-
1
-
-
0038620436
-
Codon pairs in the genome of Escherichia coli
-
Boycheva, S., Chkodrov, G., and 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
-
2
-
-
34548446795
-
Halting a cellular production line: responses to ribosomal pausing during translation
-
Buchan, J. R., and Stansfield, I. (2007). Halting a cellular production line: responses to ribosomal pausing during translation. Biol. Cell 99, 475-487. doi:10.1042/BC20070037
-
(2007)
Biol. Cell
, vol.99
, pp. 475-487
-
-
Buchan, J.R.1
Stansfield, I.2
-
3
-
-
34250189908
-
DNA synthesis and biological security
-
Bugl, H., Danner, J. P., Molinari, R. J., Mulligan, J. T., Park, H. O., Reichert, B., et al. (2007). DNA synthesis and biological security. Nat. Biotechnol. 25, 627-629. doi:10.1038/nbt0607-627
-
(2007)
Nat. Biotechnol
, vol.25
, pp. 627-629
-
-
Bugl, H.1
Danner, J.P.2
Molinari, R.J.3
Mulligan, J.T.4
Park, H.O.5
Reichert, B.6
-
4
-
-
50049093498
-
Cryptic splice site in the complementary DNA of glucocerebrosidase causes inefficient expression
-
Bukovac, S. W., Bagshaw, R. D., Rigat, B. A., Callahan, J. W., Clarke, J. T. R., and Mahuran, D. J. (2008). Cryptic splice site in the complementary DNA of glucocerebrosidase causes inefficient expression. Anal. Biochem. 381, 276-278. doi:10.1016/j.ab.2008.06.029
-
(2008)
Anal. Biochem
, vol.381
, pp. 276-278
-
-
Bukovac, S.W.1
Bagshaw, R.D.2
Rigat, B.A.3
Callahan, J.W.4
Clarke, J.T.R.5
Mahuran, D.J.6
-
5
-
-
77951734603
-
A role for codon order in translation dynamics
-
Cannarrozzi, G., Schraudolph, N. N., Faty, M., von Rohr, P., Friberg, M. T., Roth, A. C., et al. (2010). A role for codon order in translation dynamics. Cell 141, 355-367. doi:10.1016/j.cell.2010.02.036
-
(2010)
Cell
, vol.141
, pp. 355-367
-
-
Cannarrozzi, G.1
Schraudolph, N.N.2
Faty, M.3
von Rohr, P.4
Friberg, M.T.5
Roth, A.C.6
-
6
-
-
0242391986
-
Codon adaptation index as a measure of dominating codon bias
-
Carbone, A., Zinovyev, A., and Kepes, F. (2003). Codon adaptation index as a measure of dominating codon bias. Bioinformatics 19, 2005-2015. doi:10.1093/bioinformatics/btg272
-
(2003)
Bioinformatics
, vol.19
, pp. 2005-2015
-
-
Carbone, A.1
Zinovyev, A.2
Kepes, F.3
-
7
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., et al. (2005). The transcriptional landscape of the mammalian genome. Science 309, 1559-1563. doi:10.1126/science.1112014
-
(2005)
Science
, vol.309
, pp. 1559-1563
-
-
Carninci, P.1
Kasukawa, T.2
Katayama, S.3
Gough, J.4
Frith, M.C.5
Maeda, N.6
-
8
-
-
71849095864
-
TinkerCell: modular CAD tool for synthetic biology
-
Chandran, D., Bergmann, F. T., and Sauro, H. M. (2009). TinkerCell: modular CAD tool for synthetic biology. J. Biol. Eng. 3, 19. doi:10.1186/1754-1611-3-19
-
(2009)
J. Biol. Eng
, vol.3
, pp. 19
-
-
Chandran, D.1
Bergmann, F.T.2
Sauro, H.M.3
-
9
-
-
84905001680
-
Codon optimization on-line (COOL): a web-based multi-objective optimization platform for synthetic gene design
-
Chin, J. X., Chung, B. K.-S., and Lee, D.-Y. (2014). Codon optimization on-line (COOL): a web-based multi-objective optimization platform for synthetic gene design. Bioinformatics 30, 2210-2212. doi:10.1093/bioinformatics/btu192
-
(2014)
Bioinformatics
, vol.30
, pp. 2210-2212
-
-
Chin, J.X.1
Chung, B.K.-S.2
Lee, D.-Y.3
-
10
-
-
54849441249
-
Rare codons cluster
-
Clarke, I. V., Thomas, F., and Clark, P. L. (2008). Rare codons cluster. PLoS ONE 3, e3412. doi:10.1371/journal.pone.0003412
-
(2008)
PLoS ONE
, vol.3
-
-
Clarke, I.V.1
Thomas, F.2
Clark, P.L.3
-
11
-
-
0242606472
-
Natural selection and algorithmic design of mRNA
-
Cohen, B., and Skiena, S. (2003). Natural selection and algorithmic design of mRNA. J. Comput. Biol. 10, 419-432. doi:10.1089/10665270360688101
-
(2003)
J. Comput. Biol
, vol.10
, pp. 419-432
-
-
Cohen, B.1
Skiena, S.2
-
12
-
-
46449120581
-
Virus attenuation by genome-scale changes in codon pair bias
-
Coleman, J. R., Papamichail, D., Skiena, S., Futcher, B., Wimmer, E., and 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
-
13
-
-
79954608598
-
Designed reduction of Streptococcus pneumoniae pathogenicity via synthetic changes in virulence factor codon-pair bias
-
