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David F. Savage - Publications

Affiliations: 
Molecular and Cell Biology University of California, Berkeley, Berkeley, CA, United States 
Area:
Biophysics, Synthetic Biology, and Systems Biology
Website:
www.savagelab.org
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45 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Adler BA, Trinidad MI, Bellieny-Rabelo D, Zhang E, Karp HM, Skopintsev P, Thornton BW, Weissman RF, Yoon PH, Chen L, Hessler T, Eggers AR, Colognori D, Boger R, Doherty EE, ... ... Savage DF, et al. CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes. Nucleic Acids Research. PMID 37889041 DOI: 10.1093/nar/gkad890  0.447
2023 Armbruster EG, Lee J, Hutchings J, VanderWal AR, Enustun E, Adler BA, Aindow A, Deep A, Rodriguez ZK, Morgan CJ, Ghassemian M, Charles E, Cress BF, Savage DF, Doudna JA, et al. Sequential membrane- and protein-bound organelles compartmentalize genomes during phage infection. Biorxiv : the Preprint Server For Biology. PMID 37781618 DOI: 10.1101/2023.09.20.558163  0.463
2023 Stahl EC, Sabo JK, Kang MH, Allen R, Applegate E, Kim SE, Kwon Y, Seth A, Lemus N, Salinas-Rios V, Soczek KM, Trinidad M, Vo LT, Jeans C, Wozniak A, ... ... Savage DF, et al. Genome editing in the mouse brain with minimally immunogenic Cas9 RNPs. Molecular Therapy : the Journal of the American Society of Gene Therapy. PMID 37403358 DOI: 10.1016/j.ymthe.2023.06.019  0.426
2022 Al-Shayeb B, Skopintsev P, Soczek KM, Stahl EC, Li Z, Groover E, Smock D, Eggers AR, Pausch P, Cress BF, Huang CJ, Staskawicz B, Savage DF, Jacobsen SE, Banfield JF, et al. Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors. Cell. 185: 4574-4586.e16. PMID 36423580 DOI: 10.1016/j.cell.2022.10.020  0.451
2022 Chandrasekaran SS, Agrawal S, Fanton A, Jangid AR, Charrez B, Escajeda AM, Son S, Mcintosh R, Tran H, Bhuiya A, de León Derby MD, Switz NA, Armstrong M, Harris AR, Prywes N, ... ... Savage DF, et al. Rapid detection of SARS-CoV-2 RNA in saliva via Cas13. Nature Biomedical Engineering. PMID 35953650 DOI: 10.1038/s41551-022-00917-y  0.397
2022 Perier C, Nasinghe E, Charles I, Ssetaba LJ, Ahyong V, Bangs D, Beatty PR, Czudnochowski N, Diallo A, Dugan E, Fabius JM, Fong Baker H, Gardner J, Isaacs S, Joanah B, ... ... Savage DF, et al. Workshop-based learning and networking: a scalable model for research capacity strengthening in low- and middle-income countries. Global Health Action. 15: 2062175. PMID 35730550 DOI: 10.1080/16549716.2022.2062175  0.734
2021 LaFrance BJ, Cassidy-Amstutz C, Nichols RJ, Oltrogge LM, Nogales E, Savage DF. The encapsulin from Thermotoga maritima is a flavoprotein with a symmetry matched ferritin-like cargo protein. Scientific Reports. 11: 22810. PMID 34815415 DOI: 10.1038/s41598-021-01932-w  0.412
2021 Liu TY, Knott GJ, Smock DCJ, Desmarais JJ, Son S, Bhuiya A, Jakhanwal S, Prywes N, Agrawal S, Díaz de León Derby M, Switz NA, Armstrong M, Harris AR, Charles EJ, Thornton BW, ... ... Savage DF, et al. Publisher Correction: Accelerated RNA detection using tandem CRISPR nucleases. Nature Chemical Biology. PMID 34616098 DOI: 10.1038/s41589-021-00882-8  0.385
2021 Shams A, Higgins SA, Fellmann C, Laughlin TG, Oakes BL, Lew R, Kim S, Lukarska M, Arnold M, Staahl BT, Doudna JA, Savage DF. Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules. Nature Communications. 12: 5664. PMID 34580310 DOI: 10.1038/s41467-021-25992-8  0.584
2021 Liu TY, Knott GJ, Smock DCJ, Desmarais JJ, Son S, Bhuiya A, Jakhanwal S, Prywes N, Agrawal S, Díaz de León Derby M, Switz NA, Armstrong M, Harris AR, Charles EJ, Thornton BW, ... ... Savage DF, et al. Accelerated RNA detection using tandem CRISPR nucleases. Nature Chemical Biology. PMID 34354262 DOI: 10.1038/s41589-021-00842-2  0.416
2021 Liu TY, Knott GJ, Smock DCJ, Desmarais JJ, Son S, Bhuiya A, Jakhanwal S, Prywes N, Agrawal S, de León Derby MD, Switz NA, Armstrong M, Harris AR, Charles EJ, Thornton BW, ... ... Savage DF, et al. Accelerated RNA detection using tandem CRISPR nucleases. Medrxiv : the Preprint Server For Health Sciences. PMID 33791736 DOI: 10.1101/2021.03.19.21253328  0.415
