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A systematic report on the recombinant biologics approved from January 2010 to July 2014.
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2• Walsh, G., Biopharmaceutical benchmarks 2014. Nat. Biotechnol. 32 (2014), 992–1000 A systematic report on the recombinant biologics approved from January 2010 to July 2014.
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4 Nielsen, J., Production of biopharmaceutical proteins by yeast: advances through metabolic engineering. Bioengineered 4 (2013), 207–211.
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5 Choi, B.K., Bobrowicz, P., Davidson, R.C., Hamilton, S.R., Kung, D.H., Li, H., Miele, R.G., Nett, J.H., Wildt, S., Gerngross, T.U., Use of combinatorial genetic libraries to humanize N-linked glycosylation in the yeast Pichia pastoris. Proc. Natl. Acad. Sci. U. S. A. 100 (2003), 5022–5027.
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A bacterial glycosidase enables mannose-6-phosphate modification and improved cellular uptake of yeast-produced recombinant human lysosomal enzymes
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6 Tiels, P., Baranova, E., Piens, K., De Visscher, C., Pynaert, G., Nerinckx, W., Stout, J., Fudalej, F., Hulpiau, P., Tannler, S., et al. A bacterial glycosidase enables mannose-6-phosphate modification and improved cellular uptake of yeast-produced recombinant human lysosomal enzymes. Nat. Biotechnol. 30 (2012), 1225–1231.
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7
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7 Hamilton, S.R., Davidson, R.C., Sethuraman, N., Nett, J.H., Jiang, Y.W., Rios, S., Bobrowicz, P., Stadheim, T.A., Li, H.J., Choi, B.K., et al. Humanization of yeast to produce complex terminally sialylated glycoproteins. Science 313 (2006), 1441–1443.
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Cells and cell lysates: a direct approach for engineering antibodies against membrane proteins using yeast surface display
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8 Tillotson, B.J., Cho, Y.K., Shusta, E.V., Cells and cell lysates: a direct approach for engineering antibodies against membrane proteins using yeast surface display. Methods 60 (2013), 27–37.
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Production, purification and characterization of recombinant human antithrombin III by Saccharomyces cerevisiae
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9 Mallu, M.R., Vemula, S., Ronda, S.R., Production, purification and characterization of recombinant human antithrombin III by Saccharomyces cerevisiae. Electron. J. Biotechnol. 22 (2016), 81–89.
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Engineering the oxygen sensing regulation results in an enhanced recombinant human hemoglobin production by Saccharomyces cerevisiae
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10 Martinez, J.L., Liu, L., Petranovic, D., Nielsen, J., Engineering the oxygen sensing regulation results in an enhanced recombinant human hemoglobin production by Saccharomyces cerevisiae. Biotechnol. Bioeng. 112 (2015), 181–188.
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Maximizing recombinant human serum albumin production in a Mut(s) Pichia pastoris strain
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11 Mallem, M., Warburton, S., Li, F., Shandil, I., Nylen, A., Kim, S., Jiang, Y., Meehl, M., d'Anjou, M., Stadheim, T.A., et al. Maximizing recombinant human serum albumin production in a Mut(s) Pichia pastoris strain. Biotechnol. Prog. 30 (2014), 1488–1496.
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Expression, purification and characterization of recombinant human interleukin-2-serum albumin (rhIL-2-HSA) fusion protein in Pichia pastoris
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12 Lei, J.Y., Guan, B., Li, B., Duan, Z.Y., Chen, Y., Li, H.Z., Jin, J., Expression, purification and characterization of recombinant human interleukin-2-serum albumin (rhIL-2-HSA) fusion protein in Pichia pastoris. Protein Expr. Purif. 84 (2012), 154–160.
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High-level secretory expression, purification, and characterization of an anti-human Her II monoclonal antibody, trastuzumab, in the methylotrophic yeast Pichia pastoris
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13 Shibui, T., Bando, K., Misawa, S., High-level secretory expression, purification, and characterization of an anti-human Her II monoclonal antibody, trastuzumab, in the methylotrophic yeast Pichia pastoris. Adv. Biosci. Biotechnol. 4 (2013), 640–646.
