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| {{Smolke_Top}} | | {{Smolke_Top}} |
| =Next Meeting=
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| *When: 1pm 9/6/12
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| *Where: TBD
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| *Paper: TBD
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| *Moderator: TBD
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| ==Suggested Future Papers== | | =2014-2015 Journal Club= |
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| Feel free to use PMID for new paper suggestions
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| *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.
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| *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
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| *Wargacki AJ, et al. An Engineered Microbial Platform for Direct Biofuel Production from Brown Macroalgae. Science. 2012 Jan 20;335(6066):308-13.
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| *Mutalik VK, et al. Rationally designed families of orthogonal RNA regulators of translation. Nature Chemical Biology 2012, doi:10.1038/NChemBio.919
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| *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
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| *Li G, et al. The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature, doi:10.1038/nature10965
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| *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
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| *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)
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| *Auslander S, et al. Programmable single-cell mammalian biocomputers. 2012 Nature.
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| *Sandoval NR, et al. Strategy for directing combinatorial genome engineering in E. coli. PNAS 2012 109(26):10540-5. PMID: 22689973
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| | {| border="1" |
| | |+ |
| | ! Date !! Time !! Location !! Paper !! Moderator |
| | |- |
| | ! 21-Apr |
| | | 11:00 am || Spilker 143 || Enquist-Newman || Kate |
| | |- |
| | ! 19-May |
| | | 11:00 am || Spilker 143 || Lee & Church || Joy |
| | |- |
| | ! 16-Jun |
| | | 11:00 am || Spilker 143 || Xiong || Yanran |
| | |- |
| | !21- Jul |
| | | 11:00am || SC 262 || [http://www.ncbi.nlm.nih.gov/pubmed/23446346 Hansen, et al.] || Kathy |
| | |- |
| | ! 25-Aug |
| | | 11:00am || || [http://www.pnas.org/content/early/2014/07/17/1406401111.abstract Xu, et al.] || Isis |
| | |- |
| | ! Sep |
| | | || || || Remus |
| | |- |
| | ! Oct |
| | | || || || Yen-Hsiang |
| | |- |
| | ! Nov |
| | | || || || Melina |
| | |- |
| | ! Dec |
| | | || || || Kate |
| | |- |
| | ! Jan |
| | | || || || Peter |
| | |- |
| | ! Feb |
| | | || || || Maureen |
| | |- |
| | ! Mar |
| | | || || || Michale |
| | |- |
| | ! Apr |
| | | || || || Stephanie |
| | |- |
| | ! May |
| | | || || || Shireen |
| | |- |
| | ! Jun |
| | | || || || Ben |
| | |- |
| | ! Jul |
| | | || || || Joy |
| | |- |
| | |} |
| | |
| | ==Paper to be discussed== |
| <biblio> | | <biblio> |
| | #Xiong pmid=24912182 |
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| | </biblio> |
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| | ==Interesting Papers== |
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| | *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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| | <biblio> |
| | #Duss pmid=24828038 |
| | #Wang pmid=24705516 |
| | #Annaluru pmid=24674868 |
| | #Kotula pmid=24639514 |
| | #Birmingham pmid=24657930 |
| | #Lian pmid=24853351 |
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| #paige pmid=21798953
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| #paige pmid=22403384
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| #douglas pmid=22344439
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| #fu pmid=22544021
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| #pinheiro pmid=22517858
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| #sharon pmid=22609971
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| </biblio> | | </biblio> |
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| ==Comments on Papers==
| | 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? |
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| ==Voting on Papers==
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| *'''Poliseno et al.''' and '''Salmena et al''': Jay
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| *'''Wargacki et al.''': Kate
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| *'''Paige et al. and Paige et. al.''': Kathy
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| *'''Douglas et al.''':
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| *'''Mutalik et al. and Qi et al.''': Jay, Kathy
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| *'''G. Li et al.''': Josh
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| *'''H. Li et al.''':
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| *'''Fu et al.''':
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| *'''Imai et al.''': Andy, CDS
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| *'''Pinheiro et al.''': Andy, Yen-Hsiang
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| ==Past Papers== | | ==Past Papers== |
| | * Past papers |
| <biblio> | | <biblio> |
| #sensor 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 | | #Chapman pmid=24744377 |
| | #Fica pmid=24747940 |
| | #Lee pmid=24747838 |
| | #Saldana-Meyer pmid=24696455 |
| | #Liu pmid=24695221 |
| | #Cao pmid=24677733 |
| | #Church pmid=24622617 |
| | #Karas pmid=24603933 |
| | #Lee pmid=24578530 |
| | #Ding pmid=24569486 |
| | #Velagapudi pmid=24509821 |
| | #Blazeck pmid=24445655 |
| | #Avendano pmid=24189549 |
| | #Qi pmid=22383579 |
| | #Alberts pmid=24733905 |
| | #Creasey pmid=24670663 |
| | #Olson pmid=24608181 |
| | #Fossati pmid=24513861 |
| | #Lienert pmid=24434884 |
| | #Enquist-Newman pmid=24291791 |
| | #Wang pmid=24284625 |
| | #Bogorad pmid=24077099 |
| | #Auslander pmid=22722847 |
