All papers authored by Mathias Wilhelm
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Larsen Vornholz ,
Benedict-Tilmann Berger ,
Florian Seefried,
Stephanie Wilhelm ,
Patroklos Samaras ,
Laszlo Gyenis,
David William Litchfield ,
Guillaume Médard ,
Susanne Müller ,
Jürgen Ruland,
Marko Hyvönen ,
Mathias Wilhelm ,
Bernhard Kuster
Chemical proteomics reveals the target landscape of 1,000 kinase inhibitors
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Wassim Gabriel ,
Victor‐George Giurcoiu ,
Omar Shouman ,
Firas Hamood ,
Ludwig Lautenbacher ,
Cecilia Bang Jensen ,
Julian Müller ,
Mostafa Kalhor ,
Armin Soleymaniniya ,
Bernhard Kuster ,
Matthew The ,
Mathias Wilhelm
Oktoberfest: Open‐source spectral library generation and rescoring pipeline based on Prosit
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Niklas de Andrade Krätzig ,
Matteo Pecoraro,
Sebastian Lange ,
Philipp Seifert,
Clara von Frankenberg,
Johannes Untch ,
Gabriela Zuleger ,
Mathias Wilhelm ,
Daniel P. Zolg,
Florian S. Dreyer,
Eva Bräunlein,
Thomas Engleitner,
Sebastian Uhrig,
Melanie Boxberg
and 24 other authors
Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification
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Florian P. Bayer ,
Svenja Wiechmann ,
Julia Woortman ,
Nicola Berner,
Julian Müller ,
Annika Schneider ,
Karl Kramer ,
Mar Abril-Gil ,
Thomas Hopf ,
Leonie Reichart,
Lin Chen ,
Fynn M. Hansen ,
Severin Lechner ,
Patroklos Samaras
and 22 other authors
Decrypting drug actions and protein modifications by dose- and time-resolved proteomics
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Viktoria Dorfer ,
Lennart Martens ,
Isabell Bludau,
Robbin Bouwmeester ,
Sven Degroeve ,
Eric W. Deutsch ,
Siegfried Gessulat,
Lukas Käll ,
Pawel Palczynski,
Samuel H. Payne ,
Tobias Greisager Rehfeldt ,
Tobias Schmidt ,
Veit Schwämmle ,
Julian Uszkoreit
and 3 other authors
Toward an Integrated Machine Learning Model of a Proteomics Experiment
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Patroklos Samaras ,
Yangyang Bian ,
Chen Meng,
Andrea Coluccio,
Martin Frejno ,
Hannah Jakubowsky,
Sophie Dobiasch,
Rashmi R. Hazarika,
Julia Rechenberger ,
Julia Calzada-Wack,
Johannes Krumm,
Sebastian Mueller,
Chien-Yun Lee ,
Nicole Wimberger
and 16 other authors
Mass spectrometry-based draft of the mouse proteome
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Matthew The ,
Daniel P. Zolg,
Florian P. Bayer,
Omar Shouman,
Ludwig Lautenbacher ,
Karsten Schnatbaum,
Johannes Zerweck,
Tobias Knaute,
Bernard Delanghe,
Andreas Huhmer,
Holger Wenschuh,
Ulf Reimer,
Guillaume Médard ,
Bernhard Kuster
and 1 other authors
Prosit-TMT: Deep Learning Boosts Identification of TMT-Labeled Peptides
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Patroklos Samaras ,
Julian Muller,
Andreas Grafberger,
Marwin Shraideh,
Johannes Rank,
Simon T. Fuchs,
Tobias K. Schmidt ,
Matthew The,
Christian Dallago ,
Holger Wittges,
Burkhard Rost,
Helmut Krcmar,
Bernhard Kuster,
Mathias Wilhelm
ProteomicsDB: toward a FAIR open-source resource for life-science research
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Julianus Pfeuffer,
Elizaveta M. Solovyeva ,
Jingwen Deng,
Pablo Moreno ,
Selvakumar Kamatchinathan,
Deepti Jaiswal Kundu,
