Markus Müller

Publications | Phd and Masters theses

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58 publications

In press | 2024 | 2023 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2004 | 2003 | 2002 | 2001 | 1999 |
In press
 
A comprehensive proteogenomic pipeline for neoantigen discovery to advance personalized cancer immunotherapy.
Huber F., Arnaud M., Stevenson B.J., Michaux J., Benedetti F., Thevenet J., Bobisse S., Chiffelle J., Gehert T., Müller M. et al. Nature biotechnology. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_14DC47CDBB48]
2024
Immunopeptidomics-based identification of naturally presented non-canonical circRNA-derived peptides.
Ferreira H.J., Stevenson B.J., Pak H., Yu F., Almeida Oliveira J., Huber F., Taillandier-Coindard M., Michaux J., Ricart-Altimiras E., Kraemer A.I. et al., 2024/03/15. Nature communications, 15 (1) p. 2357. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_6C0EA9079104]
2023
Machine learning methods and harmonized datasets improve immunogenic neoantigen prediction.
Müller M., Huber F., Arnaud M., Kraemer A.I., Altimiras E.R., Michaux J., Taillandier-Coindard M., Chiffelle J., Murgues B., Gehret T. et al., 2023/11/14. Immunity, 56 (11) pp. 2650-2663.e6. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_809F4EAB21AB]
The immunopeptidome landscape associated with T cell infiltration, inflammation and immune editing in lung cancer.
Kraemer A.I., Chong C., Huber F., Pak H., Stevenson B.J., Müller M., Michaux J., Altimiras E.R., Rusakiewicz S., Simó-Riudalbas L. et al., 2023/05. Nature cancer, 4 (5) pp. 608-628. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_AFB188A208B6]
2021
Sensitive Immunopeptidomics by Leveraging Available Large-Scale Multi-HLA Spectral Libraries, Data-Independent Acquisition, and MS/MS Prediction.
Pak H., Michaux J., Huber F., Chong C., Stevenson B.J., Müller M., Coukos G., Bassani-Sternberg M., 2021. Molecular & cellular proteomics, 20 p. 100080. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_DCFCF966CE50]
2020
 
Automatic Annotation and Dereplication of Tandem Mass Spectra of Peptidic Natural Products.
Ricart E., Pupin M., Müller M., Lisacek F., 2020/12/15. Analytical chemistry, 92 (24) pp. 15862-15871. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_AE3479B45287]
Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes
Chong Chloe, Müller Markus, Pak HuiSong, Harnett Dermot, Huber Florian, Grun Delphine, Leleu Marion, Auger Aymeric, Arnaud Marion, Stevenson Brian J. et al., 2020/12. Nature Communications, 11 (1). Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_03EA897A1141]
Chemical Genetics of AGC-kinases Reveals Shared Targets of Ypk1, Protein Kinase A and Sch9.
Plank M., Perepelkina M., Müller M., Vaga S., Zou X., Bourgoint C., Berti M., Saarbach J., Haesendonckx S., Winssinger N. et al., 2020/04. Molecular & cellular proteomics, 19 (4) pp. 655-671. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_4D0914B0B753]
 
Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands.
Solleder M., Guillaume P., Racle J., Michaux J., Pak H.S., Müller M., Coukos G., Bassani-Sternberg M., Gfeller D., 2020/02. Molecular & cellular proteomics, 19 (2) pp. 390-404. Peer-reviewed.
[DOI][Pmid][serval:BIB_0EBACC6764B1]
Biogenesis of HLA Ligand Presentation in Immune Cells Upon Activation Reveals Changes in Peptide Length Preference.
Marino F., Semilietof A., Michaux J., Pak H.S., Coukos G., Müller M., Bassani-Sternberg M., 2020. Frontiers in immunology, 11 p. 1981. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E06D274ABF64]
2019
rBAN: retro-biosynthetic analysis of nonribosomal peptides
Ricart Emma, Leclère Valérie, Flissi Areski, Mueller Markus, Pupin Maude, Lisacek Frédérique, 2019/12. Journal of Cheminformatics, 11 (1).
[DOI][WoS][Pmid][serval:BIB_C467C9D2EDB0]
2018
 
Large-Scale Reanalysis of Publicly Available HeLa Cell Proteomics Data in the Context of the Human Proteome Project
Robin Thibault, Bairoch Amos, Müller Markus, Lisacek Frédérique, Lane Lydie, 2018/12/07. Journal of Proteome Research, 17 (12) pp. 4160-4170.
[DOI][WoS][Pmid][serval:BIB_45FABFCB8BFB]
Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome.
Mylonas R., Beer I., Iseli C., Chong C., Pak H.S., Gfeller D., Coukos G., Xenarios I., Müller M., Bassani-Sternberg M., 2018/12. Molecular & cellular proteomics, 17 (12) pp. 2347-2357. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A79DB078A6D8]
Minimal Information About an Immuno-Peptidomics Experiment (MIAIPE).
Lill J.R., van Veelen P.A., Tenzer S., Admon A., Caron E., Elias J.E., Heck AJR, Marcilla M., Marino F., Müller M. et al., 2018/06. Proteomics, 18 (12) pp. e1800110. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_62FB4A93752F]
High-throughput and Sensitive Immunopeptidomics Platform Reveals Profound Interferonγ-Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome.
Chong C., Marino F., Pak H., Racle J., Daniel R.T., Müller M., Gfeller D., Coukos G., Bassani-Sternberg M., 2018/03. Molecular & cellular proteomics, 17 (3) pp. 533-548. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A056F0253744]
2017
 
