Smolke:Journal Club

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(Voting on Papers)
(Voting on Papers)
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*'''Paige et al. and Paige et. al.''':
*'''Paige et al. and Paige et. al.''':
*'''Douglas et al.''':
*'''Douglas et al.''':
*'''Mutalik et al. and Qi et al.''':
*'''Mutalik et al. and Qi et al.''': Yen-Hsiang
*'''G. Li et al.''':
*'''G. Li et al.''':
*'''H. Li et al.''':  
*'''H. Li et al.''':  
*'''Fu et al.''':
*'''Fu et al.''':
*'''Pinheiro et al.''':
*'''Pinheiro et al.''':
*'''uslander S, et al.''': Yen-Hsiang
*'''Auslander S, et al.''': Yen-Hsiang
==Past Papers==
==Past Papers==

Revision as of 16:24, 27 August 2012

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Next Meeting

  • When: 1pm 9/6/12
  • Where: TBD
  • Paper: TBD
  • Moderator: TBD

Suggested Future Papers

Feel free to use PMID for new paper suggestions

  • Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature. 2010 Jun 24;465(7301):1033-8.
  • Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP. A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language? Cell. 2011 Jul 27
  • Wargacki AJ, et al. An Engineered Microbial Platform for Direct Biofuel Production from Brown Macroalgae. Science. 2012 Jan 20;335(6066):308-13.
  • Mutalik VK, et al. Rationally designed families of orthogonal RNA regulators of translation. Nature Chemical Biology 2012, doi:10.1038/NChemBio.919
  • Qi L, et al. Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucl. Acids Res. (2012) doi: 10.1093/nar/gks168
  • Li G, et al. The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature, doi:10.1038/nature10965
  • Li H, et al. Integrated Electromicrobial Conversion of CO2 to Higher Alcohols. Science 30 March 2012: Vol. 335 no. 6076 p. 1596 DOI: 10.1126/science.1217643
  • Low JT, Knoepfel SA, Watts JM, Ter Brake O, Berkhout B, Weeks KM. SHAPE-directed Discovery of Potent shRNA Inhibitors of HIV-1. Mol Ther. 2012 Feb 7 (pmid=22314289)
  • Auslander S, et al. Programmable single-cell mammalian biocomputers. 2012 Nature.
  • Sandoval NR, et al. Strategy for directing combinatorial genome engineering in E. coli. PNAS 2012 109(26):10540-5. PMID: 22689973
Error fetching PMID 21798953:
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  1. Error fetching PMID 21798953: [paige]
  2. Error fetching PMID 22403384: [paige]
  3. Error fetching PMID 22344439: [douglas]
  4. Error fetching PMID 22544021: [fu]
  5. Error fetching PMID 22517858: [pinheiro]
  6. Error fetching PMID 22609971: [sharon]
All Medline abstracts: PubMed HubMed

Comments on Papers

Voting on Papers

  • Poliseno et al. and Salmena et al:
  • Wargacki et al.:
  • Paige et al. and Paige et. al.:
  • Douglas et al.:
  • Mutalik et al. and Qi et al.: Yen-Hsiang
  • G. Li et al.:
  • H. Li et al.:
  • Fu et al.:
  • Pinheiro et al.:
  • Auslander S, et al.: Yen-Hsiang

Past Papers

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  1. 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 [sensor]
  2. Error fetching PMID 22184212: [bonacci]
  3. Error fetching PMID 22194579: [carothers]
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  6. Error fetching PMID 21918511: [dymond]
  7. Error fetching PMID 20194121: [xie]
  8. Error fetching PMID 20622866: [leisner]
  9. Error fetching PMID 21245841: [saito]
  10. Error fetching PMID 21602812: [yim]
  11. Error fetching PMID 21478873: [esvelt]
  12. Error fetching PMID 20671186: [schirmer]
  13. Error fetching PMID 20453864: [sinha]
  14. Error fetching PMID 20154731: [neumann]
  15. Error fetching PMID 19745116: [drinnenberg]
  16. Error fetching PMID 19648908: [dueber]
  17. Error fetching PMID 19633652: [wang]
  18. Error fetching PMID 19079053: [yu]
  19. Error fetching PMID 19131595: [lincoln]
  20. Error fetching PMID 19234448: [lam]
  21. Error fetching PMID 19279212: [nevozhay]
  22. Error fetching PMID 22722205: [imai]
All Medline abstracts: PubMed HubMed

