A. Flamholz

Most-cited papers

SARS-CoV-2 (COVID-19) by the numbers
Y. Bar-On, A. Flamholz, R. Phillips, R. Milo
2020eLife891 citations Open access
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eQuilibrator—the biochemical thermodynamics calculator
A. Flamholz, Elad Noor, A. Bar-Even, R. Milo
2011Nucleic Acids Res.561 citations Open access
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Glycolytic strategy as a tradeoff between energy yield and protein cost
A. Flamholz, Elad Noor, A. Bar-Even, Wolfram Liebermeister +1 more
2013Proceedings of the National Academy of Sciences of the United States of America532 citations Open access
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Visual account of protein investment in cellular functions
Wolfram Liebermeister, Elad Noor, A. Flamholz, Dan Davidi +2 more
2014Proceedings of the National Academy of Sciences of the United States of America368 citations Open access
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Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants
A. Crits-Christoph, Rose S. Kantor, M. Olm, O. Whitney +15 more
2020mBio346 citations Open access
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Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism
Elad Noor, A. Bar-Even, A. Flamholz, E. Reznik +2 more
2014PLoS Comput. Biol.344 citations Open access
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The total number and mass of SARS-CoV-2 virions
R. Sender, Y. Bar-On, S. Gleizer, B. Bernshtein +3 more
2020Proceedings of the National Academy of Sciences of the United States of America262 citations Open access
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Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements
Dan Davidi, Elad Noor, Wolfram Liebermeister, A. Bar-Even +6 more
2016Proceedings of the National Academy of Sciences of the United States of America259 citations Open access
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Rethinking glycolysis: on the biochemical logic of metabolic pathways.
A. Bar-Even, A. Flamholz, Elad Noor, R. Milo
2012Nature Chemical Biology248 citations
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pH determines the energetic efficiency of the cyanobacterial CO2 concentrating mechanism
N. Mangan, A. Flamholz, Rachel D. Hood, R. Milo +1 more
2016Proceedings of the National Academy of Sciences of the United States of America213 citations Open access
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Revisiting Trade-offs between Rubisco Kinetic Parameters
A. Flamholz, Noam Prywes, Uri Moran, Dan Davidi +5 more
2019Biochemistry204 citations Open access
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Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch
Benjamin L. Oakes, Dana C Nadler, A. Flamholz, Christof Fellmann +3 more
2016Nature Biotechnology198 citations Open access
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Spanning high-dimensional expression space using ribosome-binding site combinatorics
L. Zelcbuch, Niv Antonovsky, A. Bar-Even, Ayelet Levin-Karp +11 more
2013Nucleic Acids Research194 citations Open access
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The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization
Elad Noor, A. Flamholz, A. Bar-Even, Dan Davidi +2 more
2016PLoS Comput. Biol.191 citations Open access
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Design and analysis of metabolic pathways supporting formatotrophic growth for electricity-dependent cultivation of microbes.
A. Bar-Even, Elad Noor, A. Flamholz, R. Milo
2013Biochimica et Biophysica Acta171 citations Open access
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Thermodynamic constraints shape the structure of carbon fixation pathways.
A. Bar-Even, A. Flamholz, Elad Noor, R. Milo
2012Biochimica et Biophysica Acta142 citations Open access
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An integrated open framework for thermodynamics of reactions that combines accuracy and coverage
Elad Noor, A. Bar-Even, A. Flamholz, Yaniv Lubling +2 more
2012Bioinform.132 citations Open access
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A note on the kinetics of enzyme action: A decomposition that highlights thermodynamic effects
Elad Noor, A. Flamholz, Wolfram Liebermeister, A. Bar-Even +1 more
2013FEBS Letters129 citations
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Rapid construction of metabolite biosensors using domain-insertion profiling
Dana C Nadler, Stacy-Anne Morgan, A. Flamholz, K. Kortright +1 more
2016Nature Communications122 citations Open access
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Tools for interpretation of wastewater SARS-CoV-2 temporal and spatial trends demonstrated with data collected in the San Francisco Bay Area
Hannah D. Greenwald, Lauren C. Kennedy, Adrian Hinkle, O. Whitney +17 more
2021Water Research X121 citations Open access
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The stringent response regulates adaptation to darkness in the cyanobacterium Synechococcus elongatus
Rachel D. Hood, Sean A. Higgins, A. Flamholz, R. Nichols +1 more
2016Proceedings of the National Academy of Sciences of the United States of America111 citations Open access
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Highly active rubiscos discovered by systematic interrogation of natural sequence diversity
Dan Davidi, Melina Shamshoum, Zhi-Jun Guo, Y. Bar-On +14 more
2020EMBO Journal93 citations Open access
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Nearest Neighbor Networks: clustering expression data based on gene neighborhoods
C. Huttenhower, A. Flamholz, Jess N. Landis, Sauhard Sahi +6 more
2007BMC Bioinformatics85 citations Open access
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Functional reconstitution of a bacterial CO2 concentrating mechanism in Escherichia coli
A. Flamholz, Eli J. Dugan, Cecilia Blikstad, S. Gleizer +8 more
2020eLife83 citations Open access
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Hydrophobicity and Charge Shape Cellular Metabolite Concentrations
A. Bar-Even, Elad Noor, A. Flamholz, J. Buescher +1 more
2011PLoS Comput. Biol.75 citations Open access
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eQuilibrator 3.0: a database solution for thermodynamic constant estimation
M. Beber, Mattia G. Gollub, Dana Mozaffari, Kevin M. Shebek +3 more
2021Nucleic Acids Res.72 citations Open access
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DABs are inorganic carbon pumps found throughout prokaryotic phyla
John James Desmarais, A. Flamholz, Cecilia Blikstad, Eli J. Dugan +7 more
2019Nature Microbiology66 citations Open access
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The quantified cell
A. Flamholz, R. Phillips, R. Milo
2014Molecular Biology of the Cell57 citations Open access
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A map of the rubisco biochemical landscape
Noam Prywes, Naiya R. Phillips, L. Oltrogge, Sebastian Lindner +17 more
2025Nature49 citations Open access
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Phosphoglycolate salvage in a chemolithoautotroph using the Calvin cycle
N. Claassens, G. Scarinci, A. Fischer, A. Flamholz +4 more
2020Proceedings of the National Academy of Sciences of the United States of America49 citations Open access
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Cell biology of photosynthesis over geologic time.
