TY - BOOK AU - Balbás, P. AU - Lorence, A. PY - 2004 DA - 2004// TI - Recombinant gene expression: reviews and protocols PB - Humana Press CY - Totowa UR - https://doi.org/10.1385/1592597742 DO - 10.1385/1592597742 ID - Balbás2004 ER - TY - STD TI - Elena C, Ravasi P, Castelli ME, Peirú S, and Menzella HG. “Expression of codon optimized genes in microbial systems: current industrial applications and perspectives.” Front Microbiol 2014;vol. 5. ID - ref2 ER - TY - JOUR AU - Gouy, M. AU - Gautier, C. PY - 1982 DA - 1982// TI - Codon usage in bacteria: correlation with gene expressivity JO - Nucleic Acids Res VL - 10 UR - https://doi.org/10.1093/nar/10.22.7055 DO - 10.1093/nar/10.22.7055 ID - Gouy1982 ER - TY - JOUR AU - Gustafsson, C. AU - Govindarajan, S. AU - Minshull, J. PY - 2004 DA - 2004// TI - Codon bias and heterologous protein expression JO - Trends Biotechnol VL - 22 UR - https://doi.org/10.1016/j.tibtech.2004.04.006 DO - 10.1016/j.tibtech.2004.04.006 ID - Gustafsson2004 ER - TY - JOUR AU - Henry, I. AU - Sharp, P. M. PY - 2006 DA - 2006// TI - Predicting gene expression level from codon usage bias JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msl148 DO - 10.1093/molbev/msl148 ID - Henry2006 ER - TY - JOUR AU - Sandhu, K. S. AU - Pandey, S. AU - Maiti, S. AU - Pillai, B. PY - 2008 DA - 2008// TI - GASCO: Genetic Algorithm Simulation for Codon Optimization JO - In Silico Biol VL - 8 ID - Sandhu2008 ER - TY - JOUR AU - Wu, X. AU - Jörnvall, H. AU - Berndt, K. D. AU - Oppermann, U. PY - 2004 DA - 2004// TI - Codon optimization reveals critical factors for high level expression of two rare codon genes in Escherichia coli: RNA stability and secondary structure but not tRNA abundance JO - Biochem Biophys Res Commun VL - 313 UR - https://doi.org/10.1016/j.bbrc.2003.11.091 DO - 10.1016/j.bbrc.2003.11.091 ID - Wu2004 ER - TY - JOUR AU - Bai, J. AU - Swartz, D. J. AU - Protasevich, I. I. AU - Brouillette, C. G. AU - Harrell, P. M. AU - Hildebrandt, E. AU - Gasser, B. AU - Mattanovich, D. AU - Ward, A. AU - Chang, G. AU - Urbatsch, I. L. PY - 2011 DA - 2011// TI - A gene optimization strategy that enhances production of fully functional P-glycoprotein in Pichia pastoris JO - PLoS ONE VL - 6 UR - https://doi.org/10.1371/journal.pone.0022577 DO - 10.1371/journal.pone.0022577 ID - Bai2011 ER - TY - JOUR AU - Gvritishvili, A. G. AU - Leung, K. W. AU - Tombran-Tink, J. PY - 2010 DA - 2010// TI - Codon preference optimization increases heterologous PEDF expression JO - PLoS ONE VL - 5 UR - https://doi.org/10.1371/journal.pone.0015056 DO - 10.1371/journal.pone.0015056 ID - Gvritishvili2010 ER - TY - STD TI - Li W, Ng I-S, Fang B, Yu J, Zhang G. Codon optimization of 1,3-propanediol oxidoreductase expression in Escherichia coli and enzymatic properties. Electron J Biotechnol. 