Staff information

PNNL Publications

2024

• Sarkar S., C. Dieter, J.E. Kyle, M. Guney, D. Sarbaugh, R. Yin, and X. Li, et al. 2024. "Regulation of ß-cell death by ADP-ribosylhydrolase ARH3 via lipid signaling in insulitis." Cell Communication and Signaling 22, no. _:141. PNNL-SA-152364. doi:10.1101/2020.03.23.004481
• Webb-Robertson B.M., E.S. Nakayasu, F. Dong, K.C. Waugh, J.E. Flores, L.M. Bramer, and A.A. Schepmoes, et al. 2024. "Decrease in multiple complement protein levels associated with development of islet autoimmunity and type 1 diabetes." iScience 27, no. 2:Art. No. 108769. PNNL-SA-177389. doi:10.1016/j.isci.2023.108769

2023

• Bramer L.M., R. Hontz, A.J. Eisfeld, A.C. Sims, Y. Kim, K.G. Stratton, and C.D. Nicora, et al. 2023. "Multi-omics of NET Formation and Correlations with CNDP1, PSPB, and L-Cystine Levels in Severe and Mild COVID-19 Infections." Heliyon 9, no. 3:13795. PNNL-SA-169411. doi:10.1016/j.heliyon.2023.e13795
• Couvillion S.P., K.E. Mostoller, J.L. Williams, R.M. Pace, I.L. Stohel, H.K. Peterson, and C.D. Nicora, et al. 2023. "Interrogating the role of the milk microbiome in mastitis in the multi-omics era." Frontiers in Microbiology 14. PNNL-SA-180041. doi:10.3389/fmicb.2023.1105675
• Couvillion S.P., R.E. Danczak, D.T. Naylor, M.L. Smith, K.G. Stratton, V.L. Paurus, and K.J. Bloodsworth, et al. 2023. "Rapid remodeling of the soil lipidome in response to a drying-rewetting event." Microbiome 11, no. 2023:34. PNNL-SA-172149. doi:10.1186/s40168-022-01427-4
• Diaz Ludovico I., S. Sarkar, E.C. Elliott, S.M. Virtanen, I. Erlund, S. Ramanadham, and R.G. Mirmira, et al. 2023. "Fatty acid-mediated signaling as a target for developing type 1 diabetes therapies." Expert Opinion on Therapeutic Targets 27, no. 9:793-806. PNNL-SA-185489. doi:10.1080/14728222.2023.2259099
• Nakayasu E.S., L.M. Bramer, C.K. Ansong, A.A. Schepmoes, T.L. Fillmore, M.A. Gritsenko, and T.R. Clauss, et al. 2023. "Plasma protein biomarkers predict the development of persistent autoantibodies and type 1 diabetes 6 months prior to the onset of autoimmunity." Cell Reports Medicine 4, no. 7:Art. No. 101093. PNNL-SA-137771. doi:10.1016/j.xcrm.2023.101093
• Nakayasu E.S., M.A. Gritsenko, Y. Kim, J.E. Kyle, K.G. Stratton, C.D. Nicora, and N. Munoz Munoz, et al. 2023. "Elucidating regulatory processes of intense physical activity by multi-omics analysis." Military Medical Research 10, no. 1:48. PNNL-SA-158793. doi:10.1186/s40779-023-00477-5
• Patel R., K. Negron, M. Zhou, E.S. Nakayasu, B. Drown, and C. Das. 2023. "Genetically encoded crosslinking enables identification of multivalent ubiquitin-deubiquitylating enzyme interactions." Chembiochem 24, no. 15:e202300305. PNNL-SA-188089. doi:10.1002/cbic.202300305
• Sarkar S., E.C. Elliott, H.R. Henry, I. Diaz Ludovico, J.T. Melchior, A. Frazer-Abel, and B.M. Webb-Robertson, et al. 2023. "Systematic review of type 1 diabetes biomarkers reveals regulation in circulating proteins related to complement, lipid metabolism and immune response." Clinical Proteomics 20. PNNL-ACT-SA-10706. doi:10.1186/s12014-023-09429-6
• Sims E.K., A. Kulkarni, A. Hull, S. Woerner, S. Cabrera, L. Mastrandrea, and B. Hammoud, et al. 2023. "Inhibition of polyamine biosynthesis preserves ß cell function in type 1 diabetes." Cell Reports Medicine 4, no. 11:Art. No. 101261. PNNL-SA-194634. doi:10.1016/j.xcrm.2023.101261
• Tabb D., K. Jeong, K. Druart, M. Gant, K.A. Brown, C.D. Nicora, and M. Zhou, et al. 2023. "Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection." Journal of Proteome Research 22, no. 7:2199-2217. PNNL-SA-178802. doi:10.1021/acs.jproteome.2c00673
• Tang X., W. Wei, J.M. Snowball, E.S. Nakayasu, S. Bell, C.K. Ansong, and X. Lin, et al. 2023. "EMC3 regulates mesenchymal cell survival via control of the mitotic spindle assembly." iScience 26, no. 1:Art. No. 105667. PNNL-SA-152292. doi:10.1016/j.isci.2022.105667
• Vallejo M.C., S. Sarkar, E.C. Elliott, H.R. Henry, S.M. Powell, I. Diaz Ludovico, and Y. You, et al. 2023. "A proteomic meta-analysis refinement of plasma extracellular vesicles." Scientific Data 10. PNNL-SA-178237. doi:10.1038/s41597-023-02748-1
• You Y., C. Tsai, R. Patel, S. Sarkar, G. Clair, M. Zhou, and T. Liu, et al. 2023. "Analysis of a macrophage carbamylated proteome reveals a function in post-translational modification crosstalk." Cell Communication and Signaling 21, no. 1:241. PNNL-SA-186292. doi:10.1186/s12964-023-01257-3