2020 Agrawal S, Fanton A, Chandrasekaran SS, Prywes N, Lukarska M, Biering SB, Smock DCJ, Mok A, Knott GJ, Van E, Dugan E, Kim S, Liu TY, Harris E, Stanley SA, ... ... Savage DF, et al. Rapid detection of SARS-CoV-2 with Cas13. Medrxiv : the Preprint Server For Health Sciences. PMID 33354689 DOI: 10.1101/2020.12.14.20247874  0.409
2020 Laughlin TG, Savage DF, Davies KM. Recent advances on the structure and function of NDH-1: The complex I of oxygenic photosynthesis. Biochimica Et Biophysica Acta. Bioenergetics. 1861: 148254. PMID 32645407 DOI: 10.1016/J.Bbabio.2020.148254  0.414
2020 Oltrogge LM, Chaijarasphong T, Chen AW, Bolin ER, Marqusee S, Savage DF. Multivalent interactions between CsoS2 and Rubisco mediate α-carboxysome formation. Nature Structural & Molecular Biology. 27: 281-287. PMID 32123388 DOI: 10.1038/S41594-020-0387-7  0.426
2019 Lee TH, Carpenter TS, D'haeseleer P, Savage DF, Yung MC. Encapsulin carrier proteins for enhanced expression of antimicrobial peptides. Biotechnology and Bioengineering. PMID 31709513 DOI: 10.1002/Bit.27222  0.438
2019 Desmarais JJ, Flamholz AI, Blikstad C, Dugan EJ, Laughlin TG, Oltrogge LM, Chen AW, Wetmore K, Diamond S, Wang JY, Savage DF. DABs are inorganic carbon pumps found throughout prokaryotic phyla. Nature Microbiology. PMID 31406332 DOI: 10.1038/S41564-019-0520-8  0.439
2019 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. Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. Nature Communications. 10: 2127. PMID 31073154 DOI: 10.1038/S41467-019-09985-2  0.748
2019 Savage DF. Cas14: Big Advances from Small CRISPR Proteins. Biochemistry. PMID 30740978 DOI: 10.1021/Acs.Biochem.9B00035  0.46
2019 Oakes BL, Fellmann C, Rishi H, Taylor KL, Ren SM, Nadler DC, Yokoo R, Arkin AP, Doudna JA, Savage DF. CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification. Cell. 176: 254-267.e16. PMID 30633905 DOI: 10.1016/J.Cell.2018.11.052  0.773
2017 Higgins SA, Savage DF. Protein science by DNA sequencing: how advances in molecular biology are accelerating biochemistry. Biochemistry. PMID 28992412 DOI: 10.1021/Acs.Biochem.7B00886  0.4
2017 Higgins SA, Ounkap S, Savage DF. Rapid and Programmable Protein Mutagenesis Using Plasmid Recombineering. Acs Synthetic Biology. PMID 28707884 DOI: 10.1021/Acssynbio.7B00112  0.415
2017 Nichols RJ, Cassidy-Amstutz C, Chaijarasphong T, Savage DF. Encapsulins: molecular biology of the shell. Critical Reviews in Biochemistry and Molecular Biology. 1-12. PMID 28635326 DOI: 10.1080/10409238.2017.1337709  0.42
2016 Morgan SA, Nadler DC, Yokoo R, Savage DF. Biofuel metabolic engineering with biosensors. Current Opinion in Chemical Biology. 35: 150-158. PMID 27768949 DOI: 10.1016/J.Cbpa.2016.09.020  0.75
2016 Nadler DC, Morgan SA, Flamholz A, Kortright KE, Savage DF. Rapid construction of metabolite biosensors using domain-insertion profiling. Nature Communications. 7: 12266. PMID 27470466 DOI: 10.1038/Ncomms12266  0.78
2016 Cassidy-Amstutz C, Oltrogge LM, Going CC, Lee A, Teng PK, Quintanilla D, East-Seletsky A, Williams ER, Savage DF. Identification of a minimal peptide tag for in vivo and in vitro loading of encapsulin. Biochemistry. PMID 27224728 DOI: 10.1021/Acs.Biochem.6B00294  0.382
2016 Oakes BL, Nadler DC, Flamholz A, Fellmann C, Staahl BT, Doudna JA, Savage DF. Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch. Nature Biotechnology. 34: 646-51. PMID 27136077 DOI: 10.1038/Nbt.3528  0.774
2015 Chaijarasphong T, Nichols RJ, Kortright KE, Nixon CF, Teng PK, Oltrogge LM, Savage DF. Programmed ribosomal frameshifting mediates expression of the α-carboxysome. Journal of Molecular Biology. PMID 26608811 DOI: 10.1016/J.Jmb.2015.11.017  0.377
2014 Oakes BL, Nadler DC, Savage DF. Protein engineering of Cas9 for enhanced function Methods in Enzymology. 546: 491-511. PMID 25398355 DOI: 10.1016/B978-0-12-801185-0.00024-6  0.789