2011;14(4). ID - ref10 ER - TY - JOUR AU - Menzella, H. G. PY - 2011 DA - 2011// TI - Comparison of two codon optimization strategies to enhance recombinant protein production in Escherichia coli JO - Microb Cell Factories VL - 10 UR - https://doi.org/10.1186/1475-2859-10-15 DO - 10.1186/1475-2859-10-15 ID - Menzella2011 ER - TY - JOUR AU - Wang, Q. AU - Mei, C. AU - Zhen, H. AU - Zhu, J. PY - 2012 DA - 2012// TI - Codon preference optimization increases prokaryotic Cystatin C expression JO - J Biomed Biotechnol VL - 2012 ID - Wang2012 ER - TY - JOUR AU - Grantham, R. AU - Gautier, C. AU - Gouy, M. AU - Mercier, R. AU - Pavé, A. PY - 1980 DA - 1980// TI - Codon catalog usage and the genome hypothesis JO - Nucleic Acids Res VL - 8 UR - https://doi.org/10.1093/nar/8.1.197-c DO - 10.1093/nar/8.1.197-c ID - Grantham1980 ER - TY - JOUR AU - Ikemura, T. PY - 1985 DA - 1985// TI - Codon usage and tRNA content in unicellular and multicellular organisms JO - Mol Biol Evol VL - 2 ID - Ikemura1985 ER - TY - JOUR AU - Ikemura, T. PY - 1981 DA - 1981// TI - Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes JO - J Mol Biol VL - 146 UR - https://doi.org/10.1016/0022-2836(81)90363-6 DO - 10.1016/0022-2836(81)90363-6 ID - Ikemura1981 ER - TY - JOUR AU - Fuglsang, A. PY - 2003 DA - 2003// TI - Codon optimizer: a freeware tool for codon optimization JO - Protein Expr Purif VL - 31 UR - https://doi.org/10.1016/S1046-5928(03)00213-4 DO - 10.1016/S1046-5928(03)00213-4 ID - Fuglsang2003 ER - TY - JOUR AU - Gao, W. AU - Rzewski, A. AU - Sun, H. AU - Robbins, P. D. AU - Gambotto, A. PY - 2004 DA - 2004// TI - UpGene: application of a Web-based DNA codon optimization algorithm JO - Biotechnol Prog VL - 20 UR - https://doi.org/10.1021/bp0300467 DO - 10.1021/bp0300467 ID - Gao2004 ER - TY - JOUR AU - Gaspar, P. AU - Oliveira, J. L. AU - Frommlet, J. AU - Santos, M. A. S. AU - Moura, G. PY - 2012 DA - 2012// TI - EuGene: maximizing synthetic gene design for heterologous expression JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts465 DO - 10.1093/bioinformatics/bts465 ID - Gaspar2012 ER - TY - JOUR AU - Grote, A. AU - Hiller, K. AU - Scheer, M. AU - Münch, R. AU - Nörtemann, B. AU - Hempel, D. C. AU - Jahn, D. PY - 2005 DA - 2005// TI - JCat: a novel tool to adapt codon usage of a target gene to its potential expression host JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki376 DO - 10.1093/nar/gki376 ID - Grote2005 ER - TY - JOUR AU - Hoover, D. M. PY - 2002 DA - 2002// TI - DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.10.e43 DO - 10.1093/nar/30.10.e43 ID - Hoover2002 ER - TY - JOUR AU - Supek, F. AU - Vlahoviček, K. PY - 2004 DA - 2004// TI - INCA: synonymous codon usage analysis and clustering by means of self-organizing map JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth238 DO - 10.1093/bioinformatics/bth238 ID - Supek2004 ER - TY - JOUR AU - Villalobos, A. AU - Ness, J. E. AU - Gustafsson, C. AU - Minshull, J. AU - Govindarajan, S. PY - 2006 DA - 2006// TI - Gene Designer: a synthetic biology tool for constructing artificial DNA segments JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-285 DO - 10.1186/1471-2105-7-285 ID - Villalobos2006 ER - TY - JOUR AU - Guo, Y. AU - Wallace, S. S. AU - Bandaru, V. PY - 2009 DA - 2009// TI - A novel bicistronic vector for overexpressing Mycobacterium tuberculosis proteins in Escherichia coli JO - Protein