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Publication bibliography

Airen, I. O. (2011): Genome-wide Functional Genomic Analysis for Physiological Investigation and Improvement of Cell-Free Protein Synthesis. PhD thesis.

Alexandrov, Kirill; Johnston, Wayne A.: Cell-free protein synthesis. Methods and protocols (Methods in Molecular Biology, Methods and Protocols, 1118).

Billerbeck, Sonja; Härle, Johannes; Panke, Sven (2013): The good of two worlds: increasing complexity in cell-free systems. In Current opinion in biotechnology 24 (6), pp. 1037–1043. DOI: 10.1016/j.copbio.2013.03.007

Bundy, Bradley C.; Swartz, James R. (2010): Site-Specific Incorporation of p -Propargyloxyphenylalanine in a Cell-Free Environment for Direct Protein−Protein Click Conjugation. In Bioconjugate Chem. 21 (2), pp. 255–263. DOI: 10.1021/bc9002844

Buntru, Matthias; Vogel, Simon; Stoff, Katrin; Spiegel, Holger; Schillberg, Stefan (2015): A versatile coupled cell-free transcription-translation system based on tobacco BY-2 cell lysates. In Biotechnology and bioengineering 112 (5), pp. 867–878. DOI: 10.1002/bit.25502

Cai, Qi; Hanson, Jeffrey A.; Steiner, Alexander R.; Tran, Cuong; Masikat, Mary Rose; Chen, Rishard et al. (2015): A simplified and robust protocol for immunoglobulin expression in Escherichia coli cell-free protein synthesis systems. In Biotechnology progress. DOI: 10.1002/btpr.2082

Calhoun, Kara A.; Swartz, James R. (2005): An economical method for cell-free protein synthesis using glucose and nucleoside monophosphates. In Biotechnology progress 21 (4), pp. 1146–1153. DOI: 10.1021/bp050052y

Calhoun, Kara A.; Swartz, James R. (2006): Total amino acid stabilization during cell-free protein synthesis reactions. In Journal of biotechnology 123 (2), pp. 193–203. DOI: 10.1016/j.jbiotec.2005.11.011

Caschera, Filippo; Noireaux, Vincent (2014): Synthesis of 2.3 mg/ml of protein with an all Escherichia coli cell-free transcription-translation system. In Biochimie 99, pp. 162–168. DOI: 10.1016/j.biochi.2013.11.025

Caschera, Filippo; Noireaux, Vincent (2015a): A cost-effective polyphosphate-based metabolism fuels an all E. coli cell-free expression system. In Metabolic engineering 27, pp. 29–37. DOI: 10.1016/j.ymben.2014.10.007

Caschera, Filippo; Noireaux, Vincent (2015b): Preparation of amino acid mixtures for cell-free expression systems. In BioTechniques 58 (1), pp. 40–43. DOI: 10.2144/000114249

Chappell, James; Freemont, Paul S. (2013): In vivo and in vitro characterization of σ70 constitutive promoters by real-time PCR and fluorescent measurements. In Methods in molecular biology (Clifton, N.J.) 1073, pp. 61–74. DOI: 10.1007/978-1-62703-625-2_7

Chappell, James; Jensen, Kirsten; Freemont, Paul S. (2013): Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology. In Nucleic acids research 41 (5), pp. 3471–3481. DOI: 10.1093/nar/gkt052

Chizzolini, Fabio; Forlin, Michele; Cecchi, Dario; Mansy, Sheref S. (2014): Gene position more strongly influences cell-free protein expression from operons than T7 transcriptional promoter strength. In ACS synthetic biology 3 (6), pp. 363–371. DOI: 10.1021/sb4000977

Hong, Seok Hoon; Kwon, Yong-Chan; Martin, Rey W.; Des Soye, Benjamin J; de Paz, Alexandra M; Swonger, Kirsten N. et al. (2015): Improving Cell-Free Protein Synthesis through Genome Engineering of Escherichia coli Lacking Release Factor 1. In Chembiochem : a European journal of chemical biology 16 (5), pp. 844–853. DOI: 10.1002/cbic.201402708

Jewett, Michael C.; Swartz, James R. (2004): Mimicking the Escherichia coli cytoplasmic environment activates long-lived and efficient cell-free protein synthesis. In Biotechnology and bioengineering 86 (1), pp. 19–26. DOI: 10.1002/bit.20026

Karig, David K.; Iyer, Sukanya; Simpson, Michael L.; Doktycz, Mitchel J. (2012): Expression optimization and synthetic gene networks in cell-free systems. In Nucleic acids research 40 (8), pp. 3763–3774. DOI: 10.1093/nar/gkr1191

