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  1. Ruffieux, H., Hanson, A. L., Lodge, S., Lawler, N. G., Whiley, L., Gray, N., Nolan, T. H., Bergamaschi, L., Mescia, F., Turner, L., de Sa, A., Pelly, V. S., Kotagiri, P., Kingston, N., Bradley, J. R., Holmes, E., Wist, J., Nicholson, J. K., Lyons, P. A., Smith, K. G. C., Richardson, S., Bantug, G. R. & Hess, C. A patient-centric modeling framework captures recovery from SARS-CoV-2 infection. Nature Immunology 24, 349–358 (2023). doi:10.1038/s41590-022-01380-2
  2. Mallagaray, A., Rudolph, L., Lindloge, M., Mölbitz, J., Thomsen, H., Schmelter, F., Alhabash, M. W., Abdullah, M. R., Saraei, R., Ehlers, M., Graf, T., Sina, C., Petersmann, A., Nauck, M. & Günther, U. L. Towards a Precise NMR Quantification of Acute Phase Inflammation Proteins from Human Serum. Angewandte Chemie International Edition (2023). doi:10.1002/anie.202306154
  3. Berezhnoy, G., Bissinger, R., Liu, A., Cannet, C., Schäfer, H., Kienzle, K., Bitzer, M., Häberle, H., Göpel, S., Trautwein, C. & Singh, Y. Maintained imbalance of triglycerides, apolipoproteins, energy metabolites and cytokines in long-term COVID-19 syndrome patients. Frontiers in Immunology 14, (2023). doi:10.3389/fimmu.2023.1144224
  4. Bruzzone, C., Conde, R., Embade, N., Mato, J. M. & Millet, O. Metabolomics as a powerful tool for diagnostic, pronostic and drug intervention analysis in COVID-19. Frontiers in Molecular Biosciences 10, (2023). doi:10.3389/fmolb.2023.1111482
  5. Roberts, J. L., Whiley, L., Gray, N., Gay, M. & Lawler, N. G. Advanced Microsamples: Current Applications and Considerations for Mass Spectrometry-Based Metabolic Phenotyping Pipelines. Separations 9, 175–175 (2022). doi:10.3390/separations9070175
  6. Masuda, R., Lodge, S., Whiley, L., Gray, N., Lawler, N., Nitschke, P., Bong, S.-H., Kimhofer, T., Loo, R. L., Boughton, B., Zeng, A. X., Hall, D., Schaefer, H., Spraul, M., Dwivedi, G., Yeap, B. B., Diercks, T., Bernardo-Seisdedos, G., Mato, J. M., Lindon, J. C., Holmes, E., Millet, O., Wist, J. & Nicholson, J. K. Exploration of Human Serum Lipoprotein Supramolecular Phospholipids Using Statistical Heterospectroscopy in n -Dimensions (SHY- n ): Identification of Potential Cardiovascular Risk Biomarkers Related to SARS-CoV-2 Infection. Analytical Chemistry 94, 4426–4436 (2022). doi:10.1021/acs.analchem.1c05389
  7. Nitschke, P., Lodge, S., Kimhofer, T., Masuda, R., Bong, S.-H., Hall, D., Schäfer, H., Spraul, M., Pompe, N., Diercks, T., Bernardo-Seisdedos, G., Mato, J. M., Millet, O., Susic, D., Henry, A., El-Omar, E. M., Holmes, E., Lindon, J. C., Nicholson, J. K. & Wist, J. J-Edited DIffusional Proton Nuclear Magnetic Resonance Spectroscopic Measurement of Glycoprotein and Supramolecular Phospholipid Biomarkers of Inflammation in Human Serum. Analytical Chemistry 94, 1333–1341 (2022). doi:10.1021/acs.analchem.1c04576
