Publications

  1. O'Keeffe, S., Sim, H., McCue, E., Park, J. O. Ensemble quantitation of absolute metabolite concentrations in T cells reveals conserved features of immunometabolism. bioRxiv (2025) doi: 10.1101/2025.06.09.658709
  2. Law, R. C., Pande, K., O’Keeffe, S., Nurwono, G., Ki, R., Lai, P.-K., Park, J. O. Accurate and rapid determination of metabolic flux by deep learning of isotope patterns. bioRxiv (2025) doi: 10.1101/2023.11.06.565907
  3. Erşan, S., Chen, Y., Park, J. O. Comprehensive profiling of folates across polyglutamylation and one-carbon states. Metabolomics 21,71 (2025) doi: 10.1007/s11306-025-02269-5
  4. Jung, Y.-H., Lee, D.-C., Choi, B.-H., Park, J. O., Kim, J.-H. Feature-based molecular networking updates the in vitro metabolic characterisation of fenbendazole across species. Xenobiotica (2025) doi: 10.1080/00498254.2025.2497047
  5. O'Keeffe, S., Garcia, L., Chen, Y., Law, R. C., Liu, C., Park, J. O. Bringing carbon to life via one-carbon metabolism. Trends in Biotechnology 43(3),572-585 (2025) doi: 10.1016/j.tibtech.2024.08.014
  6. Gao, Y., Xiao, M., Zou, H., Nurwono, G., Zgonc, D., Birch, Q., Nadagouda, M. N., Park, J. O., Blotevogel, J., Liu, C., Hoek, E. M. V., Mahendra, S. Laccase immobilized on arginine-functionalized boron nitride nanosheets for enhanced atrazine degradation. Environmental Science & Technology 58(34),15111-15119 (2024) doi: 10.1021/acs.est.4c02849
  7. Guan, X., Erşan, S., Xie, Y., Park, J. O., Liu, C. Redox and energy homeostasis enabled by photocatalytic material–microbial interfaces. ACS Nano 18(31),20567-20575 (2024) doi: 10.1021/acsnano.4c05763
  8. Schuman, Z., Xie, Y., O’Keeffe, S., Guan, X., Sha, J., Sun, J., Wohlschlegel, J. A., Park, J. O., Liu, C. Integrated proteomics and metabolomics reveal altered metabolic regulation of Xanthobacter autotrophicus under electrochemical water-splitting conditions. ACS Applied Materials & Interfaces 16(31),40973-40979 (2024) doi: 10.1021/acsami.4c07363
  9. Ju, S.-H., Lee, S. E., Yi, S., Choi, N. R., Kim, K. H., Kim, S. M., Koh, J-Y., Kim, S.-K., Kim S.-Y., Heo, J. Y., Park, J. O., Park, S., Koo, B. S., Kang, Y. E. Transcriptomic characteristics according to tumor size and SUVmax in papillary thyroid cancer patients. Scientific Reports 14,11005 (2024) doi: 10.1038/s41598-024-61839-0
  10. Lee, S. E., Koo, B. S., Sun, P., Yi, S., Choi, N. R., Yoon, J., Kim, S.-Y., Kim S.-K., Park, S., Lakhani, A., O’Keeffe, S., Park, J. O., Kang, D. H., Kang, Y. E. Neutrophil diversity is associated with T-cell immunity and clinical relevance in patients with thyroid cancer. Cell Death Discovery 10,222 (2024) doi: 10.1038/s41420-024-01970-z
  11. Lakhani, A., Chen, X., Chen, L. C., Hong, M., Khericha, M., Chen, Y., Chen, Y. Y., Park, J. O. Extracellular domains of CARs reprogramme T cell metabolism without antigen stimulation. Nature Metabolism (2024) doi: 10.1038/s42255-024-01034-7
  12. Law, R. C., Nurwono, G., Park, J. O. A parallel glycolysis provides a selective advantage through rapid growth acceleration. Nature Chemical Biology 20(3),314-322 (2024) doi: 10.1038/s41589-023-01395-2
  13. Lee, S. E., Park, S., Yi, S., Choi, N. R., Lim, M. A., Chang, J. W., Won, H.-R., Kim, J. R., Ko, H. M., Chung, E.-J., Park, Y. J., Cho, S. W., Yu, H. W., Choi, J. Y., Yeo, M.-K., Yi, B., Yi, K., Lim, J., Koh, J.-Y., Lee, M. J., Heo, J. Y., Yoon, S. J., Kwon, S. W., Park, J.-L., Chu, I. S., Kim, J. M., Kim, S.-Y., Shan, Y., Liu, L., Hong, S.-A., Choi, D. W., Park, J. O., Ju, Y. S., Shong, M., Kim, S.-K., Koo, B. S., Kang, Y. E. Unraveling the role of the mitochondrial one-carbon pathway in undifferentiated thyroid cancer by multi-omics analyses. Nature Communications 15:1163 (2024) doi: 10.1038/s41467-024-45366-0
