Publications citing j5

Publications citing j5

212. Alaster D Moffat, Adam Elliston, Nicola J Patron, Andrew W Truman, Jose A Carrasco Lopez, A biofoundry workflow for the identification of genetic determinants of microbial growth inhibition, Synthetic Biology, Volume 6, Issue 1, 2021, ysab004,

211. Wang, Y., Cheng, H., Liu, Y. et al. In-situ generation of large numbers of genetic combinations for metabolic reprogramming via CRISPR-guided base editing. Nat Commun 12, 678 (2021).

210. Jianzhi Zhang, Yongcan Chen, Lihao Fu, Erpeng Guo, Bo Wang, Lei Dai, Tong Si. (2021) "Accelerating strain engineering in biofuel research via build and test automation of synthetic biology" Current Opinion in Biotechnology Volume 67, February 2021, Pages 88-98

209. Pavan M. (2021) Setting Up an Automated Biomanufacturing Laboratory. In: Menolascina F. (eds) Synthetic Gene Circuits. Methods in Molecular Biology, vol 2229. Humana, New York, NY.

208. Ashty S Karim, Fungmin Eric Liew, Shivani Garg, Bastian Vögeli, Blake J Rasor, Aislinn Gonnot, Marilene Pavan, Alex Juminaga, Séan D Simpson, Michael Köpke, and Michael C Jewett. (2020) "Modular cell-free expression plasmids to accelerate biological design in cells". OUP Synthetic Biology

207. Irene Otero-Muras, Pablo Carbonell. (2020) "Automated engineering of synthetic metabolic pathways for efficient association to reaction rules.biomanufacturing". Metabolic Engineering

206. Zhongkang Li, Changhao Bi, et al. (2020) "Engineering the Calvin–Benson–Bassham cycle and hydrogen utilization pathway of Ralstonia eutropha for improved autotrophic growth and polyhydroxybutyrate production". Microbial Cell Factories

205. Stracquadanio G., Zulkower V. (2021) Computer Aided Assembly and Verification of Synthetic Chromosomes. In: Marchisio M.A. (eds) Computational Methods in Synthetic Biology. Methods in Molecular Biology, vol 2189. Humana, New York, NY.

204. Garima Goyal, Nick Elsbree, Michael Fero, Nathan J. Hillson, and Gregory Linshiz. (2020) "Repurposing a microfluidic formulation device for automated DNA construction" PLOS One

203. Chao Yang Zhi Li, Dongdong Zhao, Jing Chen, Xinna Zhu, Xueli Zhang, Changhao Bi. (2020) "Engineering an efficient H2 utilizing Escherichia coli platform by modulation of endogenous hydrogenases" Biochemical Engineering Journal 107851

202. Mitchell G. Thompson, Matthew R. Incha, Allison N. Pearson, Matthias Schmidt, William A. Sharpless, Christopher B. Eiben, Pablo Cruz-Morales, Jacquelyn M. Blake-Hedges, Yuzhong Liu, Catharine A. Adams, Robert W. Haushalter, Rohith N. Krishna, Patrick Lichtner, Lars M. Blank, Aindrila Mukhopadhyay, Adam M. Deutschbauer, Patrick M. Shih, Jay D. Keasling. (2020) "Fatty Acid and Alcohol Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing". Applied and Environmental Microbiology Oct 2020, 86 (21) e01665-20; DOI: 10.1128/AEM.01665-20

201. McLaughlin James Alastair, Beal Jacob, Mısırlı Göksel, Grünberg Raik, Bartley Bryan A., Scott-Brown James, Vaidyanathan Prashant, Fontanarrosa Pedro, Oberortner Ernst, Wipat Anil, Gorochowski Thomas E., Myers Chris J. (2020) "The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering" Frontiers in Bioengineering and Biotechnology 8, 1009. DOI 10.3389/fbioe.2020.01009

200. Maria Eugenia Inda and Timothy K. Lu. (2020). "Microbes as Biosensors". Annual Review of Microbiology 2020 74:1, 337-359.

199. Qi Gong, Bin Wang, Xubiao Lu, Jiantao Tan, Yuke Hou, Taoli Liu, Yao-Guang Liu, and Qinlong Zhu. (2020) "Nicking Endonuclease-Mediated Vector Construction Strategies for Plant Gene Functional Research" Plants 2020, 9(9), 1090;

198. Fero M.J., Craft J.K., Vu T., and Hillson N.J. (2020) "Combinatorial-Hierarchical DNA Library Design Using the TeselaGen DESIGN Module with j5". In: Chandran S., George K. (eds) DNA Cloning and Assembly. Methods in Molecular Biology, vol 2205. Humana, New York, NY.

197. Ernst Oberortner, Robert Evans, Xianwei Meng, Sangeeta Nath, Hector Plahar, Lisa Simirenko, Angela Tarver, Samuel Deutsch, Nathan J. Hillson, and Jan-Fang Cheng. (2020) "An Integrated Computer-Aided Design and Manufacturing Workflow for Synthetic Biology". In: Chandran S., George K. (eds) DNA Cloning and Assembly. Methods in Molecular Biology, vol 2205. Humana, New York, NY.

196. Machens F., Hochrein L. (2020) "The AssemblX Toolkit for Reliable and User-Friendly Multigene Assemblies". In: Chandran S., George K. (eds) DNA Cloning and Assembly. Methods in Molecular Biology, vol 2205. Humana, New York, NY.

195. Tao Zhan, Qian Chen, Chao Zhang, Changhao Bi, and Xueli Zhang. (2020) "Constructing a novel biosynthetic pathway for the production of glycolate from glycerol in Escherichia coli" ACS Synth. Biol.

194. Zhao, D., Li, J., Li, S. et al. New base editors change C to A in bacteria and C to G in mammalian cells. Nat Biotechnol (2020).

193. Li Liu, Dongdong Zhao, Lijun Ye, Tao Zhan, Bin Xiong, Muzi Hu, Changhao Bi & Xueli Zhang. (2020) "A programmable CRISPR/Cas9-based phage defense system for Escherichia coli BL21(DE3)". Microbial Cell Factories volume 19, Article number: 136.

192. Mitchell G. Thompson, Jacquelyn M. Blake-Hedges, Jose Henrique Pereira, John A. Hangasky, Michael S. Belcher, William M. Moore, Jesus F. Barajas, Pablo Cruz-Morales, Lorenzo J. Washington, Robert W. Haushalter, Christopher B. Eiben, Yuzhong Liu, Will Skyrud, Veronica T. Benites, Tyler P. Barnum, Edward E. K. Baidoo, Henrik V. Scheller, Michael A. Marletta, Patrick M. Shih, Paul D. Adams & Jay D. Keasling. (2020) "An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism". Nature Communications volume 11, Article number: 2931

191. Hu, M., Xiong, B., Li, Z. et al. A novel gene expression system for Ralstonia eutropha based on the T7 promoter. BMC Microbiol 20, 121 (2020).

