Staff information

PNNL Publications

2025

• Adamczyk P.A., H. Hwang, T. Chang, Y. Gao, E. Baidoo, J. Kim, and B.M. Webb-Robertson, et al. 2025. "The oleaginous yeast Rhodosporidium toruloides engineered for biomass hydrolysate-derived (E)-a-bisabolene production." Metabolic Engineering 90. PNNL-SA-210177. doi:10.1016/j.ymben.2025.02.014
• Czajka J.J., Z. Dai, T. Radivojevic, J. Kim, S. Deng, T.L. Lemmon, and M.S. Swita, et al. 2025. "Enabling malic acid production from corn-stover hydrolysate in Lipomyces starkeyi via metabolic engineering and bioprocess optimization." Microbial Cell Factories 24:Art. No. 117. PNNL-SA-204465. doi:10.1186/s12934-025-02705-0
• Velickovic M., L. Kadam, J. Kim, K. Zemaitis, D. Velickovic, Y. Gao, and R. Wu, et al. 2025. "Advanced multi-modal mass spectrometry imaging reveals functional differences of placental villous compartments at microscale resolution." Nature Communications 16:Art. No. 2061. PNNL-SA-201502. doi:10.1038/s41467-025-57107-y

2024

• Couvillion S.P., E.S. Nakayasu, B.M. Webb-Robertson, I.H. Yang, J.G. Eder, C.D. Nicora, and L.M. Bramer, et al. 2024. "Associations between SARS-CoV-2 Infection or COVID-19 Vaccination and Human Milk Composition: A Multi-Omics Approach." The Journal of Nutrition 154, no. 12:3566-3574. PNNL-SA-197322. doi:10.1016/j.tjnut.2024.09.032
• Gao Y., H. Kim, R. Kitata, T. Lin, A.C. Swensen, T. Shi, and T. Liu. 2024. "Multiplexed Quantitative Proteomics in Prostate Cancer Biomarker Development." In Current Status of Prostate Cancer: Diagnosis, Biomarkers and Therapies, edited by Semmes, O. John, Nyalwidhe, J.O., Swadesh, K. Das, Fisher, Paul, B. 31-70. PNNL-SA-194316.
• Harrison A.L., J.G. Eder, P.M. Lalli, N. Munoz Munoz, Y. Gao, C.S. Clendinen, and D.J. Orton, et al. 2024. "PeakQC: A Software Tool for Omics-Agnostic Automated Quality Control of Mass Spectrometry Data." Journal of the American Society for Mass Spectrometry 35, no. 11:2680-2689. PNNL-SA-197329. doi:10.1021/jasms.4c00146
• Liu J., S. Cao, K.J. Imbach, M.A. Gritsenko, T.M. Lih, J.E. Kyle, and T.M. Yaron, et al. 2024. "Multi-scale signaling and tumor evolution in high-grade gliomas." Cancer Cell 42, no. 7:P1217-1238.E19. PNNL-SA-189873. doi:10.1016/j.ccell.2024.06.004
• Okonkwo O., C. Dou, E. Oksen, A. Narani, W. Marcondes, X. Chen, and J. Kim, et al. 2024. "Corn Stover variability drives differences in bisabolene production by engineered Rhodotorula toruloides." Journal of Industrial Microbiology and Biotechnology 51, no. _:Art No. kuae034. PNNL-SA-204310. doi:10.1093/jimb/kuae034
• Ross D.H., J. Lee, Y. Gao, A.L. Hollerbach, A. Bilbao, T. Shi, and Y.M. Ibrahim, et al. 2024. "Evaluation of a Reference-Free Collision Cross Section Calibration Strategy for Proteomics Using SLIM-based High-Resolution Ion Mobility Spectrometry- Mass Spectrometry." Journal of the American Society for Mass Spectrometry 35, no. 7:1539-1549. PNNL-SA-197876. doi:10.1021/jasms.4c00141
• 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