2022

• Aguirre R., A. Kulkarni, M.W. Becker, X. Lei, S. Sarkar, S. Ramanadham, and E. Phelps, et al. 2022. "Extracellular Vesicles in ß Cell Biology: Role of Lipids in Vesicle Biogenesis, Cargo, and Intercellular Signaling." Molecular Metabolism 63. PNNL-SA-173821. doi:10.1016/j.molmet.2022.101545
• Colby S.M., C.H. Chang, J.L. Bade, J. Nunez, M.R. Blumer, D.J. Orton, and K.J. Bloodsworth, et al. 2022. "DEIMoS: An Open-Source Tool for Processing High-Dimensional Mass Spectrometry Data." Analytical Chemistry 94, no. 16:6130-6138. PNNL-SA-168444. doi:10.1021/acs.analchem.1c05017
• Feid S.C., H.E. Walukiewicz, X. Wang, E.S. Nakayasu, C.V. Rao, and A.J. Wolfe. 2022. "Regulation of translation by lysine acetylation in Escherichia coli." mBio 13, no. 3:e01224-22. PNNL-SA-173824. doi:10.1128/mbio.01224-22
• Fu J., M. Zhou, M.A. Gritsenko, E.S. Nakayasu, L. Song, and Z. Luo. 2022. "Legionella pneumophila modulates host energy metabolism by ADP-ribosylation of ADP/ATP translocases." eLife 11. PNNL-SA-165115. doi:10.7554/eLife.73611
• Lee J., H.D. Mitchell, M.C. Burnet, R. Wu, S.C. Jenson, E.D. Merkley, and E.S. Nakayasu, et al. 2022. "Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics." Journal of Proteome Research 21, no. 8:2023-2035. PNNL-SA-138497. doi:10.1021/acs.jproteome.2c00334
• Sarkar S., J.T. Melchior, H.R. Henry, F. Syed, R.G. Mirmira, E.S. Nakayasu, and T.O. Metz. 2022. "GDF15: a potential therapeutic target for type 1 diabetes." Expert Opinion on Therapeutic Targets 26, no. 1:57 - 67. PNNL-SA-168207. doi:10.1080/14728222.2022.2029410
• Shakya B., W.D. Penn, E.S. Nakayasu, G.K. Kilili, and D.J. Lacount. 2022. "Identification of Exported Plasmodium falciparum Proteins That Bind to the Erythrocyte Cytoskeleton." Microorganisms 10, no. 7:1438. PNNL-SA-139741. doi:10.3390/microorganisms10071438

