Tian Zhang Lab @ UVA

Publications

  1. Zhang T#, Keele GR#, Gyuricza IG, Vincent M, Brunton C, Bell TA, Hock P, Shaw GD, Munger SC, de Villena FP, Ferris MT, Paulo JA, Gygi SP, Churchill GA. Multi-omics analysis identifies drivers of protein phosphorylation. Genome Biol. 2023 Mar 21;24(1):52. doi: 10.1186/s13059-023-02892-2. PubMed PMID: 36944993; PubMed Central PMCID: PMC10031968.
  2. Yu Q, Liu X, Keller MP, Navarrete-Perea J, Zhang T, Fu S, Vaites LP, Shuken SR, Schmid E, Keele GR, Li J, Huttlin EL, Rashan EH, Simcox J, Churchill GA, Schweppe DK, Attie AD, Paulo JA, Gygi SP. Sample multiplexing-based targeted pathway proteomics with real-time analytics reveals the impact of genetic variation on protein expression. Nat Commun. 2023 Feb 2;14(1):555. doi: 10.1038/s41467-023-36269-7. PubMed PMID: 36732331; PubMed Central PMCID: PMC9894840.
  3. Aydin S, Pham D, Zhang T, Keele G, Skelly D, Paulo J, Pankratz M, Choi T, Gygi S, Reinholdt L, Baker C, Churchill G, Munger S. Genetic dissection of the pluripotent proteome through multi-omics data integration. Cell Genomics. 2023; 3(4). doi: 10.1016/j.xgen.2023.100283.
  4. Xiao H, Bozi LHM, Sun Y, Riley CL, Philip VM, Chen M, Li J, Zhang T, Mills EL, Emont MP, Sun W, Reddy A, Garrity R, Long J, Becher T, Vitas LP, Laznik-Bogoslavski D, Ordonez M, Liu X, Chen X, Wang Y, Liu W, Tran N, Liu Y, Zhang Y, Cypess AM, White AP, He Y, Deng R, Schöder H, Paulo JA, Jedrychowski MP, Banks AS, Tseng YH, Cohen P, Tsai LT, Rosen ED, Klein S, Chondronikola M, McAllister FE, Van Bruggen N, Huttlin EL, Spiegelman BM, Churchill GA, Gygi SP, Chouchani ET. Architecture of the outbred brown fat proteome defines regulators of metabolic physiology. Cell. 2022 Nov 23;185(24):4654-4673.e28. doi: 10.1016/j.cell.2022.10.003. Epub 2022 Nov 4. PubMed PMID: 36334589; PubMed Central PMCID: PMC10040263.
  5. Zhang T. TMT29 plex: Higher order multiplexing with inherent interference correction. Proteomics. 2022 Oct;22(19-20):e2200260. doi: 10.1002/pmic.202200260. PubMed PMID: 36263995.
  6. Si L, Bai H, Oh CY, Jiang A, Hong F, Zhang T, Ye Y, Jordan TX, Logue J, McGrath M, Belgur C, Calderon K, Nurani A, Cao W, Carlson KE, Prantil-Baun R, Gygi SP, Yang D, Jonsson CB, tenOever BR, Frieman M, Ingber DE. Self-assembling short immunostimulatory duplex RNAs with broad-spectrum antiviral activity. Mol Ther Nucleic Acids. 2022 Sep 13;29:923-940. doi: 10.1016/j.omtn.2022.08.031. Epub 2022 Aug 24. PubMed PMID: 36032397; PubMed Central PMCID: PMC9398551.
  7. Perez Verdaguer M#, Zhang T#, Surve S, Paulo JA, Wallace C, Watkins SC, Gygi SP, Sorkin A. Time-resolved proximity labeling of protein networks associated with ligand-activated EGFR. Cell Rep. 2022 Jun 14;39(11):110950. doi: 10.1016/j.celrep.2022.110950. PubMed PMID: 35705039; PubMed Central PMCID: PMC9248364.
  8. Suski JM, Ratnayeke N, Braun M, Zhang T, Strmiska V, Michowski W, Can G, Simoneau A, Snioch K, Cup M, Sullivan CM, Wu X, Nowacka J, Branigan TB, Pack LR, DeCaprio JA, Geng Y, Zou L, Gygi SP, Walter JC, Meyer T, Sicinski P. CDC7-independent G1/S transition revealed by targeted protein degradation. Nature. 2022 May;605(7909):357-365. doi: 10.1038/s41586-022-04698-x. Epub 2022 May 4. PubMed PMID: 35508654; PubMed Central PMCID: PMC9106935.