Coleman, J. R., Papamichail, D., Yano, M., Garcia-Suarez Mdel, M., and Pirofski, L. A. (2011). Designed reduction of Streptococcus pneumoniae pathogenicity via synthetic changes in virulence factor codon-pair bias. J. Infect. Dis. 203, 1264-1273. doi:10.1093/infdis/jir010
-
(2011)
J. Infect. Dis
, vol.203
, pp. 1264-1273
-
-
Coleman, J.R.1
Papamichail, D.2
Yano, M.3
Garcia-Suarez Mdel, M.4
Pirofski, L.A.5
-
14
-
-
59149092285
-
Gene synthesis demystified
-
Czar, M. J., Anderson, J. C., Bader, J. S., and Peccoud, J. (2009a). Gene synthesis demystified. Trends Biotechnol. 27, 63-72. doi:10.1016/j.tibtech.2008.10.007
-
(2009)
Trends Biotechnol
, vol.27
, pp. 63-72
-
-
Czar, M.J.1
Anderson, J.C.2
Bader, J.S.3
Peccoud, J.4
-
15
-
-
67849130568
-
Writing DNA with GenoCAD
-
Czar, M. J., Cai, Y., and Peccoud, J. (2009b). Writing DNA with GenoCAD. Nucleic Acids Res. 37, W40-W47. doi:10.1093/nar/gkp361
-
(2009)
Nucleic Acids Res
, vol.37
, pp. W40-W47
-
-
Czar, M.J.1
Cai, Y.2
Peccoud, J.3
-
16
-
-
56449093852
-
Bioinformatic and physical characterizations of genome-scale ordered RNA structure in mammalian RNA viruses
-
Davis, M., Sagan, S. M., Pezacki, J. P., Evans, D. J., and Simmonds, P. (2008). Bioinformatic and physical characterizations of genome-scale ordered RNA structure in mammalian RNA viruses. J. Virol. 82, 11824-11836. doi:10.1128/JVI.01078-08
-
(2008)
J. Virol
, vol.82
, pp. 11824-11836
-
-
Davis, M.1
Sagan, S.M.2
Pezacki, J.P.3
Evans, D.J.4
Simmonds, P.5
-
17
-
-
4644280499
-
Solving the riddle of codon usage preferences: a test for translational selection
-
Dos Reis, M., Savva, R., and Wernisch, L. (2004). Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res. 32, 5036-5044. doi:10.1093/nar/gkh834
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 5036-5044
-
-
Dos Reis, M.1
Savva, R.2
Wernisch, L.3
-
18
-
-
1842536312
-
The DNA sequence and analysis of human chromosome 13
-
Dunham, A., Matthews, L. H., Burton, J., Ashurst, J. L., Howe, K. L., Ashcroft, K. J., et al. (2004). The DNA sequence and analysis of human chromosome 13. Nature 428, 522-528. doi:10.1038/nature02379
-
(2004)
Nature
, vol.428
, pp. 522-528
-
-
Dunham, A.1
Matthews, L.H.2
Burton, J.3
Ashurst, J.L.4
Howe, K.L.5
Ashcroft, K.J.6
-
19
-
-
84895827954
-
Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites
-
Espah Borujeni, A., Channarasappa, A. S., and Salis, H. M. (2014). Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites. Nucleic Acids Res. 42, 2646-2659. doi:10.1093/nar/gkt1139
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 2646-2659
-
-
Espah Borujeni, A.1
Channarasappa, A.S.2
Salis, H.M.3
-
20
-
-
0036493203
-
Regularities of context-dependent codon bias in eukaryotic genes
-
Fedorov, A., Saxonov, S., and Gilbert, W. (2002). Regularities of context-dependent codon bias in eukaryotic genes. Nucleic Acids Res. 30, 1192-1197. doi:10.1093/nar/30.5.1192
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 1192-1197
-
-
Fedorov, A.1
Saxonov, S.2
Gilbert, W.3
-
21
-
-
0000075467
-
Improved free-energy parameters for predictions of RNA duplex stability
-
Freier, S. M., Kierzek, R., Jaeger, J. A., Sugimoto, N., Caruthers, M. H., Neilson, T., et al. (1986). Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl. Acad. Sci. U. S. A. 83, 9373-9377. doi:10.1073/pnas.83.24.9373
-
(1986)
Proc. Natl. Acad. Sci. U. S. A
, vol.83
, pp. 9373-9377
-
-
Freier, S.M.1
Kierzek, R.2
Jaeger, J.A.3
Sugimoto, N.4
Caruthers, M.H.5
Neilson, T.6
-
22
-
-
1842713354
-
UpGene: application of a web-based dna codon optimization algorithm
-
Gao, W., Rzewski, A., Sun, H., Robbins, P. D., and Gambotto, A. (2004). UpGene: application of a web-based dna codon optimization algorithm. Biotechnol. Prog. 20, 443-448. doi:10.1021/bp0300467
-
(2004)
Biotechnol. Prog
, vol.20
, pp. 443-448
-
-
Gao, W.1
Rzewski, A.2
Sun, H.3
Robbins, P.D.4
Gambotto, A.5
-
23
-
-
58149191274
-
Rfam: updates to the RNA families database
-
Gardner, P. P., Daub, J., Tate, J. G., Nawrocki, E. P., Kolbe, D. L., Lindgreen, S., et al. (2009). Rfam: updates to the RNA families database. Nucleic Acids Res. 37, D136-D140. doi:10.1093/nar/gkn766
-
(2009)
Nucleic Acids Res
, vol.37
, pp. D136-D140
-
-
Gardner, P.P.1
Daub, J.2
Tate, J.G.3
Nawrocki, E.P.4
Kolbe, D.L.5
Lindgreen, S.6
-
24
-
-
84876044227