  8. Ghini, V., Maggi, L., Mazzoni, A., Spinicci, M., Zammarchi, L., Bartoloni, A., Annunziato, F. & Turano, P. Serum NMR Profiling Reveals Differential Alterations in the Lipoproteome Induced by Pfizer-BioNTech Vaccine in COVID-19 Recovered Subjects and Naïve Subjects. Frontiers in Molecular Biosciences 9, (2022). doi:10.3389/fmolb.2022.839809
  9. Ghini, V., Meoni, G., Pelagatti, L., Celli, T., Veneziani, F., Petrucci, F., Vannucchi, V., Bertini, L., Luchinat, C., Landini, G. & Turano, P. Profiling metabolites and lipoproteins in COMETA, an Italian cohort of COVID-19 patients. PLOS Pathogens 18, e1010443–e1010443 (2022). doi:10.1371/journal.ppat.1010443
  10. Laugwitz, L., Zizmare, L., Santhanakumaran, V., Cannet, C., Böhringer, J., Okun, J. G., Spraul, M., Krägeloh‐Mann, I., Groeschel, S. & Trautwein, C. Identification of neurodegeneration indicators and disease progression in metachromatic leukodystrophy using quantitative NMR ‐based urinary metabolomics. JIMD Reports 63, 168–180 (2022). doi:10.1002/jmd2.12273
  11. Rössler, T., Berezhnoy, G., Singh, Y., Cannet, C., Reinsperger, T., Schäfer, H., Spraul, M., Kneilling, M., Merle, U. & Trautwein, C. Quantitative Serum NMR Spectroscopy Stratifies COVID-19 Patients and Sheds Light on Interfaces of Host Metabolism and the Immune Response with Cytokines and Clinical Parameters. Metabolites 12, 1277–1277 (2022). doi:10.3390/metabo12121277
  12. Nitschke, P., Lodge, S., Hall, D., Schaefer, H., Spraul, M., Embade, N., Millet, O., Holmes, E., Wist, J. & Nicholson, J. K. Direct low field J-edited diffusional proton NMR spectroscopic measurement of COVID-19 inflammatory biomarkers in human serum. The Analyst 147, 4213–4221 (2022). doi:10.1039/D2AN01097F
  13. Gil-Redondo, R., Conde, R., Bizkarguenaga, M., Bruzzone, C., Laín, A., González-Valle, B., Iriberri, M., Ramos-Acosta, C., Anguita, E., Arriaga Lariz, J. I., España Yandiola, P. P., Moran, M. Á., Jiménez-Mercado, M. E., Egia-Mendikute, L., Seco, M. L., Schäfer, H., Cannet, C., Spraul, M., Palazón, A., Embade, N., Lu, S. C., Wist, J., Nicholson, J. K., Mato, J. M. & Millet, O. An NMR-Based Model to Investigate the Metabolic Phenoreversion of COVID-19 Patients throughout a Longitudinal Study. Metabolites 12, 1206–1206 (2022). doi:10.3390/metabo12121206
  14. Egia-Mendikute, L., Bosch, A., Prieto-Fernández, E., Vila-Vecilla, L., Zanetti, S. R., Lee, S. Y., Jiménez-Lasheras, B., García del Río, A., Antoñana-Vildosola, A., de Blas, A., Velasco-Beltrán, P., Serrano-Maciá, M., Iruzubieta, P., Mehrpouyan, M., Goldberg, E. M., Bornheimer, S. J., Embade, N., Martínez-Chantar, M. L., López-Hoyos, M., Mato, J. M., Millet, Ó. & Palazón, A. A flow cytometry-based neutralization assay for simultaneous evaluation of blocking antibodies against SARS-CoV-2 variants. Frontiers in Immunology 13, (2022). doi:10.3389/fimmu.2022.1014309
  15. Stagnoli, S., Peccati, F., Connell, S. R., Martinez-Castillo, A., Charro, D., Millet, O., Bruzzone, C., Palazon, A., Ardá, A., Jiménez-Barbero, J., Ereño-Orbea, J., Abrescia, N. G. A. & Jiménez-Osés, G. Assessing the Mobility of Severe Acute Respiratory Syndrome Coronavirus-2 Spike Protein Glycans by Structural and Computational Methods. Frontiers in Microbiology 13, (2022). doi:10.3389/fmicb.2022.870938
