Picciani, Mario;Soleymaniniya, Armin;Müller, Julian;Sakhteman, Amirhossein;Tzanakis, Konstantinos;Bernett, Judith;Kahl, Elias;Hamood, Firas;Kersting, Johannes;Pourjam, Mohsen;Nagai, Luis Augusto Eijy;List, Markus;Kuster, Bernhard;The, Matthew;Wilhelm, Mathias
Mapping drug mechanisms with ProteomicsDB: unified omics and cell sensitivity data at scale
Nucleic Acids Research
2025

Lautenbacher, Ludwig;Yang, Kevin L.;Kockmann, Tobias;Panse, Christian;Gabriel, Wassim;Bold, Dulguun;Kahl, Elias;Chambers, Matthew;MacLean, Brendan X.;Li, Kai;Yu, Fengchao;Searle, Brian C.;Wilburn, Damien Beau;Shahneh, Mohammad Reza Zare;Hong, Yuhui;Tang, Haixu;Wang, Mingxun;Gabriels, Ralf;Bouwmeester, Robbin;Devreese, Robbe;Angelis, Jesse;Sabidó, Eduard;Schmidt, Tobias K.;Nesvizhskii, Alexey I.;Wilhelm, Mathias
Koina: Democratizing machine learning for proteomics research
Nature Communications
2025
16
1

Kalhor, Mostafa;Saylan, Cemil Can;Picciani, Mario;Fischer, Lutz;Schimweg, Falk Boudewijn;Lapin, Joel;Rappsilber, Juri;Wilhelm, Mathias
Prosit-XL: enhanced cross-linked peptide identification by fragment intensity prediction to study protein interactions and structures
Nature Communications
2025
16
1

Lapin, Joel;Nilsson, Alfred;Wilhelm, Mathias;Käll, Lukas
Pairwise Attention: Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra
Journal of Proteome Research
2025

Frejno, Martin;Berger, Michelle T.;Tüshaus, Johanna;Hogrebe, Alexander;Seefried, Florian;Graber, Michael;Samaras, Patroklos;Ben Fredj, Samia;Sukumar, Vishal;Eljagh, Layla;Bronshtein, Igor;Mamisashvili, Lizi;Schneider, Markus;Gessulat, Siegfried;Schmidt, Tobias;Kuster, Bernhard;Zolg, Daniel P.;Wilhelm, Mathias
Unifying the analysis of bottom-up proteomics data with CHIMERYS
Nature Methods
2025
22
5
1017-1027

Angelis, Jesse;Schröder, Eva Ayla;Xiao, Zixuan;Gabriel, Wassim;Wilhelm, Mathias
Peptide Property Prediction for Mass Spectrometry Using AI: An Introduction to State of the Art Models
PROTEOMICS
2025
25
9-10

Abdul-Khalek, Naim;Picciani, Mario;Shouman, Omar;Wimmer, Reinhard;Overgaard, Michael Toft;Wilhelm, Mathias;Gregersen Echers, Simon
To Fly, or Not to Fly, That Is the Question: A Deep Learning Model for Peptide Detectability Prediction in Mass Spectrometry
Journal of Proteome Research
2025
24
6
2709-2726

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

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

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