Publications citing j5
Publications citing j5
271. Matthew J. Szarzanowicz, Lucas M. Waldburger, Michael Busche, Gina M. Geiselman, Liam D. Kirkpatrick, Alexander J. Kehl, Claudine Tahmin, Rita C. Kuo, Joshua McCauley, Hamreet Pannu, Ruoming Cui, Shuying Liu, Nathan J. Hillson, Jacob O. Brunkard, Jay D. Keasling, John M. Gladden, Mitchell G. Thompson, Patrick M. Shih. (2024) "Binary vector copy number engineering improves Agrobacterium-mediated transformation". Nat Biotechnol https://doi.org/10.1038/s41587-024-02462-2
270. Y. Torres-Tiji, H. Sethuram, A. Gupta, J. McCauley, J.-V. Dutra-Molino, R. Pathania, L. Saxton, K. Kang, N. J. Hillson, and S. P. Mayfield. (2024) "Bioinformatic Prediction and High Throughput In Vivo Screening to Identify Cis-Regulatory Elements for the Development of Algal Synthetic Promoters" ACS Synthetic Biology 13 (7), 2150-2165 https://pubs.acs.org/doi/10.1021/acssynbio.4c00199
269. Pengju Wang, Yidan Ma, Ju Li, Junchang Su, Junxi Chi, Xingmiao Zhu, Xinna Zhu, Chunzhi Zhang, Changhao Bi, and Xueli Zhang. 2024 "Exploring the De Novo NMN Biosynthesis as an Alternative Pathway to Enhance NMN Production" ACS Synthetic Biology 13 (8), 2425-2435 https://pubs.acs.org/doi/10.1021/acssynbio.4c00115
268. Hou, Z., Yu, T., Yi, Q. et al. (2024) "High-complexity of DNA double-strand breaks is key for alternative end-joining choice" Commun Biol 7, 936. https://doi.org/10.1038/s42003-024-06640-5
267. Patarasuda Chaisupa, Md Mahbubur Rahman, Sherry B. Hildreth, Saede Moseley, Chauncey Gatling, Matthew R. Bryant, Richard F. Helm, and R. Clay Wright. (2024) "Genetically Encoded, Noise-Tolerant, Auxin Biosensors in Yeast" ACS Synthetic Biology 13 (9), 2804-2819 https://pubs.acs.org/doi/10.1021/acssynbio.4c00186
266. Chi, J., Wang, P., Ma, Y. et al. (2024) "Engineering Escherichia coli for utilization of PET degraded ethylene glycol as sole feedstock" Biotechnol Biofuels 17, 121. https://doi.org/10.1186/s13068-024-02568-4
265. Bozkurt EU, Ørsted EC, Volke DC, Nikel PI. (2024) "Accelerating enzyme discovery and engineering with high-throughput screening." Nat Prod Rep. https://pubs.rsc.org/en/content/articlelanding/2024/np/d4np00031e
264. Bryant, J.A., Wright, R.C. (2025). "Biofoundry-Assisted Golden Gate Cloning with AssemblyTron". In: Schindler, D. (eds) Golden Gate Cloning. Methods in Molecular Biology, vol 2850. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-4220-7_8
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. https://doi.org/10.1007/s13721-024-00455-4
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 https://doi.org/10.1089/apb.2023.0035
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 https://doi.org/10.1016/j.ohx.2024.e00516
260. Yuxin Ma, Zhaoyang Zhang, Bin Jia, Yingjin Yuan. (2024) "Automated high-throughput DNA synthesis and assembly" Heliyon https://doi.org/10.1016/j.heliyon.2024.e26967
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. https://doi.org/10.1021/acssynbio.4c00063
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 https://doi.org/10.1002/adbi.202300529
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 https://pubs.acs.org/doi/10.1021/acssynbio.3c00441
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 https://pubs.acs.org/doi/10.1021/acssynbio.3c00292
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. https://doi.org/10.1371/journal.pone.0294469
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. https://doi.org/10.3390/biology12111406
253. Chunlin Tan, Ping Xu, Fei Tao. (2022) "Harnessing Interactional Sensory Genes for Rationally Reprogramming Chaotic Metabolism". Research. https://doi.org/10.34133/research.0017
252. Zhandong Wei, Dongdong Zhao, Jie Wang, Ju Li, Ning Xu, Chao Ding, Jun Liu, Siwei Li, Chunzhi Zhang zhangcz@dlpu.edu.cn, 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: https://doi.org/10.1128/aem.00752-23
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 https://doi.org/10.1016/B978-0-12-824469-2.00002-6
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. https://doi.org/10.1021/acssynbio.3c00367
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: https://doi.org/10.1128/aem.00230-23
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. https://doi.org/10.1007/978-981-99-2460-8_4
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. https://doi.org/10.1002/advs.202205855
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, https://doi.org/10.1093/synbio/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. https://doi.org/10.1039/9781839162855-00193
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. https://doi.org/10.4018/978-1-6684-6952-1.ch002 https://www.igi-global.com/gateway/chapter/324986
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, https://doi.org/10.1016/j.pep.2023.106317 https://www.sciencedirect.com/science/article/pii/S1046592823000888
