This page lists the publications that have been produced by the Synthetic Yeast project.

  • Design of a synthetic yeast genome Sarah M. Richardson, Leslie A. Mitchell, Giovanni Stracquadanio, Kun Yang, Jessica S. Dymond, James E. DiCarlo, Dongwon Lee, Cheng Lai Victor Huang, Srinivasan Chandrasegaran, Yizhi Cai, Jef D. Boeke, Joel S. Bader. Science , 355 1040-1044 (2017) doi:http://dx.doi.org/10.1126/science.aaf4557
  • 3D organization of synthetic and scrambled chromosomes Guillaume Mercy, Julien Mozziconacci, Vittore F. Scolari, Kun Yang, Guanghou Zhao, Agnès Thierry, Yisha Luo, Leslie A. Mitchell, Michael Shen, Yue Shen, Roy Walker, Weimin Zhang, Yi Wu, Ze-xiong Xie, Zhouqing Luo, Yizhi Cai, Junbiao Dai, Huanming Yang, Ying-Jin Yuan, Jef D. Boeke, Joel S. Bader, Héloïse Muller, Romain Koszul. Science , 355 (2017) doi:10.1126/science.aaf4597
  • “Perfect” designer chromosome V and behavior of a ring derivative Ze-Xiong Xie, Bing-Zhi Li, Leslie A. Mitchell, Yi Wu, Xin Qi, Zhu Jin, Bin Jia, Xia Wang, Bo-Xuan Zeng, Hui-Min Liu, Xiao-Le Wu, Qi Feng, Wen-Zheng Zhang, Wei Liu, Ming-Zhu Ding, Xia Li, Guang-Rong Zhao, Jian-Jun Qiao, Jing-Sheng Cheng, Meng Zhao, Zheng Kuang, Xuya Wang, J. Andrew Martin, Giovanni Stracquadanio, Kun Yang, Xue Bai, Juan Zhao, Meng-Long Hu, Qiu-Hui Lin, Wen-Qian Zhang, Ming-Hua Shen, Si Chen, Wan Su, En-Xu Wang, Rui Guo, Fang Zhai, Xue-Jiao Guo, Hao-Xing Du, Jia-Qing Zhu, Tian-Qing Song, Jun-Jun Dai, Fei-Fei Li, Guo-Zhen Jiang, Shi-Lei Han, Shi-Yang Liu, Zhi-Chao Yu, Xiao-Na Yang, Ken Chen, Cheng Hu, Da-Shuai Li, Nan Jia, Yue Liu, Lin-Ting Wang, Su Wang, Xiao-Tong Wei, Mei-Qing Fu, Lan-Meng Qu, Si-Yu Xin, Ting Liu, Kai-Ren Tian, Xue-Nan Li, Jin-Hua Zhang, Li-Xiang Song, Jin-Gui Liu, Jia-Fei Lv, Hang Xu, Ran Tao, Yan Wang, Ting-Ting Zhang, Ye-Xuan Deng, Yi-Ran Wang, Ting Li, Guang-Xin Ye, Xiao-Ran Xu, Zheng-Bao Xia, Wei Zhang, Shi-Lan Yang, Yi-Lin Liu, Wen-Qi Ding, Zhen-Ning Liu, Jun-Qi Zhu, Ning-Zhi Liu, Roy Walker, Yisha Luo, Yun Wang, Yue Shen, Huanming Yang, Yizhi Cai, Ping-Sheng Ma, Chun-Ting Zhang, Joel S. Bader, Jef D. Boeke, Ying-Jin Yuan. Science, 355 (2017) doi:10.1126/science.aaf4704
  • Bug mapping and fitness testing of chemically synthesized chromosome X Yi Wu, Bing-Zhi Li, Meng Zhao, Leslie A. Mitchell, Ze-Xiong Xie, Qiu-Hui Lin, Xia Wang, Wen-Hai Xiao, Ying Wang, Xiao Zhou, Hong Liu, Xia Li, Ming-Zhu Ding, Duo Liu, Lu Zhang, Bao-Li Liu, Xiao-Le Wu, Fei-Fei Li, Xiu-Tao Dong, Bin Jia, Wen-Zheng Zhang, Guo-Zhen Jiang, Yue Liu, Xue Bai, Tian-Qing Song, Yan Chen, Si-Jie Zhou, Rui-Ying Zhu, Feng Gao, Zheng Kuang, Xuya Wang, Michael Shen, Kun Yang, Giovanni Stracquadanio, Sarah M. Richardson, Yicong Lin, Lihui Wang, Roy Walker, Yisha Luo, Ping-Sheng Ma, Huanming Yang, Yizhi Cai, Junbiao Dai, Joel S. Bader, Jef D. Boeke, Ying-Jin Yuan. Science , 355 (2017) doi:10.1126/science.aaf4706
  • Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome Yue Shen, Yun Wang, Tai Chen, Feng Gao, Jianhui Gong, Dariusz Abramczyk, Roy Walker, Hongcui Zhao, Shihong Chen, Wei Liu, Yisha Luo, Carolin A. Müller, Adrien Paul-Dubois-Taine, Bonnie Alver, Giovanni Stracquadanio, Leslie A. Mitchell, Zhouqing Luo, Yanqun Fan, Baojin Zhou, Bo Wen, Fengji Tan, Yujia Wang, Jin Zi, Zexiong Xie, Bingzhi Li, Kun Yang, Sarah M. Richardson, Hui Jiang, Christopher E. French, Conrad A. Nieduszynski, Romain Koszul, Adele L. Marston, Yingjin Yuan, Jian Wang, Joel S. Bader, Junbiao Dai, Jef D. Boeke, Xun Xu, Yizhi Cai, Huanming Yang. Science , 355 (2017) doi:10.1126/science.aaf4791
  • Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond Leslie A. Mitchell, Ann Wang, Giovanni Stracquadanio, Zheng Kuang, Xuya Wang, Kun Yang, Sarah Richardson, J. Andrew Martin, Yu Zhao, Roy Walker, Yisha Luo, Hongjiu Dai, Kang Dong, Zuojian Tang, Yanling Yang, Yizhi Cai, Adriana Heguy, Beatrix Ueberheide, David Fenyö, Junbiao Dai, Joel S. Bader, Jef D. Boeke. Science , 355 (2017) doi:10.1126/science.aaf4831
  • Engineering the ribosomal DNA in a megabase synthetic chromosome Weimin Zhang, Guanghou Zhao, Zhouqing Luo, Yicong Lin, Lihui Wang, Yakun Guo, Ann Wang, Shuangying Jiang, Qingwen Jiang, Jianhui Gong, Yun Wang, Sha Hou, Jing Huang, Tianyi Li, Yiran Qin, Junkai Dong, Qin Qin, Jiaying Zhang, Xinzhi Zou, Xi He, Li Zhao, Yibo Xiao, Meng Xu, Erchao Cheng, Ning Huang, Tong Zhou, Yue Shen, Roy Walker, Yisha Luo, Zheng Kuang, Leslie A. Mitchell, Kun Yang, Sarah M. Richardson, Yi Wu, Bing-Zhi Li, Ying-Jin Yuan, Huanming Yang, Jiwei Lin, Guo-Qiang Chen, Qingyu Wu, Joel S. Bader, Yizhi Cai, Jef D. Boeke, Junbiao Dai. Science , 355 (2017) doi:10.1126/science.aaf3981

