Smolke:Journal Club

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(2014-2015 Journal Club)
 
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{{Smolke_Top}}
{{Smolke_Top}}
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=Next Meeting=
 
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*When: Friday Nov. 30 2:00pm
 
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*Where:
 
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*Paper:
 
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*Moderator:
 
 +
=2014-2015 Journal Club=
-
==Suggested Future Papers==
 
-
*without pmid link here:
 
-
#Spitale RNA Shape analysis in living cells [http://www.nature.com/nchembio/journal/vaop/ncurrent/full/nchembio.1131.html link]
+
{| 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
 +
| 11:00 am || SC 262  || [http://www.ncbi.nlm.nih.gov/pubmed/23446346 Hansen, et al.] || Kathy
 +
|-
 +
! 25-Aug
 +
| 11:00 am || SC 262  || [http://www.pnas.org/content/early/2014/07/17/1406401111.abstract Xu, et al.] || Isis
 +
|-
 +
! 17-Sep
 +
| 11:00 am || SC 052  || [http://www.nature.com/nm/journal/v20/n9/full/nm.3621.html Araci, et al.] || Remus
 +
|-
 +
! Oct
 +
|  ||  ||  || Yen-Hsiang
 +
|-
 +
! Nov
 +
|  ||  ||  || Melina
 +
|-
 +
! Dec
 +
|  ||  ||  || Kate
 +
|-
 +
! Jan
 +
|  ||  ||  || Peter
 +
|-
 +
! Feb
 +
|  ||  ||  || Maureen
 +
|-
 +
! Mar
 +
|  ||  ||  || Michael
 +
|-
 +
! Apr
 +
|  ||  ||  || Stephanie
 +
|-
 +
! May
 +
|  ||  ||  || Shireen
 +
|-
 +
! Jun
 +
|  ||  ||  || Ben
 +
|-
 +
! Jul
 +
|  ||  ||  || Joy
 +
|-
 +
|}
 +
 
 +
==Paper to be discussed==
 +
<biblio>
 +
#Xiong pmid=24912182
 +
 
 +
</biblio>
 +
 
 +
==Interesting Papers==
*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.
<biblio>
<biblio>
-
#salmena pmid=21802130
+
#Duss pmid=24828038
-
#Mutalik pmid=22446835
+
#Wang pmid=24705516
 +
#Annaluru pmid=24674868
 +
#Kotula pmid=24639514
 +
#Birmingham pmid=24657930
 +
#Lian pmid=24853351
 +
#Xu pmid=25049383
 +
 
 +
 
 +
</biblio>
 +
 
 +
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?
 +
 
 +
==Past Papers==
 +
* Past papers
 +
<biblio>
 +
#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
#Qi pmid=22383579
-
#Li_G pmid=22456704
+
#Alberts pmid=24733905
-
#Li_H pmid=22461604
+
#Creasey pmid=24670663
-
#Low pmid=22314289
+
#Olson pmid=24608181
 +
#Fossati pmid=24513861
 +
#Lienert pmid=24434884
 +
#Enquist-Newman pmid=24291791
 +
#Wang pmid=24284625
 +
#Bogorad pmid=24077099
#Auslander pmid=22722847
#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
#sandoval pmid=22689973
#douglas pmid=22344439
#douglas pmid=22344439
Line 29: Line 125:
#pinheiro pmid=22517858
#pinheiro pmid=22517858
#sharon pmid=22609971
#sharon pmid=22609971
-
#regot pmid=21150900
 
#karr pmid=22817898
#karr pmid=22817898
#jinek pmid=22745249
#jinek pmid=22745249
#qi pmid=22983090
#qi pmid=22983090
-
#Moss-Racusin pmid=22988126
+
#Choi pmid=24077097
-
 
+
#salmena pmid=21802130
-
</biblio>
+
#Cong pmid=23287718
-
 
+
#Mali pmid=23287722
-
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?
+
#Hwang pmid=23360964
-
 
+
#Jiang pmid=23360965
-
==Comments on Papers==
+
#Cho pmid=23360966
-
 
+
#Coelho pmid=23258409
-
==Voting on Papers==  
+
#Spitale pmid=23178934
-
*'''Spitale et al.''': Andy, CDS, Yen-Hsiang
+
-
*'''Sandoval et al.''': Eric, SG, Isis, Kate
+
-
*'''Poliseno et al.''' and '''Salmena et al''':
+
-
*'''Paige et al. and Paige et. al.''': Ryan, Jay
+
-
*'''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
+
-
*'''Karr et al''': Ryan
+
-
*'''Moss-Racusin et al.''':
+
-
*'''Freida and Block''':
+
-
 
+
-
==Past Papers==
+
-
* Past papers
+
-
<biblio>
+
#block pmid=23087247
#block pmid=23087247
#wargacki pmid=22267807
#wargacki pmid=22267807
Line 87: Line 161:
#imai pmid=22722205
#imai pmid=22722205
#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
#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
-
</biblio>
 
-
 
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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
 
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#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.
 
