Publications citing j5

Publications citing j5

263. Matzko, R., Konur, S. (2024) "Technologies for design-build-test-learn automation and computational modelling across the synthetic biology workflow: a review." Netw Model Anal Health Inform Bioinforma 13, 22.

262. Laura Adam and George H. McArthur, IV. (2024) "Substitution Attacks: A Catalyst to Reframe the DNA Manufacturing Cyberbiosecurity Landscape in the Age of Benchtop Synthesizers" Applied Biosafety

261. Ke’Koa CDH Wells, Nawwaf Kharma, Brandon B. Jaunky, Kaiyu Nie, Gabriel Aguiar-Tawil, Daniel Berry. (2024) "BioCloneBot: A versatile, low-cost, and open-source automated liquid handler" HardwareX

260. Yuxin Ma, Zhaoyang Zhang, Bin Jia, Yingjin Yuan. (2024) "Automated high-throughput DNA synthesis and assembly" Heliyon

259. Chunhe Yang, Yi Yang, Guangyun Chu, Ruoyu Wang, Haoran Li, Yufeng Mao, Meng Wang, Jian Zhang, Xiaoping Liao*, and Hongwu Ma. (2024) "AutoESDCas: A Web-Based Tool for the Whole-Workflow Editing Sequence Design for Microbial Genome Editing Based on the CRISPR/Cas System" ACS Synth. Biol.

258. Christoph Wagner, Uriel Urquiza-Garcia, Matias D. Zurbriggen, Hannes M. Beyer. (2024) "GMOCU: Digital Documentation, Management, and Biological Risk Assessment of Genetic Parts". Advanced Biology

257. Allison N. Pearson, Matthew R. Incha, Cindy N. Ho, Matthias Schmidt, Jacob B. Roberts, Alberto A. Nava, and Jay D. Keasling. (2023) "Characterization and Diversification of AraC/XylS Family Regulators Guided by Transposon Sequencing" ACS Synthetic Biology

256. Alberto A. Nava, Anna Lisa Fear, Namil Lee, Peter Mellinger, Guangxu Lan, Joshua McCauley, Stephen Tan, Nurgul Kaplan, Garima Goyal, R. Cameron Coates, Jacob Roberts, Zahmiria Johnson, Romina Hu, Bryan Wu, Jared Ahn, Woojoo E. Kim, Yao Wan, Kevin Yin, Nathan Hillson, Robert W. Haushalter, and Jay D. Keasling. (2023) "Automated Platform for the Plasmid Construction Process" ACS Synthetic Biology 2023 12 (12), 3506-3513

255. Ataii N, Bakshi S, Chen Y, Fernandez M, Shao Z, et al. (2023) "Enabling AI in synthetic biology through Construction File specification". PLOS ONE 18(11): e0294469. 

254. Hou, Zhiyang, Zelin Xu, Mengying Wu, Liqiu Ma, Li Sui, Po Bian, and Ting Wang. 2023. "Enhancement of Repeat-Mediated Deletion Rearrangement Induced by Particle Irradiation in a RecA-Dependent Manner in Escherichia coli" Biology 12, no. 11: 1406. 

253. Chunlin Tan, Ping Xu, Fei Tao. (2022) "Harnessing Interactional Sensory Genes for Rationally Reprogramming Chaotic Metabolism". Research.

252. Zhandong Wei, Dongdong Zhao, Jie Wang, Ju Li, Ning Xu, Chao Ding, Jun Liu, Siwei Li, Chunzhi Zhang, Changhao Bi. (2023) "Targeted C-to-T and A-to-G dual mutagenesis system for RhtA transporter in vivo evolution" Genetics and Molecular Biology DOI:

251. Mansoor A. Siddiqui, Ashima Sharma, Syed Shams Yazdani, "Chapter 6 - Design, building, and challenges in synthetic genomics", Editor(s): Vijai Singh, New Frontiers and Applications of Synthetic Biology, Academic Press, 2022, Pages 67-82

250. Matthias Schmidt, Namil Lee, Chunjun Zhan, Jacob B. Roberts, Alberto A. Nava, Leah S. Keiser, Aaron A. Vilchez, Yan Chen, Christopher J. Petzold, Robert W. Haushalter, Lars M. Blank, and Jay D. Keasling. (2023) "Maximizing Heterologous Expression of Engineered Type I Polyketide Synthases: Investigating Codon Optimization Strategies" ACS Synth. Biol.

249. Yang Liu, Haijiao Cheng, Haoni Li, Yingzhe Zhang, Meng Wang. (2023) "A Programmable CRISPR/Cas9 Toolkit Improves Lycopene Production in Bacillus subtilis" Applied and Industrial Microbiology DOI:

248. Wang, B. et al. (2023). Synthetic Biology: Technical Issues. In: Ning, K., Zhan, Y. (eds) Synthetic Biology and iGEM: Techniques, Development and Safety Concerns. Springer, Singapore.

247. Wang, P., Zhao, D., Li, J., Su, J., Zhang, C., Li, S., Fan, F., Dai, Z., Liao, X., Mao, Z., Bi, C., Zhang, X., Artificial Diploid Escherichia coli by a CRISPR Chromosome-Doubling Technique. Adv. Sci. 2023, 10, 2205855. 

