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Items: 43

1.

Encapsulin carrier proteins for enhanced expression of antimicrobial peptides.

Lee TH, Carpenter TS, D'haeseleer P, Savage DF, Yung MC.

Biotechnol Bioeng. 2019 Nov 10. doi: 10.1002/bit.27222. [Epub ahead of print]

PMID:
31709513
2.

DABs are inorganic carbon pumps found throughout prokaryotic phyla.

Desmarais JJ, Flamholz AI, Blikstad C, Dugan EJ, Laughlin TG, Oltrogge LM, Chen AW, Wetmore K, Diamond S, Wang JY, Savage DF.

Nat Microbiol. 2019 Dec;4(12):2204-2215. doi: 10.1038/s41564-019-0520-8. Epub 2019 Aug 12.

PMID:
31406332
3.

Author Correction: Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors.

Huang TP, Zhao KT, Miller SM, Gaudelli NM, Oakes BL, Fellmann C, Savage DF, Liu DR.

Nat Biotechnol. 2019 Jul;37(7):820. doi: 10.1038/s41587-019-0168-1.

PMID:
31182863
4.

Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors.

Huang TP, Zhao KT, Miller SM, Gaudelli NM, Oakes BL, Fellmann C, Savage DF, Liu DR.

Nat Biotechnol. 2019 Jun;37(6):626-631. doi: 10.1038/s41587-019-0134-y. Epub 2019 May 20. Erratum in: Nat Biotechnol. 2019 Jun 10;:.

5.

Multiplexed Charge Detection Mass Spectrometry for High-Throughput Single Ion Analysis of Large Molecules.

Harper CC, Elliott AG, Oltrogge LM, Savage DF, Williams ER.

Anal Chem. 2019 Jun 4;91(11):7458-7465. doi: 10.1021/acs.analchem.9b01669. Epub 2019 May 22.

PMID:
31082222
6.

Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs.

Kundert K, Lucas JE, Watters KE, Fellmann C, Ng AH, Heineike BM, Fitzsimmons CM, Oakes BL, Qu J, Prasad N, Rosenberg OS, Savage DF, El-Samad H, Doudna JA, Kortemme T.

Nat Commun. 2019 May 9;10(1):2127. doi: 10.1038/s41467-019-09985-2.

7.

Learning to Build a β-Carboxysome.

Blikstad C, Flamholz AI, Oltrogge LM, Savage DF.

Biochemistry. 2019 Apr 23;58(16):2091-2092. doi: 10.1021/acs.biochem.9b00199. Epub 2019 Apr 10. No abstract available.

PMID:
30968695
8.

Structure of the complex I-like molecule NDH of oxygenic photosynthesis.

Laughlin TG, Bayne AN, Trempe JF, Savage DF, Davies KM.

Nature. 2019 Feb;566(7744):411-414. doi: 10.1038/s41586-019-0921-0. Epub 2019 Feb 11.

PMID:
30742075
9.

Cas14: Big Advances from Small CRISPR Proteins.

Savage DF.

Biochemistry. 2019 Feb 26;58(8):1024-1025. doi: 10.1021/acs.biochem.9b00035. Epub 2019 Feb 11. No abstract available.

PMID:
30740978
10.

CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification.

Oakes BL, Fellmann C, Rishi H, Taylor KL, Ren SM, Nadler DC, Yokoo R, Arkin AP, Doudna JA, Savage DF.

Cell. 2019 Jan 10;176(1-2):254-267.e16. doi: 10.1016/j.cell.2018.11.052.

PMID:
30633905
11.

A Hard Day's Night: Cyanobacteria in Diel Cycles.

Welkie DG, Rubin BE, Diamond S, Hood RD, Savage DF, Golden SS.

Trends Microbiol. 2019 Mar;27(3):231-242. doi: 10.1016/j.tim.2018.11.002. Epub 2018 Dec 5. Review.

PMID:
30527541
12.

Protein Science by DNA Sequencing: How Advances in Molecular Biology Are Accelerating Biochemistry.

Higgins SA, Savage DF.

Biochemistry. 2018 Jan 9;57(1):38-46. doi: 10.1021/acs.biochem.7b00886. Epub 2017 Oct 23. Review.

PMID:
28992412
13.

Rapid and Programmable Protein Mutagenesis Using Plasmid Recombineering.

Higgins SA, Ouonkap SVY, Savage DF.

ACS Synth Biol. 2017 Oct 20;6(10):1825-1833. doi: 10.1021/acssynbio.7b00112. Epub 2017 Jul 24.

14.

Encapsulins: molecular biology of the shell.

Nichols RJ, Cassidy-Amstutz C, Chaijarasphong T, Savage DF.