190. Mee‐Rye Park, Yan Chen, Mitchell Thompson, Veronica T. Benites, Bonnie Fong, Christopher J. Petzold, Edward E. K. Baidoo, John M. Gladden, Paul D. Adams, Jay D. Keasling, Blake A. Simmons, and Steven W. Singer. (2020) "Response of Pseudomonas putida to Complex, Aromatic‐Rich Fractions from Biomass" ChemSusChem

189. Nicola J. Patron. O(2020) "Beyond natural: synthetic expansions of botanical form and function" New Phytologist.

188. Changhao Bi, Bin Xiong, Muzi Hu, Zhongkang Li, Li Liu, Siwei Li, Chunzhi Zhang, Xueli Zhang. (2020) "A novel gene expression system for Ralstonia eutropha based on the T7 promoter", Applied & Industrial Microbiology - General Microbiology DOI:10.21203/rs.2.21274/v1

187. Joshua J. Timmons, Doug Densmore. (2020) "Repository-based plasmid design". PLOS

186. Matthew R. Incha, Mitchell G. Thompson, Jacquelyn M.Blake-Hedges, Yuzhong Liu, Allison N. Pearson, Matthias Schmidt, Jennifer W. Gin, Christopher J. Petzold, Adam M. Deutschbauer, Jay D. Keasling. (2019) "Leveraging host metabolism for bisdemethoxycurcumin production in Pseudomonas putida" Metabolic Engineering Communications e00119

185 . Mitchell G Thompson, Allison N. Pearson, Jesus F. Barajas, Pablo Cruz-Morales, Nima Sedaghatian, Zak Costello, Megan E. Garber, Matthew R. Incha, Luis E. Valencia, Edward E.K. Baidoo, Hector Garcia Martin, Aindrila Mukhopadhyay, and Jay D Keasling. 2019 "Identification, characterization, and application of a highly sensitive lactam biosensor from Pseudomonas putida" ACS Synth. Biol.

184. Paul R. Jaschke, Gabrielle A. Dotson, Kay S. Hung, Diane Liu, and Drew Endy. (2019) "Definitive demonstration by synthesis of genome annotation completeness" PNAS 116 (48) 24206-24213

183. Jonathan A. Goler, James M. Carothers, and Jay D. Keasling. (2014) "Dual-Selection for Evolution of In Vivo Functional Aptazymes as Riboswitch Parts" Artificial Riboswitches pp 221-235

182. Mitchell G. Thompson, Luis E. Valencia, Jacquelyn M. Blake-Hedges, Pablo Cruz-Morales, Alexandria E. Velasquez, Allison N. Pearson, Lauren N. Sermeno, William A. Sharpless, Veronica T. Benites, Yan Chen, Edward E.K. Baidoo, Christopher J. Petzold, Adam M. Deutschbauer, Jay D. Keasling. (2019) "Omics-driven identification and elimination of valerolactam catabolism in Pseudomonas putida KT2440 for increased product titer" Metabolic Engineering Communications, Volume 9, e00098

181. Fusun Yaman, Aaron Adler, and Jacob Beal. (2019) "Opportunities and Challenges in Applying Artificial Intelligence to Bioengineering" Automated Reasoning for Systems Biology and Medicine pp 425-452

180. Christophe Ladroue and Sara Kalvala. (2015) "Constraint-Based Genetic Compilation" International Conference on Algorithms for Computational Biology. AlCoB 2015: Algorithms for Computational Biology pp 25-38

179. Emily Scher, Shay B Cohen, Guido Sanguinetti. (2019) "PartCrafter: find, generate and analyze BioParts" Synthetic Biology, Volume 4, Issue 1

178. Karthik Sekar, Roberto Rusconi, John T Sauls, Tobias Fuhrer, Elad Noor, Jen Nguyen, Vicente I Fernandez, Marieke F Buffing, Michael Berney, Suckjoon Jun, Roman Stocker, Uwe Sauer. (2018) "Synthesis and degradation of FtsZ quantitatively predict the first cell division in starved bacteria" Mol Syst Biol 14:e8623

177. Jesus F. Barajas, Ryan P. McAndrew, Mitchell G. Thompson, Tyler W. H. Backman, Bo Pang, Tristan de Rond, Jose H. Pereira, Veronica T. Benites, Héctor García Martín, Edward E. K. Baidoo, Nathan J. Hillson, Paul D. Adams, Jay D. Keasling. (2019) "Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases" Journal of Industrial Microbiology & Biotechnology Volume 46, Issue 8, pp 1225–1235

176. Yang Liu, Xinyi Wan & Baojun Wang. (2019) "Engineered CRISPRa enables programmable eukaryote-like gene activation in bacteria" Nature Communications volume 10, Article number: 3693

175. Chris J. Myers, Jacob Beal, Thomas E. Gorochowski, Hiroyuki Kuwahara, Curtis Madsen, James Alastair McLaughlin, Göksel Mısırlı, Tramy Nguyen, Ernst Oberortner, Meher Samineni, Anil Wipat, Michael Zhang, Zach Zundel. (2017) "A standard-enabled workflow for synthetic biology" Biochem Soc Trans (2017) 45 (3): 793-803.

174. Weninger A., Killinger M., Vogl T. (2016) "Key Methods for Synthetic Biology: Genome Engineering and DNA Assembly". In: Glieder A., Kubicek C., Mattanovich D., Wiltschi B., Sauer M. (eds) Synthetic Biology. Springer, Cham

173. Chris J. Myers. (2015) "Computational Synthetic Biology: Progress and the Road Ahead" IEEE Transactions on Multi-Scale Computing Systems ( Volume: 1 , Issue: 1 , Page(s): 19 - 32 ) DOI: 10.1109/TMSCS.2015.2478442

172. Zaiqiang Wu, Dongdong Zhao, Siwei Li, Junsong Wang, Changhao Bi, Xueli Zhang. (2019) "Combinatorial modulation of initial codons for improved zeaxanthin synthetic pathway efficiency in Escherichia coli" Microbiology

171. Ross Kent, Neil Dixon. (2019) "Contemporary Tools for Regulating Gene Expression in Bacteria" Trends in Biotechnology

170. Jing Wui Yeoh, Salvador Gomez-Carretero, Wai Kit David Chee, Ai Ying Teh, Chueh Loo Poh. (2019) "Genetic Circuit Design Principles" Handbook of Cell Biosensors pp 1-44

169. Celia Payen, Dawn Thompson. (2019) "The renaissance of yeasts as microbial factories in the modern age of biomanufacturing" YEAST EXTRACTS

168. Xiuqing Xin, Ju Li, Dongdong Zhao, Siwei Li, Qianwen Xie, Zhongkang Li, Feiyu Fan, Changhao Bi, Xueli Zhang. (2019) "Double-Check Base Editing for Efficient A to G Conversions" ACS Synth. Biol.

167. Shuwen Liu, Haihan Xiao, Fangfang Zhang, Zheng Lu, Yun Zhang, Aihua Deng, Zhongcai Li, Cui Yang & Tingyi Wen. (2019) "A seamless and iterative DNA assembly method named PS-Brick and its assisted metabolic engineering for threonine and 1-propanol production". Biotechnology for Biofuelsvolume 12, Article number: 180

166. Wen Wang, Ping He, Dongdong Zhao, Lijun Ye, Longhai Dai, Xueli Zhang, Yuanxia Sun, Jing Zheng, and Changhao Bi. (2019) "Construction of Escherichia coli cell factories for crocin biosynthesis" Microbial Cell Factories 18:120

165. Fu Chen Le Yuan Shaozhen Ding Yu Tian Qian-Nan Hu. (2019) "Data-driven rational biosynthesis design: from molecules to cell factories". Briefings in Bioinformatics, bbz065,

164. Jesus F. Barajas, Ryan P. McAndrew, Mitchell G. Thompson, Tyler W. H. Backman, Bo Pang, Tristan de Rond, Jose H. Pereira, Veronica T. Benites, Héctor García Martín, Edward E. K. Baidoo, Nathan J. Hillson, Paul D. Adams, and Jay D. Keasling. (2019) "Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases" J Ind Microbiol Biotechnol

163. Xu P., Koffas M.A.G. (2013) Assembly of Multi-gene Pathways and Combinatorial Pathway Libraries Through ePathBrick Vectors. In: Polizzi K., Kontoravdi C. (eds) Synthetic Biology. Methods in Molecular Biology (Methods and Protocols), vol 1073. Humana Press, Totowa, NJ