2021

• Alcazar O., L.F. Hernandez, E.S. Nakayasu, C.D. Nicora, C.K. Ansong, M.J. Muehlbauer, and J.R. Bain, et al. 2021. "Parallel multi-omics in high-risk subjects for the identification of integrated biomarker signatures of type 1 diabetes." Biomolecules 11, no. 3:383. PNNL-SA-158353. doi:10.3390/biom11030383
• Anderson-Baucum E., A.R. Pineros, A. Kulkarni, B.M. Webb-Robertson, B.F. Maier, R.M. Anderson, and W. Wu, et al. 2021. "Deoxyhypusine Synthase Promotes a Pro-Inflammatory Macrophage Phenotype." Cell Metabolism 33, no. 9:1883-1893.e7. PNNL-SA-162924. doi:10.1016/j.cmet.2021.08.003
• Hernandez L.F., L. Betancourt, E.S. Nakayasu, C.K. Ansong, G.A. Ceballos, D. Paredes, and M.H. Abdulreda. 2021. "Integrated metabolomics and proteomics analyses in the local milieu of islet allografts in rejection versus tolerance." International Journal of Molecular Sciences 22, no. 16:8754. PNNL-SA-162995. doi:10.3390/ijms22168754
• Song L., Y. Xie, C. Li, L. Wang, C. He, Y. Zhang, and J. Yuan, et al. 2021. "The Legionella effector SdjA is a bifunctional enzyme that distinctly regulates phosphoribosyl ubiquitination." mBio 12, no. 5:e02316-21. PNNL-SA-166276. doi:10.1128/mBio.02316-21
• Webb-Robertson B.M., L.M. Bramer, B.A. Stanfill, S.M. Reehl, E.S. Nakayasu, T.O. Metz, and B. Frohnert, et al. 2021. "Prediction of the Development of Islet Autoantibodies through Integration of Environmental, Genetic, and Metabolic Markers." Journal of Diabetes 13, no. 2:143-153. PNNL-SA-146734. doi:10.1111/1753-0407.13093
• Zamith-Miranda D., H.M. Heyman, M.C. Burnet, S.P. Couvillion, X. Zheng, N. Munoz Munoz, and W.C. Nelson, et al. 2021. "A Histoplasma capsulatum lipid metabolic map identifies antifungal targets." mBio 12, no. 6:e02972-21. PNNL-SA-152496. doi:10.1128/mBio.02972-21
• Zamith-Miranda D., H.M. Heyman, S.P. Couvillion, R.J. Cordero, M.L. Rodrigues, L. Nimrichter, and A. Casadevall, et al. 2021. "Comparative molecular and immunoregulatory analysis of extracellular vesicles from Candida albicans and Candida auris." mSystems 6, no. 4:e00822-21. PNNL-SA-156740. doi:10.1128/mSystems.00822-21
• Zamith-Miranda D., L.R. Alves, E.S. Nakayasu, and J.D. Nosanchuk. 2021. "Lessons learned from studying Histoplasma capsulatum extracellular vesicles." In Fungal Extracellular Vesicles: Biological Roles. Current Topics in Microbiology and Immunology, edited by M. Rodrigues and G. Janbon. 13-18. PNNL-SA-169908. doi:10.1007/978-3-030-83391-6_2
• Zamith-Miranda D., R.F. Amatuzzi, I.M. da Rocha, S.T. Martins, A.R. Lucena, A.Z. Vieira, and G. Trentin, et al. 2021. "Transcriptional and translational landscape of Candida auris in response to caspofungin." Computational and Structural Biotechnology Journal 19. PNNL-SA-167223. doi:10.1016/j.csbj.2021.09.007
• Zamith-Miranda D., R.P. da Silva, S.P. Couvillion, E.L. Bredeweg, M.C. Burnet, C. Coelho, and E. Camacho, et al. 2021. "Omics approaches for understanding biogenesis, composition and functions of fungal extracellular vesicles." Frontiers in Genetics 12. PNNL-SA-161136. doi:10.3389/fgene.2021.648524
• Zhang L., K. Zhang, H. Li, C. Coelho, D. De Souza, M. Shun Fu, and X. Li, et al. 2021. "Cryptococcus neoformans-infected macrophages release proinflammatory extracellular vesicles: insight into their components by multi-omics." mBio 12, no. 2:e00279-21. PNNL-SA-160420. doi:10.1128/mBio.00279-21