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Optimization of erythropoietin production with controlled glycosylation-PEGylated erythropoietin produced in glycoengineered Pichia pastoris
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14 Nett, J.H., Gomathinayagam, S., Hamilton, S.R., Gong, B., Davidson, R.C., Du, M., Hopkins, D., Mitchell, T., Mallem, M.R., Nylen, A., et al. Optimization of erythropoietin production with controlled glycosylation-PEGylated erythropoietin produced in glycoengineered Pichia pastoris. J. Biotechnol. 157 (2012), 198–206.
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15
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The vitamin-sensitive promoter PTHI11 enables pre-defined autonomous induction of recombinant protein production in Pichia pastoris
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15 Landes, N., Gasser, B., Vorauer-Uhl, K., Lhota, G., Mattanovich, D., Maurer, M., The vitamin-sensitive promoter PTHI11 enables pre-defined autonomous induction of recombinant protein production in Pichia pastoris. Biotechnol. Bioeng. 113 (2016), 2633–2643.
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16
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Metabolic engineering of recombinant protein secretion by Saccharomyces cerevisiae
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16 Hou, J., Tyo, K.E., Liu, Z., Petranovic, D., Nielsen, J., Metabolic engineering of recombinant protein secretion by Saccharomyces cerevisiae. FEMS Yeast Res. 12 (2012), 491–510.
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Hou, J.1
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17
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Enhancing the copy number of episomal plasmids in Saccharomyces cerevisiae for improved protein production
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17 Chen, Y., Partow, S., Scalcinati, G., Siewers, V., Nielsen, J., Enhancing the copy number of episomal plasmids in Saccharomyces cerevisiae for improved protein production. FEMS Yeast Res. 12 (2012), 598–607.
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Chen, Y.1
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18
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84862807811
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Different expression systems for production of recombinant proteins in Saccharomyces cerevisiae
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This study systematically evaluates factors influencing recombinant protein secretion, including protein type, expression vector and leader peptide, and demonstrates a generally applicable strategy for initial optimization of key factors for rational engineering cell factory for novel proteins.
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18•• Liu, Z., Tyo, K.E., Martinez, J.L., Petranovic, D., Nielsen, J., Different expression systems for production of recombinant proteins in Saccharomyces cerevisiae. Biotechnol. Bioeng. 109 (2012), 1259–1268 This study systematically evaluates factors influencing recombinant protein secretion, including protein type, expression vector and leader peptide, and demonstrates a generally applicable strategy for initial optimization of key factors for rational engineering cell factory for novel proteins.
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Liu, Z.1
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19
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84989940494
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A new set of rDNA-NTS-based multiple integrative cassettes for the development of antibiotic-marker-free recombinant yeasts
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19 Moon, H.Y., Lee, D.W., Sim, G.H., Kim, H.J., Hwang, J.Y., Kwon, M.G., Kang, B.K., Kim, J.M., Kang, H.A., A new set of rDNA-NTS-based multiple integrative cassettes for the development of antibiotic-marker-free recombinant yeasts. J. Biotechnol. 233 (2016), 190–199.
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Moon, H.Y.1
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Kang, H.A.9
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20
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84960906175
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EasyCloneMulti: a set of vectors for simultaneous and multiple genomic integrations in Saccharomyces cerevisiae
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20 Maury, J., Germann, S.M., Baallal Jacobsen, S.A., Jensen, N.B., Kildegaard, K.R., Herrgard, M.J., Schneider, K., Koza, A., Forster, J., Nielsen, J., et al. EasyCloneMulti: a set of vectors for simultaneous and multiple genomic integrations in Saccharomyces cerevisiae. PLoS One, 11, 2016, e0150394.