  9. Zhang T, Fassl A, Vaites LP, Fu S, Sicinski P, Paulo JA, Gygi SP. Interrogating Kinase-Substrate Relationships with Proximity Labeling and Phosphorylation Enrichment. J Proteome Res. 2022 Feb 4;21(2):494-506. doi: 10.1021/acs.jproteome.1c00865. Epub 2022 Jan 19. PubMed PMID: 35044772; PubMed Central PMCID: PMC9142857.
  10. Si L, Bai H, Oh CY, Jiang A, Hong F, Zhang T, Ye Y, Jordan TX, Logue J, McGrath M, Belgur C, Calderon K, Nurani A, Cao W, Carlson KE, Prantil-Baun R, Gygi SP, Yang D, Jonsson CB, tenOever BR, Frieman M, Ingber DE. Self-assembling short immunostimulatory duplex RNAs with broad-spectrum antiviral activity. Mol Ther Nucleic Acids. 2022 Sep 13;29:923-940. doi: 10.1016/j.omtn.2022.08.031. Epub 2022 Aug 24. PubMed PMID: 36032397; PubMed Central PMCID: PMC9398551.
  11. Keele G#, Zhang T#, Pham D, Vincent M, Bell T, Hock P, Shaw G, Paulo J, Munger S, Pardo-Manuel de Villena F, Ferris M, Gygi S, Churchill G. Regulation of protein abundance in genetically diverse mouse populations. Cell Genomics. 2021/09; :100003.
  12. Si L, Bai H, Rodas M, Cao W, Oh CY, Jiang A, Moller R, Hoagland D, Oishi K, Horiuchi S, Uhl S, Blanco-Melo D, Albrecht RA, Liu WC, Jordan T, Nilsson-Payant BE, Golynker I, Frere J, Logue J, Haupt R, McGrath M, Weston S, Zhang T, Plebani R, Soong M, Nurani A, Kim SM, Zhu DY, Benam KH, Goyal G, Gilpin SE, Prantil-Baun R, Gygi SP, Powers RK, Carlson KE, Frieman M, tenOever BR, Ingber DE. A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics. Nat Biomed Eng. 2021 Aug;5(8):815-829. doi: 10.1038/s41551-021-00718-9. Epub 2021 May 3. PubMed PMID: 33941899; PubMed Central PMCID: PMC8387338.
  13. Perez Verdaguer M, Zhang T, Paulo JA, Gygi S, Watkins SC, Sakurai H, Sorkin A. Mechanism of p38 MAPK-induced EGFR endocytosis and its crosstalk with ligand-induced pathways. J Cell Biol. 2021 Jul 5;220(7). doi: 10.1083/jcb.202102005. Epub 2021 May 25. PubMed PMID: 34032851; PubMed Central PMCID: PMC8155814.
  14. Huttlin EL, Bruckner RJ, Navarrete-Perea J, Cannon JR, Baltier K, Gebreab F, Gygi MP, Thornock A, Zarraga G, Tam S, Szpyt J, Gassaway BM, Panov A, Parzen H, Fu S, Golbazi A, Maenpaa E, Stricker K, Guha Thakurta S, Zhang T, Rad R, Pan J, Nusinow DP, Paulo JA, Schweppe DK, Vaites LP, Harper JW, Gygi SP. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell. 2021 May 27;184(11):3022-3040.e28. doi: 10.1016/j.cell.2021.04.011. Epub 2021 May 6. PubMed PMID: 33961781; PubMed Central PMCID: PMC8165030.
  15. Zhang T, Keele GR, Churchill GA, Gygi SP, Paulo JA. Strain-Specific Peptide (SSP) Interference Reference Sample: A Genetically Encoded Quality Control for Isobaric Tagging Strategies. Anal Chem. 2021 Mar 30;93(12):5241-5247. doi: 10.1021/acs.analchem.0c05483. Epub 2021 Mar 18. PubMed PMID: 33735571; PubMed Central PMCID: PMC8210951.
  16. Zhang T, Gygi SP, Paulo JA. Temporal Proteomic Profiling of SH-SY5Y Differentiation with Retinoic Acid Using FAIMS and Real-Time Searching. J Proteome Res. 2021 Jan 1;20(1):704-714. doi: 10.1021/acs.jproteome.0c00614. Epub 2020 Oct 15. PubMed PMID: 33054241; PubMed Central PMCID: PMC8210949.
  17. Takahashi N, Cho P, Selfors LM, Kuiken HJ, Kaul R, Fujiwara T, Harris IS, Zhang T, Gygi SP, Brugge JS. 3D Culture Models with CRISPR Screens Reveal Hyperactive NRF2 as a Prerequisite for Spheroid Formation via Regulation of Proliferation and Ferroptosis. Mol Cell. 2020 Dec 3;80(5):828-844.e6. doi: 10.1016/j.molcel.2020.10.010. Epub 2020 Oct 30. PubMed PMID: 33128871; PubMed Central PMCID: PMC7718371.
