Smolke:Journal Club

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=Next Meeting=
=Next Meeting=
*When: Friday Feb. 22 3pm
*When: Thursday Feb. 28 3pm
*Where: TBA
*Where: Y2E2 101
*Paper: TBD
*Paper: <biblio>#Coelho pmid=23258409</biblio>
*Moderator: TBV (To be volunteered)
*Moderator: Stephanie
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*without pmid link here:
*without pmid link here:
1.  The 5 papers published about CRISPR-Cas based genome editing published the week of 2/11 (3 in Nature Biotech, 2 in Science)
*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.
*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.
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#Moss-Racusin pmid=22988126
#Moss-Racusin pmid=22988126
#Coelho pmid=23258409
#Coelho pmid=23258409
#Nevozhay pmid=23385595
#Na pmid=23334451
#Pezo pmid=23447021
#Berthoumieux pmid=23340840
#Hanauer pmid=23222833
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==Voting on Papers==  
==Voting on Papers==  
Vote for Feb 28th:
*'''Qi, Lucks et al.''': Jay, Eric
*'''Douglas et al.''': Kathy, Melina
*'''Karr et al.''': Steph
*'''Jinek et al.''': Kathy
*'''Coelho et al.''': Yen-Hsiang, Kate, Steph, Mike, Eric
*'''Nevozhay et al.''': Yen-Hsiang, Jay
*'''Fu et al.''': Kate, Melina
*'''H. Li et al.''': Mike
Last Vote
Last Vote
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*'''Karr et al''': Ryan
*'''Karr et al''': Ryan
*'''Moss-Racusin et al.''':
*'''Moss-Racusin et al.''':
*'''Freida and Block''':
==Past Papers==
==Past Papers==

Revision as of 11:31, 15 March 2013

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Next Meeting

  • Moderator: Stephanie

Suggested Future Papers

  • without pmid link here:

1. The 5 papers published about CRISPR-Cas based genome editing published the week of 2/11 (3 in Nature Biotech, 2 in Science)

  • 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.
Error fetching PMID 21802130:
Error fetching PMID 22446835:
Error fetching PMID 22383579:
Error fetching PMID 22456704:
Error fetching PMID 22461604:
Error fetching PMID 22314289:
Error fetching PMID 22722847:
Error fetching PMID 22689973:
Error fetching PMID 22344439:
Error fetching PMID 22544021:
Error fetching PMID 21798953:
Error fetching PMID 22403384:
Error fetching PMID 22517858:
Error fetching PMID 22609971:
Error fetching PMID 21150900:
Error fetching PMID 22817898:
Error fetching PMID 22745249:
Error fetching PMID 22983090:
Error fetching PMID 22988126:
Error fetching PMID 23258409:
Error fetching PMID 23385595:
Error fetching PMID 23334451:
Error fetching PMID 23447021:
Error fetching PMID 23340840:
Error fetching PMID 23222833:
  1. Error fetching PMID 23258409: [Coelho]
  2. Error fetching PMID 21802130: [salmena]
  3. Error fetching PMID 22446835: [Mutalik]
  4. Error fetching PMID 22383579: [Qi]
  5. Error fetching PMID 22456704: [Li_G]
  6. Error fetching PMID 22461604: [Li_H]
  7. Error fetching PMID 22314289: [Low]
  8. Error fetching PMID 22722847: [Auslander]
  9. Error fetching PMID 22689973: [sandoval]
  10. Error fetching PMID 22344439: [douglas]
  11. Error fetching PMID 22544021: [fu]
  12. Error fetching PMID 21798953: [paige]
  13. Error fetching PMID 22403384: [paige]
  14. Error fetching PMID 22517858: [pinheiro]
  15. Error fetching PMID 22609971: [sharon]
  16. Error fetching PMID 21150900: [regot]
  17. Error fetching PMID 22817898: [karr]
  18. Error fetching PMID 22745249: [jinek]
  19. Error fetching PMID 22983090: [qi]
  20. Error fetching PMID 22988126: [Moss-Racusin]
  21. Error fetching PMID 23385595: [Nevozhay]
  22. Error fetching PMID 23334451: [Na]
  23. Error fetching PMID 23447021: [Pezo]
  24. Error fetching PMID 23340840: [Berthoumieux]
  25. Error fetching PMID 23222833: [Hanauer]
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 Feb 28th:

  • Qi, Lucks et al.: Jay, Eric
  • Douglas et al.: Kathy, Melina
  • Karr et al.: Steph
  • Jinek et al.: Kathy
  • Coelho et al.: Yen-Hsiang, Kate, Steph, Mike, Eric
  • Nevozhay et al.: Yen-Hsiang, Jay
  • Fu et al.: Kate, Melina
  • H. Li et al.: Mike

Last Vote

  • Spitale et al.: Andy, CDS, Yen-Hsiang, Jay
  • Sandoval et al.: Eric, SG, Isis, Kate
  • Poliseno et al. and Salmena et al:
  • Paige et al. and Paige et. al.: Ryan
  • Douglas et al.: Maureen, Kathy
  • Mutalik et al. and Qi et al.: Eric, Jay, Yen-Hsiang
  • G. Li et al.:
  • H. Li et al.: SG, Mike, Kate
  • Fu et al.: Andy
  • Pinheiro et al.: Mike
  • Sharon et al.: Isis
  • Auslander S, et al.: Maureen, Kathy
  • Jinek et al.:
  • Qi et al.: CDS, remus
  • Karr et al: Ryan
  • Moss-Racusin et al.:

