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1. Wang, H.; Ma, Z.; Niu, K.; Xiao, Y.; Wu, X.; Pan, C.; Zhao, Y.; Wang, K.; Zhang, Y.; Liu, N., Antagonistic roles of Nibbler and Hen1 in modulating piRNA 3' ends in Drosophila. Development 2016, 143(3): 530-539.

2. Pedros, C.; Zhang, Y.; Hu, J.; Choi, Y.; Canonigo-Balancio, A.; Yates, J. R., 3rd; Altman, A.; Crotty, S.; Kong, K., TBK1 controls differentiation of germinal center T follicular helper cells via a novel TRAF-like motif of ICOS. Nature Immunology 2016 [In press].  

3. Zhang, Y.; Xu, T.; Shan, B.; Hart, J.; Aslanian, A.; Han, X.; Zong, N.; Li, H.; Choi, H.; Wang, D.; Acharya, L.; Du, L.; Vogt, P. K.; Ping, P.; Yates, J. R., 3rd, ProteinInferencer: Confident protein identification and multiple experiment comparison for large scale proteomics projects. J Proteomics 2015.

4. Xia, H. G.; Najafov, A.; Geng, J.; Galan-Acosta, L.; Han, X.; Guo, Y.; Shan, B.; Zhang, Y.; Norberg, E.; Zhang, T.; Pan, L.; Liu, J.; Coloff, J. L.; Ofengeim, D.; Zhu, H.; Wu, K.; Cai, Y.; Yates, J. R.; Zhu, Z.; Yuan, J.; Vakifahmetoglu-Norberg, H., Degradation of HK2 by chaperone-mediated autophagy promotes metabolic catastrophe and cell death. J Cell Biol 2015, 210, (5), 705-16.

5. Tang, B.; Wang, T.; Wan, H.; Han, L.; Qin, X.; Zhang, Y.; Wang, J.; Yu, C.; Berton, F.; Francesconi, W.; Yates, J. R., 3rd; Vanderklish, P. W.; Liao, L., Fmr1 deficiency promotes age-dependent alterations in the cortical synaptic proteome. Proc Natl Acad Sci U S A 2015, 112, (34), E4697-706.

6. Ofengeim, D.; Ito, Y.; Najafov, A.; Zhang, Y.; Shan, B.; DeWitt, J. P.; Ye, J.; Zhang, X.; Chang, A.; Vakifahmetoglu-Norberg, H.; Geng, J.; Py, B.; Zhou, W.; Amin, P.; Lima, J. B.; Qi, C.; Yu, Q.; Trapp, B.; Yuan, J., Activation of Necroptosis in Multiple Sclerosis. Cell Rep 2015.

7. Huang, Q.; Yang, L.; Luo, J.; Guo, L.; Wang, Z.; Yang, X.; Jin, W.; Fang, Y.; Ye, J.; Shan, B.; Zhang, Y., SWATH enables precise label-free quantification on proteome-scale. Proteomics 2015.

8. Hassler, J. R.; Scheuner, D. L.; Wang, S.; Han, J.; Kodali, V. K.; Li, P.; Nguyen, J.; George, J. S.; Davis, C.; Wu, S. P.; Bai, Y.; Sartor, M.; Cavalcoli, J.; Malhi, H.; Baudouin, G.; Zhang, Y.; Yates Iii, J. R.; Itkin-Ansari, P.; Volkmann, N.; Kaufman, R. J., The IRE1alpha/XBP1s Pathway Is Essential for the Glucose Response and Protection of beta Cells. PLoS Biol 2015, 13, (10), e1002277.

9. Hart, J. R.; Zhang, Y.; Liao, L.; Ueno, L.; Du, L.; Jonkers, M.; Yates, J. R., 3rd; Vogt, P. K., The butterfly effect in cancer: A single base mutation can remodel the cell. Proc Natl Acad Sci U S A 2015.

10. Zhang, Y.; Shan, B.; Boyle, M.; Liu, J.; Liao, L.; Xu, T.; Yates, J. R., 3rd, Brain Proteome Changes Induced by Olfactory Learning in Drosophila. J Proteome Res 2014.

11. Shan, B.; Xu, C.; Zhang, Y.; Xu, T.; Gottesfeld, J. M.; Yates, J. R., 3rd, Quantitative Proteomic Analysis Identifies Targets and Pathways of a 2-Aminobenzamide HDAC Inhibitor in Friedreich's Ataxia Patient iPSC-Derived Neural Stem Cells. J Proteome Res 2014.