Karzbrun, Eyal; Shin, Jonghyeon; Bar-Ziv, Roy H.; Noireaux, Vincent (2011): Coarse-Grained Dynamics of Protein Synthesis in a Cell-Free System. In Phys. Rev. Lett. 106 (4). DOI: 10.1103/PhysRevLett.106.048104

Kazuta, Yasuaki; Matsuura, Tomoaki; Ichihashi, Norikazu; Yomo, Tetsuya (2014): Synthesis of milligram quantities of proteins using a reconstituted in vitro protein synthesis system. In Journal of bioscience and bioengineering 118 (5), pp. 554–557. DOI: 10.1016/j.jbiosc.2014.04.019

Kelwick, Richard; MacDonald, James T.; Webb, Alexander J.; Freemont, Paul (2014): Developments in the tools and methodologies of synthetic biology. In Frontiers in bioengineering and biotechnology 2, p. 60. DOI: 10.3389/fbioe.2014.00060

Kigawa, Takanori; Yabuki, Takashi; Matsuda, Natsuko; Matsuda, Takayoshi; Nakajima, Rie; Tanaka, Akiko; Yokoyama, Shigeyuki (2004): Preparation of Escherichia coli cell extract for highly productive cell-free protein expression. In Journal of structural and functional genomics 5 (1-2), pp. 63–68. DOI: 10.1023/B:JSFG.0000029204.57846.7d

Kim, Dong-Myung; Swartz, James R. (2001): Regeneration of adenosine triphosphate from glycolytic intermediates for cell-free protein synthesis. In Biotech.

Kim, Ho-Cheol; Kim, Kwang-Soo; Kang, Taek-Jin; Choi, Jong-Hyun; Song, Jaejoon; Choi, Yun Hee et al. (2015): Implementing bacterial acid resistance into cell-free protein synthesis for buffer-free expression and screening of enzymes. In Biotechnology and bioengineering. DOI: 10.1002/bit.25671

Kim, Ho-Cheol; Kim, Tae-Wan; Kim, Dong-Myung (2011): Prolonged production of proteins in a cell-free protein synthesis system using polymeric carbohydrates as an energy source. In Process Biochemistry 46 (6), pp. 1366–1369. DOI: 10.1016/j.procbio.2011.03.008

Kim, Tae-Wan; Keum, Jung-Won; Oh, In-Seok; Choi, Cha-Yong; Park, Chang-Gil; Kim, Dong-Myung (2006): Simple procedures for the construction of a robust and cost-effective cell-free protein synthesis system. In Journal of biotechnology 126 (4), pp. 554–561. DOI: 10.1016/j.jbiotec.2006.05.014

Kim, Tae-Wan; Kim, Ho-Cheol; Kim, Dong-Myung (2008): A Highly Efficient and Economical Cell-free Protein Synthesis System Using the S12 Extract of Escherichia Coli.

Kimura-Soyema, Tomomi; Shirouzu, Mikako; Yokoyama, Shigeyuki (2014): Cell-free membrane protein expression. In Methods in molecular biology (Clifton, N.J.) 1118, pp. 267–273. DOI: 10.1007/978-1-62703-782-2_18

Kwon, Yong-Chan; Jewett, Michael C. (2015): High-throughput preparation methods of crude extract for robust cell-free protein synthesis. In Scientific reports 5, p. 8663. DOI: 10.1038/srep08663

Lentini, Roberta; Forlin, Michele; Martini, Laura; Del Bianco, Cristina; Spencer, Amy C.; Torino, Domenica; Mansy, Sheref S. (2013): Fluorescent proteins and in vitro genetic organization for cell-free synthetic biology. In ACS synthetic biology 2 (9), pp. 482–489. DOI: 10.1021/sb400003y

Lentini, Roberta; Santero, Silvia Perez; Chizzolini, Fabio; Cecchi, Dario; Fontana, Jason; Marchioretto, Marta et al. (2014): Integrating artificial with natural cells to translate chemical messages that direct E. coli behaviour. In Nature communications 5, p. 4012. DOI: 10.1038/ncomms5012

Ma, Rongrong; Yang, Zhong; Huang, Lei; Zhu, Xiangcheng; Kai, Lei; Cai, Jin et al. (2010): Construction of an efficient Escherichia coli cell-free system for in vitro expression of several kinds of proteins. In Eng. Life Sci. 10 (4), pp. 333–338. DOI: 10.1002/elsc.201000052