2014 Savage D. Sequestered: Molecular Physiology of Bacterial Microcompartments Biophysical Journal. 106: 445a. DOI: 10.1016/J.Bpj.2013.11.2517  0.366
2013 Chen AH, Robinson-Mosher A, Savage DF, Silver PA, Polka JK. The bacterial carbon-fixing organelle is formed by shell envelopment of preassembled cargo. Plos One. 8: e76127. PMID 24023971 DOI: 10.1371/Journal.Pone.0076127  0.517
2012 Chen AH, Afonso B, Silver PA, Savage DF. Spatial and temporal organization of chromosome duplication and segregation in the cyanobacterium Synechococcus elongatus PCC 7942. Plos One. 7: e47837. PMID 23112856 DOI: 10.1371/Journal.Pone.0047837  0.722
2012 Bonacci W, Teng PK, Afonso B, Niederholtmeyer H, Grob P, Silver PA, Savage DF. Modularity of a carbon-fixing protein organelle. Proceedings of the National Academy of Sciences of the United States of America. 109: 478-83. PMID 22184212 DOI: 10.1073/Pnas.1108557109  0.779
2010 Savage DF, O'Connell JD, Miercke LJ, Finer-Moore J, Stroud RM. Structural context shapes the aquaporin selectivity filter. Proceedings of the National Academy of Sciences of the United States of America. 107: 17164-9. PMID 20855585 DOI: 10.1073/Pnas.1009864107  0.511
2010 Niederholtmeyer H, Wolfstädter BT, Savage DF, Silver PA, Way JC. Engineering cyanobacteria to synthesize and export hydrophilic products. Applied and Environmental Microbiology. 76: 3462-6. PMID 20363793 DOI: 10.1128/Aem.00202-10  0.512
2010 Savage DF, Afonso B, Chen AH, Silver PA. Spatially ordered dynamics of the bacterial carbon fixation machinery. Science (New York, N.Y.). 327: 1258-61. PMID 20203050 DOI: 10.1126/Science.1186090  0.736
2009 Newby ZE, O'Connell JD, Gruswitz F, Hays FA, Harries WE, Harwood IM, Ho JD, Lee JK, Savage DF, Miercke LJ, Stroud RM. A general protocol for the crystallization of membrane proteins for X-ray structural investigation. Nature Protocols. 4: 619-37. PMID 19360018 DOI: 10.1038/Nprot.2009.27  0.678
2008 Savage DF, Way J, Silver PA. Defossiling fuel: how synthetic biology can transform biofuel production. Acs Chemical Biology. 3: 13-6. PMID 18205286 DOI: 10.1021/Cb700259J  0.48
2008 Savage DF. Cell-free protein synthesis: Methods and protocols, edited by Alexander S. Spirin and James R. Swartz. Protein Science. 17: 962-963. DOI: 10.1110/Ps.083513908  0.408
2007 Savage DF, Anderson CL, Robles-Colmenares Y, Newby ZE, Stroud RM. Cell-free complements in vivo expression of the E. coli membrane proteome. Protein Science : a Publication of the Protein Society. 16: 966-76. PMID 17456747 DOI: 10.1110/Ps.062696307  0.77
2007 Savage DF, Stroud RM. Structural basis of aquaporin inhibition by mercury. Journal of Molecular Biology. 368: 607-17. PMID 17376483 DOI: 10.1016/J.Jmb.2007.02.070  0.509
2004 Egea PF, Shan SO, Napetschnig J, Savage DF, Walter P, Stroud RM. Substrate twinning activates the signal recognition particle and its receptor. Nature. 427: 215-21. PMID 14724630 DOI: 10.1038/Nature02250  0.741
2004 Lee JK, Khademi S, Harries W, Savage D, Miercke L, Stroud RM. Water and glycerol permeation through the glycerol channel GlpF and the aquaporin family. Journal of Synchrotron Radiation. 11: 86-8. PMID 14646142 DOI: 10.1107/S0909049503023872  0.758
2003 Savage DF, Egea PF, Robles-Colmenares Y, O'Connell JD, Stroud RM. Architecture and selectivity in aquaporins: 2.5 a X-ray structure of aquaporin Z. Plos Biology. 1: E72. PMID 14691544 DOI: 10.1371/Journal.Pbio.0000072  0.763
2003 Stroud RM, Savage D, Miercke LJ, Lee JK, Khademi S, Harries W. Selectivity and conductance among the glycerol and water conducting aquaporin family of channels. Febs Letters. 555: 79-84. PMID 14630323 DOI: 10.1016/S0014-5793(03)01195-5  0.737
2003 Keatinge-Clay AT, Shelat AA, Savage DF, Tsai SC, Miercke LJ, O'Connell JD, Khosla C, Stroud RM. Catalysis, specificity, and ACP docking site of Streptomyces coelicolor malonyl-CoA:ACP transacylase. Structure (London, England : 1993). 11: 147-54. PMID 12575934 DOI: 10.1016/S0969-2126(03)00004-2  0.698
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