2020

• Alcazar O., L.F. Hernandez, E.S. Nakayasu, P.D. Piehowski, C.K. Ansong, M.H. Abdulreda, and P. Buchwald. 2020. "Longitudinal Proteomics Analysis in the Immediate Microenvironment of Islet Allografts During Progression of Rejection." Journal of Proteomics 223. PNNL-SA-152172. doi:10.1016/j.jprot.2020.103826
• Bürgel P.H., C.L. Marina, P.H. Saavedra, P. Albuquerque, S.A. De Oliveira, P.H. Holanda, and R.A. Castro, et al. 2020. "Cryptococcus neoformans secretes small molecules that inhibit IL-1ß inflammasome-dependent secretion." Mediators of Inflammation 2020. PNNL-SA-140752. doi:10.1155/2020/3412763
• Burnet M.C., D. Zamith-Miranda, H.M. Heyman, K.K. Weitz, E.L. Bredeweg, J.D. Nosanchuk, and E.S. Nakayasu. 2020. "Remodeling of the Histoplasma capsulatum membrane induced by monoclonal antibodies." Vaccines 8, no. 2:269. PNNL-SA-152362. doi:10.3390/vaccines8020269
• Cleare L.G., D. Zamith-Miranda, H.M. Heyman, S.P. Couvillion, L. Nimrichter, M.L. Rodrigues, and E.S. Nakayasu, et al. 2020. "Media Matters! Alterations in the loading and release of Histoplasma capsulatum extracellular vesicles in response to different nutritional milieus." Cellular Microbiology 22, no. 9:Article No. e13217. PNNL-SA-151908. doi:10.1111/cmi.13217
• Colli M.L., M. Ramos-Rodriquez, E.S. Nakayasu, M.I. Alvelos, M. Lopes, J.L. Hill, and J. Turatsinze, et al. 2020. "An integrated multi-omics approach identifies the landscape of interferon-a-mediated responses of human pancreatic beta cells." Nature Communications 11, no. 1:Article No. 2584. PNNL-SA-144581. doi:10.1038/s41467-020-16327-0
• Gan N., H. Guan, Y. Huang, T. Yu, J. Fu, E.S. Nakayasu, and K. Puvar, et al. 2020. "Legionella pneumophila regulates the activity of UBE2N by deamidase-mediated deubiquitination." EMBO Journal 39, no. 4:Article No. e102806. PNNL-SA-141791. doi:10.15252/embj.2019102806
• Lu C., A. Mccloskey, F. Chen, E.S. Nakayasu, L. Zhang, and Z. Luo. 2020. "Fic proteins inhibit the activity of topoisomerase IV by AMPylation in diverse bacteria." Frontiers in Microbiology 11. PNNL-SA-151977. doi:10.3389/fmicb.2020.02084
• Nakayasu E.S., F. Syed, S. Tersey, M.A. Gritsenko, H.D. Mitchell, C. Chan, and J. Turatsinze, et al. 2020. "Comprehensive proteomics analysis of stressed human islets identifies GDF15 as a target for type 1 diabetes intervention." Cell Metabolism 31, no. 2:363-374.e6. PNNL-SA-150166. doi:10.1016/j.cmet.2019.12.005
• Nakayasu E.S., T.O. Metz, and R.G. Mirmira. 2020. "Probing Islet Stress in Type 1 Diabetes." Aging 12, no. 19:18975-6. PNNL-SA-155932. doi:10.18632/aging.104157
• Nicora C.D., A. Sims, K.J. Bloodsworth, Y. Kim, R.J. Moore, J.E. Kyle, and E.S. Nakayasu, et al. 2020. "Metabolite, Protein, and Lipid Extraction (MPLEx): a method that simultaneously inactivates Middle East respiratory syndrome coronavirus and allows analysis of multiple host cell components following infection." In MERS Coronavirus: Methods and Protocols, edited by R. Vijay. 173-194. New York, New York:Humana. PNNL-SA-142077. doi:10.1007/978-1-0716-0211-9_14