-
#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
 
-
#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.
 
-
#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.
 
-
#Isaacs, F.J., et al. Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement. Science 15 July 2011: 333 (6040), 348-353.
 
-
#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.
 
-
#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
 
-
#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
 
-
#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.
 
-
#Greiss S, and Chin JW. Expanding the Genetic Code of an Animal. J Am Chem Soc. 2011 Aug 8
 
-
#Poelwijk FJ, de Vos MG, Tans SJ.  Tradeoffs and Optimality in the Evolution of Gene Regulation.  Cell, 5 August 2011
 
-
#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
 
-
#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.
 
-
#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.
 
-
#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.
 
-
#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.
 
-
#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.
 
-
#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.
 
-
#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.
 
-
#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.
 
-
<biblio>
 
-
#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
 
-
#ranguphan pmid=19151732
 
-
#han pmid=19135890
 
-
#fung pmid=15875027
 
-
#cantone pmid=19327819
 
-
#kempe pmid=19359021
 
-
#tokuriki pmid=19494908
 
-
#eldar pmid=19578359
 
</biblio>
</biblio>

Current revision

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Contents

2014-2015 Journal Club

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 11:00 am SC 262 Hansen, et al. Kathy
25-Aug 11:00 am SC 262 Xu, et al. Isis
17-Sep 11:00 am SC 052 Araci, et al. Remus
Oct Yen-Hsiang
Nov Melina
Dec Kate
Jan Peter
Feb Maureen
Mar Michael
Apr Stephanie
May Shireen
Jun Ben
Jul Joy

Paper to be discussed

Error fetching PMID 24912182:
  1. Error fetching PMID 24912182: [Xiong]

Interesting Papers

  • 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 24828038:
Error fetching PMID 24705516:
Error fetching PMID 24674868:
Error fetching PMID 24639514:
Error fetching PMID 24657930:
Error fetching PMID 24853351:
Error fetching PMID 25049383:
  1. Error fetching PMID 24828038: [Duss]
  2. Error fetching PMID 24705516: [Wang]
  3. Error fetching PMID 24674868: [Annaluru]
  4. Error fetching PMID 24639514: [Kotula]
  5. Error fetching PMID 24657930: [Birmingham]
  6. Error fetching PMID 24853351: [Lian]
  7. Error fetching PMID 25049383: [Xu]
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?

