Difference between revisions of "Smolke:Journal Club"

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#Nishimasu pmid=24529477
#Nishimasu pmid=24529477
#Fossati pmid=24513861
#Fossati pmid=24513861
#Velagapudi pmid=24509821
#Hammerling pmid=24487692
#Hammerling pmid=24487692
#Lienert pmid=24434884
#Lienert pmid=24434884
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==Voting on Papers==  
==Voting on Papers==  
Vote for Mar 17th, 2014
*'''Ding et al''': KT
*'''Nishimasu et al''':
*'''Fossati et al''':
*'''Velagapudi et al''':
*'''Moses et al''': YL, KT
*'''Enquist-Newman et al''': YL
*'''Avendaño et al''':
*'''Bogorad et al''':
*'''Mutalic et al''':
*'''Qi & Arkin et al''':
*'''Ausländer et al''':
Vote for Feb 24th, 2014:
Vote for Feb 24th, 2014:

Revision as of 19:59, 3 March 2014

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2014 Winter

Date Time Location Paper Moderator
27-Jan 1:00 pm 300 Mali et al Jay
24-Feb 1:00 pm 300 Ding et al Maureen
17-Mar 1:00 pm 300

Suggested Future 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. 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]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  13. 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]
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?

Comments on Papers

Voting on Papers

Vote for Mar 17th, 2014

  • Ding et al: KT
  • Nishimasu et al:
  • Fossati et al:
  • Velagapudi et al:
  • Hammerling:
  • Lienert:
  • Moses et al: YL, KT
  • Enquist-Newman et al: YL
  • Avendaño et al:
  • Bogorad et al:
  • Mutalic et al:
  • Qi & Arkin et al:
  • Ausländer et al:

Vote for Feb 24th, 2014:

  • Fossati et al:YL, KYW
  • Carter et al:
  • Moses et al: SG
  • Enquist-Newman et al: YL, KTm YHW
  • Ding et al:MHM, JV, SR, MM
  • Fica et al:
  • Avendaño et al:MHMm, YHW, SR
  • Bogorad et al: KT, SG
  • Paddon & Newman et al:
  • Qi & Arkin et al: JV
  • Li & Liao et al:
  • Ausländer et al: MM

Past Papers

  • Past papers
  1. 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]
  2. 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]
  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. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  13. 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]
  14. 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]
  15. 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]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. 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]
  21. 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]
  22. 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]
  23. 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]
  24. 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]
  25. 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]
  26. 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]
  27. 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]
  28. 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]
  29. 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]
  30. 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]
  31. 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]
  32. 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]
  33. 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]
  34. 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]
  35. 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]
  36. 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]
  37. 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]
  38. 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]
  39. 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]
  40. 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]
  41. 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]
  42. 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]
  43. 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]
  44. 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]
  45. Lam BJ and Joyce GF. Autocatalytic aptazymes enable ligand-dependent exponential amplification of RNA. Nat Biotechnol. 2009 Mar;27(3):288-92. DOI:10.1038/nbt.1528 | PubMed ID:19234448 | HubMed [lam]
  46. Nevozhay D, Adams RM, Murphy KF, Josic K, and Balázsi G. Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression. Proc Natl Acad Sci U S A. 2009 Mar 31;106(13):5123-8. DOI:10.1073/pnas.0809901106 | PubMed ID:19279212 | HubMed [nevozhay]
  47. Imai M, Watanabe T, Hatta M, Das SC, Ozawa M, Shinya K, Zhong G, Hanson A, Katsura H, Watanabe S, Li C, Kawakami E, Yamada S, Kiso M, Suzuki Y, Maher EA, Neumann G, and Kawaoka Y. Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets. Nature. 2012 May 2;486(7403):420-8. DOI:10.1038/nature10831 | PubMed ID:22722205 | HubMed [imai]
  48. Zhang F, Carothers J, Keasling JD. Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nature Biotechnology 2012, doi:10.1038/nbt.2149

