Our Publications

Note that plasmid reagents from the Savage Lab are available from our addgene site and that all source code from our work is available on our github site. 


Laughlin TG, Bayne A, Trempe JF, Savage DF, Davies KM. Structure of NDH the complex I-like molecule of oxygenic photosynthesis. In Press.

Oakes BL, Fellmann C, Rishi H, Taylor KL, Ren SM, Nadler DC, Yokoo R, Arkin AP, Doudna JA, Savage DF. 2019. CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification. Cell 176: 254–267.e16. Link


Flamholz A, Prywes N, Moran U, Davidi D, Bar-On Y, Oltrogge L, Alves R, Savage D, Milo R. 2018. Revisiting tradeoffs in Rubisco kinetic parameters. bioRxiv 470021. Link

Welike et al. 2018

Welike et al. 2018

Desmarais JJ, Flamholz AI, Blikstad C, Dugan EJ, Laughlin TG, Oltrogge LM, Chen AW, Wetmore K, Diamond S, Wang JY, Savage DF. 2018. Genome-wide screening reveals a novel class of carbonic anhydrase-like inorganic carbon transporters in chemoautotrophic bacteria. bioRxiv 476713. Link

Kundert K, Lucas JE, Watters KE, Fellmann C, Ng AN, Heineike BM, Fitzsimmons CM, Oakes BL, Savage DF, El-Samad H, Doudna JA, Kortemme T. Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. bioRxiv, 323105. Link

Welkie DG, Rubin BE, Diamond S, Hood RD, Savage DF, Golden SS. 2018. A Hard Day's Night: Cyanobacteria in Diel Cycles. Trends in Microbiology. Link

Chaijarasphong T, Savage DF. 2018. Sequestered: Design and Construction of Synthetic Organelles. Synthetic Biology: Parts, Devices and Applications 8.

Higgins SA, Savage DF. 2018. Protein Science by DNA Sequencing: How Advances in Molecular Biology Are Accelerating Biochemistry. Biochemistry 57: 38–46. Link


Higgins SA, Savage DF. 2018. Protein Science by DNA Sequencing: How Advances in Molecular Biology Are Accelerating Biochemistry. Biochemistry 57: 38–46. Link

Higgins, SA, Ouonkap, R, Savage, DF. 2017. Rapid and Programmable Protein Mutagenesis Using Plasmid Recombineering. ACS Synth. Biol. DOI: 10.1021/acssynbio.7b00112 Link 

Nichols RJ*, Cassidy-Amstutz C*, Chaijarasphong T, Savage DF. Encapsulins: molecular biology of the shell. Crit. Rev. Biochem. Mol. Biol. 2017 Jun 21;:1–12.  *denote equal contribution Link 



Savage D, Zhang W. 2016. Biofuels: At the crossroads. Current Opinion in Chemical Biology 35: A1–A3. Link

Morgan* S-A, Nadler* DC, Yokoo R, Savage DF. 2016. Biofuel metabolic engineering with biosensors. Current Opinion in Chemical Biology 35: 150–158. *denote equal contribution Link

Mangan NM*, Flamholz A*, Milo R, Savage DF. 2016. Efficient operation of the cyanobacterial CO2 concentrating mechanism depends strongly on pH.  PNAS. doi: 10.1073/pnas.1525145113. *denote equal contribution Link

Hood RD, Higgins S, Flamholz A, Nichols RJ, Savage DF. 2016. The stringent response regulates adaptation to darkness in a cyanobacterium. PNAS. doi:10.1073/pnas.1524915113. Link 

Oakes et al. 2016

Gerhardt KP, Olson EJ, Castillo-Hair SM, Hartsough LA, Landry BP, Ekness F, Yokoo R, Gomez EJ, Ramakrishnan P, Suh J, et al. 2016. An open-hardware platform for optogenetics and photobiology. Sci Rep 6: 35363. Link 

Nadler DC*, Morgan SA*, Flamholz A, Kortright K, Savage DF. 2016. Rapid construction of metabolite biosensors using domain-insertion profiling. Nature Communications 10.1038/ncomms12266. *denote equal contribution Link 

Cassidy-Amstutz C, Oltrogge LM, Going CC, Lee A, Teng PK, Quintanilla D, East-Seletsky A, Williams ER, Savage DF. 2016. Identification of a minimal peptide tag for in vivo and in vitro loading of encapsulin. Biochemistry. Link