-
MRNA secondary structure optimization using a correlated stem-loop prediction
-
Gaspar, P., Moura, G., Santos, M. A. S., and Oliveira, J. L. (2013). MRNA secondary structure optimization using a correlated stem-loop prediction. Nucleic Acids Res. 41, e73. doi:10.1093/nar/gks1473
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Gaspar, P.1
Moura, G.2
Santos, M.A.S.3
Oliveira, J.L.4
-
25
-
-
84870439703
-
EuGene: maximizing synthetic gene design for heterologous expression
-
Gaspar, P., Oliveira, J. L., Frommlet, J., Santos, M. A. S., and Moura, G. (2012). EuGene: maximizing synthetic gene design for heterologous expression. Bioinformatics 28, 2683-2684. doi:10.1093/bioinformatics/bts465
-
(2012)
Bioinformatics
, vol.28
, pp. 2683-2684
-
-
Gaspar, P.1
Oliveira, J.L.2
Frommlet, J.3
Santos, M.A.S.4
Moura, G.5
-
26
-
-
84899817129
-
Archaeal aminoacyl-tRNA synthetases interact with the ribosome to recycle tRNAs
-
Godinic-Mikulcic, V., Jaric, J., Greber, B. J., Franke, V., Hodnik, V., Anderluh, G., et al. (2014). Archaeal aminoacyl-tRNA synthetases interact with the ribosome to recycle tRNAs. Nucleic Acids Res. 42, 5191-5201. doi:10.1093/nar/gku164
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 5191-5201
-
-
Godinic-Mikulcic, V.1
Jaric, J.2
Greber, B.J.3
Franke, V.4
Hodnik, V.5
Anderluh, G.6
-
27
-
-
0034003829
-
Identification of a cis-acting replication element within the poliovirus coding region
-
Goodfellow, I., Chaudhry, Y., Richardson, A., Meredith, J., Almond, J. W., Barclay, W., et al. (2000). Identification of a cis-acting replication element within the poliovirus coding region. J. Virol. 74, 4590-4600. doi:10.1128/JVI.74.10.4590-4600.2000
-
(2000)
J. Virol
, vol.74
, pp. 4590-4600
-
-
Goodfellow, I.1
Chaudhry, Y.2
Richardson, A.3
Meredith, J.4
Almond, J.W.5
Barclay, W.6
-
28
-
-
0037276580
-
Structure and function analysis of the poliovirus cis-acting replication element (CRE)
-
Goodfellow, I. G., Kerrigan, D., and Evans, D. J. (2003). Structure and function analysis of the poliovirus cis-acting replication element (CRE). RNA 9, 124-137. doi:10.1261/rna.2950603
-
(2003)
RNA
, vol.9
, pp. 124-137
-
-
Goodfellow, I.G.1
Kerrigan, D.2
Evans, D.J.3
-
29
-
-
23144444226
-
JCat: a novel tool to adapt codon usage of a target gene to its potential expression host
-
Grote, A., Hiller, K., Scheer, M., Munch, R., Nortemann, B., Hempel, D. C., et al. (2005). JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Res. 33, W526-W531. doi:10.1093/nar/gki376
-
(2005)
Nucleic Acids Res
, vol.33
, pp. W526-W531
-
-
Grote, A.1
Hiller, K.2
Scheer, M.3
Munch, R.4
Nortemann, B.5
Hempel, D.C.6
-
30
-
-
58149193249
-
PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes
-
Grote, A., Klein, J., Retter, I., Haddad, I., Behling, S., Bunk, B., et al. (2009). PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes. Nucleic Acids Res. 37, D61-D65. doi:10.1093/nar/gkn837
-
(2009)
Nucleic Acids Res
, vol.37
, pp. D61-D65
-
-
Grote, A.1
Klein, J.2
Retter, I.3
Haddad, I.4
Behling, S.5
Bunk, B.6
-
31
-
-
84898903326
-
D-Tailor: automated analysis and design of DNA sequences
-
Guimaraes, J. C., Rocha, M., Arkin, A. P., and Cambray, G. (2014). D-Tailor: automated analysis and design of DNA sequences. Bioinformatics 30, 1087-1094. doi:10.1093/bioinformatics/btt742
-
(2014)
Bioinformatics
, vol.30
, pp. 1087-1094
-
-
Guimaraes, J.C.1
Rocha, M.2
Arkin, A.P.3
Cambray, G.4
-
32
-
-
3042782585
-
Codon bias and heterologous protein expression
-
Gustafsson, C., Govindarajan, S., and Minshull, J. (2004). Codon bias and heterologous protein expression. Trends Biotechnol. 22, 346-353. doi:10.1016/j.tibtech.2004.04.006
-
(2004)
Trends Biotechnol
, vol.22
, pp. 346-353
-
-
Gustafsson, C.1
Govindarajan, S.2
Minshull, J.3
-
33
-
-
0024673103
-
Nonrandom utilization of codon pairs in Escherichia coli
-
Gutman, G. A., and Hatfield, G. W. (1989). Nonrandom utilization of codon pairs in Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 86, 3699-3703. doi:10.1073/pnas.86.10.3699
-
(1989)
Proc. Natl. Acad. Sci. U. S. A
, vol.86
, pp. 3699-3703
-
-
Gutman, G.A.1
Hatfield, G.W.2
-
34
-
-
0036176720
-
Detection of genes with atypical nucleotide sequence in microbial genomes
-