Aged Out

  • Valderrama-Rincon JD, et al. An engineered eukaryotic protein glycosylation pathway in Escherichia coli. Nature Chemical Biology 2012, doi:10.1038/nchembio.921
  • The arsenic bacteria paper, the 8 technical comments, and the authors' reply.
  1. 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
  2. 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.
  3. Paige, J.S., et al. RNA Mimics of Green Fluorescent Protein. Science 29 July 2011: 333, 642-646.
  4. Wochner A, Attwater J, Coulson A, Holliger P. Ribozyme-catalyzed transcription of an active ribozyme. Science. 2011 Apr 8;332(6026):209-12.
  5. baker pmid=22194412
  6. 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.
  7. 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.
  8. Milias-Argeitis A, Summers S, Stewart-Ornstein J, Zuleta I, Pincus D, El-Samad H, Khammash M, Lygeros J. In silico feedback for in vivo regulation of a gene expression circuit. Nature Biotechnology. November 2011.
  9. Schwanhäusser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M. Global quantification of mammalian gene expression control. Nature. 2011 May 19;473(7347):337-42.
  10. Isaacs, F.J., et al. Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement. Science 15 July 2011: 333 (6040), 348-353.
  11. Huo YX, Cho KM, Rivera JG, Monte E, Shen CR, Yan Y, Liao JC. Conversion of proteins into biofuels by engineering nitrogen flux. Nat Biotechnol. 2011 Mar 6.
  12. Gevorg Grigorya, Yong Ho Kim, Rudresh Acharya, Kevin Axelrod, Rishabh M. Jain, Lauren Willis, Marija Drndic, James M. Kikkawa, William F. DeGrado. Computational Design of Virus-Like Protein Assemblies on Carbon Nanotube Surfaces. Science 332, 1071 (2011);DOI: 10.1126/science.1198841
  13. Fisher MA, McKinley KL, Bradley LH, Viola SR, Hecht MH. De novo designed proteins from a library of artificial sequences function in Escherichia coli and enable cell growth. PLoS One. 2011 Jan 4; 6(1). PMID: 21245923
  14. Marlière P, Patrouix J, Döring V, Herdewijn P, Tricot S, Cruveiller S, Bouzon M, Mutzel R. Chemical Evolution of a Bacterium's Genome. Angew Chem Int Ed Engl. 2011 Jun 27. doi: 10.1002/anie.201100535.
  15. Greiss S, and Chin JW. Expanding the Genetic Code of an Animal. J Am Chem Soc. 2011 Aug 8
  16. Poelwijk FJ, de Vos MG, Tans SJ. Tradeoffs and Optimality in the Evolution of Gene Regulation. Cell, 5 August 2011
  17. Wang, H, Claveau, D, Vaillancourt, JP, Roemer, T, Meredith, TC. High-frequency transposition for determining antibacterial mode of action. Nat Chem Biol. 2011 Sept 04. doi:10.1038/nchembio.643
  18. Leonard E, Ajikumar PK, Thayer K, Xiao WH, Mo JD, Tidor B, et al. Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control. Proc Natl Acad Sci U S A.107(31):13654-9. PMCID: 2922259.
  19. Matzas M, Stahler PF, Kefer N, Siebelt N, Boisguerin V, Leonard JT, et al. High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing. Nat Biotechnol.28(12):1291-4.
  20. Kosuri S, Eroshenko N, Leproust EM, Super M, Way J, Li JB, et al. Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips. Nat Biotechnol.28(12):1295-9.
  21. Peter Y Watson and Martha J Fedor. The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo. Nature Structural & Molecular Biology March 2011: 18 (3), 359-363.
  22. Lartigue C, Vashee S, Algire MA, Chuang RY, Benders GA, Ma L, et al. Creating bacterial strains from genomes that have been cloned and engineered in yeast. Science. 2009;325(5948):1693-6.
  23. Iliopoulos D, Hirsch HA, Struhl K. An epigenetic switch involving NF-kappaB, Lin28, Let-7 MicroRNA, and IL6 links inflammation to cell transformation. Cell. 2009;139(4):693-706. PMCID: 2783826.
  24. Agresti JJ, Antipov E, Abate AR, Ahn K, Rowat AC, Baret JC, et al. Ultrahigh-throughput screening in drop-based microfluidics for directed evolution. Proc Natl Acad Sci U S A.107(9):4004-9. PMCID: 2840095.
  25. Verhounig A, Karcher D, Bock R. Inducible gene expression from the plastid genome by a synthetic riboswitch. Proc Natl Acad Sci U S A.107(14):6204-9. PMCID: 2852001.
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  2. Error fetching PMID 19666472: [antonczak]
  3. Error fetching PMID 20175178: [zhou]
  4. Error fetching PMID 20185727: [to]
  5. Error fetching PMID 19265475: [jones]
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  9. Error fetching PMID 19478183: [friedland]
  10. Error fetching PMID 19536156: [mitchell]
  11. Error fetching PMID 19359587: [kudla]
  12. Error fetching PMID 19098893: [ray]
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  18. Error fetching PMID 19494908: [tokuriki]
  19. Error fetching PMID 19578359: [eldar]
All Medline abstracts: PubMed HubMed
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