  18. Michowski W, Chick JM, Chu C, Kolodziejczyk A, Wang Y, Suski JM, Abraham B, Anders L, Day D, Dunkl LM, Li Cheong Man M, Zhang T, Laphanuwat P, Bacon NA, Liu L, Fassl A, Sharma S, Otto T, Jecrois E, Han R, Sweeney KE, Marro S, Wernig M, Geng Y, Moses A, Li C, Gygi SP, Young RA, Sicinski P. Cdk1 Controls Global Epigenetic Landscape in Embryonic Stem Cells. Mol Cell. 2020 May 7;78(3):459-476.e13. doi: 10.1016/j.molcel.2020.03.010. Epub 2020 Apr 1. PubMed PMID: 32240602; PubMed Central PMCID: PMC7214218.
  19. Sharma S, Zhang T, Michowski W, Rebecca VW, Xiao M, Ferretti R, Suski JM, Bronson RT, Paulo JA, Frederick D, Fassl A, Boland GM, Geng Y, Lees JA, Medema RH, Herlyn M, Gygi SP, Sicinski P. Targeting the cyclin-dependent kinase 5 in metastatic melanoma. Proc Natl Acad Sci U S A. 2020 Apr 7;117(14):8001-8012. doi: 10.1073/pnas.1912617117. Epub 2020 Mar 19. PubMed PMID: 32193336; PubMed Central PMCID: PMC7149478.
  20. Zhang T, Wolfe C, Pierle A, Welle KA, Hryhorenko JR, Ghaemmaghami S. Proteome-wide modulation of degradation dynamics in response to growth arrest. Proc Natl Acad Sci U S A. 2017 Nov 28;114(48):E10329-E10338. doi: 10.1073/pnas.1710238114. Epub 2017 Nov 13. PubMed PMID: 29133406; PubMed Central PMCID: PMC5715755.
  21. Welle KA#, Zhang T#, Hryhorenko JR, Shen S, Qu J, Ghaemmaghami S. Time-resolved Analysis of Proteome Dynamics by Tandem Mass Tags and Stable Isotope Labeling in Cell Culture (TMT-SILAC) Hyperplexing. Mol Cell Proteomics. 2016 Dec;15(12):3551-3563. doi: 10.1074/mcp.M116.063230. Epub 2016 Oct 20. PubMed PMID: 27765818; PubMed Central PMCID: PMC5141271.
  22. Zhang T, Ghaemmaghami S. Global analysis of cellular protein flux quantifies the selectivity of basal autophagy. Autophagy. 2016 Aug 2;12(8):1411-2. doi: 10.1080/15548627.2016.1190891. Epub 2016 Jun 1. PubMed PMID: 27248575; PubMed Central PMCID: PMC4968234.
  23. Zhang T, Shen S, Qu J, Ghaemmaghami S. Global Analysis of Cellular Protein Flux Quantifies the Selectivity of Basal Autophagy. Cell Rep. 2016 Mar 15;14(10):2426-39. doi: 10.1016/j.celrep.2016.02.040. Epub 2016 Mar 3. PubMed PMID: 26947064; PubMed Central PMCID: PMC5470642.
  24. Zhang T, Price JC, Nouri-Nigjeh E, Li J, Hellerstein MK, Qu J, Ghaemmaghami S. Kinetics of precursor labeling in stable isotope labeling in cell cultures (SILAC) experiments. Anal Chem. 2014 Nov 18;86(22):11334-41. doi: 10.1021/ac503067a. Epub 2014 Oct 29. PubMed PMID: 25301408.
  25. Shi M, Zhang T, Sun L, Luo Y, Liu DH, Xie ST, Song XY, Wang GF, Chen XL, Zhou BC, Zhang YZ. Calpain, Atg5 and Bak play important roles in the crosstalk between apoptosis and autophagy induced by influx of extracellular calcium. Apoptosis. 2013 Apr;18(4):435-51. doi: 10.1007/s10495-012-0786-2. PubMed PMID: 23242420.
  26. Shi M, Chen L, Wang XW, Zhang T, Zhao PB, Song XY, Sun CY, Chen XL, Zhou BC, Zhang YZ. Antimicrobial peptaibols from Trichoderma pseudokoningii induce programmed cell death in plant fungal pathogens. Microbiology (Reading). 2012 Jan;158(Pt 1):166-175. doi: 10.1099/mic.0.052670-0. Epub 2011 Nov 3. PubMed PMID: 22053006.

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