2019

• Coelho C., L. Brown, M. Maryam, R. Vij, D.F. Smith, M.C. Burnet, and J.E. Kyle, et al. 2019. "Listeria monocytogenes Virulence Factors, including listeriolysin O, are Secreted in Biologically Active Extracellular Vesicles." Journal of Biological Chemistry 294, no. 4:1202-1217. PNNL-SA-128462. doi:10.1074/jbc.RA118.006472
• Gan N., E.S. Nakayasu, P.J. Hollenbeck, and Z. Luo. 2019. "Legionella pneumophila inhibits immune signalling via MavC-mediated transglutaminase-induced ubiquitination of UBE2N." Nature Microbiology 4, no. 1:134-143. PNNL-SA-129705. doi:10.1038/s41564-018-0282-8
• Gan N., X. Zhen, Y. Liu, X. Xu, C. He, J. Qiu, and Y. Liu, et al. 2019. "Regulation of phosphoribosyl ubiquitination by a calmodulin-dependent glutamylase." Nature 572, no. 7769:387-391. PNNL-SA-142888. doi:10.1038/s41586-019-1439-1
• Gibbons B.C., T.L. Fillmore, Y. Gao, R.J. Moore, T. Liu, E.S. Nakayasu, and T.O. Metz, et al. 2019. "Rapidly Assessing the Quality of Targeted Proteomics Experiments through Monitoring Stable-Isotope Labeled Standards." Journal of Proteome Research 18, no. 2:694-699. PNNL-SA-137457. doi:10.1021/acs.jproteome.8b00688
• Kilili G.K., B. Shakya, P.T. Dolan, L. Wang, E.S. Nakayasu, and D.J. Lacount. 2019. "The Plasmodium falciparum MESA erythrocyte cytoskeleton-binding (MEC) motif binds to erythrocyte ankyrin." Molecular and Biochemical Parasitology 231. PNNL-SA-139742. doi:10.1016/j.molbiopara.2019.111189
• McDermott J.E., J.R. Cort, E.S. Nakayasu, J.N. Pruneda, C.C. Overall, and J.N. Adkins. 2019. "Prediction of Bacterial E3 Ubiquitin Ligase Effectors using Reduced Amino Acid Peptide Fingerprinting." PeerJ 7. PNNL-SA-138492. doi:10.7717/peerj.7055
• Nakayasu E.S., W. Qian, C. Evans-Molina, R. Mirmira, D.L. Eizirik, and T.O. Metz. 2019. "The role of proteomics in assessing beta-cell dysfunction and death in type 1 diabetes." Expert Review of Proteomics 16, no. 7:569-582. PNNL-SA-142336. doi:10.1080/14789450.2019.1634548
• Romas-Rodriquez M., H. Raurell-Vila, M.L. Colli, M.I. Alvelos, M. Subirana, J.J. Mateu, and R. Norris, et al. 2019. "The impact of proinflammatory cytokines on the ß-cell regulatory landscape provides new insights into the genetics of type 1 diabetes." Nature Genetics 51, no. 11:1588-1595. PNNL-SA-141684. doi:10.1038/s41588-019-0524-6
• Stanfill B.A., S.M. Reehl, L.M. Bramer, E.S. Nakayasu, S.S. Rich, T.O. Metz, and M. Rewers, et al. 2019. "Extending Classification Algorithms to Case-Control Studies." Biomedical Engineering and Computational Biology 10. PNNL-SA-135302. doi:10.1177/1179597219858954
• Yin L., H. Ma, E.S. Nakayasu, S.H. Payne, D.R. Morris, and C.S. Harwood. 2019. "Bacterial Longevity Requires Protein Synthesis and a Stringent Response." mBio 10, no. 5:e02189-19. PNNL-SA-143448. doi:10.1128/mBio.02189-19
• Zamith-Miranda D., H.M. Heyman, L.G. Cleare, S.P. Couvillion, G. Clair, E.L. Bredeweg, and A. Gacser, et al. 2019. "Multi-omics signature of Candida Auris, an emerging and multidrug-resistant pathogen." mSystems 4, no. 4:e00257-19. PNNL-SA-140174. doi:10.1128/mSystems.00257-19

