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Technical University of Munich

DR. MATTHEW THE

Position:Group Leader Bioinformatics
Room:002
Category:Scientific Staff
Phone:+49 - (0)8161 xxxxxx (phone currently being repaired)
Email:matthew.the[at]tum.de

Publications

2025

  • 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 more…
  • 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 21 (3), 2025, 231-253 more…
  • 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 16 (1), 2025 more…
  • 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 more…

2024

  • Chang, Yun-Chien; Gnann, Christian; Steimbach, Raphael R.; Bayer, Florian P.; Lechner, Severin; Sakhteman, Amirhossein; Abele, Miriam; Zecha, Jana; Trendel, Jakob; The, Matthew; Lundberg, Emma; Miller, Aubry K.; Kuster, Bernhard: Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics. Cell Reports 43 (6), 2024, 114272 more…
  • The, Matthew; Picciani, Mario; Jensen, Cecilia; Gabriel, Wassim; Kuster, Bernhard; Wilhelm, Mathias: AI-Assisted Processing Pipeline to Boost Protein Isoform Detection. In: Protein Bioinformatics. Springer US, 2024 more…
  • Tüshaus, Johanna; Eckert, Stephan; Schliemann, Marius; Zhou, Yuxiang; Pfeiffer, Pauline; Halves, Christiane; Fusco, Federico; Weigel, Johannes; Hönikl, Lisa; Butenschön, Vicki; Todorova, Rumyana; Rauert-Wunderlich, Hilka; The, Matthew; Rosenwald, Andreas; Heinemann, Volker; Holch, Julian; Steiger, Katja; Delbridge, Claire; Meyer, Bernhard; Weichert, Wilko; Mogler, Carolin; Kuhn, Peer-Hendrik; Kuster, Bernhard: Towards routine proteome profiling of FFPE tissue: insights from a 1,220-case pan-cancer study. The EMBO Journal 44 (1), 2024, 304-329 more…

2023

  • Bayer, Florian P.; Gander, Manuel; Kuster, Bernhard; The, Matthew: CurveCurator: a recalibrated F-statistic to assess, classify, and explore significance of dose–response curves. Nature Communications 14 (1), 2023 more…
  • Lee, Chien-Yun; The, Matthew; Meng, Chen; Bayer, Florian P; Putzker, Kerstin; Müller, Julian; Streubel, Johanna; Woortman, Julia; Sakhteman, Amirhossein; Resch, Moritz; Schneider, Annika; Wilhelm, Stephanie; Kuster, Bernhard: Illuminating phenotypic drug responses of sarcoma cells to kinase inhibitors by phosphoproteomics. Molecular Systems Biology, 2023 more…
  • Picciani, Mario; Gabriel, Wassim; Giurcoiu, Victor‐George; Shouman, Omar; Hamood, Firas; Lautenbacher, Ludwig; Jensen, Cecilia Bang; Müller, Julian; Kalhor, Mostafa; Soleymaniniya, Armin; Kuster, Bernhard; The, Matthew; Wilhelm, Mathias: Oktoberfest: Open‐source spectral library generation and rescoring pipeline based on Prosit. PROTEOMICS, 2023 more…
  • Tüshaus, Johanna; Sakhteman, Amirhossein; Lechner, Severin; The, Matthew; Mucha, Eike; Krisp, Christoph; Schlegel, Jürgen; Delbridge, Claire; Kuster, Bernhard: A region‐resolved proteomic map of the human brain enabled by high‐throughput proteomics. The EMBO Journal, 2023 more…
  • Zecha, Jana; Bayer, Florian P.; Wiechmann, Svenja; Woortman, Julia; Berner, Nicola; Müller, Julian; Schneider, Annika; Kramer, Karl; Abril-Gil, Mar; Hopf, Thomas; Reichart, Leonie; Chen, Lin; Hansen, Fynn M.; Lechner, Severin; Samaras, Patroklos; Eckert, Stephan; Lautenbacher, Ludwig; Reinecke, Maria; Hamood, Firas; Prokofeva, Polina; Vornholz, Larsen; Falcomatà, Chiara; Dorsch, Madeleine; Schröder, Ayla; Venhuizen, Anton; Wilhelm, Stephanie; Médard, Guillaume; Stoehr, Gabriele; Ruland, Jürgen; Grüner, Barbara M.; Saur, Dieter; Buchner, Maike; Ruprecht, Benjamin; Hahne, Hannes; The, Matthew; Wilhelm, Mathias; Kuster, Bernhard: Decrypting drug actions and protein modifications by dose- and time-resolved proteomics. Science 380 (6640), 2023, 93-101 more…