Hooper, S. D., and Berg, O. G. (2002). Detection of genes with atypical nucleotide sequence in microbial genomes. J. Mol. Evol. 54, 365-375. doi:10.1007/s00239-001-0051-8
-
(2002)
J. Mol. Evol
, vol.54
, pp. 365-375
-
-
Hooper, S.D.1
Berg, O.G.2
-
35
-
-
0037095730
-
DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis
-
Hoover, D. M., and Lubkowski, J. (2002). DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis. Nucleic Acids Res. 30, e43. doi:10.1093/nar/30.10.e43
-
(2002)
Nucleic Acids Res
, vol.30
-
-
Hoover, D.M.1
Lubkowski, J.2
-
36
-
-
0019824131
-
Correlation between the abundance of Escherichia coli transfer (RNAs) and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system
-
Ikemura, T. (1981). Correlation between the abundance of Escherichia coli transfer (RNAs) and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J. Mol. Biol. 151, 389-409. doi:10.1016/0022-2836(81)90003-6
-
(1981)
J. Mol. Biol
, vol.151
, pp. 389-409
-
-
Ikemura, T.1
-
37
-
-
0029162727
-
Codon pair utilization biases influence translational elongation step times
-
Irwin, B., Heck, J. D., and Hatfield, G. W. (1995). Codon pair utilization biases influence translational elongation step times. J. Biol. Chem. 270, 22801-22806. doi:10.1074/jbc.270.39.22801
-
(1995)
J. Biol. Chem
, vol.270
, pp. 22801-22806
-
-
Irwin, B.1
Heck, J.D.2
Hatfield, G.W.3
-
38
-
-
19644370646
-
GeMS: an advanced software package for designing synthetic genes
-
Jayaraj, S., Reid, R., and Santi, D. V. (2005). GeMS: an advanced software package for designing synthetic genes. Nucleic Acids Res. 33, 3011-3016. doi:10.1093/nar/gki614
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 3011-3016
-
-
Jayaraj, S.1
Reid, R.2
Santi, D.V.3
-
39
-
-
80051630187
-
Visual gene developer: a fully programmable bioinformatics software for synthetic gene optimization
-
Jung, S.-K., and McDonald, K. (2011). Visual gene developer: a fully programmable bioinformatics software for synthetic gene optimization. BMC Bioinformatics 12, 340. doi:10.1186/1471-2105-12-340
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 340
-
-
Jung, S.-K.1
McDonald, K.2
-
40
-
-
33846056835
-
fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences
-
Kin, T., Yamada, K., Terai, G., Okida, H., Yoshinari, Y., Ono, Y., et al. (2007). fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences. Nucleic Acids Res. 35, D145-D148. doi:10.1093/nar/gkl837
-
(2007)
Nucleic Acids Res
, vol.35
, pp. D145-D148
-
-
Kin, T.1
Yamada, K.2
Terai, G.3
Okida, H.4
Yoshinari, Y.5
Ono, Y.6
-
41
-
-
33745198703
-
High guanine and cytosine content increases mRNA levels in mammalian cells
-
Kudla, G., Lipinski, L., Caffin, F., Helwak, A., and Zylicz, M. (2006). High guanine and cytosine content increases mRNA levels in mammalian cells. PLoS Biol. 4, e180. doi:10.1371/journal.pbio.0040180
-
(2006)
PLoS Biol
, vol.4
-
-
Kudla, G.1
Lipinski, L.2
Caffin, F.3
Helwak, A.4
Zylicz, M.5
-
42
-
-
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. doi:10.1126/science.1170160
-
(2009)
Science
, vol.324
, pp. 255-258
-
-
Kudla, G.1
Murray, A.W.2
Tollervey, D.3
Plotkin, J.B.4
-
43
-
-
84860231100
-
The anti-shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
-
Li, G.-W., Oh, E., and Weissman, J. S. (2012). The anti-shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature 484, 538-541. doi:10.1038/nature10965
-
(2012)
Nature
, vol.484
, pp. 538-541
-
-
Li, G.-W.1
Oh, E.2
Weissman, J.S.3
-
44
-
-
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. doi:10.1101/gr.1485203
-
(2003)
Genome Res
, vol.13
, pp. 2665-2673
-
-
Lithwick, G.1
Margalit, H.2
-
45
-
-
65649112893
-
Gene composer: database software for protein construct design, codon engineering, and gene synthesis
-
Lorimer, D., Raymond, A., Walchli, J., Mixon, M., Barrow, A., Wallace, E., et al. (2009). Gene composer: database software for protein construct design, codon engineering, and gene synthesis. BMC Biotechnol. 9, 36. doi:10.1186/1472-6750-9-36
-
(2009)
BMC Biotechnol
, vol.9
, pp. 36
-
-
Lorimer, D.1
Raymond, A.2
Walchli, J.3
Mixon, M.4
Barrow, A.5
Wallace, E.6
-
46
-
-
84934438960
-
"UNAFold: software for nucleic acid folding and hybridization,"
-
ed. J. Keith (Totowa: Humana Press Inc.)
