Publications

2025

Perez JM, Ryu J, Khan H, Shetty M, Parker E, D'Arcy P, Zhu S, Bazzaro M, Thomas SN. Proteomic Analysis of ARID1A-Deficient Ovarian Clear Cell Carcinoma Cells Reveals Differential Mitochondria ETC Subunit Abundances and Targetable Mitochondrial Pathways. Int J Mol Sci. 2025 Jun 7;26(12):5466. doi: 10.3390/ijms26125466.PMID: 40564930.

Philips TJ, Erickson BK, Thomas SN. Opportunities for predictive proteogenomic biomarkers of drug treatment sensitivity in epithelial ovarian cancer. Front Oncol. 2025 Jan 7;14:1503107. doi: 10.3389/fonc.2024.1503107. eCollection 2024. PMID: 39839766.

Perez JM, Duda JM, Ryu J, Shetty M, Mehta S, Jagtap PD, Nelson AC, Winterhoff B, Griffin TJ, Starr TK, Thomas SN. Investigating proteogenomic divergence in patient-derived xenograft models of ovarian cancer. Sci Rep. 2025 Jan 4;15(1):813. doi: 10.1038/s41598-024-84874-3. PMID: 39755759.

2024

Twigg CAI, Perez JM, Ryu J, Hanson BK, Barrera Estrada VJ, Thomas SN. Evaluation of Serum Proteome Sample Preparation Methods to Support Clinical Proteomics Applications. J Am Soc Mass Spectrom. 2024 Sep 12. doi: 10.1021/jasms.4c00131. Epub ahead of print. PMID: 39263706.

Khine H, Mathson A, Moshele PR, Thyagarajan B, Karger AB, Thomas SN. Targeted electronic health record-based recruitment strategy to enhance COVID-19 vaccine response clinical research study enrollment. Contemp Clin Trials Commun. 2023 Dec 20;37:101250. doi: 10.1016/j.conctc.2023.101250. eCollection 2024 Feb. PMID: 38312474.

Ryu J, Boylan KLM, Twigg CAI, Evans R, Skubitz APN, Thomas SN. Quantification of putative ovarian cancer serum protein biomarkers using a multiplexed targeted mass spectrometry assay. Clin Proteomics. 2024 Jan 3;21(1):1. doi: 10.1186/s12014-023-09447-4. PMID: 38172678.

2023

Jordan HA, Thomas SN. Novel proteomic technologies to address gaps in pre-clinical ovarian cancer biomarker discovery efforts. Expert Rev Proteomics. 2023 Dec 20:1-12. doi: 10.1080/14789450.2023.2295861. Online ahead of print. PMID: 38116719.

Duda JM, Thomas SN. Interactions of Histone Deacetylase 6 with DNA Damage Repair Factors Strengthen its Utility as a Combination Drug Target in High-Grade Serous Ovarian Cancer. ACS Pharmacol Transl Sci. 2023 Nov 16;6(12):1924-1933. doi: 10.1021/acsptsci.3c00215. PMID: 38107255.

Lin Y, Thomas, SN. Impact of VALID Act implementation on mass spectrometry-based clinical proteomic laboratory developed tests. Mass Spectrom Adv Clin Lab. 2023 Feb 13;28:30-34. doi: 10.1016/j.jmsacl.2023.02.001. eCollection 2023 Apr. PMID: 36865788.

2022

Thomas, S.N., French, D., Jannetto, P.J., Rappold, B.A., and Clarke, W. A. Liquid chromatography–tandem mass spectrometry for clinical diagnostics. Nat Rev Methods Primers 2, 96 (2022). doi: 10.1038/s43586-022-00175-x. PMID: 36532107.

Duda JM, Thomas SN. Combination of Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and Substrate Trapping for the Detection of Transient Protein Interactions. Methods Mol Biol. 2023;2603:219-234. doi: 10.1007/978-1-0716-2863-8_18. PMID: 36370283.

Duda JM, Twigg CAI, Thomas SN. Differential histone deacetylase inhibitor-induced perturbations of the global proteome landscape in the setting of high-grade serous ovarian cancer. Proteomics. 2022 Oct 4:e2100372. doi: 10.1002/pmic.202100372. Online ahead of print. PMID: 36193784.

Karger AB, Brien JD, Christen JM, Dhakal S, Kemp TJ, Klein SL, Pinto LA, Premkumar L, Roback JD, Binder RA, Boehme KW, Boppana S, Cordon-Cardo C, Crawford JM, Daiss JL, Dupuis AP 2nd, Espino AM, Firpo-Betancourt A, Forconi C, Forrest JC, Girardin RC, Granger DA, Granger SW, Haddad NS, Heaney CD, Hunt DT, Kennedy JL, King CL, Krammer F, Kruczynski K, LaBaer J, Lee FE, Lee WT, Liu SL, Lozanski G, Lucas T, Mendu DR, Moormann AM, Murugan V, Okoye NC, Pantoja P, Payne AF, Park J, Pinninti S, Pinto AK, Pisanic N, Qiu J, Sariol CA, Simon V, Song L, Steffen TL, Stone ET, Styer LM, Suthar MS, Thomas SN, Thyagarajan B, Wajnberg A, Yates JL, Sobhani K. The Serological Sciences Network (SeroNet) for COVID-19: Depth and Breadth of Serology Assays and Plans for Assay Harmonization. mSphere. 2022 Jun 15:e0019322. doi: 10.1128/msphere.00193-22. Online ahead of print. PMID: 35703544.