246. John A Bryant, Mason Kellinger, Cameron Longmire, Ryan Miller, R Clay Wright, AssemblyTron: flexible automation of DNA assembly with Opentrons OT-2 lab robots, Synthetic Biology, Volume 8, Issue 1, 2023, ysac032,

245. S. R. Little, J. M. Perry, K. Samlali, and S. C. C. Shih, in Droplet Microfluidics, ed. C. Ren and A. Lee, The Royal Society of Chemistry, 2020, pp. 193-222.

244. Patel, D. (2023). Exploring the Frontiers of Microfluidics: Challenges and Future Prospects. In R. Singh, R. Phanden, B. Sikarwar, & J. Davim (Eds.), Advances in MEMS and Microfluidic Systems (pp. 11-31). IGI Global. 

243. Tien T. Sword, J. William Barker, Madeline Spradley, Yan Chen, Christopher J. Petzold, Constance B. Bailey. (2023) "Expression of blue pigment synthetase a from Streptomyces lavenduale reveals insights on the effects of refactoring biosynthetic megasynthases for heterologous expression in Escherichia coli", Protein Expression and Purification, Volume 210, 106317, ISSN 1046-5928, 

242. Xue Zhao, Mahbubur Rahman, Zhiyuan Xu, Tom Kasputis, Yawen He, Lijuan Yuan, R. Clay Wright, and Juhong Chen. "Engineered Yeast Displaying Specific Norovirus-Binding Nanobodies for the Concentration and Detection of Human Norovirus in Food Matrix". Journal of Agricultural and Food Chemistry Article ASAP DOI: 10.1021/acs.jafc.3c01946

241. Pearson AN, Thompson MG, Kirkpatrick LD, Ho C, Vuu KM, Waldburger LM, Keasling JD, Shih PM. The pGinger Family of Expression Plasmids. Microbiol Spectr. 2023 May 22:e0037323. doi: 10.1128/spectrum.00373-23

240.  John A Bryant Jr, Mason Kellinger, Cameron Longmire, Ryan Miller, R Clay Wright. (2022) "AssemblyTron: Flexible automation of DNA assembly with Opentrons OT-2 lab robots" OUP Synthetic Biology,

239. Li Liu, Wenbo Li, Ju Li, Dongdong Zhao, Siwei Li, Guo Jiang, Jie Wang, Xuxu Chen, Changhao Bi*, and Xueli Zhang. (2022) "Circular Guide RNA for Improved Stability and CRISPR-Cas9 Editing Efficiency in Vitro and in Bacteria" ACS Synth. Biol.

238. Su, J., Wang, P., Li, J. et al. A CRISPR-based chromosomal-separation technique for Escherichia coli. Microb Cell Fact 21, 235 (2022). 

237. Xiaole Yang, Kimberly A. Kowallis, W. Seth Childers, Chapter Ten - Protein engineering strategies to stimulate the functions of bacterial pseudokinases, Editor(s): Natalia Jura, James M. Murphy, Methods in Enzymology, Academic Press, Volume 667, 2022, Pages 275-302,

236. Garber, M.E., Fregoso, R., Lake, J. et al. Pseudomonas response regulators produced in an E. coli heterologous expression host exhibit host-derived post-translational phosphorylation. Sci Rep 12, 10336 (2022).

235. Yi Yang, Yufeng Mao, Ruoyu Wang, Haoran Li, Ye Liu, Haijiao Cheng, Zhenkun Shi, Yu Wang, Meng Wang, Ping Zheng, Xiaoping Liao, Hongwu Ma, AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms, Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022, Pages W75–W82,

234. Lukas Buecherl, Chris J Myers. (2022) "Engineering genetic circuits: advancements in genetic design automation tools and standards for synthetic biology". Current Opinion in Microbiology, Volume 68,

233. Mori, H., Yachie, N. A framework to efficiently describe and share reproducible DNA materials and construction protocols. Nat Commun 13, 2894 (2022).

232. Xiaole Yang, Kimberly A. Kowallis, W. Seth Childers. (2022) "Chapter Ten - Protein engineering strategies to stimulate the functions of bacterial pseudokinases" Editor(s): Natalia Jura, James M. Murphy. Methods in Enzymology, Academic Press, Volume 667, Pages 275-302,

231. Liu, Y., Pinto, F., Wan, X. et al. (2022). "Reprogrammed tracrRNAs enable repurposing of RNAs as crRNAs and sequence-specific RNA biosensors". Nat Commun 13, 1937.

230. Liu L, Wang P, Zhao D, Zhu L, Tang J, Leng W, Su J, Liu Y, Bi C, Zhang X. (2022) "Engineering Circularized mRNAs for the Production of Spider Silk Proteins". Appl Environ Microbiol. 88(8):e0002822.

229. Schmidt M, Pearson AN, Incha MR, Thompson MG, Baidoo EEK, Kakumanu R, Mukhopadhyay A, Shih PM, Deutschbauer AM, Blank LM, Keasling JD. (2022) "Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing". Appl Environ Microbiol. 88(7): e0243021.

