Publications by authors named "Matthew The"

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Computational Approaches for Pathway-Centric Analysis of Protein Post-Translational Modifications.
Julian Müller, Bernhard Kuster, Matthew The

Proteomics· November 2025

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Mapping drug mechanisms with ProteomicsDB: unified omics and cell sensitivity data at scale.
Mario Picciani, Armin Soleymaniniya, Julian Müller, Amirhossein Sakhteman, Konstantinos Tzanakis, Matthew The

Nucleic Acids Res· November 2025

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Proteomic analyses identify targets, pathways, and cellular consequences of oncogenic KRAS signaling.
Nicole Kabella, Florian P Bayer, Konstantinos Stamatiou, Miriam Abele, Amirhossein Sakhteman, Matthew The

Sci Signal· July 2025

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SWAPS: A Modular Deep-Learning Empowered Peptide Identity Propagation Framework Beyond Match-Between-Run.
Zixuan Xiao, Johanna Tüshaus, Bernhard Kuster, Matthew The, Mathias Wilhelm

J Proteome Res· April 2025

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ProSIMSIt: The Best of Both Worlds in Data-Driven Rescoring and Identification Transfer.
Firas Hamood, Wassim Gabriel, Pia Pfeiffer, Bernhard Kuster, Mathias Wilhelm, Matthew The

J Proteome Res· April 2025

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Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response.
Stefanie Höfer, Larissa Frasch, Sarah Brajkovic, Kerstin Putzker, Joe Lewis, Matthew The

Mol Syst Biol· March 2025

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Towards routine proteome profiling of FFPE tissue: insights from a 1,220-case pan-cancer study.
Johanna Tüshaus, Stephan Eckert, Marius Schliemann, Yuxiang Zhou, Pauline Pfeiffer, Matthew The

EMBO J· January 2025

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

Nat Commun· January 2025

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Proceedings of the EuBIC-MS developers meeting 2023.
Pedro Beltrao, Tim Van Den Bossche, Ralf Gabriels, Tanja Holstein, Tobias Kockmann, Matthew The

J Proteomics· August 2024

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AI-Assisted Processing Pipeline to Boost Protein Isoform Detection.
Matthew The, Mario Picciani, Cecilia Jensen, Wassim Gabriel, Bernhard Kuster

Methods Mol Biol· July 2024

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Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics.
Yun-Chien Chang, Christian Gnann, Raphael R Steimbach, Florian P Bayer, Severin Lechner, Matthew The

Cell Rep· June 2024

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Oktoberfest: Open-source spectral library generation and rescoring pipeline based on Prosit.
Mario Picciani, Wassim Gabriel, Victor-George Giurcoiu, Omar Shouman, Firas Hamood, Matthew The

Proteomics· April 2024

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Deep Learning-Assisted Analysis of Immunopeptidomics Data.
Wassim Gabriel, Mario Picciani, Matthew The, Mathias Wilhelm

Methods Mol Biol· April 2024

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Illuminating phenotypic drug responses of sarcoma cells to kinase inhibitors by phosphoproteomics.
Chien-Yun Lee, Matthew The, Chen Meng, Florian P Bayer, Kerstin Putzker

Mol Syst Biol· January 2024

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A region-resolved proteomic map of the human brain enabled by high-throughput proteomics.
Johanna Tüshaus, Amirhossein Sakhteman, Severin Lechner, Matthew The, Eike Mucha

EMBO J· December 2023

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CurveCurator: a recalibrated F-statistic to assess, classify, and explore significance of dose-response curves.
Florian P Bayer, Manuel Gander, Bernhard Kuster, Matthew The

Nat Commun· November 2023

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Decrypting drug actions and protein modifications by dose- and time-resolved proteomics.
Jana Zecha, Florian P Bayer, Svenja Wiechmann, Julia Woortman, Nicola Berner, Matthew The

Science· April 2023

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Triqler for Protein Summarization of Data from Data-Independent Acquisition Mass Spectrometry.
Patrick Truong, Matthew The, Lukas Käll

J Proteome Res· April 2023

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Reanalysis of ProteomicsDB Using an Accurate, Sensitive, and Scalable False Discovery Rate Estimation Approach for Protein Groups.
Matthew The, Patroklos Samaras, Bernhard Kuster, Mathias Wilhelm

Mol Cell Proteomics· December 2022

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Integrating Identification and Quantification Uncertainty for Differential Protein Abundance Analysis with Triqler.
Matthew The, Lukas Käll

Methods Mol Biol· November 2022

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SIMSI-Transfer: Software-Assisted Reduction of Missing Values in Phosphoproteomic and Proteomic Isobaric Labeling Data Using Tandem Mass Spectrum Clustering.
Firas Hamood, Florian P Bayer, Mathias Wilhelm, Bernhard Kuster, Matthew The

Mol Cell Proteomics· August 2022

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Mass spectrometry-based draft of the mouse proteome.
Piero Giansanti, Patroklos Samaras, Yangyang Bian, Chen Meng, Andrea Coluccio, Stefanie Bärthel, Matthew The

Nat Methods· July 2022

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Prosit-TMT: Deep Learning Boosts Identification of TMT-Labeled Peptides.
Wassim Gabriel, Matthew The, Daniel P Zolg, Florian P Bayer, Omar Shouman

Anal Chem· May 2022

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ProteomicsDB: toward a FAIR open-source resource for life-science research.
Ludwig Lautenbacher, Patroklos Samaras, Julian Muller, Andreas Grafberger, Marwin Shraideh, Matthew The

Nucleic Acids Res· January 2022

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Evaluation of Disposable Trap Column nanoLC-FAIMS-MS/MS for the Proteomic Analysis of FFPE Tissue.
Stephan Eckert, Yun-Chien Chang, Florian P Bayer, Matthew The, Peer-Hendrik Kuhn

J Proteome Res· December 2021

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