2022

  • Gabriel, Wassim; The, Matthew; Zolg, Daniel P.; Bayer, Florian P.; Shouman, Omar; Lautenbacher, Ludwig; Schnatbaum, Karsten; Zerweck, Johannes; Knaute, Tobias; Delanghe, Bernard; Huhmer, Andreas; Wenschuh, Holger; Reimer, Ulf; Médard, Guillaume; Kuster, Bernhard; Wilhelm, Mathias: Prosit-TMT: Deep Learning Boosts Identification of TMT-Labeled Peptides. Analytical Chemistry 94 (20), 2022, 7181-7190 more…
  • Giansanti, Piero; Samaras, Patroklos; Bian, Yangyang; Meng, Chen; Coluccio, Andrea; Frejno, Martin; Jakubowsky, Hannah; Dobiasch, Sophie; Hazarika, Rashmi R.; Rechenberger, Julia; Calzada-Wack, Julia; Krumm, Johannes; Mueller, Sebastian; Lee, Chien-Yun; Wimberger, Nicole; Lautenbacher, Ludwig; Hassan, Zonera; Chang, Yun-Chien; Falcomatà, Chiara; Bayer, Florian P.; Bärthel, Stefanie; Schmidt, Tobias; Rad, Roland; Combs, Stephanie E.; The, Matthew; Johannes, Frank; Saur, Dieter; de Angelis, Martin Hrabe; Wilhelm, Mathias; Schneider, Günter; Kuster, Bernhard: Mass spectrometry-based draft of the mouse proteome. Nature Methods 19 (7), 2022, 803-811 more…
  • Hamood, Firas; Bayer, Florian P.; Wilhelm, Mathias; Kuster, Bernhard; The, Matthew: SIMSI-Transfer: Software-assisted reduction of missing values in phosphoproteomic and proteomic isobaric labeling data using tandem mass spectrum clustering. Molecular & Cellular Proteomics, 2022, 100238 more…
  • The, Matthew; Samaras, Patroklos; Kuster, Bernhard; Wilhelm, Mathias: Re-analysis of ProteomicsDB using an accurate, sensitive and scalable false discovery rate estimation approach for protein groups. Molecular & Cellular Proteomics, 2022, 100437 more…

2021

  • Bian, Yangyang; The, Matthew; Giansanti, Piero; Mergner, Julia; Zheng, Runsheng; Wilhelm, Mathias; Boychenko, Alexander; Kuster, Bernhard: Identification of 7 000–9 000 Proteins from Cell Lines and Tissues by Single-Shot Microflow LC–MS/MS. Analytical Chemistry, 2021 more…
  • Eckert, Stephan; Chang, Yun-Chien; Bayer, Florian P.; The, Matthew; Kuhn, Peer-Hendrik; Weichert, Wilko; Kuster, Bernhard: Evaluation of Disposable Trap Column nanoLC–FAIMS–MS/MS for the Proteomic Analysis of FFPE Tissue. Journal of Proteome Research 20 (12), 2021, 5402-5411 more…
  • Lautenbacher, Ludwig; Samaras, Patroklos; Muller, Julian; Grafberger, Andreas; Shraideh, Marwin; Rank, Johannes; Fuchs, Simon T; Schmidt, Tobias K; The, Matthew; Dallago, Christian; Wittges, Holger; Rost, Burkhard; Krcmar, Helmut; Kuster, Bernhard; Wilhelm, Mathias: ProteomicsDB: toward a FAIR open-source resource for life-science research. Nucleic Acids Research, 2021 more…
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