Publications

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* = equal contribution

  1. Y Zhu, HS Anderson, E Salcedo, SE Miller, K Longnecker, MC Kido Soule, ST, Haley, GJ Swarr, R Braakman, ST Dyhrman, EB Kujawinski (2025) Characterization of Phytoplankton-Excreted Metabolites Mediating Carbon Flux through the Surface Ocean. bioRxiv, pp.2025-11
  2. KH Halloran, R Braakman, A Coe, G Swarr, MC Kido Soule, SW Chisholm, EB Kujawinski (2025) “Uptake of Prochlorococcus-derived metabolites by Alteromonas macleodii MIT1002 shows high levels of substrate specificity”. bioRxiv, 2025-01
  3. R Braakman (2025). The chitin raft hypothesis for the colonization of the open ocean by cyanobacteria. Philosophical Transactions of the Royal Society B. 380, 20240086
  4. S Blaskowski, M Roald, PM Berube, R Braakman, EV Armbrust (2025) “Simultaneous acclimation to nitrogen and iron scarcity in open ocean cyanobacteria revealed by sparse tensor decomposition of metatranscriptomes” Science Advances 11, eadr4310
  5. Braakman, R., Satinsky, B., O’Keefe, T. J., Longnecker, K., Hogle, S. L., Becker, J. W., et al. (2025). “Global niche partitioning of purine and pyrimidine cross-feeding among ocean microbes”. Science Advances. 11(1), eadp1949
  6. A Coe*, R Braakman*, SJ Biller, A Arellano, C Bliem, NN Vo, K von Emster, E Thomas, MA DeMers, C Steglich, J Huisman, SW Chisholm (2024) “Emergence of metabolic coupling to the heterotroph Alteromonas promotes dark survival in Prochlorococcus” ISME communications 4, ycae131
  7. I Veseli*, MA DeMers*, ZS Cooper*, MS Schechter, S Miller, L Weber, CB Smith, LT Rodriguez, WF Schroer, MR McIlvin, PZ Lopez, M Saito, S Dyhrman, AM Eren, MA Moran, R Braakman (2024) “Digital Microbe: a genome-informed data integration framework for team science on emerging model organisms” Scientific Data, 11(1), p.967
  8. JW Becker, S Pollak, JW Berta-Thompson, KW Becker, R Braakman, KD Dooley, T Hackl, A Coe, A Arellano, KN LeGault, PM Berube, SJ Biller, A Cubillos-Ruiz, BAS Van Mooy, SW Chisholm (2024) “Novel isolates expand the physiological diversity of Prochlorococcus and illuminate its macroevolution”. mBio, pp.e03497-23
  9. EB Kujawinski, R Braakman, K Longnecker, JW Becker, SW Chisholm, K Dooley, MC Kido Soule, GJ Swarr, K Halloran (2023) “Metabolite diversity among Prochlorococcus strains belonging to divergent ecotypes” Msystems, 8(5), pp.e01261-22
  10. G Capovilla*, R Braakman*, GP Fournier, T Hackl, J Schwartzman, X Lu, A Yelton, K Longnecker, MC Kido Soule, E Thomas, G Swarr, A Mongera, JG Payette, KG Castro, JR Waldbauer, EB Kujawinski, OX Cordero, SW Chisholm (2023) “Chitin utilization by marine picocyanobacteria and the evolution of a planktonic lifestyle”, Proceedings of the National Academy of Sciences USA, 120(20), p.e2213271120.