  16. Bizkarguenaga, M., Bruzzone, C., Gil‐Redondo, R., SanJuan, I., Martin‐Ruiz, I., Barriales, D., Palacios, A., Pasco, S. T., González‐Valle, B., Laín, A., Herrera, L., Azkarate, A., Vesga, M. A., Eguizabal, C., Anguita, J., Embade, N., Mato, J. M. & Millet, O. Uneven metabolic and lipidomic profiles in recovered COVID‐19 patients as investigated by plasma NMR metabolomics. NMR in Biomedicine 35, (2022). doi:10.1002/nbm.4637
  17. Stagnoli, S., Peccati, F., Connell, S. R., Martinez-Castillo, A., Charro, D., Millet, O., Bruzzone, C., Palazon, A., Ardá, A., Jiménez-Barbero, J., Ereño-Orbea, J., Abrescia, N. G. A. & Jiménez-Osés, G. Assessing the Mobility of Severe Acute Respiratory Syndrome Coronavirus-2 Spike Protein Glycans by Structural and Computational Methods. Frontiers in Microbiology 13, (2022). doi:10.3389/fmicb.2022.870938
  18. Egia-Mendikute, L., Bosch, A., Prieto-Fernández, E., Vila-Vecilla, L., Zanetti, S. R., Lee, S. Y., Jiménez-Lasheras, B., García del Río, A., Antoñana-Vildosola, A., de Blas, A., Velasco-Beltrán, P., Serrano-Maciá, M., Iruzubieta, P., Mehrpouyan, M., Goldberg, E. M., Bornheimer, S. J., Embade, N., Martínez-Chantar, M. L., López-Hoyos, M., Mato, J. M., Millet, Ó. & Palazón, A. A flow cytometry-based neutralization assay for simultaneous evaluation of blocking antibodies against SARS-CoV-2 variants. Frontiers in Immunology 13, (2022). doi:10.3389/fimmu.2022.1014309
  19. Gil-Redondo, R., Conde, R., Bizkarguenaga, M., Bruzzone, C., Laín, A., González-Valle, B., Iriberri, M., Ramos-Acosta, C., Anguita, E., Arriaga Lariz, J. I., España Yandiola, P. P., Moran, M. Á., Jiménez-Mercado, M. E., Egia-Mendikute, L., Seco, M. L., Schäfer, H., Cannet, C., Spraul, M., Palazón, A., Embade, N., Lu, S. C., Wist, J., Nicholson, J. K., Mato, J. M. & Millet, O. An NMR-Based Model to Investigate the Metabolic Phenoreversion of COVID-19 Patients throughout a Longitudinal Study. Metabolites 12, 1206–1206 (2022). doi:10.3390/metabo12121206
  20. Masuda, R., Lodge, S., Nitschke, P., Spraul, M., Schaefer, H., Bong, S.-H., Kimhofer, T., Hall, D., Loo, R. L., Bizkarguenaga, M., Bruzzone, C., Gil-Redondo, R., Embade, N., Mato, J. M., Holmes, E., Wist, J., Millet, O. & Nicholson, J. K. Integrative Modeling of Plasma Metabolic and Lipoprotein Biomarkers of SARS-CoV-2 Infection in Spanish and Australian COVID-19 Patient Cohorts. Journal of Proteome Research 20, 4139–4152 (2021). doi:10.1021/acs.jproteome.1c00458
  21. Holmes, E., Wist, J., Masuda, R., Lodge, S., Nitschke, P., Kimhofer, T., Loo, R. L., Begum, S., Boughton, B., Yang, R., Morillon, A.-C., Chin, S.-T., Hall, D., Ryan, M., Bong, S.-H., Gay, M., Edgar, D. W., Lindon, J. C., Richards, T., Yeap, B. B., Pettersson, S., Spraul, M., Schaefer, H., Lawler, N. G., Gray, N., Whiley, L. & Nicholson, J. K. Incomplete Systemic Recovery and Metabolic Phenoreversion in Post-Acute-Phase Nonhospitalized COVID-19 Patients: Implications for Assessment of Post-Acute COVID-19 Syndrome. Journal of Proteome Research 20, 3315–3329 (2021). doi:10.1021/acs.jproteome.1c00224
