Difference between revisions of "Smolke:Journal Club"

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Revision as of 12:14, 10 June 2014

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2014-2015 Journal Club

Date Time Location Paper Moderator
21-Apr 11:00 am Spilker 143 Enquist-Newman Kate
19-May 11:00 am Spilker 143 Lee&Church Joy
23-Jun 11:00 am Spilker 143 Yanran
Jul Kathy
Aug Isis
Sep Remus
Oct Yen-Hsiang
Nov Melina
Dec Kate
Jan Peter
Feb Maureen
Mar Michale
Apr Ben
May Shireen
Jun Joy

Paper to be discussed

Interesting Papers

  • suggestions with pmid links. Click on an author name to go to the paper OR click on the HubMed link at the bottom of the page to see all abstracts.
  1. Duss O, Michel E, Yulikov M, Schubert M, Jeschke G, and Allain FH. Structural basis of the non-coding RNA RsmZ acting as a protein sponge. Nature. 2014 May 29;509(7502):588-92. DOI:10.1038/nature13271 | PubMed ID:24828038 | HubMed [Duss]
  2. Wang BL, Ghaderi A, Zhou H, Agresti J, Weitz DA, Fink GR, and Stephanopoulos G. Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption. Nat Biotechnol. 2014 May;32(5):473-8. DOI:10.1038/nbt.2857 | PubMed ID:24705516 | HubMed [Wang]
  3. 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, and Chandrasegaran S. Total synthesis of a functional designer eukaryotic chromosome. Science. 2014 Apr 4;344(6179):55-8. DOI:10.1126/science.1249252 | PubMed ID:24674868 | HubMed [Annaluru]
  4. Kotula JW, Kerns SJ, Shaket LA, Siraj L, Collins JJ, Way JC, and Silver PA. Programmable bacteria detect and record an environmental signal in the mammalian gut. Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):4838-43. DOI:10.1073/pnas.1321321111 | PubMed ID:24639514 | HubMed [Kotula]
  5. Birmingham WR, Starbird CA, Panosian TD, Nannemann DP, Iverson TM, and Bachmann BO. Bioretrosynthetic construction of a didanosine biosynthetic pathway. Nat Chem Biol. 2014 May;10(5):392-9. DOI:10.1038/nchembio.1494 | PubMed ID:24657930 | HubMed [Birmingham]
All Medline abstracts: PubMed | HubMed

This last HubMed link seems to work. Click on it to bring up all the abstracts. This should facilitate voting. To add your paper this way, get the pmid from pubmed, and follow the format when editing. The PubMed link doesn't seem to work. Anyone know why?

Past Papers

  • Past papers
  1. Wang X, Lu Z, Gomez A, Hon GC, Yue Y, Han D, Fu Y, Parisien M, Dai Q, Jia G, Ren B, Pan T, and He C. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature. 2014 Jan 2;505(7481):117-20. DOI:10.1038/nature12730 | PubMed ID:24284625 | HubMed [Wang]
  2. Chapman EG, Costantino DA, Rabe JL, Moon SL, Wilusz J, Nix JC, and Kieft JS. The structural basis of pathogenic subgenomic flavivirus RNA (sfRNA) production. Science. 2014 Apr 18;344(6181):307-10. DOI:10.1126/science.1250897 | PubMed ID:24744377 | HubMed [Chapman]
  3. Fica SM, Tuttle N, Novak T, Li NS, Lu J, Koodathingal P, Dai Q, Staley JP, and Piccirilli JA. RNA catalyses nuclear pre-mRNA splicing. Nature. 2013 Nov 14;503(7475):229-34. DOI:10.1038/nature12734 | PubMed ID:24196718 | HubMed [Fica]
  4. Fica SM, Mefford MA, Piccirilli JA, and Staley JP. Evidence for a group II intron-like catalytic triplex in the spliceosome. Nat Struct Mol Biol. 2014 May;21(5):464-471. DOI:10.1038/nsmb.2815 | PubMed ID:24747940 | HubMed [Fica]
  5. Lee K, Cui Y, Lee LP, and Irudayaraj J. Quantitative imaging of single mRNA splice variants in living cells. Nat Nanotechnol. 2014 Jun;9(6):474-80. DOI:10.1038/nnano.2014.73 | PubMed ID:24747838 | HubMed [Lee]