162. Mitchell G. Thompson, Jacquelyn M. Blake-Hedges, Pablo Cruz-Morales, Jesus F. Barajas, Samuel C. Curran, Christopher B. Eiben, Nicholas C. Harris, Veronica T. Benites, Jennifer W. Gin, William A. Sharpless, Frederick F. Twigg, Will Skyrud, Rohith N. Krishna, Jose Henrique Pereira, Edward E. K. Baidoo, Christopher J. Petzold, Paul D. Adams, Adam P. Arkin, Adam M. Deutschbauer, Jay D. Keasling. (2019) "Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism". mBio May 2019, 10 (3) e02577-18; DOI: 10.1128/mBio.02577-18

161. Wu, Li, Ye, Zhao, Fan, Li, Bhang, Bi, and Zhang. (2019) "Engineering an Artificial Membrane Vesicle Trafficking System (AMVTS) for the Excretion of β-Carotene in Escherichia coli". ACS Synth. Biol., DOI: 10.1021/acssynbio.8b00472

160. Jorge Gonzalez de la Cruz, Fabian Machens, Katrin Messerschmidt, and Arren Bar-Even. (2019) "Core catalysis of the reductive glycine pathway demonstrated in yeast". ACS Synth. Biol., DOI: 10.1021/acssynbio.8b00464

159. Tao Wu, Siwei Li, Lijun Ye, Dongdong Zhao, Feiyu Fan, Qinyan Li, Bolin Zhang, Changhao Bi, and Xueli Zhang. (2019) "Engineering an artificial membrane vesicle trafficking system (AMVTS) for the excretion of β-carotene in Escherichia coli". ACS Synth. Biol., DOI: 10.1021/acssynbio.8b00472

158. Naveen Venayak, Kaushik Raj, Radhakrishnan Mahadevan. (2019) "Impact framework: A python framework for writing data analysis workflows to interpretmicrobial physiology". Metabolic Engineering Communications

157. Zaiqiang Wu, Junsong Wang, Xueli Zhang, Changhao Bi. (2019) "Engineering an electroactive Escherichia coli for the microbial electrosynthesis of succinate by increasing the intracellular FAD pool". Biochemical Engineering Journal.

156. Li Z, Xiong B, Liu L, Li S, Xin X, Li Z, Zhang X, Bi C. (2019) "Development of an autotrophic fermentation technique for the production of fatty acids using an engineered Ralstonia eutropha cell factory". J Ind Microbiol Biotechnol. doi: 10.1007/s10295-019-02156-8

155. David I. Walsh, III, Marilene Pavan, Luis Ortiz, Scott Wick, Johanna Bobrow, Nicholas J. Guido, Sarah Leinicke, Dany Fu, Shreya Pandit, Lucy Qin, Peter A. Carr, Douglas Densmore. (2019) "Standardizing Automated DNA Assembly: Best Practices, Metrics, and Protocols Using Robots" SLAS Technology.

154. Zaiqiang Wu, Junsong Wang, Jun Liu, Yan Wang, Changhao Bi and Xueli Zhang. (2019) "Engineering an electroactive Escherichia coli for the microbial electrosynthesis of succinate from glucose and CO2". Microbial Cell Factories 18:15

153. Anuj Dwivedi, Kamal Kumar, and Praveen Kumar Verma. (2019) "Chapter 4 - Constructing Synthetic Pathways in Plants: Strategies and Tools" in Current Developments in Biotechnology and Bioengineering Synthetic Biology (Cell Engineering and Bioprocessing Technologies), Pages 77-113

152. R. Clay Wright, Jennifer Nemhauser. (2019) "Plant Synthetic Biology: Quantifying the Known Unknowns and Discovering the Unknown Unknowns". Plant Physiology. DOI:

151. David G. J. Mann, Scott A. Bevan, Anthony J. Harvey, Rachelle A. Leffert-Sorenson. (2018) "The Use of an Automated Platform to Assemble Multigenic Constructs for Plant Transformation" Transgenic Plants pp 19-35

150. Garima Goyal, Zak Costello, Jorge Alonso Guitierrez, Aram Kang, Taek Soon Lee, Hector Garcia Martin, and Nathan J Hillson. (2018) "Parallel Integration and Chromosomal Expansion of Metabolic Pathways" ACS Synthetic Biology DOI: 10.1021/acssynbio.8b00243

149. Lijun Ye, Xinna Zhu, Tao Wu, Wen Wang, Dongdong Zhao, Changhao Bi and Xueli Zhang. (2018) "Optimizing the localization of astaxanthin enzymes for improved productivity". Biotechnology for Biofuels201811:278

148. Victor Chubukov, Florence Mingardon, Wendy Schackwitz, Edward E. K. Baidoo, Jorge Alonso-Gutierrez, Qijun Hu, Taek Soon Lee, Jay D. Keasling, Aindrila Mukhopadhyay. (2015) "Acute Limonene Toxicity in Escherichia coli Is Caused by Limonene Hydroperoxide and Alleviated by a Point Mutation in Alkyl Hydroperoxidase AhpC". Appl. Environ. Microbiol. 81 (14) 4690-4696; DOI: 10.1128/AEM.01102-15

147. Thomas L. Ruegg, Jose H. Pereira, Joseph C. Chen, Andy DeGiovanni, Pavel Novichkov, Vivek K. Mutalik, Giovani P. Tomaleri, Steven W. Singer, Nathan J. Hillson, Blake A. Simmons, Paul D. Adams & Michael P. Thelen. (2018) "Jungle Express is a versatile repressor system for tight transcriptional control". Nature Communications 9, 3617.

146. Thomas H. Mann and Lucy Shapiro. (2018) "Integration of cell cycle signals by multi-PAS domain kinases". PNAS 201808543

145. Xu Feng, Dongdong Zhao, Xueli Zhang, Xiang Ding, and Changhao Bi. (2018) "CRISPR/Cas9 Assisted Multiplex Genome Editing Technique in Escherichia coli". Biotechnology Journal

144. Bin Xiong, Zhongkang Li, Li Liu, Dongdong Zhao, Xueli Zhang and Changhao Bi. (2018) "Genome editing of Ralstonia eutropha using an electroporation-based CRISPR-Cas9 technique" Biotechnology for Biofuels 11:172

143. Guo JY, Hu KL, Bi CH, Li QY, Zhang XL. (2018) "Construction of an alternative glycerol-utilization pathway for improved β-carotene production in Escherichia coli". J Ind Microbiol Biotechnol. doi: 10.1007/s10295-018-2045-1.

142. Erik K.R. Hanko, Charles M. Denby, Violeta Sànchez i Nogué, Weiyin Lin, Kelsey J. Ramirez, Christine A. Singer, Gregg T. Beckham, Jay D. Keasling.(2018) "Engineering β-oxidation in Yarrowia lipolytica for methyl ketone production". Metabolic Engineering

141. Wu, T., Ye, L., Zhao, D. et al. (2018) "Engineering membrane morphology and manipulating synthesis for increased lycopene accumulation in Escherichia coli cell factories" 3 Biotech 8: 269.

140. Jimmy Mevaere, Christophe Goulard, Olha Schneider, Olga N. Sekurova, Haiyan Ma, Séverine Zirah, Carlos Afonso, Sylvie Rebuffat, Sergey B. Zotchev & Yanyan Li. (2018) "An orthogonal system for heterologous expression of actinobacterial lasso peptides in Streptomyces hosts". Scientific Reports doi:10.1038/s41598-018-26620-0

139. Guo JY, Hu KL, Bi CH, Li QY, Zhang XL. (2018) "Construction of an alternative glycerol-utilization pathway for improved β-carotene production in Escherichia

coli". J Ind Microbiol Biotechnol. doi: 10.1007/s10295-018-2045-1. PubMed PMID: 29752566.

