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Paul A. Stewart, PhD

Languages spoken: English

Academic Office Information

Paul.Stewart@hci.utah.edu

Education History

Doctoral Training Florida State University
 PhD
Graduate Training Florida State University
 MS
Undergraduate Florida State University
 BS

Selected Publications

Journal Article

  1. Karolak A, Urbaniak K, Monastyrskyi A, Duckett DR, Branciamore S, Stewart PA (2024). Structure-independent machine-learning predictions of the CDK12 interactome. Biophys J, 123(17), 2910-2920. (Read full article)
  2. Alontaga AY, Cano P, Ozakinci H, Puskas JA, Stewart PA, Welsh EA, Yoder SJ, Hicks JK, Saltos AN, Bossler AD, Haura EB, Koomen JM, Boyle TA (2024). Implementation of a High-Accuracy Targeted Gene Expression Panel for Clinical Care. J Mol Diagn, 26(8), 685-699. (Read full article)
  3. Permuth JB, Park MA, Chen DT, Basinski T, Powers BD, Gwede CK, Dezsi KB, Gomez M, Vyas SL, Biachi T, Cortizas EM, Crowder S, Genilo-Delgado M, Green BL, Greene A, Gregg C, Hoffe SE, Jiang K, Kim B, Vasudevan V, Garcialopez De Llano J, Menon AA, Mo Q, MorenoUrazan LM, Mok S, Parker N, Rajasekhara S, Rasool G, Sinnamon A, Sparks L, Stewart PA, Tardif K, Tassielli AF, Teer JK, Tran DV, Turner KL, Vadaparampil ST, Whelan CJ, Douglas WG, Velanovich V, Karachristos A, Legaspi A, Meredith K, Molina-Vega MA, Huguet KL, Arnoletti JP, Bloomston M, Trevino J, Merchant NB, Pimiento JM, Hodul PJ, Malafa M, Fleming J, Judge SM, Jeong DK, Judge A (2024). Leveraging real-world data to predict cancer cachexia stage, quality of life, and survival in a racially and ethnically diverse multi-institutional cohort of treatment-naïve patients with pancreatic ductal adenocarcinoma. Front Oncol, 14, 1362244. (Read full article)
  4. Peak T, Tian Y, Patel A, Shaw T, Obermayer A, Laborde J, Kim Y, Johnson J, Stewart P, Fang B, Teer JK, Koomen J, Berglund A, Marchion D, Francis N, Echevarria PR, Dhillon J, Clark N, Chang A, Sexton W, Zemp L, Chahoud J, Wang L, Manley B (2024). Pathogenic Roles for RNASET2 in Clear Cell Renal Cell Carcinoma. Lab Invest, 104(5), 102041. (Read full article)
  5. Adhikari E, Liu Q, Johnson J, Stewart P, Marusyk V, Fang B, Izumi V, Bowers K, Guzman KM, Koomen JM, Marusyk A, Lau EK (2023). Brain metastasis-associated fibroblasts secrete fucosylated PVR/CD155 that induces breast cancer invasion. Cell Rep, 42(12), 113463. (Read full article)
  6. Maurin M, Ranjouri M, Megino-Luque C, Newberg JY, Du D, Martin K, Miner RE 3rd, Prater MS, Wee DKB, Centeno B, Pruett-Miller SM, Stewart P, Fleming JB, Yu X, Bravo-Cordero JJ, Guccione E, Black MA, Mann KM (2023). RBFOX2 deregulation promotes pancreatic cancer progression and metastasis through alternative splicing. Nat Commun, 14(1), 8444. (Read full article)
  7. Sasamoto N, Stewart PA, Wang T, Thompson ZJ, Yoder SJ, Hecht JL, Cleveland JL, Conejo-Garcia J, Fridley BL, Terry KL, Tworoger SS (2023). Associations between prediagnostic aspirin use and ovarian tumor gene expression. Cancer Med, 12(17), 18405-18417. (Read full article)
  8. Grass GD, Ercan D, Obermayer AN, Shaw T, Stewart PA, Chahoud J, Dhillon J, Lopez A, Johnstone PAS, Rogatto SR, Spiess PE, Eschrich SA (2023). An Assessment of the Penile Squamous Cell Carcinoma Surfaceome for Biomarker and Therapeutic Target Discovery. Cancers (Basel), 15(14). (Read full article)
  9. Laborde J, Stewart PA, Chen Z, Chen YA, Brownstein NC (2023). Sparse clusterability: testing for cluster structure in high dimensions. BMC Bioinformatics, 24(1), 125. (Read full article)
  10. Soupir AC, Tian Y, Stewart PA, Nunez-Lopez YO, Manley BJ, Pellini B, Bloomer AM, Zhang J, Mo Q, Marchion DC, Liu M, Koomen JM, Siegel EM, Wang L (2023). Detectable Lipidomes and Metabolomes by Different Plasma Exosome Isolation Methods in Healthy Controls and Patients with Advanced Prostate and Lung Cancer. Int J Mol Sci, 24(3). (Read full article)
  11. Sarcar B, Fang B, Izumi V, O Nunez Lopez Y, Tassielli A, Pratley R, Jeong D, Permuth JB, Koomen JM, Fleming JB, Stewart PA (2022). A comparative Proteomics Analysis Identified Differentially Expressed Proteins in Pancreatic Cancer-Associated Stellate Cell Small Extracellular Vesicles. Mol Cell Proteomics, 21(12), 100438. (Read full article)
  12. Chang A, Chakiryan NH, Du D, Stewart PA, Zhang Y, Tian Y, Soupir AC, Bowers K, Fang B, Morganti A, Teer JK, Kim Y, Spiess PE, Chahoud J, Noble JD, Putney RM, Berglund AE, Robinson TJ, Koomen JM, Wang L, Manley BJ (2022). Proteogenomic, Epigenetic, and Clinical Implications of Recurrent Aberrant Splice Variants in Clear Cell Renal Cell Carcinoma. Eur Urol, 82(4), 354-362. (Read full article)