  6. Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, Terry R, Jeanty SS, Li C, Amamoto R, Peters DT, Turczyk BM, Marblestone AH, Inverso SA, Bernard A, Mali P, Rios X, Aach J, and Church GM. Highly multiplexed subcellular RNA sequencing in situ. Science. 2014 Mar 21;343(6177):1360-3. DOI:10.1126/science.1250212 | PubMed ID:24578530 | HubMed [Lee]
  7. Saldaña-Meyer R, González-Buendía E, Guerrero G, Narendra V, Bonasio R, Recillas-Targa F, and Reinberg D. CTCF regulates the human p53 gene through direct interaction with its natural antisense transcript, Wrap53. Genes Dev. 2014 Apr 1;28(7):723-34. DOI:10.1101/gad.236869.113 | PubMed ID:24696455 | HubMed [Saldana-Meyer]
  8. Liu Y, Samuel BS, Breen PC, and Ruvkun G. Caenorhabditis elegans pathways that surveil and defend mitochondria. Nature. 2014 Apr 17;508(7496):406-10. DOI:10.1038/nature13204 | PubMed ID:24695221 | HubMed [Liu]
  9. Cao J, Arha M, Sudrik C, Schaffer DV, and Kane RS. Bidirectional regulation of mRNA translation in mammalian cells by using PUF domains. Angew Chem Int Ed Engl. 2014 May 5;53(19):4900-4. DOI:10.1002/anie.201402095 | PubMed ID:24677733 | HubMed [Cao]
  10. Church GM, Elowitz MB, Smolke CD, Voigt CA, and Weiss R. Realizing the potential of synthetic biology. Nat Rev Mol Cell Biol. 2014 Apr;15(4):289-94. DOI:10.1038/nrm3767 | PubMed ID:24622617 | HubMed [Church]
  11. Karas BJ, Jablanovic J, Irvine E, Sun L, Ma L, Weyman PD, Gibson DG, Glass JI, Venter JC, Hutchison CA 3rd, Smith HO, and Suzuki Y. Transferring whole genomes from bacteria to yeast spheroplasts using entire bacterial cells to reduce DNA shearing. Nat Protoc. 2014 Apr;9(4):743-50. DOI:10.1038/nprot.2014.045 | PubMed ID:24603933 | HubMed [Karas]
  12. Ding Y, Tang Y, Kwok CK, Zhang Y, Bevilacqua PC, and Assmann SM. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature. 2014 Jan 30;505(7485):696-700. DOI:10.1038/nature12756 | PubMed ID:24270811 | HubMed [Ding]
  13. Ding BJ, Hofvander P, Wang HL, Durrett TP, Stymne S, and Löfstedt C. A plant factory for moth pheromone production. Nat Commun. 2014 Feb 25;5:3353. DOI:10.1038/ncomms4353 | PubMed ID:24569486 | HubMed [Ding]
  14. Velagapudi SP, Gallo SM, and Disney MD. Sequence-based design of bioactive small molecules that target precursor microRNAs. Nat Chem Biol. 2014 Apr;10(4):291-7. DOI:10.1038/nchembio.1452 | PubMed ID:24509821 | HubMed [Velagapudi]
  15. Blazeck J, Hill A, Liu L, Knight R, Miller J, Pan A, Otoupal P, and Alper HS. Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production. Nat Commun. 2014;5:3131. DOI:10.1038/ncomms4131 | PubMed ID:24445655 | HubMed [Blazeck]
  16. Avendaño MS, Leidy C, and Pedraza JM. Tuning the range and stability of multiple phenotypic states with coupled positive-negative feedback loops. Nat Commun. 2013;4:2605. DOI:10.1038/ncomms3605 | PubMed ID:24189549 | HubMed [Avendano]
  17. Qi L, Lucks JB, Liu CC, Mutalik VK, and Arkin AP. Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucleic Acids Res. 2012 Jul;40(12):5775-86. DOI:10.1093/nar/gks168 | PubMed ID:22383579 | HubMed [Qi]
  18. Alberts B, Kirschner MW, Tilghman S, and Varmus H. Rescuing US biomedical research from its systemic flaws. Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):5773-7. DOI:10.1073/pnas.1404402111 | PubMed ID:24733905 | HubMed [Alberts]
  19. Creasey KM, Zhai J, Borges F, Van Ex F, Regulski M, Meyers BC, and Martienssen RA. miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis. Nature. 2014 Apr 17;508(7496):411-5. DOI:10.1038/nature13069 | PubMed ID:24670663 | HubMed [Creasey]
