Publications

  1. VS Frisbie, H Hashimoto, Y Xie, FNDL Vitorino, J Baeza, T Nguyen, Z Yuan, J Kiselar, BA Garcia, EW Debler, (2024). Two DOT1 enzymes cooperatively mediate efficient ubiquitin-independent histone H3 lysine 76 tri-methylation in kinetoplastids. Nature Communications, 15 (1), 2467. https://www.nature.com/articles/s41467-024-46637-6

  2. J Baeza, BE Coons, Z Lin, J Riley, M Mendoza, WH Peranteau, BA Garcia, (2024). In utero pulse injection of isotopic amino acids quantifies protein turnover rates during murine fetal development. Cell Reports Methods, 4 (2). https://www.cell.com/cell-reports-methods/pdf/S2667-2375(24)00028-6.pdf

  3. N Dasgupta, X Lei, R Arnold, MG Teneche, KN Miller, A Rajesh, A Davis, V Anschau, AR Campos, R Gilson, A Havas, S Yin, ZM Chua, J Proulx, M Alcaraz, MI Rather, J Baeza, DC Schultz, SL Berger, PD Adams, (2023). Histone chaperone HIRA, Promyelocytic Leukemia (PML) protein and p62/SQSTM1 coordinate to regulate inflammation during cell senescence and aging.. bioRxiv, 2023.06. 24.546372. https://www.biorxiv.org/content/10.1101/2023.06.24.546372.abstract

  4. LK Pino, J Baeza, R Lauman, B Schilling, BA Garcia, (2021). Improved SILAC quantification with data-independent acquisition to investigate bortezomib-induced protein degradation. Journal of proteome research, 20 (4), 1918-1927. https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.0c00938

  5. L Narapareddy, EA Rhon-Calderon, LA Vrooman, J Baeza, DK Nguyen, C Mesaros, Y Lan, BA Garcia, RM Schultz, MS Bartolomei, (2021). Sex-specific effects of in vitro fertilization on adult metabolic outcomes and hepatic transcriptome and proteome in mouse. FASEB journal: official publication of the Federation of American Societies …, . https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8132511/

  6. P Latorre-Muro, J Baeza, R Hurtado-Guerrero, T Hicks, I Delso, C Hernández-Ruiz, A Velázquez-Campoy, AJ Lawton, Jús Angulo, JM Denu, JéA Carrodeguas, (2021). Self-acetylation at the active site of phosphoenolpyruvate carboxykinase (PCK1) controls enzyme activity. Journal of Biological Chemistry, 296. https://www.jbc.org/article/S0021-9258(20)00201-X/abstract

  7. J Baeza, AJ Lawton, J Fan, MJ Smallegan, I Lienert, T Gandhi, OM Bernhardt, L Reiter, JM Denu, (2020). Revealing dynamic protein acetylation across subcellular compartments. Journal of proteome research, 19 (6), 2404-2418. https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.0c00088

  8. L Narapareddy, EA Rhon-Calderon, LA Vrooman, J Baeza, DK Nguyen, Y Lan, BA Garcia, RM Schultz, MS Bartolomei, (2020). Sex-specific effects of in vitro fertilization on adult metabolic phenotypes and hepatic transcriptomic and proteomic pathways in mouse. bioRxiv, 2020.09. 23.309989. https://www.biorxiv.org/content/10.1101/2020.09.23.309989.abstract

  9. X Lan, E Khandros, P Huang, SA Peslak, SK Bhardwaj, JD Grevet, O Abdulmalik, H Wang, CA Keller, B Giardine, J Baeza, ER Duffner, OE Demerdash, XS Wu, CR Vakoc, BA Garcia, RC Hardison, J Shi, GA Blobel, (2019). The E3 ligase adaptor molecule SPOP regulates fetal hemoglobin levels in adult erythroid cells. Blood Advances, 3 (10), 1586-1597. https://ashpublications.org/bloodadvances/article-abstract/3/10/1586/246655