A. Flamholz, Patrick M. Shih
2020Current Biology32 citations Open access
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Trajectories for the evolution of bacterial CO2-concentrating mechanisms
A. Flamholz, Eli J. Dugan, Justin Panich, John James Desmarais +4 more
2022Proceedings of the National Academy of Sciences of the United States of America29 citations Open access
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Quantum chemistry reveals thermodynamic principles of redox biochemistry
A. Jinich, A. Flamholz, Haniu Ren, Sung-Jin Kim +5 more
2018PLoS Comput. Biol.29 citations Open access
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A quantitative compendium of COVID-19 epidemiology
Y. Bar-On, R. Sender, A. Flamholz, R. Phillips +1 more
202027 citations
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A map of the rubisco biochemical landscape
Noam Prywes, N.R. Philips, L. Oltrogge, Sebastian Lindner +16 more
2024bioRxiv19 citations Open access
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Closed ecosystems extract energy through self-organized nutrient cycles
Akshit Goyal, A. Flamholz, A. Petroff, A. Murugan
2023bioRxiv19 citations Open access
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Competing constraints shape the nonequilibrium limits of cellular decision-making
Nicholas C. Lammers, A. Flamholz, Hernán G. García
2022bioRxiv19 citations Open access
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Electro-microbial production techno-economic viability and environmental implications
Samuel J Lovat, Roee Ben-Nissan, Eliya Milshtein, Asaf Tzachor +4 more
2025Nature Biotechnology17 citations
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Carbon isotope fractionation by an ancestral rubisco suggests that biological proxies for CO2 through geologic time should be reevaluated
Renée Z. Wang, Robert J. Nichols, A. K. Liu, A. Flamholz +6 more
2023Proceedings of the National Academy of Sciences of the United States of America17 citations Open access
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Functional reconstitution of a bacterial CO2 concentrating mechanism in E. coli
A. Flamholz, Eli J. Dugan, Cecilia Blikstad, S. Gleizer +8 more
2020bioRxiv16 citations Open access
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Protein cost minimization promotes the emergence of coenzyme redundancy
J. Goldford, Ashish B. George, A. Flamholz, D. Segrè
2021Proceedings of the National Academy of Sciences of the United States of America14 citations Open access
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US grass-fed beef is as carbon intensive as industrial beef and ≈10-fold more intensive than common protein-dense alternatives
G. Eshel, A. Flamholz, A. Shepon, Ron Milo
2025Proceedings of the National Academy of Sciences of the United States of America13 citations Open access
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Uniform binding and negative catalysis at the origin of enzymes
Elad Noor, A. Flamholz, V. Jayaraman, B. Ross +4 more
2022Protein Science13 citations Open access
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Annotation-free prediction of microbial dioxygen utilization
A. Flamholz, J. Goldford, Philipp Richter, Elin M. Larsson +3 more
2024bioRxiv11 citations Open access
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Revisiting tradeoffs in Rubisco kinetic parameters
A. Flamholz, Noam Prywes, Uri Moran, Dan Davidi +5 more
2018bioRxiv11 citations Open access
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Optical O2 Sensors Also Respond to Redox Active Molecules Commonly Secreted by Bacteria
A. Flamholz, S. Saccomano, Kevin J. Cash, D. Newman
2022bioRxiv9 citations Open access
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The proteome is a terminal electron acceptor
A. Flamholz, Akshit Goyal, W. Fischer, D. Newman +1 more
2024bioRxiv8 citations Open access
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The proteome is a terminal electron acceptor
A. Flamholz, Akshit Goyal, W. Fischer, D. Newman +1 more
2025Proceedings of the National Academy of Sciences of the United States of America7 citations Open access
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Anthroponumbers.org: A quantitative database of human impacts on Planet Earth
Griffin Chure, R. Banks, A. Flamholz, N. Sarai +5 more
2022bioRxiv7 citations Open access
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Learning to Build a β-Carboxysome
Cecilia Blikstad, A. Flamholz, L. Oltrogge, D. Savage
2019Biochemistry5 citations Open access
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