| | #Matthews pmid=24463698 |
| | #Nishimasu pmid=24529477 |
| | #Hammerling pmid=24487692 |
| | #Moses pmid=24434554 |
| | #Mutalik pmid=22446835 |
| | #Ding pmid=24270811 |
| | #Carter pmid=24468674 |
| | #Fica pmid=24196718 |
| | #Li_H pmid=22461604 |
| | #Paddon pmid=23575629 |
| | #sandoval pmid=22689973 |
| | #douglas pmid=22344439 |
| | #fu pmid=22544021 |
| | #paige pmid=21798953 |
| | #paige pmid=22403384 |
| | #pinheiro pmid=22517858 |
| | #sharon pmid=22609971 |
| | #karr pmid=22817898 |
| | #jinek pmid=22745249 |
| | #qi pmid=22983090 |
| | #Choi pmid=24077097 |
| | #salmena pmid=21802130 |
| | #Cong pmid=23287718 |
| | #Mali pmid=23287722 |
| | #Hwang pmid=23360964 |
| | #Jiang pmid=23360965 |
| | #Cho pmid=23360966 |
| | #Coelho pmid=23258409 |
| | #Spitale pmid=23178934 |
| | #block pmid=23087247 |
| | #wargacki pmid=22267807 |
| #bonacci pmid=22184212 | | #bonacci pmid=22184212 |
| #carothers pmid=22194579 | | #carothers pmid=22194579 |
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| #lam pmid=19234448 | | #lam pmid=19234448 |
| #nevozhay pmid=19279212 | | #nevozhay pmid=19279212 |
| #pmid=22722205 | | #imai pmid=22722205 |
| </biblio>
| | #sensor 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 |
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| ==Aged Out==
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| *Valderrama-Rincon JD, et al. An engineered eukaryotic protein glycosylation pathway in Escherichia coli. Nature Chemical Biology 2012, doi:10.1038/nchembio.921
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| *The arsenic bacteria paper, the 8 technical comments, and the authors' reply.
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| #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 | |
| #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.
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| #Paige, J.S., et al. RNA Mimics of Green Fluorescent Protein. Science 29 July 2011: 333, 642-646.
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| #Wochner A, Attwater J, Coulson A, Holliger P. Ribozyme-catalyzed transcription of an active ribozyme. Science. 2011 Apr 8;332(6026):209-12.
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| #baker pmid=22194412
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| #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
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| #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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| #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.
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| #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.
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| #Isaacs, F.J., et al. Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement. Science 15 July 2011: 333 (6040), 348-353.
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| #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.
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| #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
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| #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
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| #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.
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| #Greiss S, and Chin JW. Expanding the Genetic Code of an Animal. J Am Chem Soc. 2011 Aug 8
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| #Poelwijk FJ, de Vos MG, Tans SJ. Tradeoffs and Optimality in the Evolution of Gene Regulation. Cell, 5 August 2011
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| #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
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| #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.
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| #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.
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| #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.
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| #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.
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| #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.
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| #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.
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| #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.
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| #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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| <biblio>
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| #zhang pmid=14726590
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| #antonczak pmid=19666472
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| #zhou pmid=20175178
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| #to pmid=20185727
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| #jones pmid=19265475
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| #ellis pmid=19377462
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| #liu pmid=19416889
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| #burns pmid=19589923
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| #friedland pmid=19478183
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| #mitchell pmid=19536156
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| #kudla pmid=19359587
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| #ray pmid=19098893
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| #ranguphan pmid=19151732
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| #han pmid=19135890
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| #fung pmid=15875027
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| #cantone pmid=19327819
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| #kempe pmid=19359021
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| #tokuriki pmid=19494908
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| #eldar pmid=19578359
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| </biblio> | | </biblio> |