• Bilbao A., N. Munoz Munoz, J. Kim, D.J. Orton, Y. Gao, K. Poorey, and K.R. Pomraning, et al. 2023. "PeakDecoder enables machine learning-based metabolite annotation and accurate profiling in multidimensional mass spectrometry measurements." Nature Communications 14, no. 2023:2461. PNNL-SA-174727. doi:10.1038/s41467-023-37031-9
• Coradetti S.T., P.A. Adamczyk, D. Liu, Y. Gao, P.B. Otoupal, G.M. Geiselman, and B.M. Webb-Robertson, et al. 2023. "Engineering Transcriptional Regulation of Pentose Metabolism in Rhodosporidium toruloides for Improved Conversion of Xylose to Bioproducts." Microbial Cell Factories 22. PNNL-SA-177272. doi:10.1186/s12934-023-02148-5
• Dai Z., K.R. Pomraning, S. Deng, J. Kim, K.B. Campbell, A.L. Robles, and B.A. Hofstad, et al. 2023. "Metabolic engineering to improve production of 3-hydroxypropionic acid from corn-stover hydrolysate in Aspergillus species." Biotechnology for Biofuels and Bioproducts 16. PNNL-SA-182738. doi:10.1186/s13068-023-02288-1
• Deng S., J. Kim, K.R. Pomraning, Y. Gao, J.E. Evans, B.A. Hofstad, and Z. Dai, et al. 2023. "Identification of a specific exporter that enables high production of aconitic acid in Aspergillus pseudoterreus." Metabolic Engineering 80. PNNL-SA-181297. doi:10.1016/j.ymben.2023.09.011
• Liu D., H. Hwang, P.B. Otoupal, G.M. Geiselman, J. Kim, K.R. Pomraning, and Y. Kim, et al. 2023. "Engineering Rhodosporidium toruloides for Production of 3-Hydroxypropionic Acid from Lignocellulosic Hydrolysate." Metabolic Engineering 78. PNNL-SA-185285. doi:10.1016/j.ymben.2023.05.001
• 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

2022

• Pomraning K.R., Z. Dai, N. Munoz Munoz, Y. Kim, Y. Gao, S. Deng, and T.L. Lemmon, et al. 2022. "Itaconic acid production is regulated by laeA in Aspergillus pseudoterreus." Metabolic Engineering Communications 15. PNNL-SA-171876. doi:10.1016/j.mec.2022.e00203

2021

• Kim J., S.T. Coradetti, Y. Kim, Y. Gao, J. Yaegashi, J.D. Zucker, and N. Munoz Munoz, et al. 2021. "Multi-omics driven metabolic network reconstruction and analysis of lignocellulosic carbon utilization in Rhodosporidium toruloides." Frontiers in Bioengineering and Biotechnology 8. PNNL-SA-156767. doi:10.3389/fbioe.2020.612832
• Kirby J., G.M. Geiselman, J. Yaegashi, J. Kim, X. Zhuang, M. Tran-Gyamfi, and J. Prahl, et al. 2021. "Further engineering of R. toruloides for the production of terpenes from lignocellulosic biomass." Biotechnology for Biofuels 14, no. 1:Article No. 101. PNNL-SA-162406. doi:10.1186/s13068-021-01950-w
• Pomraning K.R., Z. Dai, N. Munoz Munoz, Y. Kim, Y. Gao, S. Deng, and J. Kim, et al. 2021. "Integration of proteomics and metabolomics into the Design, Build, Test, Learn cycle to improve 3-hydroxypropionic acid production in Aspergillus pseudoterreus." Frontiers in Bioengineering and Biotechnology 9. PNNL-SA-149911. doi:10.3389/fbioe.2021.603832
• Wu R., M.R. Davison, Y. Gao, C.D. Nicora, J.E. McDermott, K.E. Burnum-Johnson, and K.S. Hofmockel, et al. 2021. "Moisture Modulates Soil Reservoirs of Active DNA and RNA Viruses." Communications Biology 4, no. 1:992. PNNL-SA-160635. doi:10.1038/s42003-021-02514-2

2020

• Chaves J.E., R. Wilton, Y. Gao, N. Munoz Munoz, M.C. Burnet, Z. Schmitz, and J. Rowan, et al. 2020. "Evaluation of chromosomal insertion loci in the Pseudomonas putida KT2440 genome for predictable biosystems design." Metabolic Engineering Communications 11. PNNL-SA-155823. doi:10.1016/j.mec.2020.e00139
• Gao Y., Y. Wang, Y. Chen, H. Wang, D. Young, T. Shi, and Y. Song, et al. 2020. "Proteomic Tissue-based Classifier for Early Prediction of Prostate Cancer Progression." Cancers 12, no. 5:1268. PNNL-SA-149705. doi:10.3390/cancers12051268
• Geiselman G.M., X. Zhuang, J. Kirby, M. Tran-Gyamfi, J. Prahl, E.R. Sundstrom, and Y. Gao, et al. 2020. "Production of ent-kaurene from lignocellulosic hydrolysate in Rhodosporidium toruloides." Microbial Cell Factories 19, no. 1:Article No. 24. PNNL-SA-150034. doi:10.1186/s12934-020-1293-8
• Li M., R. Li, Y. Gao, C.T. Resch, W. Qian, T. Shi, and L. Shi, et al. 2020. "Nitrate bioreduction dynamics in hyporheic zone sediments under cyclic changes of chemical compositions." Journal of Hydrology 585. PNNL-SA-152190. doi:10.1016/j.jhydrol.2020.124836
• Orwoll E.S., J. Wiedrick, C. Nielson, J.M. Jacobs, E.S. Baker, P.D. Piehowski, and V.A. Petyuk, et al. 2020. "Proteomic assessment of serum biomarkers of longevity in older men." Aging Cell 19, no. 11:Article No. e13253. PNNL-SA-155940. doi:10.1111/acel.13253
• Piehowski P.D., Y. Zhu, L.M. Bramer, K.G. Stratton, R. Zhao, D.J. Orton, and R.J. Moore, et al. 2020. "Automated mass spectrometry imaging of over 2000 proteins from tissue sections at 100-µm spatial resolution." Nature Communications 11, no. 1:Article No. 8. PNNL-SA-138884. doi:10.1038/s41467-019-13858-z

