PNNL

Dr. Aivett Bilbao is a computational scientist with the Systems Modeling and Computational Science team in PNNL’s Environmental Molecular Sciences Division and the Environmental Molecular Sciences Laboratory (EMSL) user program. She leads the development and application of advanced algorithms and software tools for mass spectrometry (MS) and artificial intelligence/machine learning (AI/ML) integration in scientific research and instrumentation. She works directly with biologists and chemists in interdisciplinary teams.

Her expertise and interests encompass various omics, MS instrumentation, analytical separations, programming languages, and leveraging modern AI for understanding microbial processes at the molecular scale and for advancing several interdisciplinary research projects spanning biology, biotechnology, and environmental sciences. Bilbao is passionate about creating user-friendly scientific software, utilizing AI for science, mentoring interns, and promoting diversity through inclusive research practices.

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.

• Artificial intelligence
• Machine learning
• Mass spectrometry
• Ion mobility spectrometry
• Data-independent acquisition
• Proteomics
• Metabolomics
• Multiomics
• Microbial activity
• Systems and Synthetic biology
• Computational methods
• Algorithm development
• Data science
• Scientific instrumentation,

• Scientific software

   

• Postdoc in Computational Mass Spectrometry, PNNL, 2016 – 2019 
• PhD in Computational Mass Spectrometry, University of Geneva, 2011 – 2015 
• MSc in Automatic Data Processing, TELECOM SubParis 2009 – 2011 
• BSc in Computer Engineering, Universidad de Oriente, 2002 – 2007 

American Society for Mass Spectrometry

• 2024 Emerging Investigators Special Issue in the Journal of the American Society for Mass Spectrometry (2024).
• PNNL Outstanding Performance Award for above and beyond contribution organizing the TechFest Conference (2024).
• Outstanding Reviewer Award from the Journal of the American Society for Mass Spectrometry (2023).
• 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 studies in France (2009-2011)
• Cum Laude BSc degree (2007)

2020 

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. https://doi.org/10.1021/jasms.0c00282 

2019 

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. https://doi.org/10.1002/mas.21585.  

2018 

Bilbao, A. 2018. “Proteomics Mass Spectrometry Data Analysis Tools.” In Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, 84-95. https://doi.org/10.1016/B978-0-12-809633-8.20274-4.  

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. https://doi.org/10.1016/j.ijms.2017.11.003.  

Bilbao, A., and F. Lisacek. 2018. “Bioinformatics Support for Farm Animal Proteomics.” In Proteomics in Domestic Animals: From Farm to Systems Biology, 361-386. https://doi.org/10.1007/978-3-319-69682-9_18.  

2017 

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. https://doi.org/10.1016/j.rhisph.2017.05.001.  

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. https://doi.org/10.1016/j.rhisph.2017.05.003.  

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. https://doi.org/10.1039/c7sc03464d.