  20. Olson EJ, Hartsough LA, Landry BP, Shroff R, and Tabor JJ. Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals. Nat Methods. 2014 Apr;11(4):449-55. DOI:10.1038/nmeth.2884 | PubMed ID:24608181 | HubMed [Olson]
  21. Fossati E, Ekins A, Narcross L, Zhu Y, Falgueyret JP, Beaudoin GA, Facchini PJ, and Martin VJ. Reconstitution of a 10-gene pathway for synthesis of the plant alkaloid dihydrosanguinarine in Saccharomyces cerevisiae. Nat Commun. 2014;5:3283. DOI:10.1038/ncomms4283 | PubMed ID:24513861 | HubMed [Fossati]
  22. Lienert F, Lohmueller JJ, Garg A, and Silver PA. Synthetic biology in mammalian cells: next generation research tools and therapeutics. Nat Rev Mol Cell Biol. 2014 Feb;15(2):95-107. DOI:10.1038/nrm3738 | PubMed ID:24434884 | HubMed [Lienert]
  23. Enquist-Newman M, Faust AM, Bravo DD, Santos CN, Raisner RM, Hanel A, Sarvabhowman P, Le C, Regitsky DD, Cooper SR, Peereboom L, Clark A, Martinez Y, Goldsmith J, Cho MY, Donohoue PD, Luo L, Lamberson B, Tamrakar P, Kim EJ, Villari JL, Gill A, Tripathi SA, Karamchedu P, Paredes CJ, Rajgarhia V, Kotlar HK, Bailey RB, Miller DJ, Ohler NL, Swimmer C, and Yoshikuni Y. Efficient ethanol production from brown macroalgae sugars by a synthetic yeast platform. Nature. 2014 Jan 9;505(7482):239-43. DOI:10.1038/nature12771 | PubMed ID:24291791 | HubMed [Enquist-Newman]
  24. Bogorad IW, Lin TS, and Liao JC. Synthetic non-oxidative glycolysis enables complete carbon conservation. Nature. 2013 Oct 31;502(7473):693-7. DOI:10.1038/nature12575 | PubMed ID:24077099 | HubMed [Bogorad]
  25. Ausländer S, Ausländer D, Müller M, Wieland M, and Fussenegger M. Programmable single-cell mammalian biocomputers. Nature. 2012 Jul 5;487(7405):123-7. DOI:10.1038/nature11149 | PubMed ID:22722847 | HubMed [Auslander]
  26. Matthews ML, Chang WC, Layne AP, Miles LA, Krebs C, and Bollinger JM Jr. Direct nitration and azidation of aliphatic carbons by an iron-dependent halogenase. Nat Chem Biol. 2014 Mar;10(3):209-15. DOI:10.1038/nchembio.1438 | PubMed ID:24463698 | HubMed [Matthews]
  27. Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, and Nureki O. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell. 2014 Feb 27;156(5):935-49. DOI:10.1016/j.cell.2014.02.001 | PubMed ID:24529477 | HubMed [Nishimasu]
  28. Hammerling MJ, Ellefson JW, Boutz DR, Marcotte EM, Ellington AD, and Barrick JE. Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness. Nat Chem Biol. 2014 Mar;10(3):178-80. DOI:10.1038/nchembio.1450 | PubMed ID:24487692 | HubMed [Hammerling]
  29. Moses T, Pollier J, Almagro L, Buyst D, Van Montagu M, Pedreño MA, Martins JC, Thevelein JM, and Goossens A. Combinatorial biosynthesis of sapogenins and saponins in Saccharomyces cerevisiae using a C-16α hydroxylase from Bupleurum falcatum. Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):1634-9. DOI:10.1073/pnas.1323369111 | PubMed ID:24434554 | HubMed [Moses]
  30. Mutalik VK, Qi L, Guimaraes JC, Lucks JB, and Arkin AP. Rationally designed families of orthogonal RNA regulators of translation. Nat Chem Biol. 2012 Mar 25;8(5):447-54. DOI:10.1038/nchembio.919 | PubMed ID:22446835 | HubMed [Mutalik]
  31. Carter GT. NP/MS since 1970: from the basement to the bench top. Nat Prod Rep. 2014 Jun;31(6):711-7. DOI:10.1039/c3np70085b | PubMed ID:24468674 | HubMed [Carter]