2019

• 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
• Horta M.A., N. Thieme, Y. Gao, K.E. Burnum-Johnson, C.D. Nicora, M.A. Gritsenko, and M.S. Lipton, et al. 2019. "Broad substrate-specific phosphorylation events are associated with the initial stage of plant cell wall recognition in Neurospora crassa." Frontiers in Microbiology 10. PNNL-SA-143199. doi:10.3389/fmicb.2019.02317
• Singer R.A., L. Arnes, Y. Cui, J. Wang, Y. Gao, M. Guney, and K.E. Burnum-Johnson, et al. 2019. "The Long Noncoding RNA Paupar Modulates PAX6 Regulatory Activities to Promote Alpha Cell Development and Function." Cell Metabolism 30, no. 6:1091-1106.e8. PNNL-SA-146887. doi:10.1016/j.cmet.2019.09.013

2018

• Orwoll E.S., J. Wiedrick, J.M. Jacobs, E.M. Baker, P.D. Piehowski, V.A. Petyuk, and Y. Gao, et al. 2018. "High-throughput serum proteomics for the identification of protein biomarkers of mortality in older men." Aging Cell 17, no. 2:Article No. e12717. PNNL-SA-131443. doi:10.1111/acel.12717

2017

• Li M., W. Qian, Y. Gao, L. Shi, and C. Liu. 2017. "Functional Enzyme-based Approach for Linking Microbial Community Functions with Biogeochemical Process Kinetics." Environmental Science & Technology 51, no. 20:11848-11857. PNNL-SA-127385. doi:10.1021/acs.est.7b03158
• Li M., Y. Gao, W. Qian, L. Shi, Y. Liu, W.C. Nelson, and C.D. Nicora, et al. 2017. "Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes." Environmental Microbiology Reports 9, no. 5:512-521. PNNL-SA-120732. doi:10.1111/1758-2229.12558
• Nie S., T. Shi, T.L. Fillmore, A.A. Schepmoes, H.M. Brewer, Y. Gao, and E. Song, et al. 2017. "Deep-dive Targeted Quantification for Ultrasensitive Analysis of Proteins in Nondepleted Human Blood Plasma/Serum and Tissues." Analytical Chemistry 89, no. 17:9139-9146. PNNL-SA-126297. doi:10.1021/acs.analchem.7b01878
• Shi T., S. Quek, Y. Gao, C.D. Nicora, S. Nie, T.L. Fillmore, and T. Liu, et al. 2017. "Multiplexed targeted mass spectrometry assays for prostate cancer-associated urinary proteins." Oncotarget 8, no. 60:101887-101898. PNNL-SA-128413. doi:10.18632/oncotarget.21710
• Song E., Y. Gao, C. Wu, T. Shi, S. Nie, T.L. Fillmore, and A.A. Schepmoes, et al. 2017. "Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer." Scientific Data. PNNL-SA-122408. doi:10.1038/sdata.2017.91
• Wang H., C.E. Barbieri, J. He, Y. Gao, T. Shi, C. Wu, and A.A. Schepmoes, et al. 2017. "Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics." Journal of Translational Medicine 15. PNNL-SA-125993. doi:10.1186/s12967-017-1276-7
• Yang L., T. Stewart, M. Shi, G. Pottiez, R. Dator, R. Wu, and P. Aro, et al. 2017. "An alpha-synuclein MRM assay with diagnostic potential for Parkinson’s disease and monitoring disease progression." Proteomics - Clinical Applications 11, no. 7-8:Article No. 1700045. PNNL-SA-124743. doi:10.1002/prca.201700045