2018

• Akberdin I., D. Collins, R. Hamilton, D.Y. Oshchepkov, A.K. Shukla, C.D. Nicora, and E.S. Nakayasu, et al. 2018. "Rare Earth Elements Alter Redox Balance in Methylomicrobium alcaliphilum 20ZR." Frontiers in Microbiology 27. PNNL-SA-139645. doi:10.3389/fmicb.2018.02735
• Baltazar L.M., D. Zamith-Miranda, M.C. Burnet, H. Choi, L. Nimrichter, E.S. Nakayasu, and J.D. Nosanchuk. 2018. "Concentration-dependent protein loading of extracellular vesicles released by Histoplasma capsulatum after antibody treatment and its modulatory action upon macrophages." Scientific Reports 8, no. 1:Article No. 8065. PNNL-SA-124828. doi:10.1038/s41598-018-25665-5
• Callister S.J., T.L. Fillmore, C.D. Nicora, J.B. Shaw, S.O. Purvine, D.J. Orton, and R.A. White, et al. 2018. "Addressing the challenge of soil metaproteome complexity by improving metaproteome depth of coverage Through two-dimensional liquid chromatography." Soil Biology and Biochemistry 125. PNNL-SA-131999. doi:10.1016/j.soilbio.2018.07.018
• Nicora C.D., K.E. Burnum-Johnson, E.S. Nakayasu, C.P. Casey, R.A. White, T. Roy Chowdhury, and J.E. Kyle, et al. 2018. "The MPLEx Protocol for Multi-Omic Analyses of Soil Samples." Journal of Visualized Experiments e57343, no. 135. PNNL-SA-129344. doi:10.3791/57343
• Stanfill B.A., E.S. Nakayasu, L.M. Bramer, A.M. Thompson, C.K. Ansong, T. Clauss, and M.A. Gritsenko, et al. 2018. "Quality Control Analysis in Real-time (QC-ART): A Tool for Real-time Quality Control Assessment of Mass Spectrometry-based Proteomics Data." Molecular & Cellular Proteomics 17, no. 9:1824-1836. PNNL-SA-129934. doi:10.1074/mcp.RA118.000648

2017

• Burnum-Johnson K.E., J.E. Kyle, A.J. Eisfeld, C.P. Casey, K.G. Stratton, J.F. Gonzalez, and F. Habyarimana, et al. 2017. "MPLEx: A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling." Analyst 142, no. 3:442-448. PNNL-SA-116063. doi:10.1039/c6an02486f
• Liu Y., W. Zhu, Y. Tan, E.S. Nakayasu, C.J. Staiger, and Z. Luo. 2017. "A Legionella Effector Disrupts Host Cytoskeletal Structure by Cleaving Actin." PLoS Pathogens 13, no. 1:e1006186. PNNL-SA-124050. doi:10.1371/journal.ppat.1006186
• Muralimanoharan S., C. Li, E.S. Nakayasu, C.P. Casey, T.O. Metz, P.W. Nathanielsz, and A. Maloyan. 2017. "Sexual dimorphism in the fetal cardiac response to maternal nutrient restriction." Journal of Molecular and Cellular Cardiology 108. PNNL-SA-123734. doi:10.1016/j.yjmcc.2017.06.006
• Nakayasu E.S., M.C. Burnet, H.E. Walukiewicz, C.S. Wilkins, A.K. Shukla, S.M. Brooks, and M.J. Plutz, et al. 2017. "Ancient regulatory role of lysine acetylation in central metabolism." mBio 8, no. 6:Article No. e01894-17. PNNL-SA-124565. doi:10.1128/mBio.01894-17
• Qiu J., K. Yu, X. Fei, Y. Liu, E.S. Nakayasu, P.D. Piehowski, and J.B. Shaw, et al. 2017. "A unique deubiquitinase that deconjugates phosphoribosyl-linked protein ubiquitination." Cell Research 27, no. 7:865-881. PNNL-SA-123995. doi:10.1038/cr.2017.66
• Shakya B., W.D. Penn, E.S. Nakayasu, and D.J. Lacount. 2017. "The Plasmodium falciparum exported protein PF3D7_0402000 binds to erythrocyte ankyrin and band 4.1." Molecular and Biochemical Parasitology 216. PNNL-SA-127217. doi:10.1016/j.molbiopara.2017.06.002
• Wang L., X. Cai, S. Wu, R. Bomjan, E.S. Nakayasu, K. Händler, and J.C. Hinton, et al. 2017. "InvS Coordinates Expression of PrgH and FimZ and Is Required for Invasion of Epithelial Cells by Salmonella enterica serovar Typhimurium." Journal of Bacteriology 199, no. 13:00824-16. PNNL-SA-127078. doi:10.1128/JB.00824-16
• Yang J., L. Yin, F.H. Lessner, E.S. Nakayasu, S.H. Payne, K. Fixen, and L.A. Gallagher, et al. 2017. "Genes essential for phototrophic growth by a purple alphaproteobacterium." Environmental Microbiology 19, no. 9:3567-3578. PNNL-SA-124648. doi:10.1111/1462-2920.13852