Mavelli, Fabio; Marangoni, Roberto; Stano, Pasquale (2015): A Simple Protein Synthesis Model for the PURE System Operation. In Bulletin of mathematical biology. DOI: 10.1007/s11538-015-0082-8

Miller, Corwin; Bröcker, Markus J.; Prat, Laure; Ip, Kevan; Chirathivat, Napon; Feiock, Alexander et al. (2015): A synthetic tRNA for EF-Tu mediated selenocysteine incorporation in vivo and in vitro. In FEBS letters. DOI: 10.1016/j.febslet.2015.06.039

Olins, Peter O.; Devine, Catherine S.; Rangwala, Shaukat H.; Kavka, Kamilla S. (1988): The T7 phage gene 10 leader RNA, a ribosome-binding site that dramatically enhances the expression of foreign genes in Escherichia coli. In Gene 73 (1), pp. 227–235.

Olins, Peter O.; Rangwala, Shaukat H. (1989): A novel sequence element derived from bacteriophage T7 mRNA acts as an enhancer of translation of the lacZ gene in Escherichia coli. In J Biol Chem.

Park, Nokyoung; Kahn, Jason S.; Rice, Edward J.; Hartman, Mark R.; Funabashi, Hisakage; Xu, Jianfeng et al. (2009): High-yield cell-free protein production from P-gel. In Nature protocols 4 (12), pp. 1759–1770. DOI: 10.1038/nprot.2009.174

Pedersen, Anders; Hellberg, Kristofer; Enberg, Johan; Karlsson, B. Göran (2011): Rational improvement of cell-free protein synthesis. In New biotechnology 28 (3), pp. 218–224. DOI: 10.1016/j.nbt.2010.06.015

Pratt, J. M. (1984): Coupled Transcription-Translation in Prokaryotic Cell-Free Systems. In B. D. Hames, S. J. Higgins (Eds.): Transcription and translation. A practical approach. Oxford, Washington, D.C.: IRL Press (Practical approach series).

Quast, Robert B.; Kortt, Oliver; Henkel, Jörg; Dondapati, Srujan K.; Wüstenhagen, Doreen A.; Stech, Marlitt; Kubick, Stefan (2015a): Automated production of functional membrane proteins using eukaryotic cell-free translation systems. In Journal of biotechnology 203, pp. 45–53. DOI: 10.1016/j.jbiotec.2015.03.015

Quast, Robert B.; Mrusek, Devid; Hoffmeister, Christian; Sonnabend, Andrei; Kubick, Stefan (2015b): Cotranslational incorporation of non-standard amino acids using cell-free protein synthesis. In FEBS letters. DOI: 10.1016/j.febslet.2015.04.041

Roos, Christian; Kai, Lei; Haberstock, Stefan; Proverbio, Davide; Ghoshdastider, Umesh; Ma, Yi et al. (2014): High-level cell-free production of membrane proteins with nanodiscs. In Methods in molecular biology (Clifton, N.J.) 1118, pp. 109–130. DOI: 10.1007/978-1-62703-782-2_7

Rosenblum, Gabriel; Cooperman, Barry S. (2014): Engine out of the chassis: cell-free protein synthesis and its uses. In FEBS letters 588 (2), pp. 261–268. DOI: 10.1016/j.febslet.2013.10.016

Shimizu, Yoshihiro; Ueda, Takuya (2010): PURE technology. In Methods in molecular biology (Clifton, N.J.) 607, pp. 11–21. DOI: 10.1007/978-1-60327-331-2_2

Shin, Jonghyeon; Noireaux, Vincent (2010): Efficient cell-free expression with the endogenous E. Coli RNA polymerase and sigma factor 70. In Journal of biological engineering 4, p. 8. DOI: 10.1186/1754-1611-4-8

Shin, Jonghyeon; Noireaux, Vincent (2012): An E. coli cell-free expression toolbox: application to synthetic gene circuits and artificial cells. In ACS synthetic biology 1 (1), pp. 29–41. DOI: 10.1021/sb200016s

Shrestha, Prashanta; Holland, Troy Michael; Bundy, Bradley Charles (2012): Streamlined extract preparation for Escherichia coli-based cell-free protein synthesis by sonication or bead vortex mixing. In BioTechniques 53 (3), pp. 163–174. DOI: 10.2144/0000113924

Sousa, Rui; Mukherjee, Srabani (2003): T7 RNA Polymerase. In, vol. 73: Elsevier (Progress in Nucleic Acid Research and Molecular Biology), pp. 1–41.

Spirin, Alexander S.; Swartz, James R. (2008): Cell-Free Protein Synthesis Systems: Historical Landmarks, Classification, and General Methods.