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 https://pubs.acs.org/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 https://journals.asm.org/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, https://doi.org/10.1093/synbio/ysac032
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. https://doi.org/10.1021/acssynbio.2c00381
238. Su, J., Wang, P., Li, J. et al. A CRISPR-based chromosomal-separation technique for Escherichia coli. Microb Cell Fact 21, 235 (2022). https://doi.org/10.1186/s12934-022-01957-4 https://microbialcellfactories.biomedcentral.com/articles/10.1186/s12934-022-01957-4
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, https://doi.org/10.1016/bs.mie.2022.03.030 https://www.sciencedirect.com/science/article/pii/S0076687922001215
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). https://doi.org/10.1038/s41598-022-13525-2
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, https://doi.org/10.1093/nar/gkac417
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, https://doi.org/10.1016/j.mib.2022.102155
233. Mori, H., Yachie, N. A framework to efficiently describe and share reproducible DNA materials and construction protocols. Nat Commun 13, 2894 (2022). https://doi.org/10.1038/s41467-022-30588-x
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, https://doi.org/10.1016/bs.mie.2022.03.030
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. https://doi.org/10.1038/s41467-022-29604-x
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. https://doi.org/10.1128/aem.00028-22
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. https://doi.org/10.1128/aem.02430-21
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, https://doi.org/10.1016/j.jbc.2022.101683
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. https://doi.org/10.1021/acssynbio.1c00433
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 https://doi.org/10.1515/psr-2021-0102
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 https://doi.org/10.1021/acssynbio.1c00293
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, https://doi.org/10.1016/j.ymben.2021.10.007
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. https://www.frontiersin.org/article/10.3389/fbioe.2021.768289
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. https://doi.org/10.1007/978-3-030-23217-7_171
221. Gupta, D., Sharma, G., Saraswat, P. et al. (2021) "Synthetic Biology in Plants, a Boon for Coming Decades". Mol Biotechnol 63, 1138–1154. https://doi.org/10.1007/s12033-021-00386-9
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, https://doi.org/10.1016/j.ymben.2021.08.005
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 https://doi.org/10.1039/D1LC00415H
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. https://doi.org/10.1021/acssynbio.1c00143
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, https://doi.org/10.1016/j.coisb.2021.100362
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 https://doi.org/10.1093/synbio/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 https://doi.org/10.1042/EBC20200132
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. https://doi.org/10.1016/j.tibtech.2021.05.001
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, https://doi.org/10.1093/synbio/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). https://doi.org/10.1038/s41467-021-21003-y
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 https://doi.org/10.1016/j.copbio.2021.01.010
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. https://doi.org/10.1007/978-1-0716-1032-9_5
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 https://doi.org/10.1093/synbio/ysaa019
207. Irene Otero-Muras, Pablo Carbonell. (2020) "Automated engineering of synthetic metabolic pathways for efficient association to reaction rules.biomanufacturing". Metabolic Engineering https://doi.org/10.1016/j.ymben.2020.11.012
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 doi.org/10.1186/s12934-020-01494-y
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. https://doi.org/10.1007/978-1-0716-0822-7_13
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 https://doi.org/10.1371/journal.pone.0242157
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 https://doi.org/10.1016/j.bej.2020.107851
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. https://doi.org/10.1146/annurev-micro-022620-081059
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; https://doi.org/10.3390/plants9091090
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. https://doi.org/10.1007/978-1-0716-0908-8_2
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. https://doi.org/10.1007/978-1-0716-0908-8_1
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. https://doi.org/10.1007/978-1-0716-0908-8_3
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. https://doi.org/10.1021/acssynbio.0c00404
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). https://doi.org/10.1038/s41587-020-0592-2
