Metabolomics & Diagnostics
Reading the body's small-molecule signatures to detect disease earlier.
Our metabolomics and lipidomics programs search for the small-molecule signatures of health and disease. A long-standing focus is the early detection of ovarian cancer, alongside work on inflammatory bowel disease, traumatic brain injury, and other conditions — combining high-resolution mass spectrometry with machine learning to turn molecular data into candidate biomarkers.
Selected publications
All publications→- 2025
Senescence-Induced Lipidome Alterations in Mesenchymal Stromal Cells
Molly E. Ogle, Joseph L. Corstvet, Reesha K. Vayalakkara, Facundo M. Fernández, Johnna S. Temenoff*, J. Proteome Res. 2025, 24(12), 5986–5994
- 2025
A Large Language Model–Powered Map of Metabolomics Research
, Olatomiwa O. Bifarin1, Varun S. Yelluru, Aditya Simhadri, Facundo M. Fernández*. Anal. Chem., 2025, 97, 27, 14088–14096
- 2025
Beyond Targeted Newborn Screening: A Non-targeted Metabolomics Workflow to Investigate Birthweight-Metabolome Correlations
, Carter K. Asef, Samuel G. Moore, C. Austin Pickens, Carlos A. Saavedra-Matiz, Joseph J. Orsini, Konstantinos Petritis, David A. Gaul, Facundo M. Fernández*. Anal. Chem., 2025, 97, 6563-6570
- 2024
Integrative Analysis of Cytokine and Lipidomics Datasets Following Mild Traumatic Brain Injury in Rats
, Alexis N Pulliam, Alyssa F Pybus, David A Gaul, Samuel G Moore, Levi B Wood, Facundo M Fernández, Michelle C LaPlaca. Metabolites, 2024, 14(3) 133.
- 2024
Automated machine learning and explainable AI (AutoML-XAI) for metabolomics: improving cancer diagnostics
, Olatomiwa O. Bifarin, and Facundo M. Fernández*. J. Am. Soc. Mass Spectrom. 2024, 35, 6, 1089–1100
- 2024
metabCombiner 2.0: Disparate Multi-Dataset Feature Alignment for LC-MS Metabolomics
, Hani Habra*, Jennifer Lynn Meijer, Tong Shen, Oliver Fiehn, David A. Gaul, Facundo M. Fernández, Kaitlin R. Rempfert, Thomas O. Metz, Karen E. Peterson, Charles Robert Evans, Alla Karnovsky. Metabolites, 2024, 14(2), 125
- 2024
Comparing Brain and Blood Lipidome Changes following Single and Repetitive Mild Traumatic Brain Injury in Rats
Alexis Pulliam, Eric Gier, David A. Gaul, Samuel Moore, Facundo M. Fernández, Michelle LaPlaca*, ACS Chem. Neurosci., 2024, 15, 2, 300–314
- 2024
Divergent Skeletal Muscle Metabolomic Signatures of Different Exercise Training Modes Independently Predict Cardiometabolic Risk Factors
, Mark W. Pataky, Arathi Prabha Kumar, David A. Gaul, Surendra Dasari, Matthew M. Robinson, Katherine A. Klaus, Facundo M. Fernandez, & K. Sreekumaran Nair*, Diabetes, Diabetes, 2024, 73(1):23–37.
- 2024
Serum Lipidome Profiling Reveals a Distinct Signature of Ovarian Cancer in Korean Women
Samyukta Sah, Olatomiwa O. Bifarin, Samuel G. Moore, David A. Gaul, Sun Young Kwon, Hyewon Chung, Hanbyoul Cho, Chi-Heum Cho, Jae-Hoon Kim, Jaeyeon Kim*, Facundo M. Fernández*. Cancer Epidemiol. Biomarkers Prev. (2024) 33(5), 681–693 [Lipidomics study of Korean ovarian cancer human cohort (80% contribution)]. Featured in a section of the journal called "Cancer Epidemiology, Biomarkers & Prevention Highlights: Selected Articles from This Issue.”
- 2024
Advances in Mass Spectrometry Imaging for Spatial Cancer Metabolomics
. Xin Ma, Facundo M. Fernández*. Mass Spectrom Rev., 2024, 43(2), 235-268
- 2023
Development of a Robust Consensus Modeling Approach for Identifying Cellular and Media Metabolites Predictive of Mesenchymal Stromal Cell Potency
Alexandria Van Grouw, Maxwell B. Colonna, Ty S. Maughon, Xunan Shen, Andrew M. Larey, Samuel G. Moore, Carolyn Yeago, Facundo M. Fernández, Arthur S. Edison, Steven L. Stice, Annie C. Bowles-Welch*, Ross A. Marklein*, Stem Cells, 2023, 41(8), 792–808.
- 2023
Identifying Metabolic Shifts in Crohn's Disease Using' Omics-Driven Contextualized Computational Metabolic Network Models
, Philip Fernandes, Yash Sharma, Brooklyn McGrew, Fatima Zulqarnain, Aman Shrivastava, Lubaina Ehsan, Dawson Payne, Lillian Dillard, Deborah Powers, Isabelle Aldridge, Samuel G Moore, Jason Matthews, Subra Kugathasan, Jason Papin, Facundo M Fernández, David A. Gaul, Sana Syed*, Sci. Rep., 2023, 203.
+ 43 more in this area on the publications page.