-
Markham, N. R., and Zuker, M. (2008). "UNAFold: software for nucleic acid folding and hybridization," in Bioinformatics: Volume 2 Data, Sequence Analysis, and Evolution, Chapter 1. ed. J. Keith (Totowa: Humana Press Inc.), 3-31. doi:10.1007/978-1-60327-429-6_1
-
(2008)
Bioinformatics: Volume 2 Data, Sequence Analysis, and Evolution
, Issue.1
, pp. 3-31
-
-
Markham, N.R.1
Zuker, M.2
-
47
-
-
0026332291
-
Evidence for horizontal gene transfer in Escherichia coli speciation
-
Medigue, C., Rouxel, T., Vigier, P., Henaut, A., and Danchin, A. (1991). Evidence for horizontal gene transfer in Escherichia coli speciation. J. Mol. Biol. 222, 851-856. doi:10.1016/0022-2836(91)90575-Q
-
(1991)
J. Mol. Biol
, vol.222
, pp. 851-856
-
-
Medigue, C.1
Rouxel, T.2
Vigier, P.3
Henaut, A.4
Danchin, A.5
-
48
-
-
79956291154
-
Optimizing restriction site placement for synthetic genomes
-
Montes, P., Memelli, H., Ward, C., Kim, J., Mitchell, J. S. B., and Skiena, S. (2010). Optimizing restriction site placement for synthetic genomes. Comb. Pattern Matching Proc. 6129, 323-337. doi:10.1007/978-3-642-13509-5_29
-
(2010)
Comb. Pattern Matching Proc
, vol.6129
, pp. 323-337
-
-
Montes, P.1
Memelli, H.2
Ward, C.3
Kim, J.4
Mitchell, J.S.B.5
Skiena, S.6
-
49
-
-
33644889434
-
Comparative context analysis of codon pairs on an ORFeome scale
-
Moura, G., Pinheiro, M., Silva, R., Miranda, I., Afreixo, V., Dias, G., et al. (2005). Comparative context analysis of codon pairs on an ORFeome scale. Genome Biol. 6, R28. doi:10.1186/gb-2005-6-3-r28
-
(2005)
Genome Biol
, vol.6
-
-
Moura, G.1
Pinheiro, M.2
Silva, R.3
Miranda, I.4
Afreixo, V.5
Dias, G.6
-
50
-
-
77954482089
-
Live attenuated influenza virus vaccines by computer-aided rational design
-
Mueller, S., Coleman, J. R., Papamichail, D., Ward, C. B., Nimnual, A., Futcher, B., et al. (2010). Live attenuated influenza virus vaccines by computer-aided rational design. Nat. Biotechnol. 28, 723-726. doi:10.1038/nbt.1636
-
(2010)
Nat. Biotechnol
, 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
-
51
-
-
0037250153
-
PRODORIC: prokaryotic database of gene regulation
-
Münch, R., Hiller, K., Barg, H., Heldt, D., Linz, S., Wingender, E., et al. (2003). PRODORIC: prokaryotic database of gene regulation. Nucleic Acids Res. 31, 266-269. doi:10.1093/nar/gkg037
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 266-269
-
-
Münch, R.1
Hiller, K.2
Barg, H.3
Heldt, D.4
Linz, S.5
Wingender, E.6
-
52
-
-
77957797837
-
RBSDesigner: software for designing synthetic ribosome binding sites that yields a desired level of protein expression
-
Na, D., and Lee, D. (2010). RBSDesigner: software for designing synthetic ribosome binding sites that yields a desired level of protein expression. Bioinformatics 26, 2633-2634. doi:10.1093/bioinformatics/btq458
-
(2010)
Bioinformatics
, vol.26
, pp. 2633-2634
-
-
Na, D.1
Lee, D.2
-
53
-
-
77952611328
-
Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with desired expression levels in prokaryotes
-
Na, D., Lee, S., and Lee, D. (2010). Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with desired expression levels in prokaryotes. BMC Syst. Biol. 4, 71. doi:10.1186/1752-0509-4-71
-
(2010)
BMC Syst. Biol
, vol.4
, pp. 71
-
-
Na, D.1
Lee, S.2
Lee, D.3
-
54
-
-
0342614926
-
Codon usage tabulated from the international DNA sequence databases; its status 1999
-
Nakamura, Y., Gojobori, T., and Ikemura, T. (1999). Codon usage tabulated from the international DNA sequence databases; its status 1999. Nucleic Acids Res. 27, 292. doi:10.1093/nar/27.1.292
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 292
-
-
Nakamura, Y.1
Gojobori, T.2
Ikemura, T.3
-
55
-
-
0345346377
-
Codon usage tabulated from international DNA sequence databases: status for the year 2000 [In Process Citation]
-
