Papers
Relevant and mostly recent papers by topic. See Google Scholar for a complete listing.
A. I. Flamholz, A. Goyal, W. W. Fischer, D. K. Newman, R. Phillips, The proteome is a terminal electron acceptor. PNAS 122, e2404048121 (2025).
A. I. Flamholz, J. E. Goldford, P. A. Richter, E. M. Larsson, A. Jinich, W. W. Fischer, D. K. Newman, Annotation-free prediction of microbial dioxygen utilization. mSystems 0, e0076324 (2024).
A. Goyal, A. I. Flamholz, A. P. Petroff, A. Murugan, Closed ecosystems extract energy through self-organized nutrient cycles. PNAS 120, e2309387120 (2023).
A. I. Flamholz, S. Saccomano, K. Cash, D. K. Newman, Optical O2 Sensors Also Respond to Redox Active Molecules Commonly Secreted by Bacteria. MBio, e0207622 (2022).
J. E. Goldford, A. B. George, A. I. Flamholz, D. Segrè, Protein cost minimization promotes the emergence of coenzyme redundancy. PNAS 119, e2110787119 (2022).
N. Prywes, N. R. Phillips, L. M. Oltrogge, S. Lindner, L. J. Taylor-Kearney, Y.-C. C. Tsai, B. de Pins, A. E. Cowan, H. A. Chang, R. Z. Wang, L. N. Hall, D. Bellieny-Rabelo, H. M. Nisonoff, R. F. Weissman, A. I. Flamholz, D. Ding, A. Y. Bhatt, O. Mueller-Cajar, P. M. Shih, R. Milo, D. F. Savage, A map of the rubisco biochemical landscape. Nature, 1–6 (2025).
R. Z. Wang, R. J. Nichols, A. K. Liu, A. I. Flamholz, J. Artier, D. M. Banda, D. F. Savage, J. M. Eiler, P. M. Shih, W. W. Fischer, Carbon isotope fractionation by an ancestral rubisco suggests that biological proxies for CO2 through geologic time should be reevaluated. PNAS 120, e2300466120 (2023).
A. I. Flamholz, E. Dugan, J. Panich, J. J. Desmarais, L. M. Oltrogge, W. W. Fischer, S. W. Singer, D. F. Savage, Trajectories for the evolution of bacterial CO2-concentrating mechanisms. PNAS 119, e2210539119 (2022).
A. I. Flamholz, E. Dugan, C. Blikstad, S. Gleizer, R. Ben-Nissan, S. Amram, N. Antonovsky, S. Ravishankar, E. Noor, A. Bar-Even, R. Milo, D. F. Savage, Functional reconstitution of a bacterial CO2 concentrating mechanism in Escherichia coli. Elife 9, e59882 (2020).
A. Flamholz, P. M. Shih, Cell biology of photosynthesis over geologic time. Curr. Biol. 30, R490–R494 (2020).
A. I. Flamholz, N. Prywes, U. Moran, D. Davidi, Y. M. Bar-On, L. M. Oltrogge, R. Alves, D. Savage, R. Milo, Revisiting trade-offs between Rubisco kinetic parameters. Biochemistry 58, 3365–3376 (2019).
J. J. Desmarais, A. I. Flamholz, C. Blikstad, E. J. Dugan, T. G. Laughlin, L. M. Oltrogge, A. W. Chen, K. Wetmore, S. Diamond, J. Y. Wang, D. F. Savage, DABs are inorganic carbon pumps found throughout prokaryotic phyla. Nature Microbiology 4, 2204–2215 (2019).