Smolke:Journal Club

Next Meeting

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Suggested Future Papers

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

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. 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.
3. O'Shaughnessy EC, Palani S, Collins JJ, Sarkar CA. Tunable Signal Processing in Synthetic MAP Kinase Cascades. Cell.144(1):119-31.
4. 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.
5. 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.
6. Wolfe-Simon F, Blum JS, Kulp TR, Gordon GW, Hoeft SE, Pett-Ridge J, Stolz JF, Webb SM, Weber PK, Davies PC, Anbar AD, Oremland RS. A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science. 2010 Dec 2.
7. Churchman LS, Weissman JS. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature.469(7330):368-73.
8. Tamsir, A, Tabor, JJ, Voigt, CA. Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’. Nature 469,212–215(13 January 2011)
9. Regot S, Macia J. et. al. Distributed biological computation with multicellular engineered networks. Nature. 2011 Jan 13;469(7329):207-11

Comments on Papers

Voting on Papers

• Leonard et al.:Mike, Josh, Stephanie
• Poliseno et al.:Kathy, Yen-Hsiang, Joe, Jay
• O'Shaughnessy et al.: PDJ, Joe, Ryan
• Matzas et al. and Kosuri et al.:Mike
• Wolfe-Simon et al.:
• Churchman and Weissman: Josh, PDJ, Megan, Andy
• Tamsir et. al. and Regot et. al.:Kathy, Yen-Hsiang, Megan, Andy, Stephanie, Ryan, Brent

Past Papers

2. Schirmer A, Rude MA, Li X, Popova E, and del Cardayre SB. . pmid:20671186. PubMed HubMed [schirmer]
3. Sinha J, Reyes SJ, and Gallivan JP. . pmid:20453864. PubMed HubMed [sinha]
4. Neumann H, Wang K, Davis L, Garcia-Alai M, and Chin JW. . pmid:20154731. PubMed HubMed [neumann]
5. Drinnenberg IA, Weinberg DE, Xie KT, Mower JP, Wolfe KH, Fink GR, and Bartel DP. . pmid:19745116. PubMed HubMed [drinnenberg]
6. Dueber JE, Wu GC, Malmirchegini GR, Moon TS, Petzold CJ, Ullal AV, Prather KL, and Keasling JD. . pmid:19648908. PubMed HubMed [dueber]
7. Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, and Church GM. . pmid:19633652. PubMed HubMed [wang]
8. 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]
9. Lincoln TA and Joyce GF. . pmid:19131595. PubMed HubMed [lincoln]
10. Lam BJ and Joyce GF. . pmid:19234448. PubMed HubMed [lam]
11. Nevozhay D, Adams RM, Murphy KF, Josic K, and Balázsi G. . pmid:19279212. PubMed HubMed [nevozhay]

Aged Out

1. 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.
2. 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.
3. 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.
4. 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.

12. Zhang Z, Gildersleeve J, Yang YY, Xu R, Loo JA, Uryu S, Wong CH, and Schultz PG. . pmid:14726590. PubMed HubMed [zhang]
13. Antonczak AK, Simova Z, and Tippmann EM. . pmid:19666472. PubMed HubMed [antonczak]
14. Zhou M, Liang X, Mochizuki T, and Asanuma H. . pmid:20175178. PubMed HubMed [zhou]
15. To TL and Maheshri N. . pmid:20185727. PubMed HubMed [to]
16. 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]
17. Ellis T, Wang X, and Collins JJ. . pmid:19377462. PubMed HubMed [ellis]
18. Kowtoniuk WE, Shen Y, Heemstra JM, Agarwal I, and Liu DR. . pmid:19416889. PubMed HubMed [liu]
19. Burns WR, Zheng Z, Rosenberg SA, and Morgan RA. . pmid:19589923. PubMed HubMed [burns]
20. Friedland AE, Lu TK, Wang X, Shi D, Church G, and Collins JJ. . pmid:19478183. PubMed HubMed [friedland]
21. Mitchell A, Romano GH, Groisman B, Yona A, Dekel E, Kupiec M, Dahan O, and Pilpel Y. . pmid:19536156. PubMed HubMed [mitchell]
22. Kudla G, Murray AW, Tollervey D, and Plotkin JB. . pmid:19359587. PubMed HubMed [kudla]
23. Ray PS, Jia J, Yao P, Majumder M, Hatzoglou M, and Fox PL. . pmid:19098893. PubMed HubMed [ray]
24. Runguphan W and O'Connor SE. . pmid:19151732. PubMed HubMed [ranguphan]
25. 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]
26. Fung E, Wong WW, Suen JK, Bulter T, Lee SG, and Liao JC. . pmid:15875027. PubMed HubMed [fung]
27. 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]
28. Kempe K, Higashi Y, Frick S, Sabarna K, and Kutchan TM. . pmid:19359021. PubMed HubMed [kempe]
29. Tokuriki N and Tawfik DS. . pmid:19494908. PubMed HubMed [tokuriki]
30. Eldar A, Chary VK, Xenopoulos P, Fontes ME, Losón OC, Dworkin J, Piggot PJ, and Elowitz MB. . pmid:19578359. PubMed HubMed [eldar]