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Maury, J.1
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21
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84947279264
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A highly efficient single-step, markerless strategy for multi-copy chromosomal integration of large biochemical pathways in Saccharomyces cerevisiae
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21 Shi, S., Liang, Y., Zhang, M.M., Ang, E.L., Zhao, H., A highly efficient single-step, markerless strategy for multi-copy chromosomal integration of large biochemical pathways in Saccharomyces cerevisiae. Metab. Eng. 33 (2016), 19–27.
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Shi, S.1
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22
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Signal peptide optimization tool for the secretion of recombinant protein from Saccharomyces cerevisiae
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22 Mori, A., Hara, S., Sugahara, T., Kojima, T., Iwasaki, Y., Kawarasaki, Y., Sahara, T., Ohgiya, S., Nakano, H., Signal peptide optimization tool for the secretion of recombinant protein from Saccharomyces cerevisiae. J. Biosci. Bioeng. 120 (2015), 518–525.
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23
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Directed evolution of a secretory leader for the improved expression of heterologous proteins and full-length antibodies in Saccharomyces cerevisiae
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23 Rakestraw, J.A., Sazinsky, S.L., Piatesi, A., Antipov, E., Wittrup, K.D., Directed evolution of a secretory leader for the improved expression of heterologous proteins and full-length antibodies in Saccharomyces cerevisiae. Biotechnol. Bioeng. 103 (2009), 1192–1201.
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Rakestraw, J.A.1
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24
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Method for producing heterologous protein using yeast with disruption of VPS gene
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24 Nishiyama T, Sakai Y: Method for producing heterologous protein using yeast with disruption of VPS gene. EP Patent 2015, EP2684948 A1.
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Nishiyama, T.1
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25
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Blocking endocytotic mechanisms to improve heterologous protein titers in Saccharomyces cerevisiae
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25 Rodriguez-Limas, W.A., Tannenbaum, V., Tyo, K.E., Blocking endocytotic mechanisms to improve heterologous protein titers in Saccharomyces cerevisiae. Biotechnol. Bioeng. 112 (2015), 376–385.
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Rodriguez-Limas, W.A.1
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26
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Heat shock response improves heterologous protein secretion in Saccharomyces cerevisiae
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26 Hou, J., Osterlund, T., Liu, Z., Petranovic, D., Nielsen, J., Heat shock response improves heterologous protein secretion in Saccharomyces cerevisiae. Appl. Microbiol. Biotechnol. 97 (2013), 3559–3568.
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Hou, J.1
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Multivariate modular engineering of the protein secretory pathway for production of heterologous glucose oxidase in Pichia pastoris
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27 Gu, L., Zhang, J., Du, G., Chen, J., Multivariate modular engineering of the protein secretory pathway for production of heterologous glucose oxidase in Pichia pastoris. Enzyme Microb. Technol. 68 (2015), 33–42.
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Gu, L.1
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28
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Engineering protein folding and translocation improves heterologous protein secretion in Saccharomyces cerevisiae
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This study demonstrates combinatorial strengthening of protein folding and translocation important for heterologous protein production in S. cerevisiae.
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28• Tang, H., Bao, X., Shen, Y., Song, M., Wang, S., Wang, C., Hou, J., Engineering protein folding and translocation improves heterologous protein secretion in Saccharomyces cerevisiae. Biotechnol. Bioeng. 112 (2015), 1872–1882 This study demonstrates combinatorial strengthening of protein folding and translocation important for heterologous protein production in S. cerevisiae.
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Tang, H.1
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29
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Overexpression of native Saccharomyces cerevisiae ER-to-Golgi SNARE genes increased heterologous cellulase secretion
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29 Van Zyl, J.H., Den Haan, R., Van Zyl, W.H., Overexpression of native Saccharomyces cerevisiae ER-to-Golgi SNARE genes increased heterologous cellulase secretion. Appl. Microbiol. Biotechnol. 100 (2016), 505–518.
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Van Zyl, J.H.1
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30
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Engineering of vesicle trafficking improves heterologous protein secretion in Saccharomyces cerevisiae
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30 Hou, J., Tyo, K., Liu, Z., Petranovic, D., Nielsen, J., Engineering of vesicle trafficking improves heterologous protein secretion in Saccharomyces cerevisiae. Metab. Eng. 14 (2012), 120–127.
