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Items: 18

1.

Design of a synthetic yeast genome.

Richardson SM, Mitchell LA, Stracquadanio G, Yang K, Dymond JS, DiCarlo JE, Lee D, Huang CL, Chandrasegaran S, Cai Y, Boeke JD, Bader JS.

Science. 2017 Mar 10;355(6329):1040-1044. doi: 10.1126/science.aaf4557.

PMID:
28280199
2.

Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond.

Mitchell LA, Wang A, Stracquadanio G, Kuang Z, Wang X, Yang K, Richardson S, Martin JA, Zhao Y, Walker R, Luo Y, Dai H, Dong K, Tang Z, Yang Y, Cai Y, Heguy A, Ueberheide B, Fenyö D, Dai J, Bader JS, Boeke JD.

Science. 2017 Mar 10;355(6329). pii: eaaf4831. doi: 10.1126/science.aaf4831.

PMID:
28280154
3.

Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome.

Shen Y, Wang Y, Chen T, Gao F, Gong J, Abramczyk D, Walker R, Zhao H, Chen S, Liu W, Luo Y, Müller CA, Paul-Dubois-Taine A, Alver B, Stracquadanio G, Mitchell LA, Luo Z, Fan Y, Zhou B, Wen B, Tan F, Wang Y, Zi J, Xie Z, Li B, Yang K, Richardson SM, Jiang H, French CE, Nieduszynski CA, Koszul R, Marston AL, Yuan Y, Wang J, Bader JS, Dai J, Boeke JD, Xu X, Cai Y, Yang H.

Science. 2017 Mar 10;355(6329). pii: eaaf4791. doi: 10.1126/science.aaf4791.

4.

Bug mapping and fitness testing of chemically synthesized chromosome X.

Wu Y, Li BZ, Zhao M, Mitchell LA, Xie ZX, Lin QH, Wang X, Xiao WH, Wang Y, Zhou X, Liu H, Li X, Ding MZ, Liu D, Zhang L, Liu BL, Wu XL, Li FF, Dong XT, Jia B, Zhang WZ, Jiang GZ, Liu Y, Bai X, Song TQ, Chen Y, Zhou SJ, Zhu RY, Gao F, Kuang Z, Wang X, Shen M, Yang K, Stracquadanio G, Richardson SM, Lin Y, Wang L, Walker R, Luo Y, Ma PS, Yang H, Cai Y, Dai J, Bader JS, Boeke JD, Yuan YJ.

Science. 2017 Mar 10;355(6329). pii: eaaf4706. doi: 10.1126/science.aaf4706.

5.

"Perfect" designer chromosome V and behavior of a ring derivative.

Xie ZX, Li BZ, Mitchell LA, Wu Y, Qi X, Jin Z, Jia B, Wang X, Zeng BX, Liu HM, Wu XL, Feng Q, Zhang WZ, Liu W, Ding MZ, Li X, Zhao GR, Qiao JJ, Cheng JS, Zhao M, Kuang Z, Wang X, Martin JA, Stracquadanio G, Yang K, Bai X, Zhao J, Hu ML, Lin QH, Zhang WQ, Shen MH, Chen S, Su W, Wang EX, Guo R, Zhai F, Guo XJ, Du HX, Zhu JQ, Song TQ, Dai JJ, Li FF, Jiang GZ, Han SL, Liu SY, Yu ZC, Yang XN, Chen K, Hu C, Li DS, Jia N, Liu Y, Wang LT, Wang S, Wei XT, Fu MQ, Qu LM, Xin SY, Liu T, Tian KR, Li XN, Zhang JH, Song LX, Liu JG, Lv JF, Xu H, Tao R, Wang Y, Zhang TT, Deng YX, Wang YR, Li T, Ye GX, Xu XR, Xia ZB, Zhang W, Yang SL, Liu YL, Ding WQ, Liu ZN, Zhu JQ, Liu NZ, Walker R, Luo Y, Wang Y, Shen Y, Yang H, Cai Y, Ma PS, Zhang CT, Bader JS, Boeke JD, Yuan YJ.

Science. 2017 Mar 10;355(6329). pii: eaaf4704. doi: 10.1126/science.aaf4704.

PMID:
28280151
6.

Low escape-rate genome safeguards with minimal molecular perturbation of Saccharomyces cerevisiae.

Agmon N, Tang Z, Yang K, Sutter B, Ikushima S, Cai Y, Caravelli K, Martin JA, Sun X, Choi WJ, Zhang A, Stracquadanio G, Hao H, Tu BP, Fenyo D, Bader JS, Boeke JD.

Proc Natl Acad Sci U S A. 2017 Feb 21;114(8):E1470-E1479. doi: 10.1073/pnas.1621250114. Epub 2017 Feb 7.

7.

BioPartsDB: a synthetic biology workflow web-application for education and research.

Stracquadanio G, Yang K, Boeke JD, Bader JS.

Bioinformatics. 2016 Nov 15;32(22):3519-3521. Epub 2016 Jul 13.

8.

CD44 SNPrs187115: A Novel Biomarker Signature that Predicts Survival in Resectable Pancreatic Ductal Adenocarcinoma.

