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Hamood, Firas;Gabriel, Wassim;Pfeiffer, Pia;Kuster, Bernhard;Wilhelm, Mathias;The, Matthew
ProSIMSIt: The Best of Both Worlds in Data-Driven Rescoring and Identification Transfer
Journal of Proteome Research
2025
24
4
2173-2180

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Xiao, Zixuan;Tüshaus, Johanna;Kuster, Bernhard;The, Matthew;Wilhelm, Mathias
SWAPS: A Modular Deep-Learning Empowered Peptide Identity Propagation Framework Beyond Match-Between-Run
Journal of Proteome Research
2025

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Zhang, Ning;Tang, Li;Li, Songgang;Liu, Lu;Gao, Mengjuan;Wang, Sisheng;Chen, Daiying;Zhao, Yichao;Zheng, Ruiqing;Soleymaniniya, Armin;Zhang, Lingran;Wang, Wenkang;Yang, Xia;Ren, Yan;Sun, Congwei;Wilhelm, Mathias;Wang, Daowen;Li, Min;Chen, Feng
Integration of multi-omics data accelerates molecular analysis of common wheat traits
Nature Communications
2025
16
1

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Müller, Julian;Bayer, Florian P.;Wilhelm, Mathias;Schuh, Maximilian G.;Kuster, Bernhard;The, Matthew
PTMNavigator: interactive visualization of differentially regulated post-translational modifications in cellular signaling pathways
Nature Communications
2025
16
1

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Abele, Miriam;Soleymaniniya, Armin;Bayer, Florian P.;Lomp, Nina;Doll, Etienne;Meng, Chen;Neuhaus, Klaus;Scherer, Siegfried;Wenning, Mareike;Wantia, Nina;Kuster, Bernhard;Wilhelm, Mathias;Ludwig, Christina
Proteomic diversity in bacteria: Insights and implications for bacterial identification
Molecular & Cellular Proteomics
2025
100917

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Gabriel, Wassim;Gonzalez, Rebecca Meelker;Laposchan, Sophia;Riedel, Erik;Dündar, Gönül;Poppenberger, Brigitte;Wilhelm, Mathias;Lee, Chien-Yun
Deep Learning Enhances Precision of Citrullination Identification in Human and Plant Tissue Proteomes
Molecular & Cellular Proteomics
2025
100924