  • GC Preps: Fast and Easy Extraction of Stable Yeast Genomic DNA. Benjamin A. Blount, Maureen R. M. Driessen and Tom Ellis. Nature Scientific Reports 6, Article number: 26863 (2016) doi:10.1038/srep26863
  • The Fifth Annual Sc2.0 and Synthetic Genomes Conference: Synthetic Genomes in High Gear. Walker RS, Cai Y. ACS Synth. Biol. 5 920-925 (2016) doi:10.1021/acssynbio.6b00227
  • Synthetic genome engineering forging new frontiers for wine yeast. Pretorius IS.Crit. Rev. Biotechnol. 18 1-25 (2016)

  • Robust orthogonal recombination system for versatile genomic elements rearrangement in yeast Saccharomyces Cerevisiae. Qiuhui Lin, Hao Qi, Yi Wu and Yingjin Yuan. Scientific Reports 5, Article number: 15249 (2015) doi:10.1038/srep15249
  • SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. Shen,Y., Stracquadanio,G., Wang,Y., Yang,K., Mitchell,L.A., Xue,Y., Cai,Y., Chen,T., Dymond,J.S., Kang,K., et al. Genome Research, 26 36-49 (2015) doi:10.1101/gr.193433.115
  • RADOM, an efficient in vivo method for assembling designed DNA fragments up to 10 kb long in Saccharomyces cerevisiae. Lin Q, Jia B, Mitchell LA, Luo J, Yang K, Zeller KI, Zhang W, Xu Z, Stracquadanio G, Bader JS, Boeke JD, Yuan YJ,.ACS Synth Biol. 4 213-220 (2015) doi:10.1021/sb500241e
  • Rewriting the blueprint of life by synthetic genomics and genome engineering. Annaluru N, Ramalingam S, Chandrasegaran S.Genome Biol. 16 125 (2015) doi:10.1186/s13059-015-0689-y
  • qPCRTag Analysis--A High Throughput, Real Time PCR Assay for Sc2.0 Genotyping. Mitchell LA, Phillips NA, Lafont A, Martin JA, Cutting R, Boeke JD. J. Vis. Exp. e52941. (2015) doi:10.3791/52941

