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 (2024) “Simultaneous acclimation to nitrogen and iron scarcity in open ocean cyanobacteria revealed by sparse tensor decomposition of metatranscriptomes” bioRxiv, pp.2024-07
  5. 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” bioRxiv, pp.2024-05
  6. 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
  7. 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
  8. 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
  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