JUMPptm: Integrated software for sensitive identification of post‐translational modifications and its application in Alzheimer's disease study von Poudel, Suresh, Vanderwall, David, Yuan, Zuo‐Fei, Wu, Zhiping, Peng, Junmin, Li, Yuxin

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EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data von Yuan, Zuo-Fei, Sidoli, Simone, Marchione, Dylan M, Simithy, Johayra, Janssen, Kevin A, Szurgot, Mary R, Garcia, Benjamin A

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Characterization of histone acylations links chromatin modifications with metabolism von Simithy, Johayra, Sidoli, Simone, Yuan, Zuo-Fei, Coradin, Mariel, Bhanu, Natarajan V., Marchione, Dylan M., Klein, Brianna J., Bazilevsky, Gleb A., McCullough, Cheryl E., Magin, Robert S., Kutateladze, Tatiana G., Snyder, Nathaniel W., Marmorstein, Ronen, Garcia, Benjamin A.

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Proteome-wide acetylation dynamics in human cells von Kori, Yekaterina, Sidoli, Simone, Yuan, Zuo-Fei, Lund, Peder J., Zhao, Xiaolu, Garcia, Benjamin A.

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One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry von Sidoli, Simone, Kori, Yekaterina, Lopes, Mariana, Yuan, Zuo-Fei, Kim, Hee Jong, Kulej, Katarzyna, Janssen, Kevin A, Agosto, Laura M, Cunha, Julia Pinheiro Chagas da, Andrews, Andrew J, Garcia, Benjamin A

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Interrogating Histone Acetylation and BRD4 as Mitotic Bookmarks of Transcription von Behera, Vivek, Stonestrom, Aaron J., Hamagami, Nicole, Hsiung, Chris C., Keller, Cheryl A., Giardine, Belinda, Sidoli, Simone, Yuan, Zuo-Fei, Bhanu, Natarajan V., Werner, Michael T., Wang, Hongxin, Garcia, Benjamin A., Hardison, Ross C., Blobel, Gerd A.

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pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry von Wang, Le-heng, Li, De-Quan, Fu, Yan, Wang, Hai-Peng, Zhang, Jing-Fen, Yuan, Zuo-Fei, Sun, Rui-Xiang, Zeng, Rong, He, Si-Min, Gao, Wen

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Naked Mole Rat Cells Have a Stable Epigenome that Resists iPSC Reprogramming von Tan, Li, Ke, Zhonghe, Tombline, Gregory, Macoretta, Nicholas, Hayes, Kevin, Tian, Xiao, Lv, Ruitu, Ablaeva, Julia, Gilbert, Michael, Bhanu, Natarajan V., Yuan, Zuo-Fei, Garcia, Benjamin A., Shi, Yujiang G., Shi, Yang, Seluanov, Andrei, Gorbunova, Vera

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Drawbacks in the use of unconventional hydrophobic anhydrides for histone derivatization in bottom-up proteomics PTM analysis von Sidoli, Simone, Yuan, Zuo-Fei, Lin, Shu, Karch, Kelly, Wang, Xiaoshi, Bhanu, Natarajan, Arnaudo, Anna M., Britton, Laura-Mae, Cao, Xing-Jun, Gonzales-Cope, Michelle, Han, Yumiao, Liu, Shichong, Molden, Rosalynn C., Wein, Samuel, Afjehi-Sadat, Leila, Garcia, Benjamin A.

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Mass Spectrometric Analysis of Histone Proteoforms von Yuan, Zuo-Fei, Arnaudo, Anna M, Garcia, Benjamin A

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Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate von Ye, Ding, Fu, Yan, Sun, Rui-Xiang, Wang, Hai-Peng, Yuan, Zuo-Fei, Chi, Hao, He, Si-Min

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Analysis of Histones H3 and H4 Reveals Novel and Conserved Post-Translational Modifications in Sugarcane von Moraes, Izabel, Yuan, Zuo-Fei, Liu, Shichong, Souza, Glaucia Mendes, Garcia, Benjamin A, Casas-Mollano, J Armando