Stögbauer, Tobias; Windhager, Lukas; Zimmer, Ralf; Rädler, Joachim O. (2012): Experiment and mathematical modeling of gene expression dynamics in a cell-free system. In Integrative biology : quantitative biosciences from nano to macro 4 (5), pp. 494–501. DOI: 10.1039/c2ib00102k

Sun, Zachary Z.; Hayes, Clarmyra A.; Shin, Jonghyeon; Caschera, Filippo; Murray, Richard M.; Noireaux, Vincent (2013): Protocols for implementing an Escherichia coli based TX-TL cell-free expression system for synthetic biology. In Journal of visualized experiments : JoVE (79), pp. e50762. DOI: 10.3791/50762

Takahashi, Melissa K.; Hayes, Clarmyra A.; Chappell, James; Sun, Zachary Z.; Murray, Richard M.; Noireaux, Vincent; Lucks, Julius B. (2015): Characterizing and prototyping genetic networks with cell-free transcription-translation reactions. In Methods (San Diego, Calif.). DOI: 10.1016/j.ymeth.2015.05.020

Takahashi, Shuntaro; Furusawa, Hiroyuki; Ueda, Takuya; Okahata, Yoshio (2013): Translation enhancer improves the ribosome liberation from translation initiation. In Journal of the American Chemical Society 135 (35), pp. 13096–13106. DOI: 10.1021/ja405967h

Taylor, Graham J.; Sarles, Stephen A. (2015): Using Cell-Free Expression to Create Light-Activated Proteins In Situ in Droplet Interface Bilayer Networks. In MRS Proc. 1720. DOI: 10.1557/opl.2015.63

Tokmakov, Alexander A.; Kurotani, Atsushi; Shirouzu, Mikako; Fukami, Yasuo; Yokoyama, Shigeyuki (2014): Bioinformatics analysis and optimization of cell-free protein synthesis. In Methods in molecular biology (Clifton, N.J.) 1118, pp. 17–33. DOI: 10.1007/978-1-62703-782-2_2

Underwood, Kelly A.; Swartz, James R.; Puglisi, Joseph D. (2005): Quantitative polysome analysis identifies limitations in bacterial cell-free protein synthesis. In Biotechnology and bioengineering 91 (4), pp. 425–435. DOI: 10.1002/bit.20529

Wang, Harris H.; Huang, Po-Yi; Xu, George; Haas, Wilhelm; Marblestone, Adam; Li, Jun et al. (2012): Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multienzyme catalysis. In ACS synthetic biology 1 (2), pp. 43–52. DOI: 10.1021/sb3000029

Xu, Zhinan; Chen, Haiqin; Yin, Xiufei; Xu, Naizheng; Cen, Peilin (2005): High-Level Expression of Soluble Human b-Defensin-2 Fused With Green Fluorescent Protein in Escherichia coli Cell-Free System. In ABAB 127 (1), pp. 053–062. DOI: 10.1385/ABAB:127:1:053

Yang, William C.; Patel, Kedar G.; Wong, H. Edward; Swartz, James R. (2012a): Simplifying and streamlining Escherichia coli-based cell-free protein synthesis. In Biotechnology progress 28 (2), pp. 413–420. DOI: 10.1002/btpr.1509

Yang, Zhong; Ma, Rongrong; Huang, Lei; Zhu, Xiangcheng; Sheng, Jiayuan; Cai, Jin et al. (2012b): High-level production of soluble adenine nucleotide translocator from Schistosoma japonicum in E. coli cell-free system. In Process Biochemistry 47 (3), pp. 395–400. DOI: 10.1016/j.procbio.2011.11.010

Zárate, Xristo; Henderson, David C.; Phillips, Keenan C.; Lake, April D.; Galbraith, David W. (2010): Development of high-yield autofluorescent protein microarrays using hybrid cell-free expression with combined Escherichia coli S30 and wheat germ extracts. In Proteome science 8, p. 32. DOI: 10.1186/1477-5956-8-32

Zheng, Qiang; Shi, Rui; Zhu, Xiangcheng; Huang, Lei; Cai, Jin; Han, Wenbiao; Xu, Zhinan (2012): Functional expression of Bacillus subtilis xylanase A in an Escherichia coli derived cell-free protein synthesis system and subsequent expression improvement via DNA gel technique. In Process Biochemistry 47 (7), pp. 1186–1191. DOI: 10.1016/j.procbio.2012.02.002

Zubay, G. (1973): In vitro synthesis of protein in microbial systems. In Annual review of genetics 7, pp. 267–287. DOI: 10.1146/annurev.ge.07.120173.001411