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Stefani N. Thomas, Ph.D. - Publications

Affiliations: 
2007 Pharmaceutical Sciences University of Southern California, Los Angeles, CA, United States 
Area:
Neuroscience Biology
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34 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Thomas SN, Friedrich B, Schnaubelt M, Chan DW, Zhang H, Aebersold R. Orthogonal Proteomic Platforms and Their Implications for the Stable Classification of High-Grade Serous Ovarian Cancer Subtypes. Iscience. 23: 101079. PMID 32534439 DOI: 10.1016/J.Isci.2020.101079  0.386
2019 Jiang H, Thomas SN, Chen Z, Chiang CY, Cole PA. Comparative analysis of the catalytic regulation of NEDD4-1 and WWP2 ubiquitin ligases. The Journal of Biological Chemistry. PMID 31578285 DOI: 10.1074/Jbc.Ra119.009211  0.314
2019 Sun S, Hu Y, Ao M, Shah P, Chen J, Yang W, Jia X, Tian Y, Thomas S, Zhang H. -GlycositeAtlas: a database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping. Clinical Proteomics. 16: 35. PMID 31516400 DOI: 10.1186/S12014-019-9254-0  0.361
2019 Huseby CJ, Hoffman CN, Cooper GL, Cocuron JC, Alonso AP, Thomas SN, Yang AJ, Kuret J. Quantification of Tau Protein Lysine Methylation in Aging and Alzheimer's Disease. Journal of Alzheimer's Disease : Jad. PMID 31450505 DOI: 10.3233/Jad-190604  0.35
2018 Mertins P, Tang LC, Krug K, Clark DJ, Gritsenko MA, Chen L, Clauser KR, Clauss TR, Shah P, Gillette MA, Petyuk VA, Thomas SN, Mani DR, Mundt F, Moore RJ, et al. Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry. Nature Protocols. PMID 29988108 DOI: 10.1038/S41596-018-0006-9  0.375
2017 Zhou JY, Chen L, Zhang B, Tian Y, Liu T, Thomas SN, Chen L, Schnaubelt M, Boja E, Hiltke T, Kinsinger CR, Rodriguez H, Davies SR, Li S, Snider JE, et al. Quality Assessments of Long-term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues. Journal of Proteome Research. PMID 29124938 DOI: 10.1021/Acs.Jproteome.7B00362  0.361
2017 Collins BC, Hunter CL, Liu Y, Schilling B, Rosenberger G, Bader SL, Chan DW, Gibson BW, Gingras AC, Held JM, Hirayama-Kurogi M, Hou G, Krisp C, Larsen B, Lin L, ... ... Thomas SN, et al. Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry. Nature Communications. 8: 291. PMID 28827567 DOI: 10.1038/S41467-017-00249-5  0.398
2017 Zhou J, Yang W, Hu Y, Hoti N, Liu Y, Shah P, Sun S, Clark DJ, Thomas SN, Zhang H. Site-specific fucosylation analysis identifies glycoproteins associated with aggressive prostate cancer cell lines using tandem affinity enrichments of intact glycopeptides followed by mass spectrometry. Analytical Chemistry. PMID 28627880 DOI: 10.1021/Acs.Analchem.7B01493  0.389
2017 Thomas SN, Yang AJ. Mass Spectrometry Analysis of Lysine Posttranslational Modifications of Tau Protein from Alzheimer's Disease Brain. Methods in Molecular Biology (Clifton, N.J.). 1523: 161-177. PMID 27975250 DOI: 10.1007/978-1-4939-6598-4_10  0.423
2016 Thomas SN, Zhang H. Targeted proteomic assays for the verification of global proteomics insights. Expert Review of Proteomics. PMID 27565203 DOI: 10.1080/14789450.2016.1229601  0.312
2016 Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou JY, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, ... ... Thomas S, et al. Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer. Cell. PMID 27372738 DOI: 10.1016/J.Cell.2016.05.069  0.365