Nakamura, Y., Gojobori, T., and Ikemura, T. (2000). Codon usage tabulated from international DNA sequence databases: status for the year 2000 [In Process Citation]. Nucleic Acids Res. 28, 292. doi:10.1093/nar/28.1.292
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 292
-
-
Nakamura, Y.1
Gojobori, T.2
Ikemura, T.3
-
56
-
-
67650663955
-
Towards programming languages for genetic engineering of living cells
-
Pedersen, M., and Phillips, A. (2009). Towards programming languages for genetic engineering of living cells. J. R. Soc. Interface 6(Suppl. 4), S437-S450. doi:10.1098/rsif.2008.0516.focus
-
(2009)
J. R. Soc. Interface
, vol.6
, pp. S437-S450
-
-
Pedersen, M.1
Phillips, A.2
-
57
-
-
0022651692
-
Differential effects of polyadenylation regions on gene expression in mammalian cells
-
Pfarr, D. S., Rieser, L. A., Woychik, R. P., Rottman, F. M., Rosenberg, M., and Reff, M. E. (1986). Differential effects of polyadenylation regions on gene expression in mammalian cells. DNA 5, 115-122. doi:10.1089/dna.1986.5.115
-
(1986)
DNA
, vol.5
, pp. 115-122
-
-
Pfarr, D.S.1
Rieser, L.A.2
Woychik, R.P.3
Rottman, F.M.4
Rosenberg, M.5
Reff, M.E.6
-
58
-
-
78650304100
-
Synonymous but not the same: the causes and consequences of codon bias
-
Plotkin, J. B., and Kudla, G. (2010). Synonymous but not the same: the causes and consequences of codon bias. Nat. Rev. Genet. 12, 32-42. doi:10.1038/nrg2899
-
(2010)
Nat. Rev. Genet
, vol.12
, pp. 32-42
-
-
Plotkin, J.B.1
Kudla, G.2
-
59
-
-
34547579086
-
Optimizer: a web server for optimizing the codon usage of DNA sequences
-
Puigbò, P., Guzmán, E., Romeu, A., and Garcia-Vallvé, S. (2007). Optimizer: a web server for optimizing the codon usage of DNA sequences. Nucleic Acids Res. 35, W126-W131. doi:10.1093/nar/gkm219
-
(2007)
Nucleic Acids Res
, vol.35
, pp. W126-W131
-
-
Puigbò, P.1
Guzmán, E.2
Romeu, A.3
Garcia-Vallvé, S.4
-
60
-
-
84911480225
-
Predicting translation initiation rates for designing synthetic biology
-
Reeve, B., Hargest, T., Gilbert, C., and Ellis, T. (2014). Predicting translation initiation rates for designing synthetic biology. Front. Bioeng. Biotechnol. 2:1. doi:10.3389/fbioe.2014.00001
-
(2014)
Front. Bioeng. Biotechnol
, vol.2
, pp. 1
-
-
Reeve, B.1
Hargest, T.2
Gilbert, C.3
Ellis, T.4
-
61
-
-
33645514473
-
GeneDesign: rapid, automated design of multikilobase synthetic genes
-
Richardson, S. M., Wheelan, S. J., Yarrington, R. M., and Boeke, J. D. (2006). GeneDesign: rapid, automated design of multikilobase synthetic genes. Genome Res. 16, 550-556. doi:10.1101/gr.4431306
-
(2006)
Genome Res
, vol.16
, pp. 550-556
-
-
Richardson, S.M.1
Wheelan, S.J.2
Yarrington, R.M.3
Boeke, J.D.4
-
62
-
-
75549086595
-
REBASE-A database for DNA restriction and modification: enzymes, genes and genomes
-
Roberts, R. J., Vincze, T., Posfai, J., and Macelis, D. (2009). REBASE-A database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res. 38, 234-236. doi:10.1093/nar/gkp874
-
(2009)
Nucleic Acids Res
, vol.38
, pp. 234-236
-
-
Roberts, R.J.1
Vincze, T.2
Posfai, J.3
Macelis, D.4
-
63
-
-
79957534528
-
The ribosome binding site calculator
-
Salis, H. M. (2011). The ribosome binding site calculator. Meth. Enzymol. 498, 19-42. doi:10.1016/B978-0-12-385120-8.00002-4
-
(2011)
Meth. Enzymol
, vol.498
, pp. 19-42
-
-
Salis, H.M.1
-
64
-
-
70349964350
-
Automated design of synthetic ribosome binding sites to control protein expression
-
Salis, H. M., Mirsky, E. A., and Voigt, C. A. (2009). Automated design of synthetic ribosome binding sites to control protein expression. Nat. Biotechnol. 27, 946-950. doi:10.1038/nbt.1568
-
(2009)
Nat. Biotechnol
, vol.27
, pp. 946-950
-
-
Salis, H.M.1
Mirsky, E.A.2
Voigt, C.A.3
-
65
-
-
70349316480
-
Quantitative correlation between mRNA secondary structure around the region downstream of the initiation codon and translational efficiency in Escherichia coli
-