  32. Li H, Opgenorth PH, Wernick DG, Rogers S, Wu TY, Higashide W, Malati P, Huo YX, Cho KM, and Liao JC. Integrated electromicrobial conversion of CO2 to higher alcohols. Science. 2012 Mar 30;335(6076):1596. DOI:10.1126/science.1217643 | PubMed ID:22461604 | HubMed [Li_H]
  33. Paddon CJ, Westfall PJ, Pitera DJ, Benjamin K, Fisher K, McPhee D, Leavell MD, Tai A, Main A, Eng D, Polichuk DR, Teoh KH, Reed DW, Treynor T, Lenihan J, Fleck M, Bajad S, Dang G, Dengrove D, Diola D, Dorin G, Ellens KW, Fickes S, Galazzo J, Gaucher SP, Geistlinger T, Henry R, Hepp M, Horning T, Iqbal T, Jiang H, Kizer L, Lieu B, Melis D, Moss N, Regentin R, Secrest S, Tsuruta H, Vazquez R, Westblade LF, Xu L, Yu M, Zhang Y, Zhao L, Lievense J, Covello PS, Keasling JD, Reiling KK, Renninger NS, and Newman JD. High-level semi-synthetic production of the potent antimalarial artemisinin. Nature. 2013 Apr 25;496(7446):528-32. DOI:10.1038/nature12051 | PubMed ID:23575629 | HubMed [Paddon]
  34. Sandoval NR, Kim JY, Glebes TY, Reeder PJ, Aucoin HR, Warner JR, and Gill RT. Strategy for directing combinatorial genome engineering in Escherichia coli. Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):10540-5. DOI:10.1073/pnas.1206299109 | PubMed ID:22689973 | HubMed [sandoval]
  35. Douglas SM, Bachelet I, and Church GM. A logic-gated nanorobot for targeted transport of molecular payloads. Science. 2012 Feb 17;335(6070):831-4. DOI:10.1126/science.1214081 | PubMed ID:22344439 | HubMed [douglas]
  36. Fu J, Bian X, Hu S, Wang H, Huang F, Seibert PM, Plaza A, Xia L, Müller R, Stewart AF, and Zhang Y. Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting. Nat Biotechnol. 2012 May;30(5):440-6. DOI:10.1038/nbt.2183 | PubMed ID:22544021 | HubMed [fu]
  37. Paige JS, Wu KY, and Jaffrey SR. RNA mimics of green fluorescent protein. Science. 2011 Jul 29;333(6042):642-6. DOI:10.1126/science.1207339 | PubMed ID:21798953 | HubMed [paige]
  38. Paige JS, Nguyen-Duc T, Song W, and Jaffrey SR. Fluorescence imaging of cellular metabolites with RNA. Science. 2012 Mar 9;335(6073):1194. DOI:10.1126/science.1218298 | PubMed ID:22403384 | HubMed [paige]
  39. Pinheiro VB, Taylor AI, Cozens C, Abramov M, Renders M, Zhang S, Chaput JC, Wengel J, Peak-Chew SY, McLaughlin SH, Herdewijn P, and Holliger P. Synthetic genetic polymers capable of heredity and evolution. Science. 2012 Apr 20;336(6079):341-4. DOI:10.1126/science.1217622 | PubMed ID:22517858 | HubMed [pinheiro]
  40. Sharon E, Kalma Y, Sharp A, Raveh-Sadka T, Levo M, Zeevi D, Keren L, Yakhini Z, Weinberger A, and Segal E. Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters. Nat Biotechnol. 2012 May 20;30(6):521-30. DOI:10.1038/nbt.2205 | PubMed ID:22609971 | HubMed [sharon]
  41. Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B Jr, Assad-Garcia N, Glass JI, and Covert MW. A whole-cell computational model predicts phenotype from genotype. Cell. 2012 Jul 20;150(2):389-401. DOI:10.1016/j.cell.2012.05.044 | PubMed ID:22817898 | HubMed [karr]
  42. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, and Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012 Aug 17;337(6096):816-21. DOI:10.1126/science.1225829 | PubMed ID:22745249 | HubMed [jinek]
  43. Qi L, Haurwitz RE, Shao W, Doudna JA, and Arkin AP. RNA processing enables predictable programming of gene expression. Nat Biotechnol. 2012 Oct;30(10):1002-6. DOI:10.1038/nbt.2355 | PubMed ID:22983090 | HubMed [qi]
  44. Choi YJ and Lee SY. Microbial production of short-chain alkanes. Nature. 2013 Oct 24;502(7472):571-4. DOI:10.1038/nature12536 | PubMed ID:24077097 | HubMed [Choi]