  14. Perez-Ramirez, C. A., Nakano, H., Law, R. C., Matulionis, N., Thompson, J., Pfeiffer, A., Park, J. O., Nakano, A., Christofk, H. R. Atlas of fetal metabolism during mid-to-late gestation and diabetic pregnancy. Cell 187,204-215 (2024) doi: 10.1016/j.cell.2023.11.011
  15. Lakhani, A., Kang, D. H., Kang, Y. E., Park, J. O. Toward systems-level metabolic analysis in endocrine disorders and cancer. Endocrinology and Metabolism 38(6),619-630 (2023) doi: 10.3803/EnM.2023.1814
  16. Xie, Y., Erşan, S., Guan, X., Wang, J., Sha, J., Xu, S., Wohlschlegel, J. A., Park, J. O., Liu, C. Unexpected metabolic rewiring of CO2 fixation in H2-mediated materials–biology hybrids. Proceedings of the National Academy of Sciences 120(42),e2308373120 (2023) doi: 10.1073/pnas.2308373120
  17. Park, J. O., Nielsen, D. R. Editorial overview: Energy biotechnology as an integral solution to global challenges. Current Opinion in Biotechnology 84,103006 (2023) doi: 10.1016/j.copbio.2023.103006
  18. Nurwono, G., O’Keeffe, S., Liu, N., Park, J. O. Sustainable metabolic engineering requires a perfect trifecta. Current Opinion in Biotechnology 83,102983 (2023) doi: 10.1016/j.copbio.2023.102983
  19. Bailleul, J., Ruan, Y., Abdulrahman, L., Scott, A. J., Yazal, T., Sung, D., Park, K., Hoang, H., Nathaniel, J., Chu, F., Palomera, D., Sehgal, A., Tsang, J. E., Nathanson, D. A., Xu, S., Park, J. O., ten Hoeve, J., Bhat, K., Qi, N., Kornblum, H. I., Schaue, D., McBride, W. H., Lyssiotis, C. A., Wahl, D. R., Vlashi, E. M2 isoform of pyruvate kinase rewires glucose metabolism during radiation therapy to promote an antioxidant response and glioblastoma radioresistance. Neuro-Oncology 25(11),1989-2000 (2023) doi: 10.1093/neuonc/noad103
  20. Park, J., Park, J. O., Choi, J., Kwon, T. T. D-SCAN: Toward collaborative multi-radio coexistence in mobile devices via deep learning. Internet of Things 21,100646 (2023) doi: 10.1016/j.iot.2022.100646
  21. Guan, X., Erşan, S., Hu, X., Atallah, T. L., Xie, Y., Lu, S., Cao, B., Sun, J., Wu, K., Huang, Y., Duan, X., Caram, J. R., Yu, Y., Park, J. O., Liu, C. Maximizing light-driven CO2 and N2 fixation efficiency in quantum dot–bacteria hybrids. Nature Catalysis 5,1019-1029 (2022) doi: 10.1038/s41929-022-00867-3
  22. Law, R. C., Lakhani, A., O’Keeffe, S., Erşan, S., Park, J. O. Integrative metabolic flux analysis reveals an indispensable dimension of phenotypes. Current Opinion in Biotechnology 75,102701 (2022) doi: 10.1016/j.copbio.2022.102701
  23. Polasko, A. L., Miao, Y., Kwok, I., Park, K., Park, J. O., Mahendra, S. Vinyl chloride and 1,4-dioxane metabolism by Pseudonocardia dioxanivorans CB1190. Journal of Hazardous Materials Letters 2,100039 (2021) doi: 10.1016/j.hazl.2021.100039
  24. Erşan, S., Park, J. O. Light-independent biological conversion of CO2. Joule 4(10),2047-2051 (2020) doi: 10.1016/j.joule.2020.08.007
  25. Xu, J., Martien, J., Gilbertson, C., Ma, J., Amador-Noguez, D., Park, J. O. Metabolic flux analysis and fluxomics-driven determination of Gibbs free energy using multiple isotopes. Current Opinion in Biotechnology 64,151-160 (2020) doi: 10.1016/j.copbio.2020.02.018
  26. Park, J. O., Tanner, L. B., Wei, M. H., Khana, D. B., Jacobson, T. B., Zhang, Z., Rubin, S. A., Li, S. H. J., Higgins, M. B., Stevenson, D. M., Amador-Noguez, D., Rabinowitz, J. D. Near-equilibrium glycolysis supports metabolic homeostasis and energy yield. Nature Chemical Biology 15(10),1001-1008 (2019) doi: 10.1038/s41589-019-0364-9