138. Dawn T. Eriksen, Ran Chao, Huimin Zhao. (2018) "Applying Advanced DNA Assembly Methods to Generate Pathway Libraries", in Synthetic Biology: Parts, Devices and Applications, 1.

137. Arturo Casini, Fang-Yuan Chang, Raissa Eluere, Andrew M. King, Eric M. Young, Quentin M. Dudley, Ashty Karim, Katelin Pratt, Cassandra Bristol, Anthony Forget, Amar Ghodasara, Robert Warden-Rothman, Rui Gan, Alexander Cristofaro, Amin Espah Borujeni, Min-Hyung Ryu, Jian Li, Yong-Chan Kwon, He Wang, Evangelos Tatsis, Carlos Rodriguez-Lopez, Sarah O’Connor, Marnix H. Mdema, Michael A. Fischbach, Michael C. Jewett, Christopher Voigt, and D. Benjamin Gordon. (2018) "A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology". Journal of the American Chemical Society Article ASAP DOI: 10.1021/jacs.7b13292

136. Coates, R.C., Bowen, B.P., Oberortner, E. et al. (2018) "An integrated workflow for phenazine-modifying enzyme characterization". J Ind Microbiol Biotechnol.

135. Ellis Whitehead, Fabian Rudolf, Hans-Michael Kaltenbach, and Jörg Stelling. (2018) "Automated Planning Enables Complex Protocols on Liquid-Handling Robots". ACS Synth. Biol., Article ASAP DOI: 10.1021/acssynbio.8b00021

134. Charles M. Denby, Rachel A. Li, Van T. Vu, Zak Costello, Weiyin Lin, Leanne Jade G. Chan, Joseph Williams, Bryan Donaldson, Charles W. Bamforth, Christopher J. Petzold, Henrik V. Scheller, Hector Garcia Martin & Jay D. Keasling. (2018) "Industrial brewing yeast engineered for the production of primary flavor determinants in hopped beer". Nature Communications volume 9, Article number: 965. doi:10.1038/s41467-018-03293-x

133. Esteban Marcellin and Lars Keld Nielsen. (2018) "Advances in analytical tools for high throughput strain engineering". Current Opinion in Biotechnology, Volume 54, Pages 33–40.

132. Mitchell G. Thompson, Nima Sedaghatian, Jesus F. Barajas, Maren Wehrs, Constance B. Bailey, Nurgul Kaplan, Nathan J. Hillson, Aindrila Mukhopadhyay & Jay D. Keasling. (2018) "Isolation and characterization of novel mutations in the pSC101 origin that increase copy number". Scientific Reports 8, 1590 doi:10.1038/s41598-018-20016-w

131. Dossani ZY, Reider Apel A, Szmidt-Middleton H, Hillson NJ, Deutsch S, Keasling JD, and Mukhopadhyay A. (2017). A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering. Yeast 1–8. doi:10.1002/yea.3292

130. Dongdong Zhao, Xu Feng, Xinna Zhu, Tao Wu, Xueli Zhang & Changhao Bi. (2017) "CRISPR/Cas9-assisted gRNA-free one-step genome editing with no sequence limitations and improved targeting efficiency". Scientific Reports 7, Article number: 16624 doi:10.1038/s41598-017-16998-8

129. Heather M. Jensen, Thomas Eng, Victor Chubukov, Robin A. Herbert & Aindrila Mukhopadhyay. (2017) Improving membrane protein expression and function using genomic edits. Scientific Reports 7, Article number: 13030 doi:10.1038/s41598-017-12901-7

128. David S. Ojala, Sabrina Sun, Jorge L. Santiago-Ortiz, Mikhail G. Shapiro, Philip A. Romero, David V. Schaffer. (2017)In Vivo Selection of a Computationally Designed SCHEMA AAV Library Yields a Novel Variant for Infection of Adult Neural Stem Cells in the SVZ. Molecular Therapy

127. R. Clay Wright, Mollye L. Zahler, Stacey R. Gerben and Jennifer L. Nemhauser. (2017) Insights into the Evolution and Function of Auxin Signaling F-Box Proteins in Arabidopsis thaliana Through Synthetic Analysis of Natural Variants. Genetics October 1, 2017 vol. 207 no. 2 583-591;

126. Swapnil P. Bhatia, Michael J. Smanski, Christopher A. Voigt, and Douglas M. Densmore. (2017) Genetic Design via Combinatorial Constraint Specification. ACS Synth. Biol., DOI: 10.1021/acssynbio.7b00154

125. de Rond, Stow, Eigl, Johnson, Chan, Goyal, Baidoo, Hillson, Petzold, Sarpong, and Keasling. (2017) Oxidative cyclization of prodigiosin by an alkylglycerol monooxygenase-like enzyme.

Nature Chemical Biology doi:10.1038/nchembio.2471

124. Gach PC*, Iwai K, Kim P, Hillson NJ, and Singh AK*. (2017) Droplet Microfluidics for Synthetic Biology. Lab on a Chip. DOI: 10.1039/C7LC00576H

123. Xinna Zhu, Dongdong Zhao, Huanna Qiu, Feiyu Fan Shuli Man, Changhao Bi, Xueli Zhang. (2017) The CRISPR/Cas9-facilitated multiplex pathway optimization (CFPO) technique and its application to improve the Escherichia coli xylose utilization pathway. Metabolic Engineering

122. Matthias Christen, Luca Del Medico, Heinz Christen, Beat Christen. (2017) Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications. PLOS ONE. DOI:

121. Björn D. Heijstra, Ching Leang, and Alex Juminaga. (2017) Gas fermentation: cellular engineering possibilities and scale up. Microb Cell Fact. 2017; 16: 60. doi: 10.1186/s12934-017-0676-y

PMCID: PMC5389167

120. Appleton E, Madsen C, Roehner N, Densmore D. (2017) Design Automation in Synthetic Biology. Cold Spring Harb Perspect Biol. doi: 10.1101/cshperspect.a023978. [Epub ahead of print] PubMed PMID: 28246188.

119. Amit Ghosh, David Ando, Jennifer Gin, Weerawat Runguphan, Charles Denby, George Wang, Edward E. K. Baidoo, Chris Shymansky, Jay D. Keasling, and Héctor García Martín. (2016) 13C Metabolic Flux Analysis for Systematic Metabolic Engineering of S. cerevisiae for Overproduction of Fatty Acids. Front. Bioeng. Biotechnol.