  11. MA Moran, EB Kujawinski, WF Schroer, SA Amin, NR Bates, EM Bertrand, R Braakman, CT Brown, MW Covert, SC Doney, ST Dyhrman, AS Edison, AM Eren, NM Levine, L Li, AC Ross, MA Saito, AE Santoro, D Segrè, A Shade, MB Sullivan, A Vardi (2022) “Microbial metabolites in the marine carbon cycle”, Nature Microbiology 7 (4), 508-523
  12. JM Lauderdale, R Braakman, G Forget, S Dutkiewicz, MJ Follows (2020) “Microbial feedbacks optimize ocean iron availability”, Proceedings of the National Academies of Sciences USA 117, 4842-4849
  13. R Braakman (2019) “Evolution of cellular metabolism and the rise of a globally productive biosphere”, Free Radical Biology and Medicine 140, 172-187
  14. PM Berube, A Rasmussen, R Braakman, R Stepanauskas, SW Chisholm (2019), “Emergence of trait variability through the lens of nitrogen assimilation in Prochlorococcus” eLife 8, e41043
  15. JJ Marlow, R. Braakman (2018) “Team players: How microbial partnerships shaped life on Earth”, Scientific American 319, 32-39
  16. PM Berube, S Biller, T Hackl, S Hogle, B Satinsky, J Becker, R. Braakman, S Collins, L Kelly, J Berta-Thompson, A Coe, K Bergauer, H Bouman, TJ Browning, D De Corte, C Hassler, Y Hulata, J Jacquot, E Maas, T Reinthaler, E Sintes, T Yokokawa, D Lindell, R Stepanauskas & SW Chisholm (2018) “Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments” Scientific Data 5, 180154
  17. R Braakman, MJ Follows & SW Chisholm (2017) “Metabolic evolution and the self-organization of ecosystems” Proceeding of the National Academy of Sciences USA 114 (15), E3091 – E3100
  18. R Braakman & DE Smith (2014) “Metabolic evolution of a deep-branching hyperthermophilic chemoautotrophic bacterium” PLOS One 9 (3), e93345
  19. R Braakman (2013) “Mapping metabolism onto the prebiotic organic chemistry of hydrothermal vents” Proceeding of the National Academy of Sciences USA 110 (33), 13236 – 13237
  20. R Braakman & DE Smith (2013) “The compositional and evolutionary logic of metabolism” Physical Biology 10 (1), 011001
  21. R Braakman & DE Smith (2012) “The emergence and early evolution of biological carbon-fixation” PLoS Computational Biology 8 (4), e1002455
  22. R Braakman & GA Blake (2011) “Principles and promise of Fabry-Perot resonators at terahertz frequencies” Journal of Applied Physics 109 (6), 063102
  23. R Braakman, A Belloche, GA Blake & K Menten (2010) “Search for interstellar methoxyacetonitrile and cyanoethanol: insights into coupling of cyano- to methanol and ammonia chemistry”, Astrophysical Journal 724 (2), 994
  24. R Braakman, BJ Drouin, SL Widicus Weaver & GA Blake (2010) “Extended analysis of hydroxyacetone in the torsional ground state”, Journal of Molecular Spectroscopy 264 (1), 43
  25. R Braakman & GA Blake (2010) “The millimeter-wave spectrum of 2-cyanoethanol” Journal of Molecular Spectroscopy 262 (2), 100
  26. R Braakman & GA Blake (2010) “The millimeter-wave spectrum of methoxyacetonitrile” Journal of Molecular Spectroscopy 262 (2), 93
  27. R Braakman (2010) “Gas phase terahertz spectroscopy and the study of complex interstellar chemistry” PhD thesis, Caltech
  28. LH Xu, J Fisher, RM Lees, HY Shi, JT Hougen, JC Pearson, BJ Drouin, GA Blake & R Braakman (2008) “Torsion-rotation analysis of the first three torsional states (Vt=0,1,2) and terahertz database for methanol”, Journal of Molecular Spectroscopy 251 (1), 305
  29. SL Widicus Weaver, R Braakman, DR Kent IV & Geoffrey A. Blake (2004) “The millimeter and submillimeter rotational spectrum of 1,3-dihydroxyacetone”, Journal of Molecular Spectroscopy 224 (2), 101
  30. FFS van der Tak, AMS Boonman, R Braakman & EF van Dishoeck (2003) “Sulphur chemistry in the envelopes of massive young stars”, Astronomy & Astrophysics 412(1), 133-145