228. Chao Zhang, Wei Zhao, Samuel W. Duvall, Kimberly A. Kowallis, W. Seth Childers. (2022) "Regulation of the activity of the bacterial histidine kinase PleC by the scaffolding protein PodJ". Journal of Biological Chemistry, Volume 298, Issue 4,

227. Yisha Luo, Joshua S. James, Sally Jones, Andrea Martella, and Yizhi Cai. (2022) "EMMA-CAD: Design Automation for Synthetic Mammalian Constructs". ACS Synthetic Biology 11 (2), 579-586.

226. Madhavan, Maya and Mustafa, Sabeena. (2022) "Systems biology–the transformative approach to integrate sciences across disciplines: Systems Biology: Integrating Biological Sciences" Physical Sciences Reviews

225. Guo Jiang, Jie Wang, Dongdong Zhao, Xuxu Chen, Shiming Pu, Chunzhi Zhang, Ju Li, Yaqiu Li, Jie Yang, Siwei Li, Xiaoping Liao, Hongwu Ma, Yanhe Ma, Zuping Zhou, Changhao Bi, and Xueli Zhang (2021) "Molecular Mechanism of the Cytosine CRISPR Base Editing Process and the Roles of Translesion DNA Polymerases" ACS Synthetic Biology 10 (12), 3353-3358

224. Bo Pang, Jia Li, Christopher B. Eiben, Ethan Oksen, Carolina Barcelos, Rong Chen, Elias Englund, Eric Sundstrom, Jay D. Keasling, (2021) "Lepidopteran mevalonate pathway optimization in Escherichia coli efficiently produces isoprenol analogs for next-generation biofuels". Metabolic Engineering, Volume 68, Pages 210-219,

223. Yang Yi, Mao Yufeng, Liu Ye, Wang Ruoyu, Lu Hui, Li Haoran, Luo Jiahao, Wang Meng, Liao Xiaoping, Ma Hongwu. (2021) "GEDpm-cg: Genome Editing Automated Design Platform for Point Mutation Construction in Corynebacterium glutamicum" .  Frontiers in Bioengineering and Biotechnology 9. 

222. Yeoh J.W., Gomez-Carretero S., Chee W.K.D., Teh A.Y., Poh C.L. (2022) "Genetic Circuit Design Principles". In: Thouand G. (eds) Handbook of Cell Biosensors. Springer, Cham.

221. Gupta, D., Sharma, G., Saraswat, P. et al. (2021) "Synthetic Biology in Plants, a Boon for Coming Decades". Mol Biotechnol 63, 1138–1154.

220. Jie Wang, Dongdong Zhao, Ju Li, Muzi Hu, Xiuqing Xin, Marcus A. Price, Qingyan Li, Li Liu, Siwei Li, Susan J. Rosser, Chunzhi Zhang, Changhao Bi, Xueli Zhang. (2021) "Helicase-AID: A novel molecular device for base editing at random genomic loci" Metabolic Engineering, Volume 67, Pages 396-402,

219. Perry, Soffer, Jain, and Shih. (2021) "Expanding the limits towards ‘one-pot’ DNA assembly and transformation on a rapid-prototype microfluidic device". Lab on a Chip

218. Savas Konur*, Laurentiu Mierla, Harold Fellermann, Christophe Ladroue, Bradley Brown, Anil Wipat, Jamie Twycross, Boyang Peter Dun, Sara Kalvala, Marian Gheorghe, and Natalio Krasnogor. (2021) "Toward Full-Stack In Silico Synthetic Biology: Integrating Model Specification, Simulation, Verification, and Biological Compilation". ACS Synth.

217. Benjamin M. Gyori, John A. Bachman. (2021) "From knowledge to models: automated modeling in systems and synthetic biology". Current Opinion in Systems Biology, 100362, ISSN 2452-3100,

216. Justin Vrana, Orlando de Lange, Yaoyu Yang, Garrett Newman, Ayesha Saleem, Abraham Miller, Cameron Cordray, Samer Halabiya, Michelle Parks, Eriberto Lopez, Sarah Goldberg, Benjamin Keller, Devin Strickland, Eric Klavins. (2021) "Aquarium: open-source laboratory software for design, execution and data management".  Synthetic Biology, Volume 6, Issue 1, ysab006

215. Christopher M. Whitford, Pablo Cruz-Morales, Jay D. Keasling, Tilmann Weber. (2021) "The Design-Build-Test-Learn cycle for metabolic engineering of Streptomycetes". Essays Biochem 65 (2): 261–275

214. Jiefei Wang, Chao Zhang, and W. Seth Childers. (2021) "A Biosensor for Detection of Indole Metabolites". ACS Synthetic Biology 10 (7), 1605-1614 DOI: 10.1021/acssynbio.1c00090 

213. Thomas A. Dixon, Thomas C. Williams, Isak S. Pretorius. (2021) "Bioinformational trends in grape and wine biotechnology". Trends in Biotechnology.

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

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