  22. Kimhofer, T., Lodge, S., Whiley, L., Gray, N., Loo, R. L., Lawler, N. G., Nitschke, P., Bong, S.-H., Morrison, D. L., Begum, S., Richards, T., Yeap, B. B., Smith, C., Smith, K. G. C., Holmes, E. & Nicholson, J. K. Correction to “Integrative Modeling of Quantitative Plasma Lipoprotein, Metabolic, and Amino Acid Data Reveals a Multiorgan Pathological Signature of SARS-CoV-2 Infection.” Journal of Proteome Research 20, 3400–3400 (2021). doi:10.1021/acs.jproteome.1c00273
  23. Nicholson, J. K. Molecular Phenomic Approaches to Deconvolving the Systemic Effects of SARS-CoV-2 Infection and Post-acute COVID-19 Syndrome. Phenomics 1, 143–150 (2021). doi:10.1007/s43657-021-00020-3
  24. Lawler, N. G., Gray, N., Kimhofer, T., Boughton, B., Gay, M., Yang, R., Morillon, A.-C., Chin, S.-T., Ryan, M., Begum, S., Bong, S. H., Coudert, J. D., Edgar, D., Raby, E., Pettersson, S., Richards, T., Holmes, E., Whiley, L. & Nicholson, J. K. Systemic Perturbations in Amine and Kynurenine Metabolism Associated with Acute SARS-CoV-2 Infection and Inflammatory Cytokine Responses. Journal of Proteome Research 20, 2796–2811 (2021). doi:10.1021/acs.jproteome.1c00052
  25. Lodge, S., Nitschke, P., Kimhofer, T., Wist, J., Bong, S.-H., Loo, R. L., Masuda, R., Begum, S., Richards, T., Lindon, J. C., Bermel, W., Reinsperger, T., Schaefer, H., Spraul, M., Holmes, E. & Nicholson, J. K. Diffusion and Relaxation Edited Proton NMR Spectroscopy of Plasma Reveals a High-Fidelity Supramolecular Biomarker Signature of SARS-CoV-2 Infection. Analytical Chemistry 93, 3976–3986 (2021). doi:10.1021/acs.analchem.0c04952
  26. Kemp, S. A. et al. SARS-CoV-2 evolution during treatment of chronic infection. Nature 592, 277–282 (2021). doi:10.1038/s41586-021-03291-y
  27. Lodge, S., Nitschke, P., Loo, R. L., Kimhofer, T., Bong, S.-H., Richards, T., Begum, S., Spraul, M., Schaefer, H., Lindon, J. C., Holmes, E. & Nicholson, J. K. Low Volume in Vitro Diagnostic Proton NMR Spectroscopy of Human Blood Plasma for Lipoprotein and Metabolite Analysis: Application to SARS-CoV-2 Biomarkers. Journal of Proteome Research 20, 1415–1423 (2021). doi:10.1021/acs.jproteome.0c00815
  28. Lodge, S., Nitschke, P., Kimhofer, T., Coudert, J. D., Begum, S., Bong, S.-H., Richards, T., Edgar, D., Raby, E., Spraul, M., Schaefer, H., Lindon, J. C., Loo, R. L., Holmes, E. & Nicholson, J. K. NMR Spectroscopic Windows on the Systemic Effects of SARS-CoV-2 Infection on Plasma Lipoproteins and Metabolites in Relation to Circulating Cytokines. Journal of Proteome Research 20, 1382–1396 (2021). doi:10.1021/acs.jproteome.0c00876