  45. Salmena L, Poliseno L, Tay Y, Kats L, and Pandolfi PP. A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?. Cell. 2011 Aug 5;146(3):353-8. DOI:10.1016/j.cell.2011.07.014 | PubMed ID:21802130 | HubMed [salmena]
  46. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, and Zhang F. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013 Feb 15;339(6121):819-23. DOI:10.1126/science.1231143 | PubMed ID:23287718 | HubMed [Cong]
  47. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, and Church GM. RNA-guided human genome engineering via Cas9. Science. 2013 Feb 15;339(6121):823-6. DOI:10.1126/science.1232033 | PubMed ID:23287722 | HubMed [Mali]
  48. Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, Peterson RT, Yeh JR, and Joung JK. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol. 2013 Mar;31(3):227-9. DOI:10.1038/nbt.2501 | PubMed ID:23360964 | HubMed [Hwang]
  49. Jiang W, Bikard D, Cox D, Zhang F, and Marraffini LA. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol. 2013 Mar;31(3):233-9. DOI:10.1038/nbt.2508 | PubMed ID:23360965 | HubMed [Jiang]
  50. Cho SW, Kim S, Kim JM, and Kim JS. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol. 2013 Mar;31(3):230-2. DOI:10.1038/nbt.2507 | PubMed ID:23360966 | HubMed [Cho]
  51. Coelho PS, Brustad EM, Kannan A, and Arnold FH. Olefin cyclopropanation via carbene transfer catalyzed by engineered cytochrome P450 enzymes. Science. 2013 Jan 18;339(6117):307-10. DOI:10.1126/science.1231434 | PubMed ID:23258409 | HubMed [Coelho]
  52. Spitale RC, Crisalli P, Flynn RA, Torre EA, Kool ET, and Chang HY. RNA SHAPE analysis in living cells. Nat Chem Biol. 2013 Jan;9(1):18-20. DOI:10.1038/nchembio.1131 | PubMed ID:23178934 | HubMed [Spitale]
  53. Frieda KL and Block SM. Direct observation of cotranscriptional folding in an adenine riboswitch. Science. 2012 Oct 19;338(6105):397-400. DOI:10.1126/science.1225722 | PubMed ID:23087247 | HubMed [block]
  54. Wargacki AJ, Leonard E, Win MN, Regitsky DD, Santos CN, Kim PB, Cooper SR, Raisner RM, Herman A, Sivitz AB, Lakshmanaswamy A, Kashiyama Y, Baker D, and Yoshikuni Y. An engineered microbial platform for direct biofuel production from brown macroalgae. Science. 2012 Jan 20;335(6066):308-13. DOI:10.1126/science.1214547 | PubMed ID:22267807 | HubMed [wargacki]
  55. Bonacci W, Teng PK, Afonso B, Niederholtmeyer H, Grob P, Silver PA, and Savage DF. Modularity of a carbon-fixing protein organelle. Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):478-83. DOI:10.1073/pnas.1108557109 | PubMed ID:22184212 | HubMed [bonacci]
  56. Carothers JM, Goler JA, Juminaga D, and Keasling JD. Model-driven engineering of RNA devices to quantitatively program gene expression. Science. 2011 Dec 23;334(6063):1716-9. DOI:10.1126/science.1212209 | PubMed ID:22194579 | HubMed [carothers]
  57. Conrado RJ, Wu GC, Boock JT, Xu H, Chen SY, Lebar T, Turnšek J, Tomšič N, Avbelj M, Gaber R, Koprivnjak T, Mori J, Glavnik V, Vovk I, Benčina M, Hodnik V, Anderluh G, Dueber JE, Jerala R, and DeLisa MP. DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency. Nucleic Acids Res. 2012 Feb;40(4):1879-89. DOI:10.1093/nar/gkr888 | PubMed ID:22021385 | HubMed [conrado]
  58. Dellomonaco C, Clomburg JM, Miller EN, and Gonzalez R. Engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals. Nature. 2011 Aug 10;476(7360):355-9. DOI:10.1038/nature10333 | PubMed ID:21832992 | HubMed [dellomonaco]