Chaudhry S, Thomas SN, Simmons GE Jr. Targeting lipid metabolism in the treatment of ovarian cancer. Oncotarget. 2022 May 25;13:768-783. doi: 10.18632/oncotarget.28241. eCollection 2022. PMID: 35634242.

Thomas SN, Karger AB, Altawallbeh G, Nelson KM, Jacobs DR Jr, Gorlin J, Barcelo H, Thyagarajan B. Ultrasensitive detection of salivary SARS-CoV-2 IgG antibodies in individuals with natural and COVID-19 vaccine-induced immunity. Sci Rep. 2022 May 25;12(1):8890. doi: 10.1038/s41598-022-12869-z. PMID: 35614113.

Thomas SN, Stieglitz HM, Hackenmueller S, Suh-Lailam B, Pyle-Eilola AL. Use of cotton balls in diapers for collection of urine samples impacts the analysis of routine chemistry tests: an evaluation of cotton balls, diapers, and chemistry analyzers. J Pediatr. 2022 Mar 3:S0022-3476(22)00172-X. doi: 10.1016/j.jpeds.2022.02.051. Online ahead of print. PMID: 35248569.

2021

Perez JM, Twigg CAI, Guan W, Thomas SN. Proteomic Analysis Reveals Low-Dose PARP Inhibitor-Induced Differential Protein Expression in BRCA1-Mutated High-Grade Serous Ovarian Cancer Cells. J Am Soc Mass Spectrom. 2021 Dec 27. doi: 10.1021/jasms.1c00215. Online ahead of print. PMID: 34958553.

Li QK, Chen J, Hu Y, Höti N, Lih TM, Thomas SN, Chen L, Roy S, Meeker A, Shah P, Chen L, Bova GS, Zhang B, Zhang H. Proteomic characterization of primary and metastatic prostate cancer reveals reduced proteinase activity in aggressive tumors. Sci Rep. 2021 Sep 23;11(1):18936. doi: 10.1038/s41598-021-98410-0. PubMed PMID: 34556748; PubMed Central PMCID: PMC8460832.

Murthy V, Altawallbeh G, Larson-Nath C, Karger AB, Thomas SN. Transient hyperphosphatasemia following pediatric liver transplantation in a patient with hepatic and skeletal abnormalities. Clin Chim Acta. 2021 Aug;519:48-50. doi: 10.1016/j.cca.2021.03.030. Epub 2021 Apr 5. PubMed PMID: 33826952; NIHMSID:NIHMS1748261.

Ryu J, Thomas SN. Quantitative Mass Spectrometry-Based Proteomics for Biomarker Development in Ovarian Cancer. Molecules. 2021 May 3;26(9). doi: 10.3390/molecules26092674. Review. PubMed PMID: 34063568; PubMed Central PMCID: PMC8125593.

Thomas SN, Altawallbeh G, Zaun CP, Pape KA, Peters JM, Titcombe PJ, Dileepan T, Rapp MJ, Bold TD, Schacker TW, Arbefeville S, Ferrieri P, Thyagarajan B, Jenkins MK, Karger AB. Initial determination of COVID-19 seroprevalence among outpatients and healthcare workers in Minnesota using a novel SARS-CoV-2 total antibody ELISA. Clin Biochem. 2021 Apr;90:15-22. doi: 10.1016/j.clinbiochem.2021.01.010. Epub 2021 Feb 1. PubMed PMID: 33539808; PubMed Central PMCID: PMC7849522.

Goldman E, Vu A, Dietz K, Thomas SN. A 9-Month-Old with Skeletal Abnormalities and a Consanguineous Sibling with Mucopolysaccharidosis IVA: The Role of Urinary Glycosaminoglycan Testing in Disease Diagnosis and Treatment Monitoring. Clin Med Insights Case Rep. 2021;14:1179547621999409. doi: 10.1177/1179547621999409. eCollection 2021. PubMed PMID: 33746520; PubMed Central PMCID: PMC7940721.

2020

Seegmiller JC, Kokaisel EL, Story SJ, Zaun CP, Peters JM, Thomas SN, Karger AB. Method comparison of SARS-CoV-2 serology assays involving three commercially available platforms and a novel in-house developed enzyme-linked immunosorbent assay. Clin Biochem. 2020 Dec;86:34-35. doi: 10.1016/j.clinbiochem.2020.08.004. Epub 2020 Aug 11. PubMed PMID: 32791053; PubMed Central PMCID: PMC7417259.

A more comprehensive list of publications can be found here.