2016

• Baltazar L.M., E.S. Nakayasu, T. Sobreira, H. Choi, A. Casadevall, L. Nimrichter, and J.D. Nosanchuk. 2016. "Antibody Binding Alters the Characteristics and Contents of Extracellular Vesicles Released by Histoplasma Capsulatum." mSphere 1, no. 2:Article No. e00085-15. PNNL-SA-121346. doi:10.1128/mSphere.00085-15
• Nakayasu E.S., C.D. Nicora, A.C. Sims, K.E. Burnum-Johnson, Y. Kim, J.E. Kyle, and M.M. Matzke, et al. 2016. "MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses." mSystems 1, no. 3:e00043-16. PNNL-SA-114737. doi:10.1128/mSystems.00043-16
• Qiu J., M.J. Sheedlo, K. Yu, Y. Tan, E.S. Nakayasu, C. Das, and X. Liu, et al. 2016. "Ubiquitination independent of E1 and E2 enzymes by bacterial effectors." Nature 533, no. 7601:120-124. PNNL-SA-117267. doi:10.1038/nature17657
• Sontag R.L., E.S. Nakayasu, R.N. Brown, G.S. Niemann, M.A. Sydor, O. Sanchez, and C. Ansong, et al. 2016. "Identification of novel host interactors of effectors secreted by Salmonella and Citrobacter: SrfH regulates host kinase ERK2 phosphorylation." mSystems 1, no. 4:e00032-15. PNNL-SA-114706. doi:10.1128/mSystems.00032-15

2015

• Elfenbein J.R., L.A. Knodler, E.S. Nakayasu, C. Ansong, H.M. Brewer, L. Bogomolnaya, and L.G. Adams, et al. 2015. "Multicopy single-stranded DNA directs intestinal colonization of enteric pathogens." PLoS Genetics 11, no. 9:e1005472. PNNL-SA-112635. doi:10.1371/journal.pgen.1005472
• Li J., C.C. Overall, E.S. Nakayasu, A.S. Kidwai, M.B. Jones, R. Johnson, and N.T. Nguyen, et al. 2015. "Analysis of the Salmonella regulatory network suggests involvement of SsrB and H-NS in sE-regulated SPI-2 gene expression." Frontiers in Microbiology 6. PNNL-SA-101010. doi:10.3389/fmicb.2015.00027
• Li J., E.S. Nakayasu, C.C. Overall, R. Johnson, A.S. Kidwai, J.E. McDermott, and C. Ansong, et al. 2015. "Global analysis of Salmonella alternative sigma factor E on protein translation." Journal of Proteome Research 14, no. 4:1716-1726. PNNL-SA-105707. doi:10.1021/pr5010423
• Nakayasu E.S., M.A. Sydor, R.N. Brown, R.L. Sontag, T. Sobreira, G.W. Slysz, and D.R. Humphrys, et al. 2015. "Identification of Salmonella Typhimurium deubiquitinase SseL substrates by immunoaffinity enrichment and quantitative proteomic analysis." Journal of Proteome Research 14, no. 9:4029-4038. PNNL-SA-101042. doi:10.1021/acs.jproteome.5b00574

2014

• Malouli D., S.G. Hansen, E.S. Nakayasu, E.E. Marshall, C.M. Hughes, A.B. Ventura, and R.M. Gilbride, et al. 2014. "Cytomegalovirus pp65 limits dissemination but is dispensable for persistence." Journal of Clinical Investigation 124, no. 5:1928-1944. PNNL-SA-91084. doi:10.1172/JCI67420
• Nakayasu E.S., S. Wu, M.A. Sydor, A.K. Shukla, K.K. Weitz, R.J. Moore, and K.K. Hixson, et al. 2014. "A Method to determine lysine acetylation stoichiometries." International Journal of Proteomics 2014. PNNL-SA-96571. doi:10.1155/2014/730725