2016 Chen Z, Thomas SN, Bolduc DM, Jiang X, Zhang X, Wolberger C, Cole PA. Enzymatic Analysis of PTEN Ubiquitylation by WWP2 and NEDD4-1 E3 ligases. Biochemistry. PMID 27295432 DOI: 10.1021/Acs.Biochem.6B00448  0.324
2016 Whiteaker JR, Halusa GN, Hoofnagle AN, Sharma V, MacLean B, Yan P, Wrobel JA, Kennedy J, Mani DR, Zimmerman LJ, Meyer MR, Mesri M, Boja E, Carr SA, Chan DW, ... ... Thomas S, et al. Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays. Methods in Molecular Biology (Clifton, N.J.). 1410: 223-36. PMID 26867747 DOI: 10.1007/978-1-4939-3524-6_13  0.41
2016 Crutchfield CA, Thomas SN, Sokoll LJ, Chan DW. Advances in mass spectrometry-based clinical biomarker discovery. Clinical Proteomics. 13: 1. PMID 26751220 DOI: 10.1186/S12014-015-9102-9  0.32
2016 Hoofnagle AN, Whiteaker JR, Carr SA, Kuhn E, Liu T, Massoni SA, Thomas SN, Townsend RR, Zimmerman LJ, Boja E, Chen J, Crimmins DL, Davies SR, Gao Y, Hiltke TR, et al. Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays. Clinical Chemistry. 62: 48-69. PMID 26719571 DOI: 10.1373/Clinchem.2015.250563  0.36
2015 Aiyetan P, Thomas SN, Zhang Z, Zhang H. MRMPlus: an open source quality control and assessment tool for SRM/MRM assay development. Bmc Bioinformatics. 16: 411. PMID 26652794 DOI: 10.1186/S12859-015-0838-Z  0.327
2015 Thomas S, Harlan R, Chen J, Aiyetan P, Liu Y, Sokoll LJ, Aebersold R, Chan DW, Zhang H. Multiplexed targeted mass spectrometry-based assays for the quantification of N-linked glycosite-containing peptides in serum. Analytical Chemistry. PMID 26451657 DOI: 10.1021/Acs.Analchem.5B02063  0.372
2015 Thomas SN, Zhang H, Cotter RJ. Application of quantitative proteomics to the integrated analysis of the ubiquitylated and global proteomes of xenograft tumor tissues. Clinical Proteomics. 12: 14. PMID 26019700 DOI: 10.1186/S12014-015-9086-5  0.425
2014 Funk KE, Thomas SN, Schafer KN, Cooper GL, Liao Z, Clark DJ, Yang AJ, Kuret J. Lysine methylation is an endogenous post-translational modification of tau protein in human brain and a modulator of aggregation propensity. The Biochemical Journal. 462: 77-88. PMID 24869773 DOI: 10.1042/Bj20140372  0.351
2013 Thomas SN, Liao Z, Clark D, Chen Y, Samadani R, Mao L, Ann DK, Baulch JE, Shapiro P, Yang AJ. Exosomal Proteome Profiling: A Potential Multi-Marker Cellular Phenotyping Tool to Characterize Hypoxia-Induced Radiation Resistance in Breast Cancer. Proteomes. 1: 87-108. PMID 24860738 DOI: 10.3390/Proteomes1020087  0.301
2013 Liao Z, Thomas SN, Wan Y, Lin HH, Ann DK, Yang AJ. An Internal Standard-Assisted Synthesis and Degradation Proteomic Approach Reveals the Potential Linkage between VPS4B Depletion and Activation of Fatty Acid β-Oxidation in Breast Cancer Cells. International Journal of Proteomics. 2013: 291415. PMID 23431444 DOI: 10.1155/2013/291415  0.36
2012 Liao Z, Wan Y, Thomas SN, Yang AJ. IsoQuant: a software tool for stable isotope labeling by amino acids in cell culture-based mass spectrometry quantitation. Analytical Chemistry. 84: 4535-43. PMID 22519468 DOI: 10.1021/Ac300510T  0.392
2012 Thomas SN, Funk KE, Wan Y, Liao Z, Davies P, Kuret J, Yang AJ. Dual modification of Alzheimer's disease PHF-tau protein by lysine methylation and ubiquitylation: a mass spectrometry approach. Acta Neuropathologica. 123: 105-17. PMID 22033876 DOI: 10.1007/S00401-011-0893-0  0.363