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Hou, J.1
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31
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84879345901
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Rate-limiting steps in yeast protein translation
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The authors establish a detailed computational model based on sequencing data and identify the fast initiation or high codon bias important for protein yield of a transgene in S. cerevisiae.
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31• Shah, P., Ding, Y., Niemczyk, M., Kudla, G., Plotkin, J.B., Rate-limiting steps in yeast protein translation. Cell 153 (2013), 1589–1601 The authors establish a detailed computational model based on sequencing data and identify the fast initiation or high codon bias important for protein yield of a transgene in S. cerevisiae.
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Shah, P.1
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32
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The cost of protein production
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32 Kafri, M., Metzl-Raz, E., Jona, G., Barkai, N., The cost of protein production. Cell Rep. 14 (2016), 22–31.
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Kafri, M.1
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Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources
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33 Li, G.W., Burkhardt, D., Gross, C., Weissman, J.S., Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. Cell 157 (2014), 624–635.
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Li, G.W.1
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34
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Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation
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This study provides improved ribosome-footprint profiles and mRNA abundances confirming the slow translation of the beginning of coding regions and codons matching rare tRNAs in S. cerevisiae.
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34• Weinberg, D.E., Shah, P., Eichhorn, S.W., Hussmann, J.A., Plotkin, J.B., Bartel, D.P., Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation. Cell Rep 14 (2016), 1787–1799 This study provides improved ribosome-footprint profiles and mRNA abundances confirming the slow translation of the beginning of coding regions and codons matching rare tRNAs in S. cerevisiae.
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Weinberg, D.E.1
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35
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84876309308
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Anaerobic alpha-amylase production and secretion with fumarate as the final electron acceptor in Saccharomyces cerevisiae
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35 Liu, Z., Osterlund, T., Hou, J., Petranovic, D., Nielsen, J., Anaerobic alpha-amylase production and secretion with fumarate as the final electron acceptor in Saccharomyces cerevisiae. Appl. Environ. Microbiol. 79 (2013), 2962–2967.
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Liu, Z.1
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36
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Transcriptome analysis of recombinant protein secretion by Aspergillus nidulans and the unfolded-protein response in vivo
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36 Sims, A.H., Gent, M.E., Lanthaler, K., Dunn-Coleman, N.S., Oliver, S.G., Robson, G.D., Transcriptome analysis of recombinant protein secretion by Aspergillus nidulans and the unfolded-protein response in vivo. Appl. Environ. Microbiol. 71 (2005), 2737–2747.
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Sims, A.H.1
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Robson, G.D.6
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37
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Correlation of cell growth and heterologous protein production by Saccharomyces cerevisiae
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37 Liu, Z., Hou, J., Martinez, J.L., Petranovic, D., Nielsen, J., Correlation of cell growth and heterologous protein production by Saccharomyces cerevisiae. Appl. Microbiol. Biotechnol. 97 (2013), 8955–8962.
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Liu, Z.1
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38
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Imbalance of heterologous protein folding and disulfide bond formation rates yields runaway oxidative stress
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38 Tyo, K.E., Liu, Z., Petranovic, D., Nielsen, J., Imbalance of heterologous protein folding and disulfide bond formation rates yields runaway oxidative stress. BMC Biol., 10, 2012, 16.
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Transcriptomics-based identification of novel factors enhancing heterologous protein secretion in yeasts
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39 Gasser, B., Sauer, M., Maurer, M., Stadlmayr, G., Mattanovich, D., Transcriptomics-based identification of novel factors enhancing heterologous protein secretion in yeasts. Appl. Environ. Microbiol. 73 (2007), 6499–6507.
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40
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84922471043
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Engineering the supply chain for protein production/secretion in yeasts and mammalian cells
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An excellent review on optimization of supply chain for building blocks and energy for protein production.
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40•• Klein, T., Niklas, J., Heinzle, E., Engineering the supply chain for protein production/secretion in yeasts and mammalian cells. J. Ind. Microbiol. Biotechnol. 42 (2015), 453–464 An excellent review on optimization of supply chain for building blocks and energy for protein production.
