Francois Ribalet

I am a marine ecologist studying how the environment shapes the distribution and abundance of plankton in the ocean. I am interested in where these organisms are found, how many occur there, and why.

last modified: April 2017

Senior Research Scientist
ribalet at

I am interested predominantly in the physiology and ecology of marine microbes and their adaptation to different environments. As part of the Simons Collaboration on Ocean Process and Ecosystems project, I am investigating the interaction between cyanobacteria and their consumers and its effects on ecosystem stability.

I use SeaFlow, our underway flow cytometer developed in the Armbrust lab, to collect continuous information about the abundance and optical properties of marine microbes. Since its launch in 2008, we have collected over 150,000 discrete observations of plankton at the surface of the ocean. I develop tools to process the high-volume of SeaFlow data and extract information such as rates of cell division and cell mortality. For more information about our cytometry facility and software tools, go to


  • 2007 Ph.D in Biological Sciences – Open University of London, UK, hosted by the Stazione Zoologica Anton Dohrn, Naples, IT. Thesis title: The role of polyunsaturated aldehyde production in the physiology and ecology of diatoms, 270 pp.
  • 2003 M.Sc in Biological Oceanology and Marine Environment – University Pierre & Marie Curie, Paris, FR
  • 2001 B.Sc in Population Biology and Ecosystems – University Pierre & Marie Curie, Paris, FR

Positions Held

  • Research Senior Scientist, School of Oceanography, University of Washington, USA, 2015-present
  • Research Assistant Professor, School of Oceanography, University of Washington, USA, 2012-2015
  • Postdoctoral Fellow, School of Oceanography, University of Washington, USA, 2008-2012
  • Graduate Research Assistant, Stazione Zoologica di Napoli, IT, 2003-2007
  • Undergraduate Research Assistant, Station Biologique de Roscoff, FR, 2001-2003