2011 Thomas SN, Wan Y, Liao Z, Hanson PI, Yang AJ. Stable isotope labeling with amino acids in cell culture based mass spectrometry approach to detect transient protein interactions using substrate trapping. Analytical Chemistry. 83: 5511-8. PMID 21619060 DOI: 10.1021/Ac200950K  0.407
2009 Thomas SN, Cripps D, Yang AJ. Proteomic analysis of protein phosphorylation and ubiquitination in Alzheimer's disease. Methods in Molecular Biology (Clifton, N.J.). 566: 109-21. PMID 20058168 DOI: 10.1007/978-1-59745-562-6_8  0.394
2008 Wan Y, Cripps D, Thomas S, Campbell P, Ambulos N, Chen T, Yang A. PhosphoScan: a probability-based method for phosphorylation site prediction using MS2/MS3 pair information. Journal of Proteome Research. 7: 2803-11. PMID 18549264 DOI: 10.1021/Pr700773P  0.325
2007 Tekirian TL, Thomas SN, Yang A. Advancing signaling networks through proteomics. Expert Review of Proteomics. 4: 573-83. PMID 17705714 DOI: 10.1586/14789450.4.4.573  0.355
2007 Lee YK, Thomas SN, Yang AJ, Ann DK. Doxorubicin down-regulates Kruppel-associated box domain-associated protein 1 sumoylation that relieves its transcription repression on p21WAF1/CIP1 in breast cancer MCF-7 cells. The Journal of Biological Chemistry. 282: 1595-606. PMID 17079232 DOI: 10.1074/Jbc.M606306200  0.317
2006 Cripps D, Thomas SN, Jeng Y, Yang F, Davies P, Yang AJ. Alzheimer disease-specific conformation of hyperphosphorylated paired helical filament-Tau is polyubiquitinated through Lys-48, Lys-11, and Lys-6 ubiquitin conjugation. The Journal of Biological Chemistry. 281: 10825-38. PMID 16443603 DOI: 10.1074/Jbc.M512786200  0.389
2005 Soreghan BA, Lu BW, Thomas SN, Duff K, Rakhmatulin EA, Nikolskaya T, Chen T, Yang AJ. Using proteomics and network analysis to elucidate the consequences of synaptic protein oxidation in a PS1 + AbetaPP mouse model of Alzheimer's disease. Journal of Alzheimer's Disease : Jad. 8: 227-41. PMID 16340081 DOI: 10.3233/Jad-2005-8302  0.411
2005 Thomas SN, Soreghan BA, Nistor M, Sarsoza F, Head E, Yang AJ. Reduced neuronal expression of synaptic transmission modulator HNK-1/neural cell adhesion molecule as a potential consequence of amyloid beta-mediated oxidative stress: a proteomic approach. Journal of Neurochemistry. 92: 705-17. PMID 15686472 DOI: 10.1111/J.1471-4159.2004.02892.X  0.332
2004 Schiewe AJ, Margol L, Soreghan BA, Thomas SN, Yang AJ. Rapid characterization of amyloid-beta side-chain oxidation by tandem mass spectrometry and the scoring algorithm for spectral analysis. Pharmaceutical Research. 21: 1094-102. PMID 15290847 DOI: 10.1023/B:Pham.0000032994.36343.02  0.37
2003 Soreghan BA, Yang F, Thomas SN, Hsu J, Yang AJ. High-throughput proteomic-based identification of oxidatively induced protein carbonylation in mouse brain. Pharmaceutical Research. 20: 1713-20. PMID 14661913 DOI: 10.1023/B:Pham.0000003366.25263.78  0.341
2003 Soreghan B, Thomas SN, Yang AJ. Aberrant sphingomyelin/ceramide metabolic-induced neuronal endosomal/lysosomal dysfunction: potential pathological consequences in age-related neurodegeneration. Advanced Drug Delivery Reviews. 55: 1515-24. PMID 14597144 DOI: 10.1016/J.Addr.2003.07.007  0.312
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