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Contents

2014 Winter

Date Time Location Paper Moderator
9-Jan 3:15 pm 300
13-Feb 3:15 pm 300
13-Mar 3:15 pm Spilker-232


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.
  1. 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. . pmid:24291791. PubMed HubMed [Enquist-Newman]
  2. Bogorad IW, Lin TS, and Liao JC. . pmid:24077099. PubMed HubMed [Bogorad]
  3. Choi YJ and Lee SY. . pmid:24077097. PubMed HubMed [Choi]
  4. 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. . pmid:23575629. PubMed HubMed [Paddon]
  5. Salmena L, Poliseno L, Tay Y, Kats L, and Pandolfi PP. . pmid:21802130. PubMed HubMed [salmena]
  6. Mutalik VK, Qi L, Guimaraes JC, Lucks JB, and Arkin AP. . pmid:22446835. PubMed HubMed [Mutalik]
  7. Qi L, Lucks JB, Liu CC, Mutalik VK, and Arkin AP. . pmid:22383579. PubMed HubMed [Qi]
  8. Li GW, Oh E, and Weissman JS. . pmid:22456704. PubMed HubMed [Li_G]
  9. Li H, Opgenorth PH, Wernick DG, Rogers S, Wu TY, Higashide W, Malati P, Huo YX, Cho KM, and Liao JC. . pmid:22461604. PubMed HubMed [Li_H]
  10. Low JT, Knoepfel SA, Watts JM, ter Brake O, Berkhout B, and Weeks KM. . pmid:22314289. PubMed HubMed [Low]
  11. Ausländer S, Ausländer D, Müller M, Wieland M, and Fussenegger M. . pmid:22722847. PubMed HubMed [Auslander]
  12. Sandoval NR, Kim JY, Glebes TY, Reeder PJ, Aucoin HR, Warner JR, and Gill RT. . pmid:22689973. PubMed HubMed [sandoval]
  13. Douglas SM, Bachelet I, and Church GM. . pmid:22344439. PubMed HubMed [douglas]
  14. Fu J, Bian X, Hu S, Wang H, Huang F, Seibert PM, Plaza A, Xia L, Müller R, Stewart AF, and Zhang Y. . pmid:22544021. PubMed HubMed [fu]
  15. Paige JS, Wu KY, and Jaffrey SR. . pmid:21798953. PubMed HubMed [paige]
  16. Paige JS, Nguyen-Duc T, Song W, and Jaffrey SR. . pmid:22403384. PubMed HubMed [paige]
  17. 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. . pmid:22517858. PubMed HubMed [pinheiro]
  18. Sharon E, Kalma Y, Sharp A, Raveh-Sadka T, Levo M, Zeevi D, Keren L, Yakhini Z, Weinberger A, and Segal E. . pmid:22609971. PubMed HubMed [sharon]
  19. Regot S, Macia J, Conde N, Furukawa K, Kjellén J, Peeters T, Hohmann S, de Nadal E, Posas F, and Solé R. . pmid:21150900. PubMed HubMed [regot]
  20. Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B Jr, Assad-Garcia N, Glass JI, and Covert MW. . pmid:22817898. PubMed HubMed [karr]
  21. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, and Charpentier E. . pmid:22745249. PubMed HubMed [jinek]
  22. Qi L, Haurwitz RE, Shao W, Doudna JA, and Arkin AP. . pmid:22983090. PubMed HubMed [qi]
  23. Moss-Racusin CA, Dovidio JF, Brescoll VL, Graham MJ, and Handelsman J. . pmid:22988126. PubMed HubMed [Moss-Racusin]
  24. Nevozhay D, Zal T, and Balázsi G. . pmid:23385595. PubMed HubMed [Nevozhay]
  25. Na D, Yoo SM, Chung H, Park H, Park JH, and Lee SY. . pmid:23334451. PubMed HubMed [Na]
  26. Pezo V, Louis D, Guérineau V, Le Caer JP, Gaillon L, Mutzel R, and Marlière P. . pmid:23447021. PubMed HubMed [Pezo]
