PNNL

Lummy Monteiro is a data scientist in the Biological Sciences Division at Pacific Northwest National Laboratory (PNNL), working at the intersection of multi-omics data integration, metabolic network reconstruction, and artificial intelligence.

She is interested in species-independent approaches that build metabolic networks directly from experimental evidence, integrating proteomics, metabolomics, and transcriptomics measurements either individually or in combination, and in coupling those networks with machine learning and large language models so that the resulting hypotheses stay grounded in measured data rather than prior annotation. She works with organisms that conventional pipelines handle poorly: non-model fungi, oleaginous yeasts, and complex microbial communities.

This focus is motivated by what these organisms are capable of. Understanding how they build and break down molecules opens routes to converting plant and plastic waste into fuels and chemicals, recovering critical minerals without destructive mining, and remediating contaminated environments. Monteiro is also interested in predictive phenomics: connecting molecular measurements to observable cellular behavior so that phenotype can be anticipated rather than only measured after the fact.

Monteiro joined PNNL in 2025 after postdoctoral appointments at the National Laboratory of the Rockies and the University of Delaware, and a visiting research year in bioinformatics at Universität Leipzig and the Helmholtz Centre for Environmental Research in Germany. She completed her PhD in biochemistry and systems biology at the University of São Paulo in Brazil, where she also earned a degree in Analysis and Systems Development. Her experience spans both laboratory and computational research, which shapes how she designs tools meant to be used by experimentalists.

• AI-driven metabolic pathway discovery
• Multi-omics data integration (proteomics, metabolomics, transcriptomics, lipidomics)
• Large language models and knowledge graphs for biological reasoning
• Genome-scale metabolic modeling
• Systems and synthetic biology
• Microbiome and metagenomic analysis
• Non-model fungi and oleaginous yeasts
• Predictive phenomics and cellular morphology prediction
• Bioengineering for the bioeconomy and environmental remediation

• PhD in biochemistry and systems biology, University of São Paulo, 2020
• BS in analysis and systems development, Ribeirão Preto Technological College (FATEC-RP), 2020
• MS in biochemistry, University of São Paulo, 2016
• BS in biochemistry, Federal University of Viçosa, 2014

• PNNL Rising Leader Development Program, 2026
• EBSD BESTie Award, creativity category, PNNL, 2025
• Thesis Award, Department of Biochemistry, University of São Paulo, 2020
• Valedictorian Award: Conferred for achieving the highest GPA in the graduating class, Analysis and Systems Development, FATEC-RP, 2020
• FAPESP - doctoral fellowships, National and International Award , 2016 and 2018
• CNPq - Ciência sem Fronteiras Undergraduate Exchange Scholarship Award, 2012

• Methods for improving plastic substrate degradation using darkling beetle larvae and isolated microbial peroxidase enzymes. U.S. Patent Application US20250289043A1.

Visit Google Scholar for a complete, updated list of publications

2026

• Monteiro L.M.O., N.B. Chowdhury, M.T. Oostrom, J.E. McDermott, K.G. Stratton, S. Choudhury, and J.P. Bardhan. 2026. “PathwaySeeker: Evidence-Grounded AI Reasoning over Organism-Specific Metabolic Networks.” bioRxiv. doi:10.64898/2026.04.14.718256
• Choudhury S., J.J. Czajka, L.M.O. Monteiro, et al. 2026. “Networked Intelligence: Active Shared Context Graphs for Human-AI Team Science.” arXiv:2607.13220. doi:10.48550/arXiv.2607.13220
• Monteiro L.M.O., et al. 2026. “Carbon source–driven metabolic and regulatory remodeling defines phenomic states in Lipomyces starkeyi.” Scientific Reports. doi: 10.1038/s41598-026-53531-2

2025

• Monteiro L.M.O., C. del Cerro, T. Kijpornyongpan, A. Yaguchi, A. Bennett, and B.S. Donohoe, et al. 2025. “Metabolic profiling of two white-rot fungi during 4-hydroxybenzoate conversion reveals biotechnologically relevant biosynthetic pathways.” Communications Biology 8, no. 1:Art. No. 224. doi:10.1038/s42003-025-07640-9

2024

• Klauer R., D.A. Hansen, D. Wu, L.M.O. Monteiro, K.V. Solomon, and M.A. Blenner. 2024. “Biological Upcycling of Plastics Waste.” Annual Review of Chemical and Biomolecular Engineering 15:315–340. doi:10.1146/annurev-chembioeng-100522-115850

2023

• Ganesan V., L.M.O. Monteiro, D. Pedada, A. Stohr, and M.A. Blenner. 2023. “High-Efficiency Multiplexed Cytosine Base Editors for Natural Product Synthesis in Yarrowia lipolytica.” ACS Synthetic Biology 12, no. 10:3082–3091. doi:10.1021/acssynbio.3c00435

2022

• Monteiro L.M.O., J.P. Saraiva, P.F. Stadler, R. Silva-Rocha, and U. Nunes da Rocha. 2022. “PredicTF: a tool to predict bacterial transcription factors in complex microbial communities.” Environmental Microbiome 17, no. 1:Art. No. 7. doi:10.1186/s40793-021-00394-x

2020

• Monteiro L.M.O., A. Sanches-Medeiros, C.A. Westmann, and R. Silva-Rocha. 2020. “Unraveling the Complex Interplay of Fis and IHF Through Synthetic Promoter Engineering.” Frontiers in Bioengineering and Biotechnology 8:510. doi:10.3389/fbioe.2020.00510
• Monteiro L.M.O., A.C. Vici, M.P. Pinheiro, P.R. Heinen, A.H.C. de Oliveira, R.J. Ward, and R.A. Prade, et al. 2020. “A Highly Glucose Tolerant β-Glucosidase from Malbranchea pulchella (MpBg3) Enables Cellulose Saccharification.” Scientific Reports 10, no. 1:Art. No. 6998. doi:10.1038/s41598-020-63972-y

2019

• Monteiro L.M.O., L.M. Arruda, A. Sanches-Medeiros, C.A. Westmann, and R. Silva-Rocha. 2019. “Reverse Engineering of an Aspirin-Responsive Transcriptional Regulator in Escherichia coli.” ACS Synthetic Biology 8, no. 8:1890–1900. doi:10.1021/acssynbio.9b00191

2018

• Monteiro L.M.O., L.M. Arruda, and R. Silva-Rocha. 2018. “Emergent Properties in Complex Synthetic Bacterial Promoters.” ACS Synthetic Biology 7, no. 2:602–612. doi:10.1021/acssynbio.7b00344