118. William Henry Bothfeld, Grace Kapov, and Keith Tyo. (2017) A glucose-sensing toggle switch for autonomous, high productivity genetic control. ACS Synth. Biol. DOI: 10.1021/acssynbio.6b00257

117. Neta Agmon, Zuojian Tang, Kun Yang, Ben Sutter, Shigehito Ikushima, Yizhi Cai, Katrina Caravelli, James A. Martin, Xiaoji Sun, Woo Jin Choi, Allen Zhang, Giovanni Stracquadanio, Haiping Hao, Benjamin P. Tu, David Fenyo, Joel S. Bader, and Jef D. Boeke. (2017) Low escape-rate genome safeguards with minimal molecular perturbation of Saccharomyces cerevisiae

PNAS doi:10.1073/pnas.1621250114

116. Lena Hochrein, Fabian Machens, Juergen Gremmels, Karina Schulz, Katrin Messerschmidt, Bernd Mueller-Roeber. (2017) AssemblX: a user-friendly toolkit for rapid and reliable multi-gene assemblies. Nucl Acids Res gkx034. DOI:

115. Marta Vazquez-Vilar, Alfredo Quijano-Rubio, Asun Fernandez-del-Carmen, Alejandro Sarrion-Perdigones, Rocio Ochoa-Fernandez, Peio Ziarsolo, José Blanca, Antonio Granell and Diego Orzaez. (2016) GB3.0: a platform for plant bio-design that connects functional DNA elements with associated biological data. Nucl. Acids Res. doi: 10.1093/nar/gkw1326

114. Victor Chubukov, John James Desmarais, George Wang, Leanne Jade G Chan, Edward EK Baidoo, Christopher J Petzold, Jay D Keasling & Aindrila Mukhopadhyay. (2017) Engineering glucose metabolism of Escherichia coli under nitrogen starvation. npj Systems Biology and Applications 3, Article number: 16035 doi:10.1038/npjsba.2016.35

113. Lauren B. A. Woodruff, Thomas E. Gorochowski, Nicholas Roehner, Tarjei S. Mikkelsen, Douglas Densmore, D. Benjamin Gordon, Robert Nicol and Christopher A. Voigt. (2016) Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration. Nucl. Acids Res. (2016) doi: 10.1093/nar/gkw1226

112. Ernst Oberortner, Jan-Fang Cheng, Nathan J. Hillson, and Samuel Deutsch. (2016) Streamlining the Design-to-Build Transition with Build-Optimization Software Tools. ACS Synth. Biol., Article ASAP

DOI: 10.1021/acssynbio.6b00200

111. Zhao, Yuan, Xiong, Sun, Ye, Li, Zhang, Bi. (2016) Development of a fast and easy method for Escherichia coli genome editing with CRISPR/Cas9.

Microbial Cell Factories 15(1)

110. Hans J Genee, Anne P Bali, Søren D Petersen, Solvej Siedler, Mads T Bonde, Luisa S Gronenberg, Mette Kristensen, Scott J Harrison, and Morten O A Sommer. (2016) Functional mining of transporters using synthetic selections. Nature Chemical Biology doi:10.1038/nchembio.2189

109. Garcia-Ruiz, E., HamediRad, M., and Zhao, H. (2016) Pathway Design, Engineering, and Optimization, pp 1-40, Springer Berlin Heidelberg, Berlin, Heidelberg. DOI 10.1007/10_2016_12

108. Shi, Z., Vickers, C.E. (2016) Molecular Cloning Designer Simulator (MCDS): All-in-one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects. Metabolic Engineering Open volume 3, pp. 173 - 186.

107. Hongnian Sun, Dongdong Zhao, Bin Xiong, Chunzhi Zhang, Changhao Bi. (2016) Engineering Corynebacterium glutamicum for violacein hyper production. Microbial Cell Factories 2016 15:148. DOI: 10.1186/s12934-016-0545-0

106. Brian Chaikind, Jeffrey L. Bessen, David B. Thompson, Johnny H. Hu and David R. Liu. (2016) A programmable Cas9-serine recombinase fusion protein that operates on DNA sequences in mammalian cells. Nucl. Acids Res. doi: 10.1093/nar/gkw707

105. Trinh, C.T., Mendoza, B., 2016. Modular Cell Design for Rapid, Efficient Strain Engineering towards Industrialization of Biology, Curr Opin Chem Eng, 14:18–25

104. Olga N. Sekurova, Jianhai Zhang, Kåre A. Kristiansen and Sergey B. Zotchev. (2016) Activation of chloramphenicol biosynthesis in Streptomyces venezuelae ATCC 10712 by ethanol shock: insights from the promoter fusion studies. Microbial Cell Factories 2016 15:85. DOI: 10.1186/s12934-016-0484-9

103. Pablo Carbonell, Andrew Currin, Adrian J. Jervis, Nicholas J. W. Rattray, Neil Swainston, Cunyu Yan, Eriko Takano, and Rainer Breitling. (2016) Bioinformatics for the synthetic biology of natural products: integrating across the Design–Build–Test cycle. Nat. Prod. Rep., 2016, Advance Article. DOI: 10.1039/C6NP00018E

102. Marijke Frederix, Florence Mingardon, Matthew Hu, Ning Sun, Todd Pray, Seema Singh, Blake A. Simmons, Jay D. Keasling and Aindrila Mukhopadhyay. (2015) Development of an E. coli strain for one-pot biofuel production from ionic liquid pretreated cellulose and switchgrass. Green Chem., 2016, Advance Article. DOI: 10.1039/C6GC00642F

101. Thomas H. Mann, W. Seth Childers, Jimmy A. Blair, Michael R. Eckart, and Lucy Shapiro. (2016) A cell cycle kinase with tandem sensory PAS domains integrates cell fate cues. Nature Communications 7 (11454). doi:10.1038/ncomms11454

100. Sadowski, Michael I.; Grant, Chris; Fell, Tim S. (2016) Harnessing QbD, Programming Languages, and Automation for Reproducible Biology. TRENDS IN BIOTECHNOLOGY 34 (3), 214-227.

99. Beck, D. A. C., Carothers, J. M., Subramanian, V. R. and Pfaendtner, J. (2016), Data science: Accelerating innovation and discovery in chemical engineering. AIChE J., 62: 1402–1416. doi:10.1002/aic.15192

98. Javidpour P, Deutsch S, Mutalik VK, Hillson NJ, Petzold CJ, Keasling JD, et al. (2016) Investigation of Proposed Ladderane Biosynthetic Genes from Anammox Bacteria by Heterologous Expression in E. coli. PLoS ONE 11(3): e0151087. doi:10.1371/journal.pone.0151087

97. Sarah Rodriguez, Charles M. Denby, T. Van Vu, Edward E. K. Baidoo, George Wang and Jay D. Keasling. (2016) ATP citrate lyase mediated cytosolic acetyl-CoA biosynthesis increases mevalonate production in Saccharomyces cerevisiae. Microbial Cell Factories 201615:48 DOI: 10.1186/s12934-016-0447-1

96. Sekar K, Gentile AM, Bostick JW, Tyo KEJ (2016) N-Terminal-Based Targeted, Inducible Protein Degradation in Escherichia coli. PLoS ONE 11(2): e0149746. doi:10.1371/journal.pone.0149746

95. Miguel Suástegui, Meirong Gao, Zengyi Shao. (2016) Chapter 6 – Pathway Assembly and Optimization. Biotechnology for Biofuel Production and Optimization, Pages 139–164. doi:10.1016/B978-0-444-63475-7.00006-6

94. Justin Hsia, William J. Holtz, Michel M. Maharbiz, Murat Arcak,Jay D. Keasling. (2016) Modular Synthetic Inverters from Zinc Finger Proteins and Small RNAs. PLOS ONE DOI: 10.1371/journal.pone.0149483

93. Linshiz, Jensen, Stawski, Bi, Elsbree, Jiao, Kim, Mathies, Keasling, Hillson. (2016) End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis. Journal of Biological Engineering 10

92. Henrique Cestari De Paoli, Gerald A. Tuskan & Xiaohan Yang. (2016) An innovative platform for quick and flexible joining of assorted DNA fragments. Scientific Reports 6, Article number: 19278 doi:10.1038/srep19278

91. G.H. McArthur IV, P.P. Nanjannavar, E.H. Miller, S.S. Fong. Integrative metabolic engineering. AIMS Bioengineering, 2015, 2(3): 93-103. doi: 10.3934/bioeng.2015.3.93

90. Kun Yang, Giovanni Stracquadanio, Jingchuan Luo, Jef D. Boeke, Joel S. Bader. (2015) BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts. Bioinformatics:btv664

89. Douglas Densmore, Soha Hassoun (2012). Design Automation for Synthetic Biological Systems. IEEE Design & Test of Computers 29:7-20

88. A. Casini, J. T. MacDonald, J. D. Jonghe, G. Christodoulou, P. S. Freemont, G. S. Baldwin, T. Ellis. (2014) One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy. Nucleic Acids Research 42:e7-e7.