Past Papers

  • Past papers
Error fetching PMID 23178934:
Error fetching PMID 23087247:
Error fetching PMID 22267807:
Error fetching PMID 22184212:
Error fetching PMID 22194579:
Error fetching PMID 22021385:
Error fetching PMID 21832992:
Error fetching PMID 21918511:
Error fetching PMID 20194121:
Error fetching PMID 20622866:
Error fetching PMID 21245841:
Error fetching PMID 21602812:
Error fetching PMID 21478873:
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:
Error fetching PMID 22722205:
  1. Error fetching PMID 23178934: [Spitale]
  2. Error fetching PMID 23087247: [block]
  3. Error fetching PMID 22267807: [wargacki]
  4. Error fetching PMID 22184212: [bonacci]
  5. Error fetching PMID 22194579: [carothers]
  6. Error fetching PMID 22021385: [conrado]
  7. Error fetching PMID 21832992: [dellomonaco]
  8. Error fetching PMID 21918511: [dymond]
  9. Error fetching PMID 20194121: [xie]
  10. Error fetching PMID 20622866: [leisner]
  11. Error fetching PMID 21245841: [saito]
  12. Error fetching PMID 21602812: [yim]
  13. Error fetching PMID 21478873: [esvelt]
  14. Error fetching PMID 20671186: [schirmer]
  15. Error fetching PMID 20453864: [sinha]
  16. Error fetching PMID 20154731: [neumann]
  17. Error fetching PMID 19745116: [drinnenberg]
  18. Error fetching PMID 19648908: [dueber]
  19. Error fetching PMID 19633652: [wang]
  20. Error fetching PMID 19079053: [yu]
  21. Error fetching PMID 19131595: [lincoln]
  22. Error fetching PMID 19234448: [lam]
  23. Error fetching PMID 19279212: [nevozhay]
  24. Error fetching PMID 22722205: [imai]
  25. 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]
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.
  1. Zhang Z, Gildersleeve J, Yang YY, Xu R, Loo JA, Uryu S, Wong CH, and Schultz PG. . pmid:14726590. PubMed HubMed [zhang]
  2. Antonczak AK, Simova Z, and Tippmann EM. . pmid:19666472. PubMed HubMed [antonczak]
  3. Zhou M, Liang X, Mochizuki T, and Asanuma H. . pmid:20175178. PubMed HubMed [zhou]
  4. To TL and Maheshri N. . pmid:20185727. PubMed HubMed [to]
  5. Jones S, Peng PD, Yang S, Hsu C, Cohen CJ, Zhao Y, Abad J, Zheng Z, Rosenberg SA, and Morgan RA. . pmid:19265475. PubMed HubMed [jones]
  6. Ellis T, Wang X, and Collins JJ. . pmid:19377462. PubMed HubMed [ellis]
  7. Kowtoniuk WE, Shen Y, Heemstra JM, Agarwal I, and Liu DR. . pmid:19416889. PubMed HubMed [liu]
  8. Burns WR, Zheng Z, Rosenberg SA, and Morgan RA. . pmid:19589923. PubMed HubMed [burns]
  9. Friedland AE, Lu TK, Wang X, Shi D, Church G, and Collins JJ. . pmid:19478183. PubMed HubMed [friedland]
  10. Mitchell A, Romano GH, Groisman B, Yona A, Dekel E, Kupiec M, Dahan O, and Pilpel Y. . pmid:19536156. PubMed HubMed [mitchell]
  11. Kudla G, Murray AW, Tollervey D, and Plotkin JB. . pmid:19359587. PubMed HubMed [kudla]
  12. Ray PS, Jia J, Yao P, Majumder M, Hatzoglou M, and Fox PL. . pmid:19098893. PubMed HubMed [ray]
  13. Runguphan W and O'Connor SE. . pmid:19151732. PubMed HubMed [ranguphan]
  14. Han J, Pedersen JS, Kwon SC, Belair CD, Kim YK, Yeom KH, Yang WY, Haussler D, Blelloch R, and Kim VN. . pmid:19135890. PubMed HubMed [han]
  15. Fung E, Wong WW, Suen JK, Bulter T, Lee SG, and Liao JC. . pmid:15875027. PubMed HubMed [fung]
  16. Cantone I, Marucci L, Iorio F, Ricci MA, Belcastro V, Bansal M, Santini S, di Bernardo M, di Bernardo D, and Cosma MP. . pmid:19327819. PubMed HubMed [cantone]
  17. Kempe K, Higashi Y, Frick S, Sabarna K, and Kutchan TM. . pmid:19359021. PubMed HubMed [kempe]
  18. Tokuriki N and Tawfik DS. . pmid:19494908. PubMed HubMed [tokuriki]
  19. Eldar A, Chary VK, Xenopoulos P, Fontes ME, Losón OC, Dworkin J, Piggot PJ, and Elowitz MB. . pmid:19578359. PubMed HubMed [eldar]
All Medline abstracts: PubMed HubMed
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