  29. Meoni, G., Ghini, V., Maggi, L., Vignoli, A., Mazzoni, A., Salvati, L., Capone, M., Vanni, A., Tenori, L., Fontanari, P., Lavorini, F., Peris, A., Bartoloni, A., Liotta, F., Cosmi, L., Luchinat, C., Annunziato, F. & Turano, P. Metabolomic/lipidomic profiling of COVID-19 and individual response to tocilizumab. PLOS Pathogens 17, e1009243–e1009243 (2021). doi:10.1371/journal.ppat.1009243
  30. Schmelter, F., Föh, B., Mallagaray, A., Rahmöller, J., Ehlers, M., Lehrian, S., von Kopylow, V., Künsting, I., Lixenfeld, A. S., Martin, E., Ragab, M., Meyer-Saraei, R., Kreutzmann, F., Eitel, I., Taube, S., Käding, N., Jantzen, E., Graf, T., Sina, C. & Günther, U. L. Metabolic and Lipidomic Markers Differentiate COVID-19 From Non-Hospitalized and Other Intensive Care Patients. Frontiers in Molecular Biosciences 8, (2021). doi:10.3389/fmolb.2021.737039
  31. Singh, Y., Trautwein, C., Fendel, R., Krickeberg, N., Berezhnoy, G., Bissinger, R., Ossowski, S., Salker, M. S., Casadei, N. & Riess, O. SARS-CoV-2 infection paralyzes cytotoxic and metabolic functions of the immune cells. Heliyon 7, e07147–e07147 (2021). doi:10.1016/j.heliyon.2021.e07147
  32. Millet, O., Cortajarena, A. L., Salvatella, X., Kiessling, L. L. & Jiménez-Barbero, J. Scientific Response to the Coronavirus Crisis in Spain: Collaboration and Multidisciplinarity. ACS chemical biology 15, 1722–1723 (2020). doi:10.1021/acschembio.0c00496
  33. San Juan, I., Bruzzone, C., Bizkarguenaga, M., Bernardo-Seisdedos, G., Laín, A., Gil-Redondo, R., Diercks, T., Gil-Martínez, J., Urquiza, P., Arana, E., Seco, M., García de Vicuña, A., Embade, N., Mato, J. M. & Millet, O. Abnormal concentration of porphyrins in serum from COVID-19 patients. British journal of haematology 190, e265–e267 (2020). doi:10.1111/bjh.17060
  34. Lenza, M. P., Oyenarte, I., Diercks, T., Quintana, J. I., Gimeno, A., Coelho, H., Diniz, A., Peccati, F., Delgado, S., Bosch, A., Valle, M., Millet, O., Abrescia, N. G. A., Palazón, A., Marcelo, F., Jiménez‐Osés, G., Jiménez‐Barbero, J., Ardá, A. & Ereño‐Orbea, J. Structural Characterization of N‐Linked Glycans in the Receptor Binding Domain of the SARS‐CoV‐2 Spike Protein and their Interactions with Human Lectins. Angewandte Chemie International Edition 59, 23763–23771 (2020). doi:10.1002/anie.202011015
  35. Bruzzone, C., Bizkarguenaga, M., Gil-Redondo, R., Diercks, T., Arana, E., García de Vicuña, A., Seco, M., Bosch, A., Palazón, A., San Juan, I., Laín, A., Gil-Martínez, J., Bernardo-Seisdedos, G., Fernández-Ramos, D., Lopitz-Otsoa, F., Embade, N., Lu, S., Mato, J. M. & Millet, O. SARS-CoV-2 Infection Dysregulates the Metabolomic and Lipidomic Profiles of Serum. iScience 23, 101645–101645 (2020). doi:10.1016/j.isci.2020.101645
  36. Bruzzone, C., Bizkarguenaga, M., Gil-Redondo, R., Diercks, T., Arana, E., García de Vicuña, A., Seco, M., Bosch, A., Palazón, A., San Juan, I., Laín, A., Gil-Martínez, J., Bernardo-Seisdedos, G., Fernández-Ramos, D., Lopitz-Otsoa, F., Embade, N., Lu, S., Mato, J. M. & Millet, O. SARS-CoV-2 Infection Dysregulates the Metabolomic and Lipidomic Profiles of Serum. iScience 23, 101645–101645 (2020). doi:10.1016/j.isci.2020.101645