  • Total Synthesis of a Functional Designer Eukaryotic Chromosome. Narayana Annaluru, Héloïse Muller, Leslie A. Mitchell, Sivaprakash Ramalingam, Giovanni Stracquadanio, Sarah M. Richardson, Jessica S. Dymond, Zheng Kuang, Lisa Z. Scheifele, Eric M. Cooper, Yizhi Cai, Karen Zeller, Neta Agmon, Jeffrey S. Han, Michalis Hadjithomas, Jennifer Tullman, Katrina Caravelli, Kimberly Cirelli, Zheyuan Guo, Viktoriya London, Apurva Yeluru, Sindurathy Murugan, Karthikeyan Kandavelou, Nicolas Agier, Gilles Fischer, Kun Yang, J. Andrew Martin, Murat Bilgel, Pavlo Bohutski, Kristin M. Boulier, Brian J. Capaldo, Joy Chang, Kristie Charoen, Woo Jin Choi, Peter Deng, James E. DiCarlo, Judy Doong, Jessilyn Dunn, Jason I. Feinberg, Christopher Fernandez, Charlotte E. Floria, David Gladowski, Pasha Hadidi, Isabel Ishizuka, Javaneh Jabbari, Calvin Y.L. Lau, Pablo A. Lee, Sean Li, Denise Lin, Matthias E. Linder, Jonathan Ling, Jaime Liu, Jonathan Liu, Mariya London, Henry Ma, Jessica Mao, Jessica E. McDade, Alexandra McMillan, Aaron M. Moore, Won Chan Oh, Yu Ouyang, Ruchi Patel, Marina Paul, Laura C. Paulsen, Judy Qiu, Alex Rhee, Matthew G. Rubashkin, Ina Y. Soh, Nathaniel E. Sotuyo, Venkatesh Srinivas, Allison Suarez, Andy Wong, Remus Wong, Wei Rose Xie, Yijie Xu, Allen T. Yu, Romain Koszul, Joel S. Bader, Jef D. Boeke, and Srinivasan Chandrasegaran. Science. 344, 55-58 (2014) doi:10.1126/science.1249252
  • The Sixth International Meeting on Synthetic Biology (SB6. 0). Cai Y, Ellis T. Special Issue Editorial. ACS Synthetic Biology 3: 107-107 (2014) doi:10.1021/sb500085b
  • Total synthesis of a eukaryotic chromosome: Redesigning and SCRaMbLE-ing yeast. Jovicevic D, Blount BA, Ellis T. Bioessays 36 855-60. (2014) doi:10.1002/bies.201400086
  • Circular permutation of a synthetic eukaryotic chromosome with the telomerator. Mitchell LA, Boeke JD. Proc Natl Acad Sci USA. 111 17003-17010 (2014) doi:10.1073/pnas.1414399111

  • The Saccharomyces cerevisiae SCRaMbLE system and genome minimization. Jessica Dymond and Jef Boeke. Bioengineered. 3, 170-173 (2012) doi: 10.4161/bbug.19543
  • The Build-a-Genome course. Cooper EM1, Müller H, Chandrasegaran S, Bader JS, Boeke JD.Methods Mol. Biol. 852 273-283 (2012) doi:10.1007/978-1-61779-564-0_20
  • Assembling large DNA segments in yeast. Muller H, Annaluru N, Schwerzmann JW, Richardson SM, Dymond JS, Cooper EM, Bader JS, Boeke JD, Chandrasegaran S.Methods Mol Biol. 852133-50 (2012) doi:10.1007/978-1-61779-564-0_11
  • Design-A-Gene with GeneDesign. Richardson SM, Liu S, Boeke JD, Bader JS.Methods Mol Biol. 852 235-247 (2012) doi:10.1007/978-1-61779-564-0_18

  • Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Jessica S. Dymond, Sarah M. Richardson, Candice E. Coombes, Timothy Babatz, Héloïse Muller, Narayana Annaluru, William J. Blake, Joy W. Schwerzmann, Junbiao Dai, Derek L. Lindstrom, Annabel C. Boeke, Daniel E. Gottschling, Srinivasan Chandrasegaran, Joel S. Bader and Jef D. Boeke. Nature. 477, 471-476 (2011) doi:10.1038/nature10403

  • GeneDesign 3.0 is an updated synthetic biology toolkit. Richardson SM1, Nunley PW, Yarrington RM, Boeke JD, Bader JS. Nucleic Acids Res. 38 2603-2606 (2010) doi:10.1093/nar/gkq143

  • Teaching synthetic biology, bioinformatics and engineering to undergraduates: the interdisciplinary Build-a-Genome course. Dymond JS, Scheifele LZ, Richardson S, Lee P, Chandrasegaran S, Bader JS, Boeke JD.Genetics 181 13-21 (2009) doi:10.1534/genetics.108.096784

  • GeneDesign: Rapid, automated design of multikilobase synthetic genesSarah M. Richardson, Sarah J. Wheelan, Robert M. Yarrington, and Jef D. Boeke. Genome Research. 16, 550-556 (2006) doi:10.1101/gr.4431306