David F Savage (David Savage)

ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 42

Top Venues

Nature communications

Proceedings of the National Academy of Sciences of the United States of America

Biochemistry

bioRxiv : the preprint server for biology

UC Berkeley

UCSF (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

UC Berkeley Jul 01 2011

United States

Associate Professor :: Molecular & Cell Biology

Education History

UCSF Sep 12 2001 - Apr 01 2007

United States

PHD :: Graduate Group in Biophyiscs

Publications

David Ding, Ada Y Shaw, Sam Sinai, Nathan Rollins, Noam Prywes, David F Savage, Michael T Laub, Debora S Marks
Protein design using structure-based residue preferences. Nature communications 15 (1) (2024)
Chintan Soni, Noam Prywes, Matthew Hall, Malavika A Nair, David F Savage, Alanna Schepartz, Abhishek Chatterjee
A Translation-Independent Directed Evolution Strategy to Engineer Aminoacyl-tRNA Synthetases. ACS central science 10 (6) (2024)
Luis E Valentin-Alvarado, Kathryn E Appler, Valerie De Anda, Marie C Schoelmerich, Jacob West-Roberts, Veronika Kivenson, Alexander Crits-Christoph, Lynn Ly, Rohan Sachdeva, Chris Greening, David F Savage, Brett J Baker, Jillian F Banfield
Asgard archaea modulate potential methanogenesis substrates in wetland soil. Nature communications 15 (1) (2024)
Noam Prywes, Naiya R Phillips, Luke M Oltrogge, Sebastian Lindner, Yi-Chin Candace Tsai, Benoit de Pins, Aidan E Cowan, Leah J Taylor-Kearney, Hana A Chang, Laina N Hall, Daniel Bellieny-Rabelo, Hunter M Nisonoff, Rachel F Weissman, Avi I Flamholz, David Ding, Abhishek Y Bhatt, Patrick M Shih, Oliver Mueller-Cajar, Ron Milo, David F Savage
A map of the rubisco biochemical landscape. bioRxiv : the preprint server for biology (2024)
Luis E Valentin-Alvarado, Kathryn E Appler, Valerie De Anda, Marie C Schoelmerich, Jacob West-Roberts, Veronika Kivenson, Alexander Crits-Christoph, Lynn Ly, Rohan Sachdeva, Chris Greening, David F Savage, Brett J Baker, Jillian F Banfield
Asgard archaea modulate potential methanogenesis substrates in wetland soil. Nature communications 15 (1) (2024)
Noam Prywes, Naiya R Phillips, Luke M Oltrogge, Sebastian Lindner, Yi-Chin Candace Tsai, Benoit de Pins, Aidan E Cowan, Leah J Taylor-Kearney, Hana A Chang, Laina N Hall, Daniel Bellieny-Rabelo, Hunter M Nisonoff, Rachel F Weissman, Avi I Flamholz, David Ding, Abhishek Y Bhatt, Patrick M Shih, Oliver Mueller-Cajar, Ron Milo, David F Savage
A map of the rubisco biochemical landscape. bioRxiv : the preprint server for biology (2024)
David Ding, Ada Y Shaw, Sam Sinai, Nathan Rollins, Noam Prywes, David F Savage, Michael T Laub, Debora S Marks
Protein design using structure-based residue preferences. Nature communications 15 (1) (2024)
Chintan Soni, Noam Prywes, Matthew Hall, Malavika A Nair, David F Savage, Alanna Schepartz, Abhishek Chatterjee
A Translation-Independent Directed Evolution Strategy to Engineer Aminoacyl-tRNA Synthetases. ACS central science 10 (6) (2024)
David Ding, Ada Y Shaw, Sam Sinai, Nathan Rollins, Noam Prywes, David F Savage, Michael T Laub, Debora S Marks
Protein design using structure-based residue preferences. Nature communications 15 (1) (2024)