Expr Purif VL - 65 UR - https://doi.org/10.1016/j.pep.2008.12.013 DO - 10.1016/j.pep.2008.12.013 ID - Guo2009 ER - TY - JOUR AU - Rosano, G. L. AU - Ceccarelli, E. A. PY - 2009 DA - 2009// TI - Rare codon content affects the solubility of recombinant proteins in a codon bias-adjusted Escherichia coli strain JO - Microb Cell Factories VL - 8 UR - https://doi.org/10.1186/1475-2859-8-41 DO - 10.1186/1475-2859-8-41 ID - Rosano2009 ER - TY - JOUR AU - Widmann, M. AU - Clairo, M. AU - Dippon, J. AU - Pleiss, J. PY - 2008 DA - 2008// TI - Analysis of the distribution of functionally relevant rare codons JO - BMC Genomics VL - 9 UR - https://doi.org/10.1186/1471-2164-9-207 DO - 10.1186/1471-2164-9-207 ID - Widmann2008 ER - TY - JOUR AU - Zhou, Z. AU - Schnake, P. AU - Xiao, L. AU - Lal, A. A. PY - 2004 DA - 2004// TI - Enhanced expression of a recombinant malaria candidate vaccine in Escherichia coli by codon optimization JO - Protein Expr Purif VL - 34 UR - https://doi.org/10.1016/j.pep.2003.11.006 DO - 10.1016/j.pep.2003.11.006 ID - Zhou2004 ER - TY - JOUR AU - Raab, D. AU - Graf, M. AU - Notka, F. AU - Schödl, T. AU - Wagner, R. PY - 2010 DA - 2010// TI - The GeneOptimizer Algorithm: using a sliding window approach to cope with the vast sequence space in multiparameter DNA sequence optimization JO - Syst Synth Biol VL - 4 UR - https://doi.org/10.1007/s11693-010-9062-3 DO - 10.1007/s11693-010-9062-3 ID - Raab2010 ER - TY - JOUR AU - Jung, S. -. K. AU - McDonald, K. PY - 2011 DA - 2011// TI - Visual gene developer: a fully programmable bioinformatics software for synthetic gene optimization JO - BMC Bioinformatics VL - 12 UR - https://doi.org/10.1186/1471-2105-12-340 DO - 10.1186/1471-2105-12-340 ID - Jung2011 ER - TY - JOUR AU - Solis-Escalante, D. AU - Kuijpers, N. G. A. AU - Bongaerts, N. AU - Bolat, I. AU - Bosman, L. AU - Pronk, J. T. AU - Daran, J. -. M. AU - Daran-Lapujade, P. PY - 2013 DA - 2013// TI - amdSYM, a new dominant recyclable marker cassette for Saccharomyces cerevisiae JO - FEMS Yeast Res VL - 13 UR - https://doi.org/10.1111/1567-1364.12024 DO - 10.1111/1567-1364.12024 ID - Solis-Escalante2013 ER - TY - JOUR AU - Blackburn, M. C. AU - Petrova, E. AU - Correia, B. E. AU - Maerkl, S. J. PY - 2016 DA - 2016// TI - Integrating gene synthesis and microfluidic protein analysis for rapid protein engineering JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1497 DO - 10.1093/nar/gkv1497 ID - Blackburn2016 ER - TY - JOUR AU - Stammen, S. AU - Muller, B. K. AU - Korneli, C. AU - Biedendieck, R. AU - Gamer, M. AU - Franco-Lara, E. AU - Jahn, D. PY - 2010 DA - 2010// TI - High-yield intra- and extracellular protein production using bacillus megaterium JO - Appl Environ Microbiol VL - 76 UR - https://doi.org/10.1128/AEM.00431-10 DO - 10.1128/AEM.00431-10 ID - Stammen2010 ER - TY - STD TI - Tuan-Anh T, Nam V, Hoang N, Bao P. “A Novel Method to Highly Expressed Genes Prediction Using Radius Clustering and Relative Synonymous Codon Usage.” J Comput Biol. 2015;1086–96. ID - ref32 ER - TY - JOUR AU - Marin, M. PY - 2008 DA - 2008// TI - Folding at the rhythm of the rare