2013

• Ansong C., S. Wu, D. Meng, X. Liu, H.M. Brewer, B. Kaiser, and E.S. Nakayasu, et al. 2013. "Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typimurium in response to infection-like conditions." Proceedings of the National Academy of Sciences of the United States of America 110, no. 25:10153-10158. PNNL-SA-92306. doi:10.1073/pnas.1221210110
• Conlon B.P., E.S. Nakayasu, L.E. Fleck, M.D. LaFleur, V.M. Isabella, K. Coleman, and S.N. Leonard, et al. 2013. "Activated ClpP kills persisters and eradicates a chronic biofilm infection." Nature 503, no. 7476:365-370. PNNL-SA-98792. doi:10.1038/nature12790
• Nakayasu E.S., C. Ansong, J.N. Brown, F. Yang, D. Lopez-Ferrer, W. Qian, and R.D. Smith, et al. 2013. "Evaluation of selected binding domains for the analysis of ubiquitinated proteomes." Journal of the American Society for Mass Spectrometry 24, no. 8:1214-1223. PNNL-SA-83169. doi:10.1007/s13361-013-0619-8
• Nakayasu E.S., R. Tempel, X.A. Cambronne, V.A. Petyuk, M.B. Jones, M.A. Gritsenko, and M.E. Monroe, et al. 2013. "Comparative phosphoproteomics reveals components of host cell invasion and post-transcriptional regulation during Francisella infection." Molecular and Cellular Proteomics 12, no. 11:3297-3309. PNNL-SA-93942. doi:10.1074/mcp.M113.029850
• Nakayasu E.S., R.N. Brown, C. Ansong, M.A. Sydor, S. Imtiaz, C. Mihai, and R.L. Sontag, et al. 2013. "Multi-omic data integration links Deleted in Breast Cancer 1 (DBC1) Degradation to Chromatin Remodeling in Inflammatory Response." Molecular & Cellular Proteomics. MCP 12, no. 8:2136-2147. PNNL-SA-88392. doi:10.1074/mcp.M112.026138
• Su D., A.K. Shukla, B. Chen, J. Kim, E.S. Nakayasu, Y. Qu, and U.K. Aryal, et al. 2013. "Quantitative Site-specific Reactivity Profiling of S-Nitrosylation in Mouse Skeletal Muscle Using Cysteinyl Peptide Enrichment Coupled with Mass Spectrometry." Free Radical Biology & Medicine 57. PNNL-SA-89035. doi:10.1016/j.freeradbiomed.2012.12.010

2012

• Ansong C.K., B.L. Deatherage, D.R. Hyduke, B. Schmidt, J.E. McDermott, M.B. Jones, and S. Chauhan, et al. 2012. "Studying Salmonellae and Yersiniae Host-Pathogen Interactions Using Integrated ‘Omics and Modeling." In Systems Biology. Current Topics in Microbiology and Immunology, edited by M Katze. 21-41. PNNL-SA-135981. doi:10.1007/82_2012_247
• Bordbar A., M.L. Mo, E.S. Nakayasu, A.C. Rutledge, Y. Kim, T.O. Metz, and M.B. Jones, et al. 2012. "Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation." Molecular Systems Biology 8. PNNL-SA-87903. doi:10.1038/msb.2012.21
• Malouli D., E.S. Nakayasu, K. Viswanathan, D.G. Camp, W.L. Chang, P.A. Barry, and R.D. Smith, et al. 2012. "Reevaluation of the Coding Potential and Proteomic Analysis of the BAC Derived Rhesus Cytomegalovirus Strain 68-1." Journal of Virology 86, no. 17:8959-8973. PNNL-SA-87442. doi:10.1128/JVI.01132-12

2011

• McDermott J.E., H. Yoon, E.S. Nakayasu, T.O. Metz, D.R. Hyduke, A.S. Kidwai, and B.O. Palsson, et al. 2011. "Technologies and Approaches to Elucidate and Model the Virulence Program of Salmonella." Frontiers in Microbiology 2. PNNL-SA-78291. doi:10.3389/fmicb.2011.00121