87. Michal Galdzicki, Kevin P Clancy, Ernst Oberortner, Matthew Pocock, Jacqueline Y Quinn, Cesar A Rodriguez, Nicholas Roehner, Mandy L Wilson, Laura Adam, J Christopher Anderson, Bryan A Bartley, Jacob Beal, Deepak Chandran, Joanna Chen, Douglas Densmore, Drew Endy, Raik Grünberg, Jennifer Hallinan, Nathan J Hillson, Jeffrey D Johnson, Allan Kuchinsky, Matthew Lux, Goksel Misirli, Jean Peccoud, Hector A Plahar, Evren Sirin, Guy-Bart Stan, Alan Villalobos, Anil Wipat, John H Gennari, Chris J Myers, Herbert M Sauro. (2014). The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nature Biotechnology 32:545-550.

86. Richard Kelwick, James T. MacDonald, Alexander J. Webb, Paul Freemont. (2014) Developments in the Tools and Methodologies of Synthetic Biology

Front Bioeng Biotechnol. 2014 Nov 26;2:60. doi: 10.3389/fbioe.2014.00060.

85. Chris J. Myers. (2013) Platforms for Genetic Design Automation. Methods in Microbiology Volume 40, 2013, Pages 177–202.

84. Ran Chao, Yongbo Yuan, Huimin Zhao. (2014) Recent advances in DNA assembly technologies. FEMS Yeast Res. 2014 Jun 5. doi: 10.1111/1567-1364.12171.

83. Hagen A, Poust S, de Rond T, Fortman JL, Katz L, Petzold CJ, Keasling JD. (2015) Engineering a polyketide synthase for in vitro production of adipic acid. ACS Synth Biol. DOI: 10.1021/acssynbio.5b00153

82. Bertram M. Berla, Rajib Saha, Costas D. Maranas & Himadri B. Pakrasi. (2015). Cyanobacterial Alkanes Modulate Photosynthetic Cyclic Electron Flow to Assist Growth under Cold Stress. Scientific Reports 5, Article number: 14894 doi:10.1038/srep14894

81. Beal J, Adler A, Yaman F. Managing Bioengineering Complexity with AI Techniques. Biosystems. 2015 Sep 3. pii: S0303-2647(15)00129-X. doi: 10.1016/j.biosystems.2015.08.006

80. Steven C. Slater, Blake A. Simmons, Tamara S. Rogers, Margaret F. Phillips, Kristy Nordahl, Brian H. Davison. (2015) The DOE Bioenergy Research Centers: History, Operations, and Scientific Output. Bioenerg. Res. DOI 10.1007/s12155-015-9660-8.

79. Kelly A. Markham and Hal S. Alper. (2015) Synthetic Biology for Specialty Chemicals. Annual Review of Chemical and Biomolecular Engineering

Vol. 6: 35-52 DOI: 10.1146/annurev-chembioeng-061114-123303

78. Poust S, Piety J, Bar-Even A, Louw C, Baker D, Keasling JD, Siegel JB. (2015) Mechanistic Analysis of an Engineered Enzyme that Catalyzes the Formose Reaction.. Chembiochem. doi: 10.1002/cbic.201500228

77. Thomas Vogl, Mudassar Ahmad, Florian W Krainer, Helmut Schwab, Anton Glieder. (2015) Restriction site free cloning (RSFC) plasmid family for seamless, sequence independent cloning in Pichia pastoris. Microbial Cell Factories 14:103 doi:10.1186/s12934-015-0293-6.

76. George H McArthur IV, Pooja P Nanjannavar, Emily H Miller, and Stephen S Fong. (2015) Integrative metabolic engineering. Biengineering Volume 2, Issue 3, 93-103.

DOI: 10.3934/bioeng.2015.3.93

75. Matthias Christen, Samuel Deutsch, and Beat Christen. (2015) Genome Calligrapher: A Web Tool for Refactoring Bacterial Genome Sequences for de Novo DNA Synthesis ACS Synth. Biol., Article ASAP DOI: 10.1021/acssynbio.5b00087

74. Arturo Casini, Marko Storch, Geoffrey S. Baldwin, & Tom Ellis. (2015) Bricks and blueprints: methods and standards for DNA assembly. Nature Reviews Molecular Cell Biology doi:10.1038/nrm4014

73. Steve C. C. Shih, Garima Goyal, Peter W. Kim, Nicolas Koutsoubelis, Jay D. Keasling, Paul D. Adams, Nathan J. Hillson, and Anup K. Singh. (2015) A Versatile Microfluidic Device for Automating Synthetic Biology. ACS Synthetic Biology Article ASAP. DOI:10.1021/acssynbio.5b00062

72. Courbet A, Endy D, Renard E, Molina F, Bonnet J. Detection of pathologicalbiomarkers in human clinical samples via amplifying genetic switches and logic gates. SciTransl Med. 2015 May 27;7(289):289ra83. doi: 10.1126/scitranslmed.aaa3601.

71. Chao R, Yuan Y, Zhao H. Building biological foundries for next-generation synthetic biology. Sci China Life Sci. 2015 May 19. [Epub ahead of print] PubMed

PMID: 25985756.

70. Filipa Pereira, Flávio Azevedo, Ângela Carvalho, Gabriela F Ribeiro, Mark W Budde, Björn Johansson (2015). Pydna: a simulation and documentation tool for DNA assembly strategies using python. BMC Bioinformatics 2015, 16:142. doi:10.1186/s12859-015-0544-x

69. Hao Qi, Bing-Zhi Li, Wen-Qian Zhang, Duo Liu, Ying-Jin Yuan. (2015) Modularization of genetic elements promotes synthetic metabolic engineering. Biotechnology Advances doi:10.1016/j.biotechadv.2015.04.002

68. Mateus Schreiner Garcez Lopes. (2015) Engineering biological systems toward a sustainable bioeconomy. J Ind Microbiol Biotechnol DOI 10.1007/s10295-015-1606-9

67. Wentao Kong, Venhar Celik, Chen Liao, Qiang Hua, Ting Lu. (2014) Programming the group behaviors of bacterial communities with synthetic cellular communication. Bioresources and Bioprocessing 1:24.

66. Cai Y, Agmon N, Choi WJ, Ubide A, Stracquadanio G, Caravelli K, Hao H, Bader JS, Boeke JD. (2015) Intrinsic biocontainment: Multiplex genome safeguards combine

transcriptional and recombinational control of essential yeast genes. Proc Natl Acad Sci U S A. PubMed PMID: 25624482.

65. Nelson R. Barton, Anthony P. Burgard, Mark J. Burk, Jason S. Crater, Robin E. Osterhout, Priti Pharkya, Brian A. Steer, Jun Sun, John D. Trawick, Stephen J. Van Dien, Tae Hoon Yang, and Harry Yim. (2015) An integrated biotechnology platform for developing sustainable chemical processes. Journal of Industrial Microbiology & Biotechnology 42:349-360.