codon beat JO - Biotechnol J VL - 3 UR - https://doi.org/10.1002/biot.200800089 DO - 10.1002/biot.200800089 ID - Marin2008 ER - TY - JOUR AU - Purvis, I. J. AU - Bettany, A. J. E. AU - Santiago, T. C. AU - Coggins, J. R. AU - Duncan, K. AU - Eason, R. AU - Brown, A. J. P. PY - 1987 DA - 1987// TI - The efficiency of folding of some proteins is increased by controlled rates of translation in vivo JO - J Mol Biol VL - 193 UR - https://doi.org/10.1016/0022-2836(87)90230-0 DO - 10.1016/0022-2836(87)90230-0 ID - Purvis1987 ER - TY - JOUR AU - Sharp, P. M. AU - Li, W. -. H. PY - 1987 DA - 1987// TI - The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications JO - Nucleic Acids Res VL - 15 UR - https://doi.org/10.1093/nar/15.3.1281 DO - 10.1093/nar/15.3.1281 ID - Sharp1987 ER - TY - JOUR AU - Sharp, P. M. AU - Tuohy, T. M. F. AU - Mosurski, K. R. PY - 1986 DA - 1986// TI - Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes JO - Nucleic Acids Res VL - 14 UR - https://doi.org/10.1093/nar/14.13.5125 DO - 10.1093/nar/14.13.5125 ID - Sharp1986 ER - TY - BOOK AU - Duda, R. O. AU - Hart, P. E. AU - Stork, D. G. PY - 2001 DA - 2001// TI - Pattern classification PB - Wiley CY - New York ID - Duda2001 ER - TY - BOOK AU - Jolliffe, I. T. PY - 1986 DA - 1986// TI - Principal Component Analysis PB - Springer New York CY - New York UR - https://doi.org/10.1007/978-1-4757-1904-8 DO - 10.1007/978-1-4757-1904-8 ID - Jolliffe1986 ER - TY - BOOK AU - Mitchell, T. M. PY - 1997 DA - 1997// TI - Machine Learning PB - McGraw-Hill, Inc. CY - New York ID - Mitchell1997 ER - TY - JOUR AU - Huang, G. -. B. PY - 2003 DA - 2003// TI - Learning capability and storage capacity of two-hidden-layer feedforward networks JO - IEEE Trans Neural Netw VL - 14 UR - https://doi.org/10.1109/TNN.2003.809401 DO - 10.1109/TNN.2003.809401 ID - Huang2003 ER - TY - BOOK AU - Yan, X. PY - 2009 DA - 2009// TI - Linear Regression Analysis: Theory and Computing UR - https://doi.org/10.1142/6986 DO - 10.1142/6986 ID - Yan2009 ER - TY - BOOK AU - Michalewicz, Z. PY - 1996 DA - 1996// TI - Genetic algorithms + data structures = evolution programs, 3rd rev. and extended ed. Berlin PB - Springer CY - New York ID - Michalewicz1996 ER - TY - BOOK AU - Mitchel, M. PY - 1996 DA - 1996// TI - An introduction to genetic algorithms PB - MIT Press CY - Cambridge ID - Mitchel1996 ER - TY - JOUR AU - Royston, J. P. PY - 1982 DA - 1982// TI - An extension of Shapiro and Wilk’s W test for normality to large samples JO - Appl Stat VL - 31 UR - https://doi.org/10.2307/2347973 DO - 10.2307/2347973 ID - Royston1982 ER - TY - BOOK AU - Hollander, M. AU - Wolfe, D. A. PY - 1999 DA - 1999// TI - Nonparametric statistical methods PB - Wiley CY - New York ID - Hollander1999 ER - TY - JOUR AU - Welch, M. AU - Govindarajan, S. AU - Ness, J. E. AU - Villalobos, A. AU - Gurney, A. AU - Minshull, J. AU - Gustafsson, C. PY - 2009 DA - 2009// TI - Design parameters to control synthetic gene expression in Escherichia coli JO - PLoS ONE VL - 4 UR - https://doi.org/10.1371/journal.pone.0007002 DO - 10.1371/journal.pone.0007002 ID - Welch2009 ER -