Journal Publications

  1. Hamilton, M., Hennon, G.M., Morales, R., Needoba, J., Peterson, T.D., Schatz, M., Swalwell, J., Armbrust, E.V. and Ribalet, F. 2017. Dynamics of Teleaulax-like cryptophytes during the decline of a red water bloom in the Columbia River Estuary. Journal of Plankton Research, in press
  2. Heal, K., Qin, W., Ribalet, F., Bertagnolli, A., Coyote-Maestes, W., Hmelo, L. Moffett, J., Devol, A., Armbrust, E.V., Stahl, D. and Ingalls, A. 2017. Two distinct pools of B12 analogs reveal community interdependencies in the ocean. Proceedings of the National Academy of Sciences USA, 114:364-369
  3. Hyrkas, J., Clayton, S., Ribalet, F., Halperin, D., Armbrust, E.V. and Howe, B. 2016. Scalable clustering algorithms for continuous environmental flow cytometry. Bioinformatics 32:417-423
  4. Ribalet, F., Swalwell, J., Clayton, S., Jimenez, V., Sudek, S., Lin, Y., Johnson, Z.I., Worden, A.Z. and Armbrust, E.V. 2015. Light-driven synchrony of Prochlorococcus cell growth and mortality in the subtropical Pacific gyre. Proceedings of the National Academy of Sciences USA 112:8008-8012
  5. Ribalet, F., Bastianini, M., Vidoudez, C., Acri, F., Berges, J., Ianora, A., Miralto, A., Pohnert, G., Romano, G., Wichard, T., and Casotti, R. 2014. Phytoplankton cell lysis associated with polyunsaturated aldehyde release in the northern Adriatic Sea. PLoS ONE 9(1):e85947
  6. Halperin, D., Weitz, K., Howe, B., Ribalet, F., Saito, M., and Armbrust, E.V. 2013. Real-Time Collaborative Analysis with (Almost) Pure SQL: A Case Study in Biogeochemical Oceanography. Proceedings of the 25th International Conference on Scientific and Statistical Database Management, 28:1-12
  7. Pavlesky, H., Ribalet, F., Swalwell, J., Cosca, C.E., Cokelet, E., Feely, R., Armbrust, E.V., and Quay, P. 2013. The influence of net community production and phytoplankton community structure on CO2 uptake in the Gulf of Alaska. Global Biogeochemical Cycles 27: 664-676
  8. Howe, B., Halperin, D., Ribalet, F., Sagar, C., and Armbrust, E.V. 2013. SQLShare: Scientific Workflow Management via Relational View Sharing. Computing in Science & Engineering, 15: 22-31
  9. Ribalet, F. 2012. Toward an adaptive sampling strategy to understand the sensitivity of biogeochemical province boundaries to climate change. Journal of Marine Biology and Oceanography 1:2 (Editorial)
  10. Swalwell, J.E., Ribalet, F., and Armbrust, E.V. 2011. SeaFlow: A novel underway flow-cytometer for continuous observations of phytoplankton in the ocean. Limnology & Oceanography Methods 9: 466-477
  11. Ribalet, F., Schruth, D., and Armbrust, E.V. 2011. flowPhyto: enabling automated analysis of microscopic algae from continuous flow cytometric data. Bioinformatics 27:732-733
  12. Ribalet, F., Marchetti, A., Hubbard, K.A., Brown, K., Durkin, C.A., Morales, R., Robert, M., Swalwell, J.E, Tortell, P.D., and Armbrust, E.V. 2010. Unveiling a phytoplankton hotspot at a narrow boundary between coastal and oceanic waters. Proceedings of the National Academy of Sciences USA 107:16571-16576
  13. Ribalet, F., Vidoudez, C., Cassin, D., Pohnert, G., Ianora, A., Miralto, A., and Casotti, R. 2009. High plasticity in the production of diatom-polyunsaturated aldehydes under nutrient limitation: Physiological and ecological implications. Protist 160:444-451
  14. Marchetti, A., Parker, M.S., Moccia, L.P., Lin, E.O., Arrieta, A.L., Ribalet, F., Murphy, M.E.P., Maldonado, M.T., and Armbrust, V.E. 2009. Iron storage by ferritin in bloom-forming marine pennate diatoms. Nature 457:467-470
  15. Ribalet, F., Intertaglia, L., Lebaron, P., and Casotti, R. 2008. Differential effect of three polyunsaturated aldehydes on marine bacterial isolates. Aquatic Toxicology 86: 249-255
  16. Ribalet, F., Berges, J.A., Ianora, A., and Casotti, R. 2007. Growth inhibition of cultured marine phytoplankton by toxic algal-derived polyunsaturated aldehydes. Aquatic Toxicology 85:219-227
  17. Ribalet, F., Wichard, T., Pohnert, G., Ianora, A., Miralto, A., and Casotti, R. 2007. Age and nutrient limitations enhance aldehyde production in marine diatoms. Phytochemistry 68: 2059-2067
  18. Vardi, A., Formiggini, F., Casotti, R., de Martino, A., Ribalet, F., Miralto, A., and Bowler, C. 2006. A stress surveillance system based on calcium and nitric oxide in marine diatoms. PLoS Biology 4: 411-419A

Open Source Software

  • popcycle is a R/python package that process in real-time continuous flow cytometry data from SeaFlow. The software is built to be operated remotely via satellite connection.
  • ssPopModel is a R package that uses a size-structured matrix population model to estimate hourly division rates of phytoplankton populations based on the dynamics of their size distribution. These estimates are independent of variations in cell abundance and can be used to study physiologically-driven changes in population dynamics. The model is described in Sosik, H. et al. 2003 Limnology & Oceanography 48, 1756:1765
  • cytDiv is a R function that calculates ecological diversity indices for a microbial community based on its bio-optical properties measured at the single cell level by flow cytometry. The indices express the organization and structure of a community, its richness in physiological and genetic variations. The equations used to calculate the indices are described in Li, W. 1997 Limnology & Oceanography 42, 874:880
  • clusterPop is a R package that performs a mixture of manual and automated clustering analysis of phytoplankton populations. It provides a collection of functions that performs rapid classification of a fixed, predefined number of phytoplankton populations using multivariate gating and k-means statistical clustering method. The package is compatible with our software package flowPhyto
  • flowPhyto is a package for the R statistical programming language that uses automated computational methods to cluster phytoplankton populations, perform aggregate statistics and create maps of phytoplankton distribution from georeferenced flow cytometry data in a highly parallel fashion using file-based wrapper functions. For more details, see Ribalet, F. et al. 2011 Bioinformatics 27, 732:733