64. Jacob Beal. (2015) Bridging the gap: a roadmap to breaking the biological design barrier. Front. Bioeng. Biotechnol., DOI: 10.3389/fbioe.2014.00087

63. Jee Loon Foo, Heather M. Jensen, Robert H. Dahl, Kevin George, Jay D. Keasling, Taek Soon Lee, Susanna Leong, and Aindrila Mukhopadhyay. (2014) Improving Microbial Biogasoline Production in Escherichia coli Using Tolerance Engineering. mBio vol. 5 no. 6 e01932-14 doi: 10.1128/mBio.01932-14

62. Patron NJ. (2014) DNA assembly for plant biology: techniques and tools. Curr Opin Plant Biol. 19:14-9. doi: 10.1016/j.pbi.2014.02.004

61. Ding, Yunfeng; Wu, Fan; Tan, Cheemeng. (2014) "Synthetic Biology: A Bridge between Artificial and Natural Cells." Life 4, no. 4: 1092-1116.

60. Wright RC, Khakhar A, Eshleman JR, Ostermeier M. (2014) Advancements in the Development of HIF-1α-Activated Protein Switches for Use in Enzyme Prodrug

Therapy. PLoS One. 9(11):e114032. doi: 10.1371/journal.pone.0114032.

59. Kelwick R, MacDonald JT, Webb AJ, Freemont P. (2014) Developments in the tools and methodologies of synthetic biology. Front Bioeng Biotechnol. doi: 10.3389/fbioe.2014.00060

58. Wentao Kong, Venhar Celik, Chen Liao, Qiang Hua, and Ting Lu. (2014) Programming the group behaviors of bacterial communities with synthetic cellular communication. Bioresources and Bioprocessing 1:24 doi:10.1186/s40643-014-0024-6

57. Mingji Li, Irina Borodina. (2014) Application of synthetic biology for production of chemicals in yeast Saccharomyces cerevisiae. FEMS Yeast Research DOI: 10.1111/1567-1364.12213

56. Tanveer S. Batth, Pragya Singh, Vikram R. Ramakrishnan, Mirta M.L. Sousa, Leanne Jade G. Chan, Huu M. Tran, Eric. G. Luning, Eva H.Y. Pan, Khanh M. Vuu, Jay D. Keasling, Paul D. Adams, and Christopher J. Petzold. (2014) A targeted proteomics toolkit for High-throughput absolute quantification of Escherichia coli proteins. Metabolic Engineering. DOI: 10.1016/j.ymben.2014.08.004

55. Evan Appleton, Jenhan Tao, Traci Haddock, and Douglas Densmore. (2014) Interactive assembly algorithms for molecular cloning. Nature Methods 11, 657–662.

54. Orit Shaer, Consuelo Valdes, Sirui Liu, Kara Lu, Kimberly Chang, Wendy Xu, Traci L. Haddock, Swapnil Bhatia, Douglas Densmore, Robert Kincaid. (2014) Designing reality-based interfaces for experiential bio-design. Personal and Ubiquitous Computing 18(6):1515

53. H. Huang and D. Densmore. (2014) Integration of microfluidics into the synthetic biology design flow. Lab Chip. DOI: 10.1039/C4LC00509K

52. Nicholas Roehner, Ernst Oberortner, Matthew Pocock, Jacob Beal, Kevin Clancy, Curtis Madsen, Goksel Misirli, Anil Wipat, Herbert Sauro, and Chris J. Myers. (2014)

Proposed Data Model for the Next Version of the Synthetic Biology Open Language. ACS Synthetic Biology. DOI: 10.1021/sb500176h

51. Cyrille Pauthenier and Jean-Loup Faulon. (2014) PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling. Nucl. Acids Res. DOI: 10.1093/nar/gku393

50. Sean Poust, Andrew Hagen, Leonard Katz, Jay D Keasling. (2014) Narrowing the gap between the promise and reality of polyketide synthases as a synthetic biology platform. Current Opinion in Biotechnology 30:32.

49. Jennifer A N Brophy, Christopher A Voigt. (2014) Principles of genetic circuit design. Nature Methods 11(5):508.

48. Evan Appleton, Jenhan Tao, Traci Haddock, & Douglas Densmore. (2014) Interactive assembly algorithms for molecular cloning. Nature Methods. DOI:10.1038/nmeth.2939

47. Ryan E. Cobb, Jonathan C. Ning, Huimin Zhao. (2014) DNA assembly techniques for next-generation combinatorial biosynthesis of natural products. Journal of Industrial Microbiology & Biotechnology 41(2):469

46. Chris J. Paddon and Jay D. Keasling. (2014) Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development. Nature Reviews Microbiology doi:10.1038/nrmicro3240

45. Church GM, Elowitz MB, Smolke CD, Voigt CA, Weiss R. (2014) Realizing the potential of synthetic biology. Nat Rev Mol Cell Biol. DOI: 10.1038/nrm3767

44. Daniel Camsund, Thorsten Heidorn, and Peter Lindblad. (2014). Design and analysis of LacI-repressed promoters and DNA-looping in a cyanobacterium. Journal of Biological Engineering 8(1):4. DOI: 10.1186/1754-1611-8-4

43. Linshiz, G., Stawski, N., Goyal, G., Bi, C., Poust, S., Sharma, M., Mutalik, V., Keasling, J.D., and Hillson, N.J. (2014). PR-PR: Cross-Platform Laboratory Automation System. ACS Synthetic Biology. DOI: 10.1021/sb4001728

42. Douglas M. Densmore, Swapnil Bhatia. (2013) "Bio-design automation: software + biology + robots". Trends in Biotechnology. DOI: 10.1016/j.tibtech.2013.10.005.

41. Liu, Wusheng; Yuan, Joshua S.; Stewart, C. Neal, Jr. (2013) "Advanced genetic tools for plant biotechnology". Nature Reviews Genetics 14 (11), 781-793. DOI: 10.1038/nrg3583.

40. Bi, C., Su, P., Müller, J., Yeh, Y.C., Chhabra, S.R., Beller, H.R., Singer, S.W., and Hillson, N.J. (2013) "Development of a broad-host synthetic biology toolbox for ralstonia eutropha and its application to engineering hydrocarbon biofuel production". Microbial Cell Factories 12:107. DOI: 10.1186/1475-2859-12-107

39. Fisher, A.B., Canfield, A.B., Hayward, L.C., Fong, S.S., and McArthur IV, G.H. (2013) "Ex vivo DNA assembly". Front. Bioeng. Biotechnol. DOI: 10.3389/fbioe.2013.00012.

38. Cobb RE, Ning JC, Zhao H. (2013) "DNA assembly techniques for next-generation combinatorial biosynthesis of natural products". J Ind Microbiol Biotechnol. Oct 15. [Epub ahead of print] PubMed PMID: 24127070.

37. Yifan Li , Qun Gu , Zhenquan Lin , Zhiwen Wang , Tao Chen *, and Xueming Zhao. (2013) "Multiplex Iterative Plasmid Engineering for Combinatorial Optimization of Metabolic Pathways and Diversification of Protein Coding Sequences". ACS Synth. Biol. DOI: 10.1021/sb400051t

36. Sang Yup Lee, Seung Bum Sohn, Yu Bin Kim, Jae Ho Shin, Jin Eyun Kim, Tae Yong Kim. (2013) "Chapter 8 – Computational Methods for Strain Design" in Synthetic Biology Tools and Applications. Huimin Zhao, Editor(s), Academic Press, Boston, Pages 141-156.