  10. LM Agosto, MR Gazzara, CM Radens, S Sidoli, J Baeza, BA Garcia, KW Lynch, (2019). Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing. Genome research, 29 (12), 2046-2055. https://genome.cshlp.org/content/29/12/2046.short

  11. AJ Lindahl, AJ Lawton, J Baeza, JA Dowell, JM Denu, (2019). Site-specific lysine acetylation stoichiometry across subcellular compartments. Protein Acetylation: Methods and Protocols, 79-106. https://link.springer.com/protocol/10.1007/978-1-4939-9434-2_6

  12. P Latorre-Muro, J Baeza, EA Armstrong, R Hurtado-Guerrero, F Corzana, LE Wu, DA Sinclair, P Lopez-Buesa, JA Carrodeguas, JM Denu, (2018). Dynamic acetylation of phosphoenolpyruvate carboxykinase toggles enzyme activity between gluconeogenic and anaplerotic reactions. Molecular cell, 71 (5), 718-732. e9. https://www.cell.com/molecular-cell/pdf/S1097-2765(18)30600-2.pdf

  13. J Baeza, AJ Lawton, J Fan, MJ Smallegan, I Lienert, T Gandhi, OM Bernhardt, L Reiter, JM Denu, AG Biognosys, (2018). Quantifying dynamic protein acetylation using quantitative stoichiometry. bioRxiv, 472530. https://www.biorxiv.org/content/10.1101/472530v3

  14. I Galleano, J Nielsen, AS Madsen, CA Olsen, (2017). Scalable and purification-free synthesis of a myristoylated fluorogenic sirtuin substrate. Synlett, 28 (16), 2169-2173. https://www.thieme-connect.com/products/ejournals/html/10.1055/s-0036-1588875

  15. J Baeza, MJ Smallegan, JM Denu, (2016). Mechanisms and dynamics of protein acetylation in mitochondria. Trends in biochemical sciences, 41 (3), 231-244. https://www.cell.com/trends/biochemical-sciences/fulltext/S0968-0004(15)00256-X

  16. J Fan, J Baeza, JM Denu, (2016). Investigating histone acetylation stoichiometry and turnover rate. Methods in Enzymology, 574, 125-148. https://www.sciencedirect.com/science/article/pii/S0076687916000203

  17. J Baeza, MJ Smallegan, JM Denu, (2015). Site-specific reactivity of nonenzymatic lysine acetylation. ACS chemical biology, 10 (1), 122-128. https://pubs.acs.org/doi/abs/10.1021/cb500848p

  18. J Baeza, JA Dowell, MJ Smallegan, J Fan, D Amador-Noguez, Z Khan, JM Denu, (2014). Stoichiometry of Site-specific Lysine Acetylation in an Entire Proteome♦. Journal of Biological Chemistry, 289 (31), 21326-21338. https://www.jbc.org/article/S0021-9258(20)47518-0/abstract

  19. JL Feldman, J Baeza, JM Denu, (2013). Activation of the Protein Deacetylase SIRT6 by Long-chain Fatty Acids and Widespread Deacylation by Mammalian Sirtuins♦. Journal of Biological Chemistry, 288 (43), 31350-31356. https://www.jbc.org/article/S0021-9258(20)48735-6/abstract

  20. JY Ho, NJ Cira, JA Crooks, J Baeza, DB Weibel, (2012). Rapid identification of ESKAPE bacterial strains using an autonomous microfluidic device. PLoS One, 7 (7), e41245. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0041245

  21. X Zhang, M Daucher, J Baeza, C‐W Kim, R Russell, S Kottilil, (2012). Human immunodeficiency virus enhances hepatitis C virus replication by differential regulation of IFN and TGF family genes. Journal of medical virology, 84 (9), 1344-1352. https://onlinelibrary.wiley.com/doi/abs/10.1002/jmv.23315

♦ This article was selected as a Paper of the Week.