  27. Berthoumieux S, de Jong H, Baptist G, Pinel C, Ranquet C, Ropers D, and Geiselmann J. . pmid:23340840. PubMed HubMed [Berthoumieux]
  28. Hanauer DI, Frederick J, Fotinakes B, and Strobel SA. . pmid:23222833. PubMed HubMed [Hanauer]
  29. Hajdin CE, Bellaousov S, Huggins W, Leonard CW, Mathews DH, and Weeks KM. . pmid:23503844. PubMed HubMed [Hajdin]
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
  1. Coelho PS, Brustad EM, Kannan A, and Arnold FH. . pmid:23258409. PubMed HubMed [Coelho]
  2. Spitale RC, Crisalli P, Flynn RA, Torre EA, Kool ET, and Chang HY. . pmid:23178934. PubMed HubMed [Spitale]
  3. Frieda KL and Block SM. . pmid:23087247. PubMed HubMed [block]
  4. 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. . pmid:22267807. PubMed HubMed [wargacki]
  5. Bonacci W, Teng PK, Afonso B, Niederholtmeyer H, Grob P, Silver PA, and Savage DF. . pmid:22184212. PubMed HubMed [bonacci]
  6. Carothers JM, Goler JA, Juminaga D, and Keasling JD. . pmid:22194579. PubMed HubMed [carothers]
  7. 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. . pmid:22021385. PubMed HubMed [conrado]
  8. Dellomonaco C, Clomburg JM, Miller EN, and Gonzalez R. . pmid:21832992. PubMed HubMed [dellomonaco]
  9. 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. . pmid:21918511. PubMed HubMed [dymond]
  10. Xie Z, Liu SJ, Bleris L, and Benenson Y. . pmid:20194121. PubMed HubMed [xie]
  11. Leisner M, Bleris L, Lohmueller J, Xie Z, and Benenson Y. . pmid:20622866. PubMed HubMed [leisner]
  12. Saito H, Fujita Y, Kashida S, Hayashi K, and Inoue T. . pmid:21245841. PubMed HubMed [saito]
  13. 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. . pmid:21602812. PubMed HubMed [yim]
  14. Esvelt KM, Carlson JC, and Liu DR. . pmid:21478873. PubMed HubMed [esvelt]
  15. Schirmer A, Rude MA, Li X, Popova E, and del Cardayre SB. . pmid:20671186. PubMed HubMed [schirmer]
  16. Sinha J, Reyes SJ, and Gallivan JP. . pmid:20453864. PubMed HubMed [sinha]
  17. Neumann H, Wang K, Davis L, Garcia-Alai M, and Chin JW. . pmid:20154731. PubMed HubMed [neumann]
  18. Drinnenberg IA, Weinberg DE, Xie KT, Mower JP, Wolfe KH, Fink GR, and Bartel DP. . pmid:19745116. PubMed HubMed [drinnenberg]
  19. Dueber JE, Wu GC, Malmirchegini GR, Moon TS, Petzold CJ, Ullal AV, Prather KL, and Keasling JD. . pmid:19648908. PubMed HubMed [dueber]
  20. Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, and Church GM. . pmid:19633652. PubMed HubMed [wang]
  21. Yu RC, Pesce CG, Colman-Lerner A, Lok L, Pincus D, Serra E, Holl M, Benjamin K, Gordon A, and Brent R. . pmid:19079053. PubMed HubMed [yu]
  22. Lincoln TA and Joyce GF. . pmid:19131595. PubMed HubMed [lincoln]
  23. Lam BJ and Joyce GF. . pmid:19234448. PubMed HubMed [lam]
  24. Nevozhay D, Adams RM, Murphy KF, Josic K, and Balázsi G. . pmid:19279212. PubMed HubMed [nevozhay]
  25. 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. . pmid:22722205. PubMed HubMed [imai]
  26. 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. dx.doi.org/10.1021/ja203972q
  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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