Smolke:Journal Club

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(Voting on Papers)
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*'''Chen et al''':
*'''Chen et al''':
*'''Huo et al.''':
*'''Huo et al.''':
-
*'''Bond-Watts et al.''' and '''Shen et al.''': Joe, Stephanie, Josh
+
*'''Bond-Watts et al.''' and '''Shen et al.''': Joe, Stephanie, Josh, Isis
-
*'''Yim et al.''': Joe, Stephanie, Ryan, Josh
+
*'''Yim et al.''': Joe, Stephanie, Ryan, Josh, Isis
*'''Schwanhäusser et al.''': DK, Megan, Ryan, Andy, Yen-Hsiang
*'''Schwanhäusser et al.''': DK, Megan, Ryan, Andy, Yen-Hsiang

Revision as of 23:15, 31 May 2011

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Contents

Next Meeting

  • When: Monday, June 6, 2pm
  • Where: Y2E2 270
  • Paper: TBD
  • Moderator: TBD

Suggested Future Papers

Note: The biblio extension is broken. Suggested papers need full references.

  1. 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.465(7301):1033-8.
  2. O'Shaughnessy EC, Palani S, Collins JJ, Sarkar CA. Tunable Signal Processing in Synthetic MAP Kinase Cascades. Cell.144(1):119-31.
  3. Churchman LS, Weissman JS. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature.469(7330):368-73.
  4. Wörsdörfer B, Woycechowsky KJ, and Hilvert, D. Directed Evolution of a Protein Container. Science 4 February 2011: 331 (6017), 589-592.
  5. Chen X, Denison L, Levy M, Ellington AD. Direct selection for ribozyme cleavage activity in cells. RNA 23 November 2009: 15 (11), 2035-45.
  6. 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.
  7. 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.
  8. 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
  9. 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, Van Dien S. Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nat Chem Biol. 2011 May 22
  10. 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.

For next month

  1. The arsenic bacteria paper, the 8 technical comments, and the authors' reply.
  2. 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
  3. 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

Comments on Papers

Voting on Papers

  • Poliseno et al.:
  • O'Shaughnessy et al.:
  • Churchman and Weissman:
  • Wörsdörfer et al.:
  • Chen et al:
  • Huo et al.:
  • Bond-Watts et al. and Shen et al.: Joe, Stephanie, Josh, Isis
  • Yim et al.: Joe, Stephanie, Ryan, Josh, Isis
  • Schwanhäusser et al.: DK, Megan, Ryan, Andy, Yen-Hsiang

Past Papers

Error fetching PMID 20671186:
Error fetching PMID 20453864:
Error fetching PMID 20154731:
Error fetching PMID 19745116:
Error fetching PMID 19648908:
Error fetching PMID 19633652:
Error fetching PMID 19079053:
Error fetching PMID 19131595:
Error fetching PMID 19234448:
Error fetching PMID 19279212:
  1. KM, Carlson JC, Liu DR. A system for the continuous directed evolution of biomolecules. Nature. 2011. [Esvelt]
  2. Error fetching PMID 20671186: [schirmer]
  3. Error fetching PMID 20453864: [sinha]
  4. Error fetching PMID 20154731: [neumann]
  5. Error fetching PMID 19745116: [drinnenberg]
  6. Error fetching PMID 19648908: [dueber]
  7. Error fetching PMID 19633652: [wang]
  8. Error fetching PMID 19079053: [yu]
  9. Error fetching PMID 19131595: [lincoln]
  10. Error fetching PMID 19234448: [lam]
  11. Error fetching PMID 19279212: [nevozhay]
All Medline abstracts: PubMed HubMed

Aged Out

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
Error fetching PMID 14726590:
Error fetching PMID 19666472:
Error fetching PMID 20175178:
Error fetching PMID 20185727:
Error fetching PMID 19265475:
Error fetching PMID 19377462:
Error fetching PMID 19416889:
Error fetching PMID 19589923:
Error fetching PMID 19478183:
Error fetching PMID 19536156:
Error fetching PMID 19359587:
Error fetching PMID 19098893:
Error fetching PMID 19151732:
Error fetching PMID 19135890:
Error fetching PMID 15875027:
Error fetching PMID 19327819:
Error fetching PMID 19359021:
Error fetching PMID 19494908:
Error fetching PMID 19578359:
  1. Error fetching PMID 14726590: [zhang]
  2. Error fetching PMID 19666472: [antonczak]
  3. Error fetching PMID 20175178: [zhou]
  4. Error fetching PMID 20185727: [to]
  5. Error fetching PMID 19265475: [jones]
  6. Error fetching PMID 19377462: [ellis]
  7. Error fetching PMID 19416889: [liu]
  8. Error fetching PMID 19589923: [burns]
  9. Error fetching PMID 19478183: [friedland]
  10. Error fetching PMID 19536156: [mitchell]
  11. Error fetching PMID 19359587: [kudla]
  12. Error fetching PMID 19098893: [ray]
  13. Error fetching PMID 19151732: [ranguphan]
  14. Error fetching PMID 19135890: [han]
  15. Error fetching PMID 15875027: [fung]
  16. Error fetching PMID 19327819: [cantone]
  17. Error fetching PMID 19359021: [kempe]
  18. Error fetching PMID 19494908: [tokuriki]
  19. Error fetching PMID 19578359: [eldar]
All Medline abstracts: PubMed HubMed
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