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

Ourailidis, Iordanis;Stögbauer, Fabian;Zhou, Yuxiang;Beck, Susanne;Romanovsky, Eva;Eckert, Stephan;Wollenberg, Barbara;Wirth, Markus;Steiger, Katja;Kuster, Bernhard;Gires, Olivier;Stenzinger, Albrecht;Schirmacher, Peter;Weichert, Wilko;Kuhn, Peer-Hendrik;Boxberg, Melanie;Budczies, Jan
Multi-omics analysis to uncover the molecular basis of tumor budding in head and neck squamous cell carcinoma
npj Precision Oncology
2025
9
1

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

Höfer, Stefanie;Frasch, Larissa;Brajkovic, Sarah;Putzker, Kerstin;Lewis, Joe;Schürmann, Hendrik;Leone, Valentina;Sakhteman, Amirhossein;The, Matthew;Bayer, Florian P;Müller, Julian;Hamood, Firas;Siveke, Jens T;Reichert, Maximilian;Kuster, Bernhard
Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response
Molecular Systems Biology
2025
21
3
231-253

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

Miletić, Nebojša;Weckesser, Janik;Mosler, Thorsten;Rathore, Rajeshwari;Hoffmann, Marina E.;Gehrtz, Paul;Schlesiger, Sarah;Hartung, Ingo V.;Berner, Nicola;Wilhelm, Stephanie;Müller, Juliane;Adhikari, Bikash;Němec, Václav;Sivashanmugam, Saran Aswathaman;Elson, Lewis;Holzmann, Hanna;Schwalm, Martin P.;Hoffmann, Lasse;Abdul Azeez, Kamal Rayees;Müller, Susanne;Kuster, Bernhard;Wolf, Elmar;Đikić, Ivan;Knapp, Stefan
Workflow for E3 Ligase Ligand Validation for PROTAC Development
ACS Chemical Biology
2025
20
2
507-521

Kardell, Oliver;Gronauer, Thomas;von Toerne, Christine;Merl-Pham, Juliane;König, Ann-Christine;Barth, Teresa K.;Mergner, Julia;Ludwig, Christina;Tüshaus, Johanna;Giesbertz, Pieter;Breimann, Stephan;Schweizer, Lisa;Müller, Torsten;Kliewer, Georg;Distler, Ute;Gomez-Zepeda, David;Popp, Oliver;Qin, Di;Teupser, Daniel;Cox, Jürgen;Imhof, Axel;Küster, Bernhard;Lichtenthaler, Stefan F.;Krijgsveld, Jeroen;Tenzer, Stefan;Mertins, Philipp;Coscia, Fabian;Hauck, Stefanie M.
Multicenter Longitudinal Quality Assessment of MS-Based Proteomics in Plasma and Serum
Journal of Proteome Research
2025
24
3
1017-1029

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
24
3
100917