35. Sean C. Sleight and Herbert M. Sauro. (2013) "Visualization of Evolutionary Stability Dynamics and Competitive Fitness of Escherichia coli Engineered with Randomized Multigene Circuits". ACS Synth. Biol. DOI: 10.1021/sb400055h

34. Thomas Landrain, Morgan Meyer, Ariel Martin Perez, and Remi Sussan. (2013) "Do-it-yourself biology: challenges and promises for an open science and technology movement". Systems and Synthetic Biology. DOI: 10.1007/s11693-013-9116-4

33. Carothers, J. (2013) "Design-driven, multi-use research agendas to enable applied synthetic biology for global health". Syst Synth Biol. DOI 10.1007/s11693-013-9118-2

32. Narjeskhatoon Habibi, Siti Zaiton Mohd Hashim, Cesar A. Rodriguez, Mohd Razip Samian. (2013) "A Review of CADs, Languages and Data Models for Synthetic Biology" Jurnal Teknologi 63 (1): DOI: 10.11113/jt.v63.1644

31. Sleight, S.C. and Sauro, H.M. (2013) "Randomized BioBrick Assembly: A novel DNA assembly method for randomizing and optimizing genetic circuits and metabolic pathways" ACS Synth. Biol., DOI: 10.1021/sb4000542

30. Cox III, R.S., Koro Nishikata, K., Shimoyama, S., Yoshida, Y., Matsui, M., Makita, Y., and Toyoda, T. (2013) PromoterCAD: data-driven design of plant regulatory DNA. Nucl. Acids Res. DOI: 10.1093/nar/gkt518

29. Kahl, L.J., and Endy, D. (2013) A survey of enabling technologies in synthetic biology. Journal of Biological Engineering 7:13 DOI:10.1186/1754-1611-7-13.

28. Chen, W.H., Qin, Z.J., Zhao, G.P. (2013) The MASTER (methylation-assisted tailorable ends rational) ligation method for seamless DNA assembly. Nucleic Acids Research 41 (8), e93. DOI:10.1093/nar/gkt122

27. Mackenzie, A. (2013) Realizing the promise of biotechnology: Infrastructural-icons in synthetic biology. Futures. DOI:10.1016/j.futures.2013.02.003

26. Linshiz, G., Goldberg, A., Konry, T., and Hillson, N.J. (2013) The Fusion of Biology, Computer Science, and Engineering – towards efficient and successful synthetic biology. Perspectives in Biology and Medicine 55 (4), 503-520. DOI: 10.1353/pbm.2012.0044

25. Stephen Van Dien. (2013) From the first drop to the first truckload: commercialization of microbial processes for renewable chemicals. Current Opinion in Biotechnology. DOI:10.1016/j.copbio.2013.03.002

24. Peng Xu, Namita Bhan, and Mattheos AG Koffas. (2013). "Engineering plant metabolism into microbes: from systems biology to synthetic biology". Current Opinion in Biotechnology 24(2):291.

23. Chen, J, Densmore, D, Ham, TS, Keasling, JD and Hillson, N.J. (2012) "DeviceEditor visual biological CAD canvas". Journal of Biological Engineering 6:1

22. Vivek K Mutalik, Joao C Guimaraes, Guillaume Cambray, Quynh-Anh Mai, Marc Juul Christoffersen, Lance Martin, Ayumi Yu, Colin Lam, Cesar Rodriguez, Gaymon Bennett, Jay D Keasling, Drew Endy, and Adam P Arkin. (2013) Quantitative estimation of activity and quality for collections of functional genetic elements. Nature Methods. doi:10.1038/nmeth.2403

21. W.H. Chen, Z.J. Qin, J. Wang, G.P. Zhao, (2013)The MASTER (methylation-assisted tailorable ends rational) ligation method for seamless DNA assembly. Nucleic Acids Research. doi:10.1093/nar/gkt122

20. Esvelt, K.M., and Wang, H.H. (2013) Genome-scale engineering for systems and synthetic biology. Molecular Systems Biology 9:641. doi:10.1038/msb.2012.66

19. Stevens, J.T., and Myers, C.J. (2012) Dynamic Modeling of Cellular Populations within iBioSim. ACS Synthetic Biology. DOI: 10.1021/sb300082b

18. Perkel, JM. (2012). Genome engineering: writing a better genome. BioTechniques, Vol. 53, No. 4, October 2012, pp. 213–217.

17. Linshiz, G., Stawski, N., Poust, S., Bi, C., Keasling, J.D., and Hillson, N.J. (2012). PaR-PaR Laboratory Automation platform. ACS Synthetic Biology. DOI: 10.1021/sb300075t

16. Xu P, Bhan N, Koffas MA. (2012) Engineering plant metabolism into microbes: from

systems biology to synthetic biology. Curr Opin Biotechnol. doi: 10.1016/j.copbio.2012.08.010. PubMed PMID: 22985679.

15. Jacob Beal, Ron Weiss, Douglas Densmore, Aaron Adler, Evan Appleton, Jonathan Babb, Swapnil Bhatia, Noah Davidsohn, Traci Haddock, Joseph Loyall, Richard Schantz, Viktor Vasilev, and Fusun Yaman. (2012) An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications. ACS Synthetic Biology. DOI: 10.1021/sb300030d

14. Yaman F, Bhatia S, Adler A, Densmore D, and Beal J. (2012) Automated Selection of Synthetic Biology Parts for Genetic Regulatory Networks. ACS Synthetic Biology. DOI: 10.1021/sb300032y.

13. Kitney R, Freemont P. (2012) Synthetic biology - the state of play. FEBS Lett. DOI: 10.1016/j.febslet.2012.06.002 PubMed PMID: 22704968.

12. Ham, T.S., Dmytriv, Z. Plahar, H., Chen, J., Hillson, N.J., and Keasling, J.D. (2012) Design, Implementation and Practice of JBEI-ICE: An Open Source Biological Part Registry Platform and Tools. Nucleic Acids Research. DOI: 10.1093/nar/gks531.

11. Allen Cheng and Timothy K. Lu. (2012) Synthetic Biology: An Emerging Engineering Discipline. Annu. Rev. Biomed. Eng. 2012. 14:155–78. DOI: 10.1146/annurev-bioeng-071811–150118.

10. Michael G Montague, Carole Lartigue, Sanjay Vashee. (2012) Synthetic genomics: potential and limitations. Current Opinion in Biotechnology, DOI:10.1016/j.copbio.2012.01.014.

9. Synthetic Biology. Wikigenes collaborative publishing.

8. Artificial gene synthesis. Wikipedia, the free encyclopedia.

7. (2012) In This Issue. ACS Synthetic Biology 1 (1), 3-3. DOI: 10.1021/sb3000047.

6. Holtz, William J (2011) Engineering Scalable Combinational Logic in Escherichia coli Using Zinc Finger Proteins. UC Berkeley Technical Report EECS-2011-59.

5. Baker M. (2011) Synthetic genomes: The next step for the synthetic genome. Nature. 473(7347):403, 405-8. DOI:10.1038/473403a. PubMed PMID: 21593873.

4. Hillson NJ. (2011) "DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems" in Design and Analysis of Bio-molecular Circuits, Koeppl H., Densmore, D., di Bernardo, M., and Setti, G. (Editors), Springer-Verlag, 1st Edition, 295-314.

3. Beal, J., Phillips, A., Densmore, D., and Cai, Y.(2011) "High-Level Programming Languages for Bio-Molecular Systems" in Design and Analysis of Bio-molecular Circuits, Koeppl H., Densmore, D., di Bernardo, M., and Setti, G. (Editors), Springer-Verlag, 1st Edition, 225-252.

2. Chandran D, Bergmann FT, Sauro HM, Densmore D. (2011) "Computer-Aided Design for Synthetic Biology" in Design and Analysis of Bio-molecular Circuits, Koeppl H., Densmore, D., di Bernardo, M., and Setti, G. (Editors), Springer-Verlag, 1st Edition, 203-224.

1. Ellis T, Adie T, Baldwin GS. DNA assembly for synthetic biology: from parts to pathways and beyond (2011). Integr Biol (Camb). 3, 109-118. DOI: 10.1039/C0IB00070A. PubMed PMID: 21246151.doi:10.1186/1754-1611-8-4Recent advances in DNA assembly technologies