Noam Prywes, Naiya R Phillips, Luke M Oltrogge, Sebastian Lindner, Yi-Chin Candace Tsai, Benoit de Pins, Aidan E Cowan, Leah J Taylor-Kearney, Hana A Chang, Laina N Hall, Daniel Bellieny-Rabelo, Hunter M Nisonoff, Rachel F Weissman, Avi I Flamholz, David Ding, Abhishek Y Bhatt, Patrick M Shih, Oliver Mueller-Cajar, Ron Milo, David F Savage
A map of the rubisco biochemical landscape. bioRxiv : the preprint server for biology (2024)
Luis E Valentin-Alvarado, Kathryn E Appler, Valerie De Anda, Marie C Schoelmerich, Jacob West-Roberts, Veronika Kivenson, Alexander Crits-Christoph, Lynn Ly, Rohan Sachdeva, Chris Greening, David F Savage, Brett J Baker, Jillian F Banfield
Asgard archaea modulate potential methanogenesis substrates in wetland soil. Nature communications 15 (1) (2024)
David Ding, Ada Y Shaw, Sam Sinai, Nathan Rollins, Noam Prywes, David F Savage, Michael T Laub, Debora S Marks
Protein design using structure-based residue preferences. Nature communications 15 (1) (2024)
Renée Z Wang, Robert J Nichols, Albert K Liu, Avi I Flamholz, Juliana Artier, Douglas M Banda, David F Savage, John M Eiler, Patrick M Shih, Woodward W Fischer
Carbon isotope fractionation by an ancestral rubisco suggests that biological proxies for CO 2 through geologic time should be reevaluated. Proceedings of the National Academy of Sciences of the United States of America 120 (20) (2023)
Cecilia Blikstad, Eli J Dugan, Thomas G Laughlin, Julia B Turnšek, Mira D Liu, Sophie R Shoemaker, Nikoleta Vogiatzi, Jonathan P Remis, David F Savage
Identification of a carbonic anhydrase-Rubisco complex within the alpha-carboxysome. Proceedings of the National Academy of Sciences of the United States of America 120 (43) (2023)
Renée Z Wang, Robert J Nichols, Albert K Liu, Avi I Flamholz, Juliana Artier, Douglas M Banda, David F Savage, John M Eiler, Patrick M Shih, Woodward W Fischer
Carbon isotope fractionation by an ancestral rubisco suggests that biological proxies for CO 2 through geologic time should be reevaluated. Proceedings of the National Academy of Sciences of the United States of America 120 (20) (2023)
Benja-Min A Adler, Marena I Trinidad, Daniel Bellieny Rabelo, Elaine Zhang, Hannah M Karp, Petr Skopintsev, Brittney W Thornton, Rachel F Weissman, Peter H Yoon, Lin-Xing Chen, Tomas Hessler, Amy R Eggers, David Colognori, Ron S Boger, Erin E Doherty, Connor A Tsuchida, Ryan V Tran, Laura Hofman, Honglue Shi, Kevin M Wasko, Zehan Zhou, Chenglong Xia, Muntathar J Al-Shimary, Jaymin R Patel, Vienna C J X Thomas, Rithu Pattali, Matthew J Kan, Anna Vardapetyan, Alana Yang, Arushi Lahiri, Michaela F Maxwell, Andrew G Murdock, Glenn C Ramit, Hope R Henderson, Roland W Calvert, Rebecca S Bamert, Gavin J Knott, Audrone Lapinaite, Patrick Pausch, Joshua C Cofsky, Erik J Sontheimer, Blake Wiedenheft, Peter C Fineran, Stan J J Brouns, Dipali G Sashital, Brian C Thomas, Christopher T Brown, Daniela S A Goltsman, Rodolphe Barrangou, Virginijus Siksnys, Jillian F Banfield, David F Savage, Jennifer A Doudna
CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes. Nucleic acids research (2023)
Luke M Oltrogge, Allen W Chen, Thawatchai Chaijarasphong, Julia B Turnšek, David F Savage
α-Carboxysome Size Is Controlled by the Disordered Scaffold Protein CsoS2. Biochemistry (2023)
Emily G Armbruster, Jina Lee, Joshua Hutchings, Arica R VanderWal, Eray Enustun, Benja-Min A Adler, Ann Aindow, Amar Deep, Zaida K Rodriguez, Chase J Morgan, Majid Ghassemian, Emeric Charles, Brady F Cress, David F Savage, Jennifer A Doudna, Kit Pogliano, Kevin D Corbett, Elizabeth Villa, Joe Pogliano