Stracquadanio G, Vrugt B, Flury R, Schraml P, Würl P, Müller TH, Knippschild U, Henne-Bruns D, Breitenstein S, Clavien PA, Graf R, Bond GL, Grochola LF.

Clin Cancer Res. 2016 Dec 15;22(24):6069-6077. Epub 2016 Jun 9.

9.

The importance of p53 pathway genetics in inherited and somatic cancer genomes.

Stracquadanio G, Wang X, Wallace MD, Grawenda AM, Zhang P, Hewitt J, Zeron-Medina J, Castro-Giner F, Tomlinson IP, Goding CR, Cygan KJ, Fairbrother WG, Thomas LF, Sætrom P, Gemignani F, Landi S, Schuster-Böckler B, Bell DA, Bond GL.

Nat Rev Cancer. 2016 Apr;16(4):251-65. doi: 10.1038/nrc.2016.15. Review.

PMID:
27009395
10.

BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts.

Yang K, Stracquadanio G, Luo J, Boeke JD, Bader JS.

Bioinformatics. 2016 Mar 15;32(6):937-9. doi: 10.1093/bioinformatics/btv664. Epub 2015 Nov 14.

11.

SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes.

Shen Y, Stracquadanio G, Wang Y, Yang K, Mitchell LA, Xue Y, Cai Y, Chen T, Dymond JS, Kang K, Gong J, Zeng X, Zhang Y, Li Y, Feng Q, Xu X, Wang J, Wang J, Yang H, Boeke JD, Bader JS.

Genome Res. 2016 Jan;26(1):36-49. doi: 10.1101/gr.193433.115. Epub 2015 Nov 13.

12.

Yeast Golden Gate (yGG) for the Efficient Assembly of S. cerevisiae Transcription Units.

Agmon N, Mitchell LA, Cai Y, Ikushima S, Chuang J, Zheng A, Choi WJ, Martin JA, Caravelli K, Stracquadanio G, Boeke JD.

ACS Synth Biol. 2015 Jul 17;4(7):853-9. doi: 10.1021/sb500372z. Epub 2015 Mar 23.

PMID:
25756291
13.

Intrinsic biocontainment: multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes.

Cai Y, Agmon N, Choi WJ, Ubide A, Stracquadanio G, Caravelli K, Hao H, Bader JS, Boeke JD.

Proc Natl Acad Sci U S A. 2015 Feb 10;112(6):1803-8. doi: 10.1073/pnas.1424704112. Epub 2015 Jan 26.

14.

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. 2015 Mar 20;4(3):213-20. doi: 10.1021/sb500241e. Epub 2014 Jun 4.

PMID:
24895839
15.

Total synthesis of a functional designer eukaryotic chromosome.

Annaluru N, Muller H, Mitchell LA, Ramalingam S, Stracquadanio G, Richardson SM, Dymond JS, Kuang Z, Scheifele LZ, Cooper EM, Cai Y, Zeller K, Agmon N, Han JS, Hadjithomas M, Tullman J, Caravelli K, Cirelli K, Guo Z, London V, Yeluru A, Murugan S, Kandavelou K, Agier N, Fischer G, Yang K, Martin JA, Bilgel M, Bohutski P, Boulier KM, Capaldo BJ, Chang J, Charoen K, Choi WJ, Deng P, DiCarlo JE, Doong J, Dunn J, Feinberg JI, Fernandez C, Floria CE, Gladowski D, Hadidi P, Ishizuka I, Jabbari J, Lau CY, Lee PA, Li S, Lin D, Linder ME, Ling J, Liu J, Liu J, London M, Ma H, Mao J, McDade JE, McMillan A, Moore AM, Oh WC, Ouyang Y, Patel R, Paul M, Paulsen LC, Qiu J, Rhee A, Rubashkin MG, Soh IY, Sotuyo NE, Srinivas V, Suarez A, Wong A, Wong R, Xie WR, Xu Y, Yu AT, Koszul R, Bader JS, Boeke JD, Chandrasegaran S.

Science. 2014 Apr 4;344(6179):55-8. doi: 10.1126/science.1249252. Epub 2014 Mar 27. Erratum in: Science. 2014 May 23;344(6186):816.

16.

Efficient behavior of photosynthetic organelles via Pareto optimality, identifiability, and sensitivity analysis.

Carapezza G, Umeton R, Costanza J, Angione C, Stracquadanio G, Papini A, Lió P, Nicosia G.

ACS Synth Biol. 2013 May 17;2(5):274-88. doi: 10.1021/sb300102k. Epub 2013 Jan 24.

PMID:
23654280
17.

Identification of sensitive enzymes in the photosynthetic carbon metabolism.

Umeton R, Stracquadanio G, Papini A, Costanza J, Liò P, Nicosia G.

Adv Exp Med Biol. 2012;736:441-59. doi: 10.1007/978-1-4419-7210-1_26.

PMID:
22161345
18.

Generalized pattern search algorithm for Peptide structure prediction.

Nicosia G, Stracquadanio G.

Biophys J. 2008 Nov 15;95(10):4988-99. doi: 10.1529/biophysj.107.124016. Epub 2008 May 16.

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