Oakes BL, Nadler DC, Flamholz A, Fellmann C, Staahl BT, Doudna JA, Savage DF. 2016. Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch. Nat Biotechnol. Link

Chaijarasphong T, Nichols RJ, Kortright KE, Nixon CF, Teng PK, Oltrogge LM, Savage DF. 2016. Programmed Ribosomal Frameshifting Mediates Expression of the α-Carboxysome. J Mol Biol 428: 153–164. Link


Yokoo et al. 2014

Yokoo R, Hood RD, Savage DF. 2015. Live-cell imaging of cyanobacteria. Photosynthesis Research 126: 33–46. Link


Oakes BL, Nadler DC, Savage DF. 2014. Protein engineering of Cas9 for enhanced function. Methods in enzymology 546: 491–511. Link


Chen AH, Robinson-Mosher A, Savage DF, Silver PA, Polka JK. 2013. The bacterial carbon-fixing organelle is formed by shell envelopment of preassembled cargo. PLoS ONE 8: e76127. Link


Chen AH, Afonso B, Silver PA, Savage DF. 2012. Spatial and temporal organization of chromosome duplication and segregation in the cyanobacterium Synechococcus elongatus PCC 7942. PLoS ONE 7: e47837. Link

Bonacci et al. 2012

Bonacci W, Teng PK, Afonso B, Niederholtmeyer H, Grob P, Silver PA, Savage DF. 2012. Modularity of a carbon-fixing protein organelle. Proc Natl Acad Sci USA 109: 478–483. Link


Niederholtmeyer H, Wolfstädter BT, Savage DF, Silver PA, Way JC. 2010. Engineering cyanobacteria to synthesize and export hydrophilic products. Appl Environ Microbiol 76: 3462–3466. Link

Savage DF*, Afonso B*, Chen AH, Silver PA. 2010. Spatially ordered dynamics of the bacterial carbon fixation machinery. Science 327: 1258–1261. *denote equal contribution Link

older work from Savage et alia

Structural context shapes the aquaporin selectivity filter. Savage, D.F., O’Connell III, J.D., Stroud R.M. (2010) PNAS. 107:17164-9. 

A general protocol for the crystallization of membrane proteins for X-ray structural investi gation. Newby, Z.E., O'Connell 3rd, J.D., Gruswitz, F., Hays, F.A., Harries, W.E., Harwood, I.M., Ho, J.D., Lee, J.K., Savage, D.F., Miercke, L.J., Stroud, R.M. (2009) Nat Protoc. 4:619-37. 

Defossiling fuel: How synthetic biology can transform biofuel production. Savage, D.F., Way, J., Silver, P.A. (2008) ACS Chem. Biol. 3:13-6. 

Structural basis of aquaporin inhibition by mercury. Savage, D.F. and Stroud, R.M. (2007) J. Mol. Biol. 368: 607-17. 

Cell-free complements in vivo expression of the E. coli membrane proteome. Savage, D.F., Anderson C.L, Robles-Colmenares, Y., Newby, Z.A., Stroud R.M. (2007) Protein Sci. 16:966-76. 

Substrate twinning activates the signal recognition particle and its receptor. Egea P.F., Shan S.O., Napetschnig J., Savage D.F., Walter P., Stroud R.M. (2004) Nature, 426:215-221.

Water and glycerol permeation through the glycerol channel GlpF and the aquaporin family. Lee, J.K., Khademi, S., Harries, W., Savage, D., Miercke, L, Stroud, R.M. (2004) J. Synchrotron Radiat. 11:86-88

Architecture and selectivity in aquaporins: 2.5Å x-ray structure of aquaporin Z. Savage, D. F., Egea, P.F., Robles, Y.C., O’Connell III, J.D., and Stroud, R.M. (2003) PLoS Biology, 1:334-340. 

Selectivity and conductance among the glycerol and water conducting aquaporin family of channels. Stroud, R.M., Savage, D.F., Miercke, L.J., Lee, J.K., Khademi, S., Harries, W. (2003). FEBS Letters, 555:79-84. 

Catalysis, specificity, and ACP docking site of Streptomyces coelicolor malonyl-CoA: ACP transacylase. Keatinge-Clay, A.T., Shelat, A.A., Savage, D.F., Tsai, S.C., Miercke, L.J.W., O'Connell 3rd, J.D., Khosla, C., and Stroud, R.M. (2003) Structure, 11:147-154.