All Medline abstracts: PubMed | HubMed

Aged Out

  1. Li GW, Oh E, and Weissman JS. The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature. 2012 Mar 28;484(7395):538-41. DOI:10.1038/nature10965 | PubMed ID:22456704 | HubMed [Li_G]
  2. Low JT, Knoepfel SA, Watts JM, ter Brake O, Berkhout B, and Weeks KM. SHAPE-directed discovery of potent shRNA inhibitors of HIV-1. Mol Ther. 2012 Apr;20(4):820-8. DOI:10.1038/mt.2011.299 | PubMed ID:22314289 | HubMed [Low]
  3. Regot S, Macia J, Conde N, Furukawa K, Kjellén J, Peeters T, Hohmann S, de Nadal E, Posas F, and Solé R. Distributed biological computation with multicellular engineered networks. Nature. 2011 Jan 13;469(7329):207-11. DOI:10.1038/nature09679 | PubMed ID:21150900 | HubMed [regot]
  4. Moss-Racusin CA, Dovidio JF, Brescoll VL, Graham MJ, and Handelsman J. Science faculty's subtle gender biases favor male students. Proc Natl Acad Sci U S A. 2012 Oct 9;109(41):16474-9. DOI:10.1073/pnas.1211286109 | PubMed ID:22988126 | HubMed [Moss-Racusin]
  5. Nevozhay D, Zal T, and Balázsi G. Transferring a synthetic gene circuit from yeast to mammalian cells. Nat Commun. 2013;4:1451. DOI:10.1038/ncomms2471 | PubMed ID:23385595 | HubMed [Nevozhay]
  6. Na D, Yoo SM, Chung H, Park H, Park JH, and Lee SY. Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nat Biotechnol. 2013 Feb;31(2):170-4. DOI:10.1038/nbt.2461 | PubMed ID:23334451 | HubMed [Na]
  7. Pezo V, Louis D, Guérineau V, Le Caer JP, Gaillon L, Mutzel R, and Marlière P. A metabolic prototype for eliminating tryptophan from the genetic code. Sci Rep. 2013;3:1359. DOI:10.1038/srep01359 | PubMed ID:23447021 | HubMed [Pezo]
  8. Berthoumieux S, de Jong H, Baptist G, Pinel C, Ranquet C, Ropers D, and Geiselmann J. Shared control of gene expression in bacteria by transcription factors and global physiology of the cell. Mol Syst Biol. 2013;9:634. DOI:10.1038/msb.2012.70 | PubMed ID:23340840 | HubMed [Berthoumieux]
  9. Hanauer DI, Frederick J, Fotinakes B, and Strobel SA. Linguistic analysis of project ownership for undergraduate research experiences. CBE Life Sci Educ. 2012 Winter;11(4):378-85. DOI:10.1187/cbe.12-04-0043 | PubMed ID:23222833 | HubMed [Hanauer]
  10. Hajdin CE, Bellaousov S, Huggins W, Leonard CW, Mathews DH, and Weeks KM. Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots. Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5498-503. DOI:10.1073/pnas.1219988110 | PubMed ID:23503844 | HubMed [Hajdin]
All Medline abstracts: PubMed | HubMed
  1. Valderrama-Rincon JD, et al. An engineered eukaryotic protein glycosylation pathway in Escherichia coli. Nature Chemical Biology 2012, doi:10.1038/nchembio.921
  2. The arsenic bacteria paper, the 8 technical comments, and the authors' reply.
  3. Shen, Claire R., Lan, Ethan I., Dekishima, Yasumasa, Baez, Antonino, Cho, Kwang Myung, Liao, James C. High titer anaerobic 1-butanol synthesis in Escherichia coli enabled by driving forces. Appl. Environ. Microbiol. 2011 0: AEM.03034-10
  4. Bond-Watts BB, Bellerose RJ and Chang MC. Enzyme mechanism as a kinetic control element for designing synthetic biofuel pathways. Nature Chemical Biology. April 2011. 222-227.
  5. Paige, J.S., et al. RNA Mimics of Green Fluorescent Protein. Science 29 July 2011: 333, 642-646.
  6. Wochner A, Attwater J, Coulson A, Holliger P. Ribozyme-catalyzed transcription of an active ribozyme. Science. 2011 Apr 8;332(6026):209-12.
  7. baker pmid=22194412
  8. Brown ME, Walker MC, Nakashige TG, Iavarone AT, Chang MC. Discovery and characterization of heme enzymes from unsequenced bacteria: Application to microbial lignin degradation. JACS 2011, 133, 18006-18009. dx.doi.org/10.1021/ja203972q
  9. Porter DL, Levine BL, Kalos M, Bagg A, June CH. Chimeric Antigen Receptor-Modified T Cells in Chronic Lymphoid Leukemia. N Engl J Med. 2011 Aug 10.
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