  59. Dymond JS, Richardson SM, Coombes CE, Babatz T, Muller H, Annaluru N, Blake WJ, Schwerzmann JW, Dai J, Lindstrom DL, Boeke AC, Gottschling DE, Chandrasegaran S, Bader JS, and Boeke JD. Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature. 2011 Sep 14;477(7365):471-6. DOI:10.1038/nature10403 | PubMed ID:21918511 | HubMed [dymond]
  60. Xie Z, Liu SJ, Bleris L, and Benenson Y. Logic integration of mRNA signals by an RNAi-based molecular computer. Nucleic Acids Res. 2010 May;38(8):2692-701. DOI:10.1093/nar/gkq117 | PubMed ID:20194121 | HubMed [xie]
  61. Leisner M, Bleris L, Lohmueller J, Xie Z, and Benenson Y. Rationally designed logic integration of regulatory signals in mammalian cells. Nat Nanotechnol. 2010 Sep;5(9):666-70. DOI:10.1038/nnano.2010.135 | PubMed ID:20622866 | HubMed [leisner]
  62. Saito H, Fujita Y, Kashida S, Hayashi K, and Inoue T. Synthetic human cell fate regulation by protein-driven RNA switches. Nat Commun. 2011 Jan 18;2:160. DOI:10.1038/ncomms1157 | PubMed ID:21245841 | HubMed [saito]
  63. Yim H, Haselbeck R, Niu W, Pujol-Baxley C, Burgard A, Boldt J, Khandurina J, Trawick JD, Osterhout RE, Stephen R, Estadilla J, Teisan S, Schreyer HB, Andrae S, Yang TH, Lee SY, Burk MJ, and Van Dien S. Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nat Chem Biol. 2011 May 22;7(7):445-52. DOI:10.1038/nchembio.580 | PubMed ID:21602812 | HubMed [yim]
  64. Esvelt KM, Carlson JC, and Liu DR. A system for the continuous directed evolution of biomolecules. Nature. 2011 Apr 28;472(7344):499-503. DOI:10.1038/nature09929 | PubMed ID:21478873 | HubMed [esvelt]
  65. Schirmer A, Rude MA, Li X, Popova E, and del Cardayre SB. Microbial biosynthesis of alkanes. Science. 2010 Jul 30;329(5991):559-62. DOI:10.1126/science.1187936 | PubMed ID:20671186 | HubMed [schirmer]
  66. Sinha J, Reyes SJ, and Gallivan JP. Reprogramming bacteria to seek and destroy an herbicide. Nat Chem Biol. 2010 Jun;6(6):464-70. DOI:10.1038/nchembio.369 | PubMed ID:20453864 | HubMed [sinha]
  67. Neumann H, Wang K, Davis L, Garcia-Alai M, and Chin JW. Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome. Nature. 2010 Mar 18;464(7287):441-4. DOI:10.1038/nature08817 | PubMed ID:20154731 | HubMed [neumann]
  68. Drinnenberg IA, Weinberg DE, Xie KT, Mower JP, Wolfe KH, Fink GR, and Bartel DP. RNAi in budding yeast. Science. 2009 Oct 23;326(5952):544-550. DOI:10.1126/science.1176945 | PubMed ID:19745116 | HubMed [drinnenberg]
  69. Dueber JE, Wu GC, Malmirchegini GR, Moon TS, Petzold CJ, Ullal AV, Prather KL, and Keasling JD. Synthetic protein scaffolds provide modular control over metabolic flux. Nat Biotechnol. 2009 Aug;27(8):753-9. DOI:10.1038/nbt.1557 | PubMed ID:19648908 | HubMed [dueber]
  70. Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, and Church GM. Programming cells by multiplex genome engineering and accelerated evolution. Nature. 2009 Aug 13;460(7257):894-898. DOI:10.1038/nature08187 | PubMed ID:19633652 | HubMed [wang]
  71. Yu RC, Pesce CG, Colman-Lerner A, Lok L, Pincus D, Serra E, Holl M, Benjamin K, Gordon A, and Brent R. Negative feedback that improves information transmission in yeast signalling. Nature. 2008 Dec 11;456(7223):755-61. DOI:10.1038/nature07513 | PubMed ID:19079053 | HubMed [yu]
  72. Lincoln TA and Joyce GF. Self-sustained replication of an RNA enzyme. Science. 2009 Feb 27;323(5918):1229-32. DOI:10.1126/science.1167856 | PubMed ID:19131595 | HubMed [lincoln]
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