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Paul Stewart, PhD

Program: Biostatistics and Bioinformatics

Overview

Proteomics, Metabolomics, Multi-omics, Bioinformatics 


Associations

    • Biostatistics and Bioinformatics
    • Cancer Biology and Evolution Program

Education & Training

Research

Dr. Stewart has expertise in computational proteomics and metabolomics, integration of multi-omics datasets, and development of novel bioinformatics tools. He is broadly interested in cancer metabolism and how its dysregulation impacts the tumor microenvironment, host immune response, and therapeutic efficacy. 

Publications

  • Laborde J, Stewart PA, Chen Z, Chen YA, Brownstein NC. Sparse clusterability: testing for cluster structure in high dimensions. BMC Bioinformatics. 2023 Mar.24(1):125. Pubmedid: 37003995. Pmcid: PMC10064666.
  • 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. 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. 2023 Jan.24(3). Pubmedid: 36768152. Pmcid: PMC9916336.
  • 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. Proteogenomic, Epigenetic, and Clinical Implications of Recurrent Aberrant Splice Variants in Clear Cell Renal Cell Carcinoma. Eur Urol. 2022 Oct.82(4):354-362. Pubmedid: 35718636.
  • Shaw TI, Zhao B, Li Y, Wang H, Wang L, Manley B, Stewart PA, Karolak A. Multi-omics approach to identifying isoform variants as therapeutic targets in cancer patients. Front Oncol. 2022 Nov.12:1051487. Pubmedid: 36505834. Pmcid: PMC9730332.
  • Sasamoto N, Stewart PA, Wang T, Yoder SJ, Chellappan S, Hecht JL, Fridley BL, Terry KL, Tworoger SS. Lifetime ovulatory years and ovarian cancer gene expression profiles. J Ovarian Res. 2022 May.15(1):59. Pubmedid: 35562768. Pmcid: PMC9102743.
  • 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, Boca SM. Ten quick tips for deep learning in biology. PLoS Comput Biol. 2022 Mar.18(3):e1009803. Pubmedid: 35324884. Pmcid: PMC8946751.
  • Sarcar B, Fang B, Izumi V, Nunez-Lopez Y, Tassielli A, Pratley R, Jeong D, Permuth JB, Koomen JM, Fleming JB, Stewart PA. A comparative Proteomics Analysis Identified Differentially Expressed Proteins in Pancreatic Cancer-Associated Stellate Cell Small Extracellular Vesicles. Mol Cell Proteomics. 2022 Dec.21(12):100438. Pubmedid: 36332889. Pmcid: PMC9792568.
  • 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. Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration. Mol Cancer Res. 2022 Apr.20(4):542-555. Pubmedid: 35022314. Pmcid: PMC8983558.
  • Mahajan S, Majumder A, Stewart PA, Chen YA, Adhikari E, Fang B, Yang Y, Lawrence H, Kinose F, Koomen JM, Haura EB. Deubiquitinase Vulnerabilities Identified through Activity-Based Protein Profiling in Non-Small Cell Lung Cancer. Acs Chem Biol. 2022 Apr.17(4):776-784. Pubmedid: 35311290.
  • 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. The harsh microenvironment in early breast cancer selects for a Warburg phenotype. Proc Natl Acad Sci U S A. 2021 Jan.118(3). Pubmedid: 33452133. Pmcid: PMC7826394.
  • 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. Managing a Large-Scale Multiomics Project: A Team Science Case Study in Proteogenomics. Methods Mol Biol. 2020 Sep.2194:187-221. Pubmedid: 32926368. Pmcid: PMC7771375.
  • Cook LM, Frieling JS, Nerlakanti N, McGuire JJ, Stewart PA, Burger KL, Cleveland JL, Lynch CC. Betaglycan drives the mesenchymal stromal cell osteogenic program and prostate cancer-induced osteogenesis. Oncogene. 2019 Oct.38(44):6959-6969. Pubmedid: 31409900. Pmcid: PMC7771554.
  • 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. Proteogenomic landscape of squamous cell lung cancer. Nat Commun. 2019 Aug.10(1):3578. Pubmedid: 31395880. Pmcid: PMC6687710.
  • Stewart PA, Kuenzi BM, Mehta S, Kumar P, Johnson JE, Jagtap P, Griffin TJ, Haura EB. The Galaxy Platform for Reproducible Affinity Proteomic Mass Spectrometry Data Analysis. Methods Mol Biol. 2019 Apr.1977:249-261. Pubmedid: 30980333. Pmcid: PMC7787333.
  • Welsh EA, Stewart PA, Kuenzi BM, Eschrich JA. Escape Excel: A tool for preventing gene symbol and accession conversion errors. PLoS One. 2017 Sep.12(9):e0185207. Pubmedid: 28953918. Pmcid: PMC5617173.
  • Stewart PA, Fang B, Slebos RJ, Zhang G, Borne AL, Fellows K, Teer JK, Chen YA, Welsh E, Eschrich SA, Haura EB, Koomen JM. Relative protein quantification and accessible biology in lung tumor proteomes from four LC-MS/MS discovery platforms. Proteomics. 2017 Mar.17(6). Pubmedid: 28195392. Pmcid: PMC5606153.
  • Kuenzi BM, Remsing Rix LL, Stewart PA, Fang B, Kinose F, Bryant AT, Boyle TA, Koomen JM, Haura EB, Rix U. Polypharmacology-based ceritinib repurposing using integrated functional proteomics. Nat Chem Biol. 2017 Dec.13(12):1222-1231. Pubmedid: 28991240. Pmcid: PMC5909815.
  • Kim JY, Stewart PA, Borne AL, Fang B, Welsh EA, Chen YA, Eschrich SA, Koomen JM, Haura EB. Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer. Proteomes. 2016 Jun.4(2):16. Pubmedid: 28154798. Pmcid: PMC5217344.
  • Kuenzi BM, Borne AL, Li J, Haura EB, Eschrich SA, Koomen JM, Rix U, Stewart PA. APOSTL: An Interactive Galaxy Pipeline for Reproducible Analysis of Affinity Proteomics Data. J Proteome Res. 2016 Dec.15(12):4747-4754. Pubmedid: 27680298. Pmcid: PMC5231908.
  • Stewart PA, Parapatics K, Welsh EA, Müller AC, Cao H, Fang B, Koomen JM, Eschrich SA, Bennett KL, Haura EB. A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma. PLoS One. 2015 Nov.10(11):e0142162. Pubmedid: 26539827. Pmcid: PMC4634858.
  • Stewart PA, Luks J, Roycik MD, Sang QX, Zhang J. Differentially expressed transcripts and dysregulated signaling pathways and networks in African American breast cancer. PLoS One. 2013 Dec.8(12):e82460. Pubmedid: 24324792. Pmcid: PMC3853650.
  • Wang X, Stewart PA, Cao Q, Sang QX, Chung LW, Emmett MR, Marshall AG. Characterization of the phosphoproteome in androgen-repressed human prostate cancer cells by Fourier transform ion cyclotron resonance mass spectrometry. J Proteome Res. 2011 Sep.10(9):3920-3928. Pubmedid: 21786837.

Grants

  • Title: Innovative Proteogenomics to Investigate Tertiary Lymphoid Structures in Lung Cancer
    Sponsor: Cancer Research Institute
    PI: Stewart, P.
  • Title: A Flexible, Robust, and Reproducible Proteogenomic Pipeline
    Sponsor: Moffitt Cancer Center
    PI: Stewart, P., CO-PI: Jaeger, A.