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Klein, T.1
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41
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Enhanced protein and biochemical production using CRISPRi-based growth switches
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41 Li, S., Jendresen, C.B., Grunberger, A., Ronda, C., Jensen, S.I., Noack, S., Nielsen, A.T., Enhanced protein and biochemical production using CRISPRi-based growth switches. Metab. Eng. 38 (2016), 274–284.
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Li, S.1
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Jensen, S.I.5
Noack, S.6
Nielsen, A.T.7
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42
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84961654631
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Increasing pentose phosphate pathway flux enhances recombinant protein production in Pichia pastoris
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The authors combinatorially overexpress genes involved in pentose phosphate pathway (PPP), enhancing the PPP flux ratio and recombinant hSOD production in P. pastoris.
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42• Nocon, J., Steiger, M., Mairinger, T., Hohlweg, J., Russmayer, H., Hann, S., Gasser, B., Mattanovich, D., Increasing pentose phosphate pathway flux enhances recombinant protein production in Pichia pastoris. Appl. Microbiol. Biotechnol. 100 (2016), 5955–5963 The authors combinatorially overexpress genes involved in pentose phosphate pathway (PPP), enhancing the PPP flux ratio and recombinant hSOD production in P. pastoris.
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Nocon, J.1
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Hann, S.6
Gasser, B.7
Mattanovich, D.8
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43
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Metabolomics-driven approach for the improvement of Chinese hamster ovary cell growth: overexpression of malate dehydrogenase II
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43 Chong, W.P., Reddy, S.G., Yusufi, F.N., Lee, D.Y., Wong, N.S., Heng, C.K., Yap, M.G., Ho, Y.S., Metabolomics-driven approach for the improvement of Chinese hamster ovary cell growth: overexpression of malate dehydrogenase II. J. Biotechnol. 147 (2010), 116–121.
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Chong, W.P.1
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Yap, M.G.7
Ho, Y.S.8
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44
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Integration of expression data in genome-scale metabolic network reconstructions
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44 Blazier, A.S., Papin, J.A., Integration of expression data in genome-scale metabolic network reconstructions. Front. Physiol., 3, 2012, 299.
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Blazier, A.S.1
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45
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Model based engineering of Pichia pastoris central metabolism enhances recombinant protein production
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The authors utilized genome scale metabolic modeling to predict targets for enhancing recombinant protein production in P. pastoris. A high accuracy in the positive target prediction demonstrates the promising application of model guided strain development.
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45•• Nocon, J., Steiger, M.G., Pfeffer, M., Sohn, S.B., Kim, T.Y., Maurer, M., Russmayer, H., Pflugl, S., Ask, M., Haberhauer-Troyer, C., et al. Model based engineering of Pichia pastoris central metabolism enhances recombinant protein production. Metab. Eng. 24 (2014), 129–138 The authors utilized genome scale metabolic modeling to predict targets for enhancing recombinant protein production in P. pastoris. A high accuracy in the positive target prediction demonstrates the promising application of model guided strain development.
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Nocon, J.1
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Russmayer, H.7
Pflugl, S.8
Ask, M.9
Haberhauer-Troyer, C.10
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46
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84949257152
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Genome-scale metabolic model of Pichia pastoris with native and humanized glycosylation of recombinant proteins
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46 Irani, Z.A., Kerkhoven, E.J., Shojaosadati, S.A., Nielsen, J., Genome-scale metabolic model of Pichia pastoris with native and humanized glycosylation of recombinant proteins. Biotechnol. Bioeng. 113 (2016), 961–969.
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Irani, Z.A.1
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Shojaosadati, S.A.3
Nielsen, J.4
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47
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84877119088
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Genome-scale modeling of the protein secretory machinery in yeast
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The authors construct a genome-scale model for protein secretion in S. cerevisiae using a bottom-up approach. This model covers the entire secretory process to provide a more detailed comprehensive view of the secretory machinery.