Sang, W. S., Yang, J., and Jung, G. Y. (2009). Quantitative correlation between mRNA secondary structure around the region downstream of the initiation codon and translational efficiency in Escherichia coli. Biotechnol. Bioeng. 104, 611-616. doi:10.1002/bit.22431
-
(2009)
Biotechnol. Bioeng
, vol.104
, pp. 611-616
-
-
Sang, W.S.1
Yang, J.2
Jung, G.Y.3
-
66
-
-
0028196714
-
From sequences to shapes and back: a case study in RNA secondary structures
-
Schuster, P., Fontana, W., Stadler, P. F., and Hofacker, I. L. (1994). From sequences to shapes and back: a case study in RNA secondary structures. Proc. Biol. Sci. 255, 279-284. doi:10.1098/rspb.1994.0040
-
(1994)
Proc. Biol. Sci
, vol.255
, pp. 279-284
-
-
Schuster, P.1
Fontana, W.2
Stadler, P.F.3
Hofacker, I.L.4
-
67
-
-
8144223724
-
The ambush hypothesis: hidden stop codons prevent off-frame gene reading
-
Seligmann, H., and Pollock, D. D. (2004). The ambush hypothesis: hidden stop codons prevent off-frame gene reading. DNA Cell Biol. 23, 701-705. doi:10.1089/dna.2004.23.701
-
(2004)
DNA Cell Biol
, vol.23
, pp. 701-705
-
-
Seligmann, H.1
Pollock, D.D.2
-
68
-
-
84870851210
-
Predictive design of mRNA translation initiation region to control prokaryotic translation efficiency
-
Seo, S. W., Yang, J. S., Kim, I., Yang, J., Min, B. E., Kim, S., et al. (2013). Predictive design of mRNA translation initiation region to control prokaryotic translation efficiency. Metab. Eng. 15, 67-74. doi:10.1016/j.ymben.2012.10.006
-
(2013)
Metab. Eng
, vol.15
, pp. 67-74
-
-
Seo, S.W.1
Yang, J.S.2
Kim, I.3
Yang, J.4
Min, B.E.5
Kim, S.6
-
69
-
-
0029100233
-
Predicting thermodynamic properties of RNA
-
Serra, M. J., and Turner, D. H. (1995). Predicting thermodynamic properties of RNA. Methods Enzymol. 259, 242-261. doi:10.1016/0076-6879(95)59047-1
-
(1995)
Methods Enzymol
, vol.259
, pp. 242-261
-
-
Serra, M.J.1
Turner, D.H.2
-
70
-
-
0036677820
-
Computational identification of putative programmed translational frameshift sites
-
Shah, A. A., Giddings, M. C., Parvaz, J. B., Gesteland, R. F., Atkins, J. F., and Ivanov, I. P. (2002). Computational identification of putative programmed translational frameshift sites. Bioinformatics 18, 1046-1053. doi:10.1093/bioinformatics/18.8.1046
-
(2002)
Bioinformatics
, vol.18
, pp. 1046-1053
-
-
Shah, A.A.1
Giddings, M.C.2
Parvaz, J.B.3
Gesteland, R.F.4
Atkins, J.F.5
Ivanov, I.P.6
-
71
-
-
0023046211
-
Codon usage in regulatory genes in Escherichia coli does not reflect selection for "rare" codons
-
Sharp, P. M., and Li, W. H. (1986). Codon usage in regulatory genes in Escherichia coli does not reflect selection for "rare" codons. Nucleic Acids Res. 14, 7737-7749. doi:10.1093/nar/14.19.7737
-
(1986)
Nucleic Acids Res
, vol.14
, pp. 7737-7749
-
-
Sharp, P.M.1
Li, W.H.2
-
72
-
-
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. doi:10.1093/nar/15.3.1281
-
(1987)
Nucleic Acids Res
, vol.15
, pp. 1281-1295
-
-
Sharp, P.M.1
Li, W.H.2
-
73
-
-
0023046874
-
Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes
-
Sharp, P. M., Tuohy, T. M., and Mosurski, K. R. (1986). Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 14, 5125-5143. doi:10.1093/nar/14.13.5125
-
(1986)
Nucleic Acids Res
, vol.14
, pp. 5125-5143
-
-
Sharp, P.M.1
Tuohy, T.M.2
Mosurski, K.R.3
-
74
-
-
45149118469
-
Engineering BioBrick vectors from BioBrick parts
-
Shetty, R. P., Endy, D., and Knight, T. F. (2008). Engineering BioBrick vectors from BioBrick parts. J. Biol. Eng. 2, 5. doi:10.1186/1754-1611-2-5
-
(2008)
J. Biol. Eng
, vol.2
, pp. 5
-
-
Shetty, R.P.1
Endy, D.2
Knight, T.F.3
-
75
-
-
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., and Evans, D. J. (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. doi:10.1261/rna.7640104
-
(2004)
RNA
, vol.10
, pp. 1337-1351
-
-
Simmonds, P.1
Tuplin, A.2
Evans, D.J.3
-
76
-
-
0037203041
-
Effect of gene location, mRNA secondary structures, and RNase sites on expression of two genes in an engineered operon
