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Markus Muller
Markus Muller
Department of Oncology, CHUV and Vital-IT, SIB Swiss Institute of Bioinformatics
Verified email at sib.swiss
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Cited by
Year
pROC: an open-source package for R and S+ to analyze and compare ROC curves
X Robin, N Turck, A Hainard, N Tiberti, F Lisacek, JC Sanchez, M Müller
BMC bioinformatics 12 (1), 1-8, 2011
79012011
SuperHirn – a novel tool for high resolution LC‐MS‐based peptide/protein profiling
LN Mueller, O Rinner, A Schmidt, S Letarte, B Bodenmiller, MY Brusniak, ...
Proteomics 7 (19), 3470-3480, 2007
9252007
Reproducible isolation of distinct, overlapping segments of the phosphoproteome
B Bodenmiller, LN Mueller, M Mueller, B Domon, R Aebersold
Nature methods 4 (3), 231-237, 2007
6282007
Identification of cross-linked peptides from large sequence databases
O Rinner, J Seebacher, T Walzthoeni, LN Mueller, M Beck, A Schmidt, ...
Nature methods 5 (4), 315-318, 2008
4772008
Processing and classification of protein mass spectra
M Hilario, A Kalousis, C Pellegrini, M Müller
Mass spectrometry reviews 25 (3), 409-449, 2006
2372006
Automated protein identification by tandem mass spectrometry: issues and strategies
P Hernandez, M Müller, RD Appel
Mass spectrometry reviews 25 (2), 235-254, 2006
2242006
An integrated mass spectrometric and computational framework for the analysis of protein interaction networks
O Rinner, LN Mueller, M Hubálek, M Müller, M Gstaiger, R Aebersold
Nature biotechnology 25 (3), 345-352, 2007
2042007
Improving protein identification from peptide mass fingerprinting through a parameterized multi‐level scoring algorithm and an optimized peak detection
R Gras, M Müller, E Gasteiger, S Gay, PA Binz, W Bienvenut, C Hoogland, ...
ELECTROPHORESIS: An International Journal 20 (18), 3535-3550, 1999
1971999
A molecular scanner to automate proteomic research and to display proteome images
PA Binz, M Müller, D Walther, WV Bienvenut, R Gras, C Hoogland, ...
Analytical Chemistry 71 (21), 4981-4988, 1999
1791999
Processing strategies and software solutions for data‐independent acquisition in mass spectrometry
A Bilbao, E Varesio, J Luban, C Strambio‐De‐Castillia, G Hopfgartner, ...
Proteomics 15 (5-6), 964-980, 2015
1712015
An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures
A Schmidt, N Gehlenborg, B Bodenmiller, LN Mueller, D Campbell, ...
Molecular & Cellular Proteomics 7 (11), 2138-2150, 2008
1592008
pROC: display and analyze ROC curves
X Robin, N Turck, A Hainard, N Tiberti, F Lisacek, JC Sanchez, M Müller, ...
R package version 1, 2018
1532018
Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes
C Chong, M Müller, HS Pak, D Harnett, F Huber, D Grun, M Leleu, ...
Nature communications 11 (1), 1-21, 2020
1322020
Quantitative proteomic analysis of protein complexes: concurrent identification of interactors and their state of phosphorylation
D Pflieger, MA Jünger, M Müller, O Rinner, H Lee, PM Gehrig, M Gstaiger, ...
Molecular & cellular proteomics 7 (2), 326-346, 2008
1262008
High-throughput and sensitive immunopeptidomics platform reveals profound interferonγ-mediated remodeling of the human leukocyte antigen (HLA) ligandome
C Chong, F Marino, HS Pak, J Racle, RT Daniel, M Müller, D Gfeller, ...
Molecular & Cellular Proteomics 17 (3), 533-548, 2018
1222018
Unrestricted identification of modified proteins using MS/MS
E Ahrné, M Müller, F Lisacek
Proteomics 10 (4), 671-686, 2010
992010
Analysis of Cell Surface Proteome Changes via Label-free, Quantitative Mass Spectrometry* S
R Schiess, LN Mueller, A Schmidt, M Mueller, B Wollscheid, R Aebersold
Molecular & cellular proteomics 8 (4), 624-638, 2009
972009
Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective
Y Perez-Riverol, R Wang, H Hermjakob, M Müller, V Vesada, JA Vizcaíno
Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1844 (1), 63-76, 2014
892014
Machine learning approaches to lung cancer prediction from mass spectra
M Hilario, A Kalousis, M Müller, C Pellegrini
Proteomics 3 (9), 1716-1719, 2003
852003
Estimating the contribution of proteasomal spliced peptides to the HLA-I ligandome
R Mylonas, I Beer, C Iseli, C Chong, HS Pak, D Gfeller, G Coukos, ...
Molecular & Cellular Proteomics 17 (12), 2347-2357, 2018
842018
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