2016

• Guo X., T.L. Fillmore, Y. Gao, and K. Tang. 2016. "Capillary Electrophoresis-nanoelectrospray Ionization-selected Reaction Monitoring Mass Spectrometry Via A True Sheathless Metal-coated Emitter Interface For Robust And High Sensitivity Sample Quantification." Analytical Chemistry 88, no. 8:4418-4425. PNNL-SA-115236. doi:10.1021/acs.analchem.5b04912
• Ho M.E., S. Quek, L.D. True, R. Seiler, A. Fleischmann, L. Bagryanova, and S.R. Kim, et al. 2016. "Bladder cancer cells secrete while normal bladder cells express but do not secrete AGR2." Oncotarget 7, no. 13:15747-15756. PNNL-SA-114369. doi:10.18632/oncotarget.7400
• Hoofnagle A.N., J.R. Whiteaker, S.A. Carr, E. Kuhn, T. Liu, S.A. Massoni, and S.N. Thomas, et al. 2016. "Recommendations for the generation, quantification, storage and handling of peptides used for mass spectrometry-based assays." Clinical Chemistry 62, no. 1:48-69. PNNL-SA-113208. doi:10.1373/clinchem.2015.250563
• Nielson C., K. Jones, R.F. Chun, J.M. Jacobs, Y. Wang, M. Hewison, and J.S. Adams, et al. 2016. "Free 25-Hydroxyvitamin D: Impact of Vitamin D Binding Protein Assays on Racial-Genotypic Associations." Journal of Clinical Endocrinology and Metabolism 101, no. 5:2226-2234. PNNL-SA-120076. doi:10.1210/jc.2016-1104
• Nielson C., K. Jones, R.F. Chun, J.M. Jacobs, Y. Wang, M. Hewison, and J.S. Adams, et al. 2016. "Role of Assay Type in Determining Free 25-Hydroxyvitamin D Levels in Diverse Populations." The New England Journal of Medicine 374, no. 17:1695-1696. PNNL-SA-108708. doi:10.1056/NEJMc1513502
• Shi T., M. Niepel, J.E. McDermott, Y. Gao, C.D. Nicora, W.B. Chrisler, and L.M. Markillie, et al. 2016. "Conservation of Protein Abundance Patterns Reveals the Regulatory Architecture of the of the EGFR-MAPK Pathway." Science Signaling 9, no. 436:rs6. PNNL-SA-115056. doi:10.1126/scisignal.aaf0891
• Sigdel T.K., Y. Gao, J. He, A. Wang, C.D. Nicora, T.L. Fillmore, and T. Shi, et al. 2016. "Mining the Human Urine Proteome for Monitoring Renal Transplant Injury." Kidney International 89, no. 6:1244-1252. PNNL-SA-115293. doi:10.1016/j.kint.2015.12.049

2015

• He J., A.A. Schepmoes, T. Shi, C. Wu, T.L. Fillmore, Y. Gao, and R.D. Smith, et al. 2015. "Analytical platform evaluation for quantification of ERG in prostate cancer using protein and mRNA detection methods." Journal of Translational Medicine 13. PNNL-SA-107827. doi:10.1186/s12967-015-0418-z

2014

• Shi T., Y. Gao, M.J. Gaffrey, C.D. Nicora, T.L. Fillmore, W.B. Chrisler, and M.A. Gritsenko, et al. 2014. "Sensitive Targeted Quantification of ERK Phosphorylation Dynamics and Stoichiometry in Human Cells without Affinity Enrichment." Analytical Chemistry 87, no. 2:1103-1110. PNNL-SA-103421. doi:10.1021/ac503797x
• Shi T., Y. Gao, S. Quek, T.L. Fillmore, C.D. Nicora, D. Su, and R. Zhao, et al. 2014. "A highly sensitive targeted mass spectrometric assay for quantification of low-abundance AGR2 in human urine and serum." Journal of Proteome Research 13, no. 2:875-882. PNWD-SA-10119. doi:10.1021/pr400912c
• Wu C., T. Shi, J.N. Brown, J. He, Y. Gao, T.L. Fillmore, and A.K. Shukla, et al. 2014. "Expediting SRM assay development for large-scale targeted proteomics experiments." Journal of Proteome Research 13, no. 10:4479-87. PNNL-SA-102906. doi:10.1021/pr500500d

2013

• Shi T., T.L. Fillmore, Y. Gao, R. Zhao, J. He, A.A. Schepmoes, and C.D. Nicora, et al. 2013. "Long-Gradient Separations Coupled with Selected Reaction Monitoring for Highly Sensitive, Large Scale Targeted Protein Quantification in a Single Analysis." Analytical Chemistry 85, no. 19:9196-9203. PNNL-SA-96700. doi:10.1021/ac402105s
• Shi T., X. Sun, Y. Gao, T.L. Fillmore, A.A. Schepmoes, R. Zhao, and J. He, et al. 2013. "Targeted quantification of low ng/mL level proteins in human serum without immunoaffinity depletion." Journal of Proteome Research 12, no. 7:3353-3361. PNNL-SA-92544. doi:10.1021/pr400178v
• Zhou J., R.K. Krovvidi, Y. Gao, H. Gao, B.O. Petritis, A. De, and C. Miller-Graziano, et al. 2013. "Trauma-associated Human Neutrophil Alterations Revealed by Comparative Proteomics Profiling." Proteomics - Clinical Applications 7, no. 7-8:571-583. PNWD-SA-9434. doi:10.1002/prca.201200109