-
Smolke, C. D., and Keasling, J. D. (2002). Effect of gene location, mRNA secondary structures, and RNase sites on expression of two genes in an engineered operon. Biotechnol. Bioeng. 80, 762-776. doi:10.1002/bit.10434
-
(2002)
Biotechnol. Bioeng
, vol.80
, pp. 762-776
-
-
Smolke, C.D.1
Keasling, J.D.2
-
77
-
-
2942582578
-
The "weighted sum of relative entropy": a new index for synonymous codon usage bias
-
Suzuki, H., Saito, R., and Tomita, M. (2004). The "weighted sum of relative entropy": a new index for synonymous codon usage bias. Gene 335, 19-23. doi:10.1016/j.gene.2004.03.001
-
(2004)
Gene
, vol.335
, pp. 19-23
-
-
Suzuki, H.1
Saito, R.2
Tomita, M.3
-
78
-
-
33746788103
-
Gene designer: a synthetic biology tool for constructing artificial DNA segments
-
Villalobos, A., Ness, J. E., Gustafsson, C., Minshull, J., and Govindarajan, S. (2006). Gene designer: a synthetic biology tool for constructing artificial DNA segments. BMC Bioinformatics 7, 285. doi:10.1186/1471-2105-7-285
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 285
-
-
Villalobos, A.1
Ness, J.E.2
Gustafsson, C.3
Minshull, J.4
Govindarajan, S.5
-
79
-
-
13444269018
-
Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes
-
Wan, X. F., Xu, D., Kleinhofs, A., and Zhou, J. Z. (2004). Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes. BMC Evol. Biol. 4:19. doi:10.1186/1471-2148-4-19
-
(2004)
BMC Evol. Biol
, vol.4
, pp. 19
-
-
Wan, X.F.1
Xu, D.2
Kleinhofs, A.3
Zhou, J.Z.4
-
80
-
-
70349199628
-
Design parameters to control synthetic gene expression in Escherichia coli
-
Welch, M., Govindarajan, S., Ness, J. E., Villalobos, A., Gurney, A., Minshull, J., et al. (2009). Design parameters to control synthetic gene expression in Escherichia coli. PLoS ONE 4, e7002. doi:10.1371/journal.pone.0007002
-
(2009)
PLoS ONE
, vol.4
-
-
Welch, M.1
Govindarajan, S.2
Ness, J.E.3
Villalobos, A.4
Gurney, A.5
Minshull, J.6
-
81
-
-
42049123423
-
Codon-optimized bacterial genes improve l-Arabinose fermentation in recombinant Saccharomyces cerevisiae
-
Wiedemann, B., and Boles, E. (2008). Codon-optimized bacterial genes improve l-Arabinose fermentation in recombinant Saccharomyces cerevisiae. Appl. Environ. Microbiol. 74, 2043-2050. doi:10.1128/AEM.02395-07
-
(2008)
Appl. Environ. Microbiol
, vol.74
, pp. 2043-2050
-
-
Wiedemann, B.1
Boles, E.2
-
82
-
-
33749069702
-
"The synthetic gene designer: a flexible web platform to explore sequence space of synthetic genes for heterologous expression,"
-
2005 Aug 8-11. (California: Stanford University)
-
Wu, G., Bashir-Bello, N., and Freeland, S. (2005). "The synthetic gene designer: a flexible web platform to explore sequence space of synthetic genes for heterologous expression," in 2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts, 2005 Aug 8-11. (California: Stanford University), 258-259. Available from: http://conferences.computer.org/bioinformatics/
-
(2005)
2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts
, pp. 258-259
-
-
Wu, G.1
Bashir-Bello, N.2
Freeland, S.3
-
83
-
-
79957442875
-
Developer's and user's guide to clotho v2.0 a software platform for the creation of synthetic biological systems
-
Xia, B., Bhatia, S., Bubenheim, B., Dadgar, M., Densmore, D., and Anderson, J. C. (2011). Developer's and user's guide to clotho v2.0 a software platform for the creation of synthetic biological systems. Methods Enzymol. 498, 97-135. doi:10.1016/B978-0-12-385120-8.00005-X
-
(2011)
Methods Enzymol
, vol.498
, pp. 97-135
-
-
Xia, B.1
Bhatia, S.2
Bubenheim, B.3
Dadgar, M.4
Densmore, D.5
Anderson, J.C.6
-
84
-
-
0024477261
-
On finding all suboptimal foldings of an RNA molecule
-
Zuker, M. (1989). On finding all suboptimal foldings of an RNA molecule. Science 244, 48-52. doi:10.1126/science.2468181
-
(1989)
Science
, vol.244
, pp. 48-52
-
-
Zuker, M.1
|