Crit Rev Biochem Mol Biol. 2017 Oct;52(5):583-594. doi: 10.1080/10409238.2017.1337709. Epub 2017 Jun 21. Review.

PMID:
28635326
15.

An open-hardware platform for optogenetics and photobiology.

Gerhardt KP, Olson EJ, Castillo-Hair SM, Hartsough LA, Landry BP, Ekness F, Yokoo R, Gomez EJ, Ramakrishnan P, Suh J, Savage DF, Tabor JJ.

Sci Rep. 2016 Nov 2;6:35363. doi: 10.1038/srep35363.

16.

Biofuel metabolic engineering with biosensors.

Morgan SA, Nadler DC, Yokoo R, Savage DF.

Curr Opin Chem Biol. 2016 Dec;35:150-158. doi: 10.1016/j.cbpa.2016.09.020. Epub 2016 Oct 18. Review.

17.

pH determines the energetic efficiency of the cyanobacterial CO2 concentrating mechanism.

Mangan NM, Flamholz A, Hood RD, Milo R, Savage DF.

Proc Natl Acad Sci U S A. 2016 Sep 6;113(36):E5354-62. doi: 10.1073/pnas.1525145113. Epub 2016 Aug 22.

18.

The stringent response regulates adaptation to darkness in the cyanobacterium Synechococcus elongatus.

Hood RD, Higgins SA, Flamholz A, Nichols RJ, Savage DF.

Proc Natl Acad Sci U S A. 2016 Aug 16;113(33):E4867-76. doi: 10.1073/pnas.1524915113. Epub 2016 Aug 2.

19.

Rapid construction of metabolite biosensors using domain-insertion profiling.

Nadler DC, Morgan SA, Flamholz A, Kortright KE, Savage DF.

Nat Commun. 2016 Jul 29;7:12266. doi: 10.1038/ncomms12266.

20.

Identification of a Minimal Peptide Tag for in Vivo and in Vitro Loading of Encapsulin.

Cassidy-Amstutz C, Oltrogge L, Going CC, Lee A, Teng P, Quintanilla D, East-Seletsky A, Williams ER, Savage DF.

Biochemistry. 2016 Jun 21;55(24):3461-8. doi: 10.1021/acs.biochem.6b00294. Epub 2016 Jun 7.

PMID:
27224728
21.

Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch.

Oakes BL, Nadler DC, Flamholz A, Fellmann C, Staahl BT, Doudna JA, Savage DF.

Nat Biotechnol. 2016 Jun;34(6):646-51. doi: 10.1038/nbt.3528. Epub 2016 May 2.

22.

Programmed Ribosomal Frameshifting Mediates Expression of the α-Carboxysome.

Chaijarasphong T, Nichols RJ, Kortright KE, Nixon CF, Teng PK, Oltrogge LM, Savage DF.

J Mol Biol. 2016 Jan 16;428(1):153-164. doi: 10.1016/j.jmb.2015.11.017. Epub 2015 Dec 1.

PMID:
26608811
23.

Protein engineering of Cas9 for enhanced function.

Oakes BL, Nadler DC, Savage DF.

Methods Enzymol. 2014;546:491-511. doi: 10.1016/B978-0-12-801185-0.00024-6.

24.

Live-cell imaging of cyanobacteria.

Yokoo R, Hood RD, Savage DF.

Photosynth Res. 2015 Oct;126(1):33-46. doi: 10.1007/s11120-014-0049-x. Epub 2014 Nov 4. Review.

PMID:
25366827
25.

The bacterial carbon-fixing organelle is formed by shell envelopment of preassembled cargo.

Chen AH, Robinson-Mosher A, Savage DF, Silver PA, Polka JK.

PLoS One. 2013 Sep 4;8(9):e76127. doi: 10.1371/journal.pone.0076127. eCollection 2013.

26.

Presentation of continuous outcomes in randomised trials: an observational study.

Schriger DL, Savage DF, Altman DG.

BMJ. 2012 Dec 18;345:e8486. doi: 10.1136/bmj.e8486.

27.

Spatial and temporal organization of chromosome duplication and segregation in the cyanobacterium Synechococcus elongatus PCC 7942.

Chen AH, Afonso B, Silver PA, Savage DF.

PLoS One. 2012;7(10):e47837. doi: 10.1371/journal.pone.0047837. Epub 2012 Oct 24.

28.

Modularity of a carbon-fixing protein organelle.

Bonacci W, Teng PK, Afonso B, Niederholtmeyer H, Grob P, Silver PA, Savage DF.

Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):478-83. doi: 10.1073/pnas.1108557109. Epub 2011 Dec 19.

29.

Triazoles as γ-secretase modulators.