  27. Song, Y., Park, J. O., Tanner, L., Nagano, Y., Rabinowitz, J. D., Shvartsman, S. Y. Energy budget of Drosophila embryogenesis. Current Biology 29(12),R566-R567 (2019) doi: 10.1016/j.cub.2019.05.025
  28. Park, J. O., Liu, N., Holinski, K. M., Emerson, D. F., Qiao, K., Woolston, B. M., Xu, J., Lazar, Z., Islam, M. A., Vidoudez, C., Girguis, P. R., Stephanopoulos, G. Synergistic substrate cofeeding stimulates reductive metabolism. Nature Metabolism 1(6),643-651 (2019) doi: 10.1038/s42255-019-0077-0
  29. Schober, A. F., Mathis, A. D., Ingle, C., Park, J. O., Chen, L., Rabinowitz, J. D., Junier, I., Rivoire, O., Reynolds, K. A. A two-enzyme adaptive unit within bacterial folate metabolism. Cell Reports 27(11),3359-3370 (2019) doi: 10.1016/j.celrep.2019.05.030
  30. Li, S. H.-J., Li, Z., Park, J. O., King, C. G., Rabinowitz, J. D., Wingreen, N. S., Gitai, Z. Escherichia coli translation strategies differ across carbon, nitrogen and phosphorus limitation conditions. Nature Microbiology 3(8),939-947 (2018) doi: 10.1038/s41564-018-0199-2
  31. Tanner, L. B., Goglia, A. G., Wei, M. H., Sehgal, T., Parsons, L. R., Park, J. O., White, E., Toettcher, J. E., Rabinowitz, J. D. Four key steps control glycolytic flux in mammalian cells. Cell Systems 7(1),49-62 (2018) doi: 10.1016/j.cels.2018.06.003
  32. Miller, R. A., Shi, Y., Lu, W., Pirman, D. A., Jatkar, A., Blatnik, M., Wu, H., Cardenas, C., Wan, M., Foskett, J. K., Park, J. O., Zhang, Y., Holland, W. L., Rabinowitz, J. D., Birnbaum, M. J. Targeting hepatic glutaminase activity to ameliorate hyperglycemia. Nature Medicine 24(4),518-524 (2018) doi: 10.1038/nm.4514
  33. Song, Y., Marmion, R. A., Park, J. O., Biswas, D., Rabinowitz, J. D., Shvartsman, S. Y. Dynamic control of dNTP synthesis in early embryos. Developmental Cell 42(3),1-8 (2017) doi: 10.1016/j.devcel.2017.06.013
  34. Hackett, S. R., Zanotelli, V. R. T., Xu, W., Goya, J., Park, J. O., Perlman, D. H., Gibney, P. A., Botstein, D., Storey, J. D., Rabinowitz, J. D. Systems-level analysis of mechanisms regulating yeast metabolic flux. Science 354(6311),aaf2786 (2016) doi: 10.1126/science.aaf2786
  35. Park, J. O., Rubin, S. A., Xu, Y. F., Amador-Noguez, D., Fan, J., Shlomi, T., Rabinowitz, J. D. Metabolite concentrations, fluxes and free energies imply efficient enzyme usage. Nature Chemical Biology 12(7),482-489 (2016) doi: 10.1038/nchembio.2077
  36. Bren, A., Park, J. O., Towbin, B. D., Dekel, E., Rabinowitz, J. D., Alon, U. Glucose becomes one of the worst carbon sources for E. coli on poor nitrogen sources due to suboptimal levels of cAMP. Scientific Reports 6(1),24834 (2016) doi: 10.1038/srep24834
  37. Liu, L., Shah, S., Fan, J., Park, J. O., Wellen, K. E., Rabinowitz, J. D. Malic enzyme tracers reveal hypoxia-induced switch in adipocyte NADPH pathway usage. Nature Chemical Biology 12(5),345-352 (2016) doi: 10.1038/nchembio.2047
  38. Mok, W. W. K., Park, J. O., Rabinowitz, J. D., Brynildsen, M. P. RNA futile cycling in model persisters derived from MazF accumulation. mBio 6(6),e01588-15 (2015) doi: 10.1128/mBio.01588-15
  39. Aristilde, L., Lewis, I. A., Park, J. O., Rabinowitz, J. D. Hierarchy in pentose sugar metabolism in Clostridium acetobutylicum. Applied and Environmental Microbiology 81(4),1452-1462 (2015) doi: 10.1128/AEM.03199-14
  40. Schellenberger, J., Park, J. O., Conrad, T. M., Palsson, B. Ø. BiGG: A Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 11,213 (2010) doi: 10.1186/1471-2105-11-213

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