12. Kong, K. F.; Fu, G.; Zhang, Y.; Yokosuka, T.; Casas, J.; Canonigo-Balancio, A. J.; Becart, S.; Kim, G.; Yates, J. R., 3rd; Kronenberg, M.; Saito, T.; Gascoigne, N. R.; Altman, A., Protein kinase C-eta controls CTLA-4-mediated regulatory T cell function. Nat Immunol 2014, 15, (5), 465-72.

13. Zhang, Y.; Fonslow, B. R.; Shan, B.; Baek, M. C.; Yates, J. R., 3rd, Protein analysis by shotgun/bottom-up proteomics. Chem Rev 2013, 113, (4), 2343-94.

14. Webhofer, C.; Zhang, Y.; Brusis, J.; Reckow, S.; Landgraf, R.; Maccarrone, G.; Turck, C. W.; Filiou, M. D., (1)(5)N metabolic labeling: evidence for a stable isotope effect on plasma protein levels and peptide chromatographic retention times. J Proteomics 2013, 88, 27-33.

15. Ryan, S. D.; Dolatabadi, N.; Chan, S. F.; Zhang, X.; Akhtar, M. W.; Parker, J.; Soldner, F.; Sunico, C. R.; Nagar, S.; Talantova, M.; Lee, B.; Lopez, K.; Nutter, A.; Shan, B.; Molokanova, E.; Zhang, Y.; Han, X.; Nakamura, T.; Masliah, E.; Yates, J. R., 3rd; Nakanishi, N.; Andreyev, A. Y.; Okamoto, S.; Jaenisch, R.; Ambasudhan, R.; Lipton, S. A., Isogenic human iPSC Parkinson's model shows nitrosative stress-induced dysfunction in MEF2-PGC1alpha transcription. Cell 2013, 155, (6), 1351-64.

16. Filiou, M. D.; Webhofer, C.; Gormanns, P.; Zhang, Y.; Reckow, S.; Bisle, B.; Teplytska, L.; Frank, E.; Kessler, M. S.; Maccarrone, G.; Landgraf, R.; Turck, C. W., The (15)N isotope effect as a means for correlating phenotypic alterations and affected pathways in a trait anxiety mouse model. Proteomics 2012, 12, (15-16), 2421-7.

17. Zhang, Y.; Reckow, S.; Webhofer, C.; Boehme, M.; Gormanns, P.; Egge-Jacobsen, W. M.; Turck, C. W., Proteome scale turnover analysis in live animals using stable isotope metabolic labeling. Anal Chem 2011, 83, (5), 1665-72.

18. Zhang, Y.; Filiou, M. D.; Reckow, S.; Gormanns, P.; Maccarrone, G.; Kessler, M. S.; Frank, E.; Hambsch, B.; Holsboer, F.; Landgraf, R.; Turck, C. W., Proteomic and metabolomic profiling of a trait anxiety mouse model implicate affected pathways. Mol Cell Proteomics 2011, 10, (12), M111 008110.

19. Filiou, M. D.; Zhang, Y.; Teplytska, L.; Reckow, S.; Gormanns, P.; Maccarrone, G.; Frank, E.; Kessler, M. S.; Hambsch, B.; Nussbaumer, M.; Bunck, M.; Ludwig, T.; Yassouridis, A.; Holsboer, F.; Landgraf, R.; Turck, C. W., Proteomics and metabolomics analysis of a trait anxiety mouse model reveals divergent mitochondrial pathways. Biol Psychiatry 2011, 70, (11), 1074-82.

20. Zhang, Y.; Webhofer, C.; Reckow, S.; Filiou, M. D.; Maccarrone, G.; Turck, C. W., A MS data search method for improved 15N-labeled protein identification. Proteomics 2009, 9, (17), 4265-70.

21. Haegler, K.; Mueller, N. S.; Maccarrone, G.; Hunyadi-Gulyas, E.; Webhofer, C.; Filiou, M. D.; Zhang, Y.; Turck, C. W., QuantiSpec--Quantitative mass spectrometry data analysis of (15)N-metabolically labeled proteins. J Proteomics 2009, 71, (6), 601-8.

22. Frank, E.; Kessler, M. S.; Filiou, M. D.; Zhang, Y.; Maccarrone, G.; Reckow, S.; Bunck, M.; Heumann, H.; Turck, C. W.; Landgraf, R.; Hambsch, B., Stable isotope metabolic labeling with a novel N-enriched bacteria diet for improved proteomic analyses of mouse models for psychopathologies. PLoS One 2009, 4, (11), e7821.

 

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