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. https://microbialcellfactories.biomedcentral.com/articles/10.1186/s12934-020-01393-2
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). https://doi.org/10.1186/s12866-020-01812-9
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 https://doi.org/10.1002/cssc.202000268
189. Nicola J. Patron. O(2020) "Beyond natural: synthetic expansions of botanical form and function" New Phytologist. https://doi.org/10.1111/nph.16562
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 https://doi.org/10.1371/journal.pone.0223935
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 https://doi.org/10.1016/j.mec.2019.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. https://doi.org/10.1021/acssynbio.9b00292
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 https://doi.org/10.1073/pnas.1905990116
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 https://doi.org/10.1016/j.mec.2019.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 https://doi.org/10.1093/synbio/ysz014
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 https://doi.org/10.15252/msb.20188623
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. https://doi.org/10.1042/BST20160347
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 https://doi.org/10.1007/978-3-319-22708-5_3
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 https://doi.org/10.1002/mbo3.930
171. Ross Kent, Neil Dixon. (2019) "Contemporary Tools for Regulating Gene Expression in Bacteria" Trends in Biotechnology https://doi.org/10.1016/j.tibtech.2019.09.007
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 https://doi.org/10.1002/yea.3439
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. https://doi.org/10.1021/acssynbio.9b00284
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 https://biotechnologyforbiofuels.biomedcentral.com/articles/10.1186/s13068-019-1520-x
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 https://doi.org/10.1186/s12934-019-1166-1
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, https://doi.org/10.1093/bib/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 https://doi.org/10.1007/s10295-019-02189-z
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 https://doi.org/10.1007/978-1-62703-625-2_10
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 https://doi.org/10.1016/j.mec.2019.e00089
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. https://doi.org/10.1016/j.bej.2019.03.015
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. https://doi.org/10.1177/2472630318825335
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 https://doi.org/10.1186/s12934-019-1067-3
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 https://doi.org/10.1016/B978-0-444-64085-7.00004-6
152. R. Clay Wright, Jennifer Nemhauser. (2019) "Plant Synthetic Biology: Quantifying the Known Unknowns and Discovering the Unknown Unknowns". Plant Physiology. DOI: https://doi.org/10.1104/pp.18.01222
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 https://doi.org/10.1186/s13068-018-1270-1
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. https://doi.org/10.1038/s41467-018-05857-3
146. Thomas H. Mann and Lucy Shapiro. (2018) "Integration of cell cycle signals by multi-PAS domain kinases". PNAS 201808543 https://doi.org/10.1073/pnas.1808543115
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 https://doi.org/10.1002/biot.201700604
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 https://doi.org/10.1186/s13068-018-1170-4
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 https://doi.org/10.1016/j.ymben.2018.05.018
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. https://doi.org/10.1007/s13205-018-1298-8
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. https://doi.org/10.1002/9783527688104.ch16
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. https://doi.org/10.1007/s10295-018-2025-5
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. https://doi.org/10.1016/j.copbio.2018.01.027
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 https://doi.org/10.1016/j.ymthe.2017.09.006
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; https://doi.org/10.1534/genetics.117.300092
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 https://doi.org/10.1016/j.ymben.2017.08.003
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: https://doi.org/10.1371/journal.pone.0177234
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. https://doi.org/10.3389/fbioe.2016.00076
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:https://doi.org/10.1093/nar/gkx034
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. DOI:dx.doi.org/10.1016/j.meteno.2016.05.003
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. http://www.biotechniques.com/BiotechniquesJournal/2012/October/Genome-engineering-writing-a-better-genome/biotechniques-336011.html
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