  13. Sasamoto N, Stewart PA, Wang T, Yoder SJ, Chellappan S, Hecht JL, Fridley BL, Terry KL, Tworoger SS (2022). Lifetime ovulatory years and ovarian cancer gene expression profiles. J Ovarian Res, 15(1), 59. (Read full article)
  14. Mahajan S, Majumder A, Stewart PA, Chen YA, Adhikari E, Fang B, Yang Y, Lawrence H, Kinose F, Koomen JM, Haura EB (2022). Deubiquitinase Vulnerabilities Identified through Activity-Based Protein Profiling in Non-Small Cell Lung Cancer. ACS Chem Biol, 17(4), 776-784. (Read full article)
  15. Majumder A, Hosseinian S, Stroud M, Adhikari E, Saller JJ, Smith MA, Zhang G, Agarwal S, Creixell M, Meyer BS, Kinose F, Bowers K, Fang B, Stewart PA, Welsh EA, Boyle TA, Meyer AS, Koomen JM, Haura EB (2021). Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration. Mol Cancer Res, 20(4), 542-555. (Read full article)
  16. Lee BD, Gitter A, Greene CS, Raschka S, Maguire F, Titus AJ, Kessler MD, Lee AJ, Chevrette MG, Stewart PA, Britto-Borges T, Cofer EM, Yu KH, Carmona JJ, Fertig EJ, Kalinin AA, Signal B, Lengerich BJ, Triche TJ Jr, Boca SM (2022). Ten quick tips for deep learning in biology. PLoS Comput Biol, 18(3), e1009803. (Read full article)
  17. Damaghi M, West J, Robertson-Tessi M, Xu L, Ferrall-Fairbanks MC, Stewart PA, Persi E, Fridley BL, Altrock PM, Gatenby RA, Sims PA, Anderson ARA, Gillies RJ (2021). The harsh microenvironment in early breast cancer selects for a Warburg phenotype. Proc Natl Acad Sci U S A, 118(3). (Read full article)
  18. Cook LM, Frieling JS, Nerlakanti N, McGuire JJ, Stewart PA, Burger KL, Cleveland JL, Lynch CC (2019). Betaglycan drives the mesenchymal stromal cell osteogenic program and prostate cancer-induced osteogenesis. Oncogene, 38(44), 6959-6969. (Read full article)
  19. Stewart PA, Welsh EA, Slebos RJC, Fang B, Izumi V, Chambers M, Zhang G, Cen L, Pettersson F, Zhang Y, Chen Z, Cheng CH, Thapa R, Thompson Z, Fellows KM, Francis JM, Saller JJ, Mesa T, Zhang C, Yoder S, DeNicola GM, Beg AA, Boyle TA, Teer JK, Ann Chen Y, Koomen JM, Eschrich SA, Haura EB (2019). Proteogenomic landscape of squamous cell lung cancer. Nat Commun, 10(1), 3578. (Read full article)
  20. Kuenzi BM, Remsing Rix LL, Stewart PA, Fang B, Kinose F, Bryant AT, Boyle TA, Koomen JM, Haura EB, Rix U (2017). Polypharmacology-based ceritinib repurposing using integrated functional proteomics. Nat Chem Biol, 13(12), 1222-1231. (Read full article)
  21. Welsh EA, Stewart PA, Kuenzi BM, Eschrich JA (2017). Escape Excel: A tool for preventing gene symbol and accession conversion errors. PLoS One, 12(9), e0185207. (Read full article)
  22. Stewart PA, Khamis ZI, Zhau HE, Duan P, Li Q, Chung LWK, Sang QA (2016). Upregulation of minichromosome maintenance complex component 3 during epithelial-to-mesenchymal transition in human prostate cancer. Oncotarget, 8(24), 39209-39217. (Read full article)
  23. Stewart PA, Fang B, Slebos RJ, Zhang G, Borne AL, Fellows K, Teer JK, Chen YA, Welsh E, Eschrich SA, Haura EB, Koomen JM (2016). Relative protein quantification and accessible biology in lung tumor proteomes from four LC-MS/MS discovery platforms. Proteomics, 17(6). (Read full article)
  24. Kuenzi BM, Borne AL, Li J, Haura EB, Eschrich SA, Koomen JM, Rix U, Stewart PA (2016). APOSTL: An Interactive Galaxy Pipeline for Reproducible Analysis of Affinity Proteomics Data. J Proteome Res, 15(12), 4747-4754. (Read full article)
  25. Kim JY, Stewart PA, Borne AL, Fang B, Welsh EA, Chen YA, Eschrich SA, Koomen JM, Haura EB (2016). Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer. Proteomes, 4(2), 16. (Read full article)
  26. Stewart PA, Parapatics K, Welsh EA, Mller AC, Cao H, Fang B, Koomen JM, Eschrich SA, Bennett KL, Haura EB (2015). A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma. PLoS One, 10(11), e0142162. (Read full article)
  27. Stewart PA, Luks J, Roycik MD, Sang QX, Zhang J (2013). Differentially expressed transcripts and dysregulated signaling pathways and networks in African American breast cancer. PLoS One, 8(12), e82460. (Read full article)
  28. Wang X, Stewart PA, Cao Q, Sang QX, Chung LW, Emmett MR, Marshall AG (2011). Characterization of the phosphoproteome in androgen-repressed human prostate cancer cells by Fourier transform ion cyclotron resonance mass spectrometry. J Proteome Res, 10(9), 3920-8. (Read full article)
  29. Semaan SM, Wang X, Stewart PA, Marshall AG, Sang QX (2011). Differential phosphopeptide expression in a benign breast tissue, and triple-negative primary and metastatic breast cancer tissues from the same African-American woman by LC-LTQ/FT-ICR mass spectrometry. Biochem Biophys Res Commun, 412(1), 127-31. (Read full article)
  30. Stewart PA, Lay N, Sussman M, et al (2008). An Improved Sharp Interface Method for Viscoelastic and Viscous Two-Phase Flows. J Sci Comput, 35, 43-61.

