Paula Ramos-Silva

Paula Ramos-Silva

I am a computational and experimental biologist with background in molecular evolution, bioinformatics and biomineralization. I am fascinated by marine biodiversity and have studied evolutionary processes in mollusks, corals and bacteria. In my Marie Skłodowska-Curie project EPIC "Evolution of planktonic gastropod calcification" I am studying the evolution and mechanisms of biomineralization in planktonic gastropods, and how they can cope with ocean acidification. 


bioinformatics, biomineralization, molecular evolution, macroevolution, next generation sequencing, adaptation, ocean acidification, RNA, proteins


Biomineralization in planktonic gastropods

Holoplanktonic gastropods (pteropods and heteropods) are among the most vulnerable calcifiers to ocean acidification. They live at the ocean surface and build thin and delicate shells of aragonite, a polymorph of calcium carbonate. My research focuses on the biomineralization genes and mechanisms controlling their shell formation and aims at a better understanding of calcification by marine zooplankton and the impacts of ocean acidification on this process.


Key Publications

Ramos-Silva P,  Odendaal M, Wall-Palmer D, Mekkes L, Peijnenburg KTCA. Transcriptomic Responses of Adult Versus Juvenile Atlantids to Ocean Acidification. Frontiers in Marine Science 2022; 9: 1–12. Link

Ramos-Silva P, Wall-Palmer D, Marlétaz F, Marin F, Peijnenburg KTCA. 2021. Evolution and biomineralization of pteropod shells. Journal of Structural Biology 213: 107779. Link 

Ramos-Silva P, Serrano M, Henriques AO. 2019. From Root to Tips: Sporulation Evolution and Specialization in Bacillus subtilis and the Intestinal Pathogen Clostridioides difficile. Molecular Biology and Evolution 36:2714–2736. Link 

Ramos-Silva P, Kaandorp J, Herbst F, Plasseraud L, Alcaraz G, Stern C, Corneillat M, Guichard N, Durlet C, Luquet G, Marin F. 2014. The Skeleton of the Staghorn Coral Acropora millepora: Molecular and Structural Characterization. PLoS One 9:e97454.  Link 

Ramos-Silva P, Kaandorp J, Huisman L, Marie B, Zanella-Cléon I, Guichard N, Miller DJ, Marin F. 2013. The Skeletal Proteome of the Coral Acropora millepora: The Evolution of Calcification by Co-Option and Domain Shuffling. Molecular Biology and Evolution 30:2099–2112. Link

Ramos-Silva P, Marin F, Kaandorp J, Marie B. 2013. Biomineralization toolkit: The importance of sample cleaning prior to the characterization of biomineral proteomes. Proceedings of the National Academy of Sciences USA 110:E2144–E2146.  Link

Ramos-Silva P, Benhamada S, Le Roy N, Marie B, Guichard N, Zanella-Cléon I, Plasseraud L, Corneillat M, Alcaraz G, Kaandorp J, Marin F. 2012. Novel Molluskan Biomineralization Proteins Retrieved from Proteomics: A Case Study with Upsalin. ChemBioChem 13:1067–1078. Link 

All publications on Google Scholar


Lecturing and supervision

  • Supervision: G. Casas Canales (MSc in Freshwater and Marine Biology - Univ. Amsterdam),  Transcriptomic responses of the sub-Antarctic pteropod Limacina retroversa to ocean acidification: adults vs juveniles (Mar 2021 - Jul 2022 )
  • Supervision: M-L. Odendaal (MSc in Marine Biology - Univ. Wageningen), Transcriptomic responses of juvenile versus adult shelled heteropod species Atlanta ariejansseni under past, present and future pH conditions (May-Nov 2020)
  • Supervision: J. Smith (MSc in Biology Univ. Leiden), Screening for fast-evolving genes in pteropod species (Jan-Jun 2019)
  • Teaching Assistant: Biological Oceanography, University of Amsterdam, Netherlands (Nov 2020, 2021)
  • Teaching: Computational Biology and Bioinformatics, TiranaMathBioWorkshop, Albania  (Oct 2018)
  • Teaching Assistant: Research in Bioinformatics, University of Lisbon, Portugal (Jun 2015, 2016)
  • Teaching: Applied Genetics, University of the Nouvelle Grand’Anse, Haiti (Jan-Feb 2014, 2015)
Shell fossils


  • Promo video about sea butterflies in collaboration with Studio de Maan