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Integrated genomic and proteomic analyses identify stimulus-dependent molecular changes associated with distinct modes of skeletal muscle atrophy von Hunt, Liam C., Graca, Flavia A., Pagala, Vishwajeeth, Wang, Yong-Dong, Li, Yuxin, Yuan, Zuo-Fei, Fan, Yiping, Labelle, Myriam, Peng, Junmin, Demontis, Fabio

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Akt-Dependent Metabolic Reprogramming Regulates Tumor Cell Histone Acetylation von Lee, Joyce V., Carrer, Alessandro, Shah, Supriya, Snyder, Nathaniel W., Wei, Shuanzeng, Venneti, Sriram, Worth, Andrew J., Yuan, Zuo-Fei, Lim, Hee-Woong, Liu, Shichong, Jackson, Ellen, Aiello, Nicole M., Haas, Naomi B., Rebbeck, Timothy R., Judkins, Alexander, Won, Kyoung-Jae, Chodosh, Lewis A., Garcia, Benjamin A., Stanger, Ben Z., Feldman, Michael D., Blair, Ian A., Wellen, Kathryn E.

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A Strategy for Precise and Large Scale Identification of Core Fucosylated Glycoproteins von Jia, Wei, Lu, Zhuang, Fu, Yan, Wang, Hai-Peng, Wang, Le-Heng, Chi, Hao, Yuan, Zuo-Fei, Zheng, Zhao-Bin, Song, Li-Na, Han, Huan-Huan, Liang, Yi-Min, Wang, Jing-Lan, Cai, Yun, Zhang, Yu-Kui, Deng, Yu-Lin, Ying, Wan-Tao, He, Si-Min, Qian, Xiao-Hong

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Histone Purification Combined with High‐Resolution Mass Spectrometry to Examine Histone Post‐Translational Modifications and Histone Variants in Caenorhabditis elegans von Millan‐Ariño, Lluís, Yuan, Zuo‐Fei, Oomen, Marlies E., Brandenburg, Simone, Chernobrovkin, Alexey, Salignon, Jérôme, Körner, Lioba, Zubarev, Roman A., Garcia, Benjamin A., Riedel, Christian G.

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EpiProfile Quantifies Histone Peptides With Modifications by Extracting Retention Time and Intensity in High-resolution Mass Spectra[S] von Yuan, Zuo-Fei, Lin, Shu, Molden, Rosalynn C., Cao, Xing-Jun, Bhanu, Natarajan V., Wang, Xiaoshi, Sidoli, Simone, Liu, Shichong, Garcia, Benjamin A.

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A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics von Wang, Xiaoshi, Yuan, Zuo-Fei, Fan, Jing, Karch, Kelly R., Ball, Lauren E., Denu, John M., Garcia, Benjamin A.

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Critical Role of Histone Turnover in Neuronal Transcription and Plasticity von Maze, Ian, Wenderski, Wendy, Noh, Kyung-Min, Bagot, Rosemary C., Tzavaras, Nikos, Purushothaman, Immanuel, Elsässer, Simon J., Guo, Yin, Ionete, Carolina, Hurd, Yasmin L., Tamminga, Carol A., Halene, Tobias, Farrelly, Lorna, Soshnev, Alexey A., Wen, Duancheng, Rafii, Shahin, Birtwistle, Marc R., Akbarian, Schahram, Buchholz, Bruce A., Blitzer, Robert D., Nestler, Eric J., Yuan, Zuo-Fei, Garcia, Benjamin A., Shen, Li, Molina, Henrik, Allis, C. David

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Identifying Sex-Specific Serum Patterns of Alzheimer's Mice through Deep TMT Profiling and a Concentration-Dependent Concatenation Strategy von Dey, Kaushik Kumar, Yarbro, Jay M, Liu, Danting, Han, Xian, Wang, Zhen, Jiao, Yun, Wu, Zhiping, Yang, Shu, Lee, DongGeun, Dasgupta, Abhijit, Yuan, Zuo-Fei, Wang, Xusheng, Zhu, Liqin, Peng, Junmin

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