Review

  1. Waqas A, Tripathi A, Ramachandran RP, Stewart PA, Rasool G (2024). Multimodal data integration for oncology in the era of deep neural networks: a review. [Review]. Front Artif Intell, 7, 1408843. (Read full article)
  2. Park MA, Whelan CJ, Ahmed S, Boeringer T, Brown J, Crowder SL, Gage K, Gregg C, Jeong DK, Jim HSL, Judge AR, Mason TM, Parker N, Pillai S, Qayyum A, Rajasekhara S, Rasool G, Tinsley SM, Schabath MB, Stewart P, West J, McDonald P, Permuth JB (2024). Defining and Addressing Research Priorities in Cancer Cachexia through Transdisciplinary Collaboration. [Review]. Cancers (Basel), 16(13). (Read full article)
  3. Shaw TI, Zhao B, Li Y, Wang H, Wang L, Manley B, Stewart PA, Karolak A (2022). Multi-omics approach to identifying isoform variants as therapeutic targets in cancer patients. [Review]. Front Oncol, 12, 1051487. (Read full article)

Book Chapter

  1. Stewart PA, Welsh EA, Fang B, Izumi V, Mesa T, Zhang C, Yoder S, Zhang G, Cen L, Pettersson F, Zhang Y, Chen Z, Cheng CH, Thapa R, Thompson Z, Avedon M, Wloch M, Fournier M, Fellows KM, Francis JM, Saller JJ, Boyle TA, Chen YA, Haura EB, Teer JK, Eschrich SA, Koomen JM (2021). Managing a Large-Scale Multiomics Project: A Team Science Case Study in Proteogenomics. In Methods In Molecular Biology (2194, pp. 187-221).
  2. Stewart PA, Kuenzi BM, Mehta S, Kumar P, Johnson JE, Jagtap P, Griffin TJ, Haura EB (2019). The Galaxy Platform for Reproducible Affinity Proteomic Mass Spectrometry Data Analysis. In Methods In Molecular Biology (1977, pp. 249-261).

Commentary

  1. Stewart PA, Jaeger AM (2023). Taking the temperature of lung cancer antigens. Nat Cancer, 4(5), 586-587. (Read full article)