Fischer C, Zultanski SL, Zhou H, Methot JL, Brown WC, Mampreian DM, Schell AJ, Shah S, Nuthall H, Hughes BL, Smotrov N, Kenific CM, Cruz JC, Walker D, Bouthillette M, Nikov GN, Savage DF, Jeliazkova-Mecheva VV, Diaz D, Szewczak AA, Bays N, Middleton RE, Munoz B, Shearman MS.

Bioorg Med Chem Lett. 2011 Jul 1;21(13):4083-7. doi: 10.1016/j.bmcl.2011.04.089. Epub 2011 May 4.

PMID:
21616665
30.

Structural context shapes the aquaporin selectivity filter.

Savage DF, O'Connell JD 3rd, Miercke LJ, Finer-Moore J, Stroud RM.

Proc Natl Acad Sci U S A. 2010 Oct 5;107(40):17164-9. doi: 10.1073/pnas.1009864107. Epub 2010 Sep 20.

31.

Engineering cyanobacteria to synthesize and export hydrophilic products.

Niederholtmeyer H, Wolfstädter BT, Savage DF, Silver PA, Way JC.

Appl Environ Microbiol. 2010 Jun;76(11):3462-6. doi: 10.1128/AEM.00202-10. Epub 2010 Apr 2. Erratum in: Appl Environ Microbiol. 2010 Sep;76(17):6023.

32.

Spatially ordered dynamics of the bacterial carbon fixation machinery.

Savage DF, Afonso B, Chen AH, Silver PA.

Science. 2010 Mar 5;327(5970):1258-61. doi: 10.1126/science.1186090.

33.

A general protocol for the crystallization of membrane proteins for X-ray structural investigation.

Newby ZE, O'Connell JD 3rd, Gruswitz F, Hays FA, Harries WE, Harwood IM, Ho JD, Lee JK, Savage DF, Miercke LJ, Stroud RM.

Nat Protoc. 2009;4(5):619-37. doi: 10.1038/nprot.2009.27.

34.

Defossiling fuel: how synthetic biology can transform biofuel production.

Savage DF, Way J, Silver PA.

ACS Chem Biol. 2008 Jan 18;3(1):13-6. doi: 10.1021/cb700259j. No abstract available.

PMID:
18205286
35.

Cell-free complements in vivo expression of the E. coli membrane proteome.

Savage DF, Anderson CL, Robles-Colmenares Y, Newby ZE, Stroud RM.

Protein Sci. 2007 May;16(5):966-76.

36.

Structural basis of aquaporin inhibition by mercury.

Savage DF, Stroud RM.

J Mol Biol. 2007 May 4;368(3):607-17. Epub 2007 Mar 2.

37.

Molecular determinants of dihydrouridine synthase activity.

Savage DF, de Crécy-Lagard V, Bishop AC.

FEBS Lett. 2006 Oct 2;580(22):5198-202. Epub 2006 Sep 5.

38.

Substrate twinning activates the signal recognition particle and its receptor.

Egea PF, Shan SO, Napetschnig J, Savage DF, Walter P, Stroud RM.

Nature. 2004 Jan 15;427(6971):215-21.

PMID:
14724630
39.

Architecture and selectivity in aquaporins: 2.5 a X-ray structure of aquaporin Z.

Savage DF, Egea PF, Robles-Colmenares Y, O'Connell JD 3rd, Stroud RM.

PLoS Biol. 2003 Dec;1(3):E72. Epub 2003 Dec 22.

40.

Catalysis, specificity, and ACP docking site of Streptomyces coelicolor malonyl-CoA:ACP transacylase.

Keatinge-Clay AT, Shelat AA, Savage DF, Tsai SC, Miercke LJ, O'Connell JD 3rd, Khosla C, Stroud RM.

Structure. 2003 Feb;11(2):147-54.

41.

Recommendations on feeding infants of HIV positive mothers. WHO, UNICEF, UNAIDS guidelines.

Savage DF, Lhotska L; WHO; UNICEF; UNAIDS.

Adv Exp Med Biol. 2000;478:225-30. No abstract available.

PMID:
11065075
42.

Laser endarterectomy: a comparison of thrombotic potential following CO2 laser vs surgical endarterectomy.

McVicker JH, Day AL, Savage DF, Abela GS, Roberts AJ, Watson RL, Mehta JL.

Stroke. 1986 Mar-Apr;17(2):266-70.

PMID:
3754358
43.

Chemonucleolysis versus open discectomy: the case against chymopapain.

Day AL, Savage DF, Friedman WA, Sypert GW.

Clin Neurosurg. 1986;33:385-96. No abstract available.

PMID:
3791808

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