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Aivett Bilbao
Computational Scientist

Aivett Bilbao is a computational scientist in the Computing, Analytics, and Modeling science area. She conducts research on computational tools for mass spectrometry-based omics, working directly with experimental biologists and chemists in interdisciplinary teams. She has acquired extensive experience developing software for mass spectrometry using multiple programming languages and technologies. Projects include proteomics and and small molecule (e.g., metabolites and lipids) molecular characterization entailing both algorithm design and software implementation for data from different instruments (time-of-flight, quadrupole, and Fourier transform-based mass analyzers) and analytical separation techniques (liquid chromatography, ion mobility, solid phase extraction, and gas chromatography).

She earned her PhD from University of Geneva in Switzerland with special interest in data-independent acquisition mass spectrometry. Her bachelor’s degree is in computer engineering from Universidad de Oriente in Venezuela (cum laude) and her MSc studies were focused on machine learning algorithms and statistical methods at Telecom SudParis in France.

Research Interests

Computational methods, algorithm development, data science and artificial intelligence for mass spectrometry-based omics research


  • Postdoc in Computational Mass Spectrometry, PNNL (2019)
  • PhD in Computational Mass Spectrometry, University of Geneva, Switzerland (2015)
  • MSc in Automatic Data Processing, TELECOM SubParis, France (2011)
  • BSc in Computer Engineering, Universidad de Oriente, Venezuela (2007)

Awards and Recognition

  • PNNL Pathway to Excellence, Software creator award and Key contributor award (2022)
  • The Swiss Initiative in Systems Biology (SystemsX) IPhD funding (2015)
  • Fundayacucho Venezuelan Full Scholarship for MSc (2009-2011)
  • Cum Laude BSc degree (2007)
  • Outstanding Reviewer Award from the Journal of the American Society for Mass Spectrometry, announced at the 2023 ASMS Annual Conference.

Affiliations and Professional Service

  • American Society for Mass Spectrometry



Conant, C. R., Attah, I. K., Garimella, S. V., Nagy, G., Bilbao, A., Smith, R. D., & Ibrahim, Y. M. (2020). Evaluation of Waveform Profiles for Traveling Wave Ion Mobility Separations in Structures for Lossless Ion Manipulations. Journal of the American Society for Mass Spectrometry.


Gabelica, V., A. A. Shvartsburg, C. Afonso, P. Barran, J. L. P. Benesch, C. Bleiholder, M. T. Bowers, A. Bilbao, M. F. Bush, J. L. Campbell, I. D. G. Campuzano, T. Causon, B. H. Clowers, C. S. Creaser, E. De Pauw, J. Far, F. Fernandez-Lima, J. C. Fjeldsted, K. Giles, M. Groessl, C. J. Hogan, Jr., S. Hann, H. I. Kim, R. T. Kurulugama, J. C. May, J. A. McLean, K. Pagel, K. Richardson, M. E. Ridgeway, F. Rosu, F. Sobott, K. Thalassinos, S. J. Valentine, and T. Wyttenbach. 2019. “Recommendations for Reporting Ion Mobility Mass Spectrometry Measurements.” Mass Spectrometry Reviews 38 (3): 291-320.


Bilbao, A. 2018. “Proteomics Mass Spectrometry Data Analysis Tools.” In Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, 84-95.

Bilbao, A., B. C. Gibbons, G. W. Slysz, K. L. Crowell, M. E. Monroe, Y. M. Ibrahim, R. D. Smith, S. H. Payne, and E. S. Baker. 2018. “An Algorithm to Correct Saturated Mass Spectrometry Ion Abundances for Enhanced Quantitation and Mass Accuracy in Omic Studies.” International Journal of Mass Spectrometry 427: 91-99.

Bilbao, A., and F. Lisacek. 2018. “Bioinformatics Support for Farm Animal Proteomics.” In Proteomics in Domestic Animals: From Farm to Systems Biology, 361-386.


Allen White, R., M. I. Borkum, A. Rivas-Ubach, A. Bilbao, J. P. Wendler, S. M. Colby, M. Köberl, and C. Jansson. 2017. “From Data to Knowledge: The Future of Multi-Omics Data Analysis for the Rhizosphere.” Rhizosphere 3: 222-229.

White, R. A., III, A. Rivas-Ubach, M. I. Borkum, M. Köberl, A. Bilbao, S. M. Colby, D. W. Hoyt, K. Bingol, Y. M. Kim, J. P. Wendler, K. K. Hixson, and C. Jansson. 2017. “The State of Rhizospheric Science in the Era of Multi-Omics: A Practical Guide to Omics Technologies.” Rhizosphere 3: 212-221.

Zheng, X., N. A. Aly, Y. Zhou, K. T. Dupuis, A. Bilbao, V. L. Paurus, D. J. Orton, R. Wilson, S. H. Payne, R. D. Smith, and E. S. Baker. 2017. “A Structural Examination and Collision Cross Section Database for over 500 Metabolites and Xenobiotics Using Drift Tube Ion Mobility Spectrometry.” Chemical Science 8 (11): 7724-7736.