Sequential membrane- and protein-bound organelles compartmentalize genomes during phage infection. bioRxiv : the preprint server for biology (2023)
Renée Z Wang, Robert J Nichols, Albert K Liu, Avi I Flamholz, Juliana Artier, Douglas M Banda, David F Savage, John M Eiler, Patrick M Shih, Woodward W Fischer
Carbon isotope fractionation by an ancestral rubisco suggests that biological proxies for CO 2 through geologic time should be reevaluated. Proceedings of the National Academy of Sciences of the United States of America 120 (20) (2023)
Renée Z Wang, Robert J Nichols, Albert K Liu, Avi I Flamholz, Juliana Artier, Douglas M Banda, David F Savage, John M Eiler, Patrick M Shih, Woodward W Fischer
Carbon isotope fractionation by an ancestral rubisco suggests that biological proxies for CO 2 through geologic time should be reevaluated. Proceedings of the National Academy of Sciences of the United States of America 120 (20) (2023)
Renée Z Wang, Robert J Nichols, Albert K Liu, Avi I Flamholz, Juliana Artier, Douglas M Banda, David F Savage, John M Eiler, Patrick M Shih, Woodward W Fischer
Carbon isotope fractionation by an ancestral rubisco suggests that biological proxies for CO 2 through geologic time should be reevaluated. Proceedings of the National Academy of Sciences of the United States of America 120 (20) (2023)
Avi I Flamholz, Eli J Dugan, Justin Panich, John James Desmarais, Luke M Oltrogge, Woodward W Fischer, Steven W Singer, David F Savage
Trajectories for the evolution of bacterial CO 2 -concentrating mechanisms. Proceedings of the National Academy of Sciences of the United States of America 119 (49) (2022)
Lauren Ann Metskas, Davi Ortega, Luke M Oltrogge, Cecilia Blikstad, Derik R Lovejoy, Thomas G Laughlin, David F Savage, George J Lu
Rubisco forms a lattice inside alpha-carboxysomes. Nature communications 13 (1) (2022)
William B Carpenter, Abhijit A Lavania, Julia S Borden, Luke M Oltrogge, Davis Perez, Peter D Dahlberg, David F Savage, W E Moerner
Ratiometric Sensing of Redox Environments Inside Individual Carboxysomes Trapped in Solution. The journal of physical chemistry letters 13 (20) (2022)
Arik Shams, Sean A Higgins, Christof Fellmann, Thomas G Laughlin, Benjamin L Oakes, Rachel Lew, Shin Kim, Maria Lukarska, Madeline Arnold, Brett T Staahl, Jennifer A Doudna, David F Savage
Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules. Nature communications 12 (1) (2021)
Katie A Lien, Kayla Dinshaw, Robert J Nichols, Caleb Cassidy-Amstutz, Matthew Knight, Rahul Singh, Lindsay D Eltis, David F Savage, Sarah A Stanley
A nanocompartment system contributes to defense against oxidative stress in Mycobacterium tuberculosis. eLife 10 (2021)
Robert J Nichols, Benjamin LaFrance, Naiya R Phillips, Devon R Radford, Luke M Oltrogge, Luis E Valentin-Alvarado, Amanda J Bischoff, Eva Nogales, David F Savage
Discovery and characterization of a novel family of prokaryotic nanocompartments involved in sulfur metabolism. eLife 10 (2021)
Tina Y Liu, Gavin J Knott, Dylan C J Smock, John James Desmarais, Sungmin Son, Abdul Bhuiya, Shrutee Jakhanwal, Noam Prywes, Shreeya Agrawal, María Díaz de León Derby, Neil A Switz, Maxim Armstrong, Andrew R Harris, Emeric J Charles, Brittney W Thornton, Parinaz Fozouni, Jeffrey Shu, Stephanie I Stephens, G Renuka Kumar, Chunyu Zhao, Amanda Mok, Anthony T Iavarone, Arturo M Escajeda, Roger McIntosh, Shineui Kim, Eli J Dugan, null null, Katherine S Pollard, Ming X Tan, Melanie M Ott, Daniel A Fletcher, Liana F Lareau, Patrick D Hsu, David F Savage, Jennifer A Doudna