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47•• Feizi, A., Osterlund, T., Petranovic, D., Bordel, S., Nielsen, J., Genome-scale modeling of the protein secretory machinery in yeast. PLoS One, 8, 2013, e63284 The authors construct a genome-scale model for protein secretion in S. cerevisiae using a bottom-up approach. This model covers the entire secretory process to provide a more detailed comprehensive view of the secretory machinery.
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PLoS One
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Feizi, A.1
Osterlund, T.2
Petranovic, D.3
Bordel, S.4
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48
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Altered sterol composition renders yeast thermotolerant
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48 Caspeta, L., Chen, Y., Ghiaci, P., Feizi, A., Buskov, S., Hallstrom, B.M., Petranovic, D., Nielsen, J., Altered sterol composition renders yeast thermotolerant. Science 346 (2014), 75–78.
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Science
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Caspeta, L.1
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Feizi, A.4
Buskov, S.5
Hallstrom, B.M.6
Petranovic, D.7
Nielsen, J.8
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49
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84905917097
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Improved production of a heterologous amylase in Saccharomyces cerevisiae by inverse metabolic engineering
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49 Liu, Z., Liu, L., Osterlund, T., Hou, J., Huang, M., Fagerberg, L., Petranovic, D., Uhlen, M., Nielsen, J., Improved production of a heterologous amylase in Saccharomyces cerevisiae by inverse metabolic engineering. Appl. Environ. Microbiol. 80 (2014), 5542–5550.
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Liu, Z.1
Liu, L.2
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Fagerberg, L.6
Petranovic, D.7
Uhlen, M.8
Nielsen, J.9
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50
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84893020696
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High-throughput screening for industrial enzyme production hosts by droplet microfluidics
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50 Sjostrom, S.L., Bai, Y.P., Huang, M.T., Liu, Z.H., Nielsen, J., Joensson, H.N., Svahn, H.A., High-throughput screening for industrial enzyme production hosts by droplet microfluidics. Lab Chip 14 (2014), 806–813.
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(2014)
Lab Chip
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Sjostrom, S.L.1
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Huang, M.T.3
Liu, Z.H.4
Nielsen, J.5
Joensson, H.N.6
Svahn, H.A.7
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51
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84940521020
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Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast
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The authors isolate yeast mutant strains with significantly improved amylase production through microfluidic screening and systematical analysis of mutations and biological processes associated with improved protein secretion.
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51•• Huang, M., Bai, Y., Sjostrom, S.L., Hallstrom, B.M., Liu, Z., Petranovic, D., Uhlen, M., Joensson, H.N., Andersson-Svahn, H., Nielsen, J., Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast. Proc. Natl. Acad. Sci. U. S. A. 112 (2015), E4689–4696 The authors isolate yeast mutant strains with significantly improved amylase production through microfluidic screening and systematical analysis of mutations and biological processes associated with improved protein secretion.
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(2015)
Proc. Natl. Acad. Sci. U. S. A.
, vol.112
, pp. E4689-4696
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Huang, M.1
Bai, Y.2
Sjostrom, S.L.3
Hallstrom, B.M.4
Liu, Z.5
Petranovic, D.6
Uhlen, M.7
Joensson, H.N.8
Andersson-Svahn, H.9
Nielsen, J.10
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52
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84952682854
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CRISPR/Cas9 advances engineering of microbial cell factories
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52 Jakociunas, T., Jensen, M.K., Keasling, J.D., CRISPR/Cas9 advances engineering of microbial cell factories. Metab. Eng. 34 (2016), 44–59.
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Jakociunas, T.1
Jensen, M.K.2
Keasling, J.D.3
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53
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84925607864
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RNAi-assisted genome evolution in Saccharomyces cerevisiae for complex phenotype engineering
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53 Si, T., Luo, Y., Bao, Z., Zhao, H., RNAi-assisted genome evolution in Saccharomyces cerevisiae for complex phenotype engineering. ACS Synth. Biol. 4 (2015), 283–291.
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Si, T.1
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