Nancy George ,
Silvie Fexova,
Björn Grüning ,
Melanie Christine Föll,
Johannes Griss ,
Marc Vaudel ,
Enrique Audain
and 25 other authors
A proteomics sample metadata representation for multiomics integration and big data analysis
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Daniel P. Zolg,
Michael Graber,
Siegfried Gessulat ,
Tobias Schmidt ,
Karsten Schnatbaum,
Celina Schwencke-Westphal ,
Philipp Seifert,
Niklas de Andrade Krätzig,
Johannes Zerweck,
Tobias Knaute,
Eva Bräunlein,
Patroklos Samaras ,
Ludwig Lautenbacher ,
Susan Klaeger
and 9 other authors
Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics
Download from www.nature.com
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Patroklos Samaras,
Viktoria Dorfer ,
Christian Panse ,
Tobias Kockmann ,
Leon Bichmann ,
Bart van Puyvelde,
Yasset Perez-Riverol ,
Eric W. Deutsch ,
Bernhard Kuster ,
Mathias Wilhelm
Universal Spectrum Explorer: A standalone (web-)application for cross-resource spectrum comparison
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Chen Meng,
Benjamin Ruprecht ,
Thomas Oellerich,
Sebastian Scheich ,
Karin Kleigrewe ,
Enken Drecoll,
Patroklos Samaras ,
Alexander Hogrebe ,
Dominic Helm ,
Julia Mergner ,
Jana Zecha ,
Stephanie Heinzlmeir ,
Mathias Wilhelm ,
Julia Dorn
and 4 other authors
Proteome activity landscapes of tumor cell lines determine drug responses
Download from www.nature.com
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Nils Kurzawa ,
Thomas Hopf,
Matthias Moerch,
Jana Zecha ,
Niels Leijten ,
Yangyang Bian,
Eva Musiol,
Melanie Maschberger,
Gabriele Stoehr,
Isabelle Becher ,
Charlotte Daly,
Patroklos Samaras ,
Julia Mergner,
Britta Spanier
and 10 other authors
Meltome atlas—thermal proteome stability across the tree of life
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Markus List,
Michael Papacek,
Xia Chen,
Ajeet Chaudhary ,
Patroklos Samaras ,
Sandra Richter,
Hiromasa Shikata,
Maxim Messerer ,
Daniel Lang ,
Stefan Altmann,
Philipp Cyprys,
Daniel P. Zolg,
Toby Mathieson
and 17 other authors
Mass-spectrometry-based draft of the Arabidopsis proteome
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Tobias Schmidt,
Daniel Paul Zolg,
Patroklos Samaras ,
Karsten Schnatbaum,
Johannes Zerweck,
Tobias Knaute,
Julia Rechenberger,
Bernard Delanghe,
Andreas Huhmer,
Ulf Reimer,
Hans-Christian Ehrlich,
Stephan Aiche ,
Bernhard Kuster ,
Mathias Wilhelm
Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning
Download from www.nature.com
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Yasset Perez-Riverol ,
Robert J. Chalkley,
Mathias Wilhelm ,
Stephen Tate,
Timo Sachsenberg ,
Mathias Walzer,
Lukas Käll ,
Bernard Delanghe,
Sebastian Böcker ,
Emma L. Schymanski ,
Paul Wilmes ,
Viktoria Dorfer ,
Bernhard Kuster ,
Pieter-Jan Volders
and 15 other authors
Expanding the Use of Spectral Libraries in Proteomics
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Stephanie Heinzlmeir ,
Mathias Wilhelm ,
Harald Polzer,
Binje Vick ,
Paul-Albert Koenig ,
Maria Reinecke,
Benjamin Ruprecht,
Svenja Petzoldt,
Chen Meng,
Jana Zecha ,
Katrin Reiter ,
Huichao Qiao,
Dominic Helm ,
Heiner Koch
and 33 other authors
The target landscape of clinical kinase drugs
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