Past Papers

  • Past papers
Error fetching PMID 24744377:
Error fetching PMID 24747940:
Error fetching PMID 24747838:
Error fetching PMID 24696455:
Error fetching PMID 24695221:
Error fetching PMID 24677733:
Error fetching PMID 24622617:
Error fetching PMID 24603933:
Error fetching PMID 24578530:
Error fetching PMID 24569486:
Error fetching PMID 24509821:
Error fetching PMID 24445655:
Error fetching PMID 24189549:
Error fetching PMID 22383579:
Error fetching PMID 24733905:
Error fetching PMID 24670663:
Error fetching PMID 24608181:
Error fetching PMID 24513861:
Error fetching PMID 24434884:
Error fetching PMID 24291791:
Error fetching PMID 24284625:
Error fetching PMID 24077099:
Error fetching PMID 22722847:
Error fetching PMID 24463698:
Error fetching PMID 24529477:
Error fetching PMID 24487692:
Error fetching PMID 24434554:
Error fetching PMID 22446835:
Error fetching PMID 24270811:
Error fetching PMID 24468674:
Error fetching PMID 24196718:
Error fetching PMID 22461604:
Error fetching PMID 23575629:
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 22817898:
Error fetching PMID 22745249:
Error fetching PMID 22983090:
Error fetching PMID 24077097:
Error fetching PMID 21802130:
Error fetching PMID 23287718:
Error fetching PMID 23287722:
Error fetching PMID 23360964:
Error fetching PMID 23360965:
Error fetching PMID 23360966:
Error fetching PMID 23258409:
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 24284625: [Wang]
  2. Error fetching PMID 24744377: [Chapman]
  3. Error fetching PMID 24196718: [Fica]
  4. Error fetching PMID 24747940: [Fica]
  5. Error fetching PMID 24578530: [Lee]
  6. Error fetching PMID 24747838: [Lee]
  7. Error fetching PMID 24696455: [Saldana-Meyer]
  8. Error fetching PMID 24695221: [Liu]
  9. Error fetching PMID 24677733: [Cao]
  10. Error fetching PMID 24622617: [Church]
  11. Error fetching PMID 24603933: [Karas]
  12. Error fetching PMID 24270811: [Ding]
  13. Error fetching PMID 24569486: [Ding]
  14. Error fetching PMID 24509821: [Velagapudi]
  15. Error fetching PMID 24445655: [Blazeck]
  16. Error fetching PMID 24189549: [Avendano]
  17. Error fetching PMID 22383579: [Qi]
  18. Error fetching PMID 24733905: [Alberts]
  19. Error fetching PMID 24670663: [Creasey]
  20. Error fetching PMID 24608181: [Olson]
  21. Error fetching PMID 24513861: [Fossati]
  22. Error fetching PMID 24434884: [Lienert]
  23. Error fetching PMID 24291791: [Enquist-Newman]
  24. Error fetching PMID 24077099: [Bogorad]
  25. Error fetching PMID 22722847: [Auslander]
  26. Error fetching PMID 24463698: [Matthews]
  27. Error fetching PMID 24529477: [Nishimasu]
  28. Error fetching PMID 24487692: [Hammerling]
  29. Error fetching PMID 24434554: [Moses]
  30. Error fetching PMID 22446835: [Mutalik]
  31. Error fetching PMID 24468674: [Carter]
  32. Error fetching PMID 22461604: [Li_H]
  33. Error fetching PMID 23575629: [Paddon]
  34. Error fetching PMID 22689973: [sandoval]
  35. Error fetching PMID 22344439: [douglas]
  36. Error fetching PMID 22544021: [fu]
  37. Error fetching PMID 21798953: [paige]
  38. Error fetching PMID 22403384: [paige]
  39. Error fetching PMID 22517858: [pinheiro]
  40. Error fetching PMID 22609971: [sharon]
  41. Error fetching PMID 22817898: [karr]
  42. Error fetching PMID 22745249: [jinek]
  43. Error fetching PMID 22983090: [qi]
  44. Error fetching PMID 24077097: [Choi]
  45. Error fetching PMID 21802130: [salmena]
  46. Error fetching PMID 23287718: [Cong]
  47. Error fetching PMID 23287722: [Mali]
  48. Error fetching PMID 23360964: [Hwang]
  49. Error fetching PMID 23360965: [Jiang]
  50. Error fetching PMID 23360966: [Cho]
  51. Error fetching PMID 23258409: [Coelho]
  52. Error fetching PMID 23178934: [Spitale]
  53. Error fetching PMID 23087247: [block]
  54. Error fetching PMID 22267807: [wargacki]
  55. Error fetching PMID 22184212: [bonacci]
  56. Error fetching PMID 22194579: [carothers]
  57. Error fetching PMID 22021385: [conrado]
  58. Error fetching PMID 21832992: [dellomonaco]
  59. Error fetching PMID 21918511: [dymond]
  60. Error fetching PMID 20194121: [xie]
  61. Error fetching PMID 20622866: [leisner]
  62. Error fetching PMID 21245841: [saito]
  63. Error fetching PMID 21602812: [yim]
  64. Error fetching PMID 21478873: [esvelt]
  65. Error fetching PMID 20671186: [schirmer]
  66. Error fetching PMID 20453864: [sinha]
  67. Error fetching PMID 20154731: [neumann]
  68. Error fetching PMID 19745116: [drinnenberg]
  69. Error fetching PMID 19648908: [dueber]
  70. Error fetching PMID 19633652: [wang]
  71. Error fetching PMID 19079053: [yu]
  72. Error fetching PMID 19131595: [lincoln]
  73. Error fetching PMID 19234448: [lam]
  74. Error fetching PMID 19279212: [nevozhay]
  75. Error fetching PMID 22722205: [imai]
  76. 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
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