Gene Ther
, vol.16
, pp. 605-619
-
-
Zanta-Boussif, M.A.1
Charrier, S.2
Brice-Ouzet, A.3
Martin, S.4
Opolon, P.5
Thrasher, A.J.6
Hope, T.J.7
Galy, A.8
-
82
-
-
26444621352
-
Why highly expressed proteins evolve slowly
-
Drummond,D.A., Bloom,J.D., Adami,C., Wilke,C.O. and Arnold,F.H. (2005) Why highly expressed proteins evolve slowly. Proc. Natl Acad. Sci. U.S.A., 102, 14338-14343.
-
(2005)
Proc. Natl Acad. Sci. U.S.A.
, vol.102
, pp. 14338-14343
-
-
Drummond, D.A.1
Bloom, J.D.2
Adami, C.3
Wilke, C.O.4
Arnold, F.H.5
-
83
-
-
84870717729
-
Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells
-
Dana,A. and Tuller,T. (2012) Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells. PLoS Comput. Biol., 8, e1002755.
-
(2012)
PLoS Comput. Biol.
, vol.8
, pp. e1002755
-
-
Dana, A.1
Tuller, T.2
-
84
-
-
84890072854
-
Exonic transcription factor binding directs codon choice and affects protein evolution
-
Stergachis,A.B., Haugen,E., Shafer,A., Fu,W., Vernot,B., Reynolds,A., Raubitschek,A., Ziegler,S., LeProust,E.M., Akey,J.M. et al. (2013) Exonic transcription factor binding directs codon choice and affects protein evolution. Science, 342, 1367-1372.
-
(2013)
Science
, vol.342
, pp. 1367-1372
-
-
Stergachis, A.B.1
Haugen, E.2
Shafer, A.3
Fu, W.4
Vernot, B.5
Reynolds, A.6
Raubitschek, A.7
Ziegler, S.8
Leproust, E.M.9
Akey, J.M.10
-
86
-
-
0026906491
-
Development of an all-fish gene cassette for gene transfer in aquaculture
-
Du,S.J., Gong,Z., Hew,C.L., Tan,C.H. and Fletcher,G.L. (1992) Development of an all-fish gene cassette for gene transfer in aquaculture. Mol. Mar. Biol. Biotechnol., 1, 290-300.
-
(1992)
Mol. Mar. Biol. Biotechnol.
, vol.1
, pp. 290-300
-
-
Du, S.J.1
Gong, Z.2
Hew, C.L.3
Tan, C.H.4
Fletcher, G.L.5
-
87
-
-
84878922026
-
Yin Yang 1 intronic binding sequences and splicing elicit intron-mediated enhancement of ubiquitin C gene expression
-
Bianchi,M., Crinelli,R., Giacomini,E., Carloni,E., Radici,L. and Magnani,M. (2013) Yin Yang 1 intronic binding sequences and splicing elicit intron-mediated enhancement of ubiquitin C gene expression. PLoS One, 8, e65932.
-
(2013)
PLoS One
, vol.8
, pp. e65932
-
-
Bianchi, M.1
Crinelli, R.2
Giacomini, E.3
Carloni, E.4
Radici, L.5
Magnani, M.6
-
88
-
-
10344233719
-
The effect of intron location on intron-mediated enhancement of gene expression in Arabidopsis
-
Rose,A.B. (2004) The effect of intron location on intron-mediated enhancement of gene expression in Arabidopsis. Plant J., 40, 744-751.
-
(2004)
Plant J.
, vol.40
, pp. 744-751
-
-
Rose, A.B.1
-
89
-
-
0023884698
-
Replication, integration and stable germ-line transmission of foreign sequences injected into early zebrafish embryos
-
Stuart,G.W., McMurray,J.V. and Westerfield,M. (1988) Replication, integration and stable germ-line transmission of foreign sequences injected into early zebrafish embryos. Development, 103, 403-412.
-
(1988)
Development
, vol.103
, pp. 403-412
-
-
Stuart, G.W.1
McMurray, J.V.2
Westerfield, M.3
-
90
-
-
33947307492
-
A histological survey of green fluorescent protein expression in 'green' mice: Implications for stem cell research
-
Biankin,S.A., Collector,M.I., Biankin,A.V., Brown,L.J., Kleeberger,W., Devereux,W.L., Zahnow,C.A., Baylin,S.B., Watkins,D.N., Sharkis,S.J. et al. (2007) A histological survey of green fluorescent protein expression in 'green' mice: Implications for stem cell research. Pathology, 39, 247-251.
-
(2007)
Pathology
, vol.39
, pp. 247-251
-
-
Biankin, S.A.1
Collector, M.I.2
Biankin, A.V.3
Brown, L.J.4
Kleeberger, W.5
Devereux, W.L.6
Zahnow, C.A.7
Baylin, S.B.8
Watkins, D.N.9
Sharkis, S.J.10
-
91
-
-
70249128067
-
Transcriptional silencing and reactivation in transgenic zebrafish
-
Goll,M.G., Anderson,R., Stainier,D.Y.R., Spradling,A.C. and Halpern,M.E. (2009) Transcriptional silencing and reactivation in transgenic zebrafish. Genetics, 182, 747-755.
-
(2009)
Genetics
, vol.182
, pp. 747-755
-
-
Goll, M.G.1
Anderson, R.2
Stainier, D.Y.R.3
Spradling, A.C.4
Halpern, M.E.5
-
92
-
-
58149139574
-
V2a and V2b neurons are generated by the final divisions of pair-producing progenitors in the zebrafish spinal cord
-
Kimura,Y., Satou,C. and Higashijima,S. (2008) V2a and V2b neurons are generated by the final divisions of pair-producing progenitors in the zebrafish spinal cord. Development, 135, 3001-3005.
-
(2008)
Development
, vol.135
, pp. 3001-3005
-
-
Kimura, Y.1
Satou, C.2
Higashijima, S.3
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