Accelerated RNA detection using tandem CRISPR nucleases. Nature chemical biology 17 (9) (2021)
Avi I Flamholz, Eli J Dugan, Cecilia Blikstad, Shmuel Gleizer, Roee Ben-Nissan, Shira Amram, Niv Antonovsky, Sumedha Ravishankar, Elad Noor, Arren Bar-Even, Ron Milo, David F Savage
Functional reconstitution of a bacterial CO2 concentrating mechanism in Escherichia coli. eLife 9 (2020)
Luke M Oltrogge, Thawatchai Chaijarasphong, Allen W Chen, Eric R Bolin, Susan Marqusee, David F Savage
Multivalent interactions between CsoS2 and Rubisco mediate α-carboxysome formation. Nature structural & molecular biology 27 (3) (2020)
John J Desmarais, Avi I Flamholz, Cecilia Blikstad, Eli J Dugan, Thomas G Laughlin, Luke M Oltrogge, Allen W Chen, Kelly Wetmore, Spencer Diamond, Joy Y Wang, David F Savage
DABs are inorganic carbon pumps found throughout prokaryotic phyla. Nature microbiology 4 (12) (2019)
Conner C Harper, Andrew G Elliott, Luke M Oltrogge, David F Savage, Evan R Williams
Multiplexed Charge Detection Mass Spectrometry for High-Throughput Single Ion Analysis of Large Molecules. Analytical chemistry 91 (11) (2019)
David F Savage
Cas14: Big Advances from Small CRISPR Proteins. Biochemistry 58 (8) (2019)
Cecilia Blikstad, Avi I Flamholz, Luke M Oltrogge, David F Savage
Learning to Build a β-Carboxysome. Biochemistry 58 (16) (2019)
Avi I Flamholz, Noam Prywes, Uri Moran, Dan Davidi, Yinon M Bar-On, Luke M Oltrogge, Rui Alves, David F Savage, Ron Milo
Revisiting Trade-offs between Rubisco Kinetic Parameters. Biochemistry 58 (31) (2019)
Sean A Higgins, Sorel V Y Ouonkap, David F Savage
Rapid and Programmable Protein Mutagenesis Using Plasmid Recombineering. ACS synthetic biology 6 (10) (2017)
Sean A Higgins, David F Savage
Protein Science by DNA Sequencing: How Advances in Molecular Biology Are Accelerating Biochemistry. Biochemistry 57 (1) (2017)
Robert J Nichols, Caleb Cassidy-Amstutz, Thawatchai Chaijarasphong, David F Savage
Encapsulins: molecular biology of the shell. Critical reviews in biochemistry and molecular biology 52 (5) (2017)
Dana C Nadler, Stacy-Anne Morgan, Avi Flamholz, Kaitlyn E Kortright, David F Savage
Rapid construction of metabolite biosensors using domain-insertion profiling. Nature communications 7 (2016)
Benjamin L Oakes, Dana C Nadler, Avi Flamholz, Christof Fellmann, Brett T Staahl, Jennifer A Doudna, David F Savage
Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch. Nature biotechnology 34 (6) (2016)
Rachel D Hood, Sean A Higgins, Avi Flamholz, Robert J Nichols, David F Savage
The stringent response regulates adaptation to darkness in the cyanobacterium Synechococcus elongatus. Proceedings of the National Academy of Sciences of the United States of America 113 (33) (2016)
Niall M Mangan, Avi Flamholz, Rachel D Hood, Ron Milo, David F Savage
pH determines the energetic efficiency of the cyanobacterial CO2 concentrating mechanism. Proceedings of the National Academy of Sciences of the United States of America 113 (36) (2016)

David F Savage.css-eqlu8i{font-size:small;padding-left:4px;} (David Savage)

Publication Activity (10 Years)

Top Topics

Top Venues

David F Savage (David Savage)