M
Markus Mueller
Researcher at ETH Zurich
Publications - 22
Citations - 1920
Markus Mueller is an academic researcher from ETH Zurich. The author has contributed to research in topics: Automatic target recognition & Argonaute. The author has an hindex of 10, co-authored 22 publications receiving 1666 citations. Previous affiliations of Markus Mueller include Swiss Institute of Bioinformatics & École Polytechnique Fédérale de Lausanne.
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Journal ArticleDOI
Reproducible isolation of distinct, overlapping segments of the phosphoproteome
Bernd Bodenmiller,Lukas N. Mueller,Markus Mueller,Bruno Domon,Ruedi Aebersold,Ruedi Aebersold,Ruedi Aebersold +6 more
TL;DR: The results suggest that the three methods detect different, partially overlapping segments of the phosphoproteome and that, at present, no single method is sufficient for a comprehensive phosphopeptides analysis.
Journal ArticleDOI
Identification of cross-linked peptides from large sequence databases
Oliver Rinner,Jan Seebacher,Thomas Walzthoeni,Thomas Walzthoeni,Lukas N. Mueller,Martin Beck,Alexander Schmidt,Alexander Schmidt,Markus Mueller,Ruedi Aebersold,Ruedi Aebersold,Ruedi Aebersold +11 more
TL;DR: It is shown that xQuest can identify cross-linked peptides from a total Escherichia coli lysate with an unrestricted database search and reduces the search space by an upstream candidate-peptide search before the recombination step.
Journal ArticleDOI
Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction
Daniel K. Wells,Marit M. van Buuren,Kristen K. Dang,Vanessa M. Hubbard-Lucey,Kathleen C. F. Sheehan,Katie M. Campbell,Andrew Lamb,Jeffrey P. Ward,John Sidney,Ana Belen Blazquez,Andrew J. Rech,Jesse M. Zaretsky,Begonya Comin-Anduix,Alphonsus H. C. Ng,William Chour,Thomas Yu,Hira Rizvi,Jia M. Chen,Patrice Manning,Gabriela Steiner,Xengie Doan,Aly A. Khan,Amit A. Lugade,Ana M. Mijalkovic Lazic,Angela Frentzen,Arbel D. Tadmor,Ariella Sasson,Arjun A. Rao,Baikang Pei,Barbara Schrörs,Beata Berent-Maoz,Beatriz M. Carreno,Bin Song,Bjoern Peters,Bo Li,Brandon W. Higgs,Brian Stevenson,Christian Iseli,Christopher A. Miller,Christopher A. Morehouse,Cornelis J. M. Melief,Cristina Puig-Saus,Daphne van Beek,David Balli,David Gfeller,David Haussler,Dirk Jäger,Eduardo Cortes,Ekaterina Esaulova,Elham Sherafat,Francisco Arcila,Gabor Bartha,Geng Liu,George Coukos,Guilhem Richard,Han Chang,Han Si,Inka Zörnig,Ioannis Xenarios,Ion I. Mandoiu,Irsan Kooi,James P. Conway,Jan H. Kessler,Jason A. Greenbaum,Jason Perera,Jason Harris,Jasreet Hundal,Jennifer M. Shelton,Jianmin Wang,Jiaqian Wang,Joel Greshock,Jonathon Blake,Joseph D. Szustakowski,Julia Kodysh,Juliet Forman,Lei Wei,Leo J. Lee,Lorenzo F. Fanchi,Maarten Slagter,Maren Lang,Markus Mueller,Martin Löwer,Mathias Vormehr,Maxim N. Artyomov,Michael A. Kuziora,Michael F. Princiotta,Michal Bassani-Sternberg,Mignonette H. Macabali,Milica R. Kojicic,Naibo Yang,Nevena M. Ilic Raicevic,Nicolas Guex,Nicolas Robine,Niels Halama,Nikola M. Skundric,Ognjen Milicevic,Pascal Gellert,Patrick Jongeneel,Pornpimol Charoentong,Pramod K. Srivastava,Prateek Tanden,Priyanka Shah,Qiang Hu,Ravi Gupta,Richard Chen,Robert A. Petit,Robert Ziman,Rolf Hilker,Sachet A. Shukla,Sahar Al Seesi,Sean Michael Boyle,Si Qiu,Siranush Sarkizova,Sofie R. Salama,Song Liu,Song Wu,Sriram Sridhar,Steven L. C. Ketelaars,Suchit Jhunjhunwala,Tatiana Shcheglova,Thierry Schuepbach,Todd Creasy,Veliborka Josipovic,Vladimir B. Kovacevic,Weixuan Fu,Willem-Jan Krebber,Yi-Hsiang Hsu,Yinong Sebastian,Zeynep Kosaloglu Yalcin,Zhiqin Huang,Taha Merghoub,Taha Merghoub,Justin Guinney,Justin Guinney,Adam Kolom,Cheryl Selinsky,Antoni Ribas,Antoni Ribas,Matthew D. Hellmann,Nir Hacohen,Nir Hacohen,Alessandro Sette,Alessandro Sette,James R. Heath,Nina Bhardwaj,Fred Ramsdell,Robert D. Schreiber,Ton N. Schumacher,Pia Kvistborg,Nadine Defranoux +149 more
TL;DR: A model of tumor epitope immunogenicity was developed that filtered out 98% of non-immunogenic peptides with a precision above 0.70 and was validated in an independent cohort of 310 epitopes prioritized from tumor sequencing data and assessed for T cell binding.
Journal ArticleDOI
Corrigendum: Identification of cross-linked peptides from large sequence databases
Oliver Rinner,Jan Seebacher,Thomas Walzthoeni,Lukas N. Mueller,Martin Beck,Alexander Schmidt,Markus Mueller,Ruedi Aebersold +7 more
TL;DR: In the version of this Brief Communication initially published, an author name (Lukas Mueller) was incorrect and the correct author name is Lukas N. Mueller.
Journal ArticleDOI
An Integrated, Directed Mass Spectrometric Approach for In-depth Characterization of Complex Peptide Mixtures
Alexander Schmidt,Nils Gehlenborg,Bernd Bodenmiller,Lukas N. Mueller,D. Campbell,Markus Mueller,Ruedi Aebersold,Bruno Domon +7 more
TL;DR: A directed LC-MS/MS approach that alleviates the limitations of DDA precursor ion selection by decoupling peak detection and sequencing of selected precursor ions is presented.