Glycoforest 1.0
Horlacher Oliver, Jin Chunsheng, Alocci Davide, Mariethoz Julien, Müller Markus, Karlsson Niclas G., Lisacek Frederique, 2017/10/17. Analytical Chemistry, 89 (20) pp. 10932-10940.
[DOI][WoS][Pmid][serval:BIB_9B87323150CF]
 
Optimization by infusion of multiple reaction monitoring transitions for sensitive quantification of peptides by liquid chromatography/mass spectrometry : Optimizing MRM transitions by FIA
Alghanem Bandar, Nikitin Frédéric, Stricker Thomas, Duchoslav Eva, Luban Jeremy, Strambio-De-Castillia Caterina, Muller Markus, Lisacek Frédérique, Varesio Emmanuel, Hopfgartner Gérard, 2017/05/15. Rapid Communications in Mass Spectrometry, 31 (9) pp. 753-761.
[DOI][Pmid][serval:BIB_C59D86E11BC9]
'Hotspots' of Antigen Presentation Revealed by Human Leukocyte Antigen Ligandomics for Neoantigen Prioritization.
Müller M., Gfeller D., Coukos G., Bassani-Sternberg M., 2017. Frontiers in Immunology, 8 p. 1367. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A4DBE7C295A9]
2016
 
Detection of busulfan adducts on proteins : Detection of busulfan adducts on proteins
Acosta-Martin Adelina E., Antinori Paola, Uppugunduri Chakradhara Rao S., Daali Youssef, Ansari Marc, Scherl Alexander, Müller Markus, Lescuyer Pierre, 2016/12/15. Rapid Communications in Mass Spectrometry, 30 (23) pp. 2517-2528.
[DOI][WoS][Pmid][serval:BIB_81C2787188F3]
2015
 
Comparative Proteomic Profiling of Ehrlichia ruminantium Pathogenic Strain and Its High-Passaged Attenuated Strain Reveals Virulence and Attenuation-Associated Proteins
Marcelino Isabel, Ventosa Miguel, Pires Elisabete, Müller Markus, Lisacek Frédérique, Lefrançois Thierry, Vachiery Nathalie, Coelho Ana Varela, 2015/12/21. PLOS ONE, 10 (12) pp. e0145328.
[DOI][WoS][Pmid][serval:BIB_3E2008107A93]
 
MzJava: An open source library for mass spectrometry data processing
Horlacher Oliver, Nikitin Frederic, Alocci Davide, Mariethoz Julien, Müller Markus, Lisacek Frederique, 2015/11. Journal of Proteomics, 129 pp. 63-70.
[DOI][WoS][Pmid][serval:BIB_B015F9DC7B94]
 
Unrestricted modification search reveals lysine methylation as major modification induced by tissue formalin fixation and paraffin embedding
Zhang Ying, Muller Markus, Xu Bo, Yoshida Yutaka, Horlacher Oliver, Nikitin Frederic, Garessus Samuel, Magdeldin Sameh, Kinoshita Naohiko, Fujinaka Hidehiko et al., 2015/08. PROTEOMICS, 15 (15) pp. 2568-2579.
[DOI][WoS][Pmid][serval:BIB_7FE3B905C9D3]
 
Processing strategies and software solutions for data-independent acquisition in mass spectrometry
Bilbao Aivett, Varesio Emmanuel, Luban Jeremy, Strambio-De-Castillia Caterina, Hopfgartner Gérard, Müller Markus, Lisacek Frédérique, 2015/03. PROTEOMICS, 15 (5-6) pp. 964-980.
[DOI][WoS][Pmid][serval:BIB_F784D7B261E0]
2014
 
Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective
Perez-Riverol Yasset, Wang Rui, Hermjakob Henning, Müller Markus, Vesada Vladimir, Vizcaíno Juan Antonio, 2014/01. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1844 (1) pp. 63-76.
[DOI][WoS][Pmid][serval:BIB_65ECF64021DE]
2013
 
Clustering and Filtering Tandem Mass Spectra Acquired in Data-Independent Mode
Pak Huisong, Nikitin Frederic, Gluck Florent, Lisacek Frederique, Scherl Alexander, Muller Markus, 2013/12. Journal of The American Society for Mass Spectrometry, 24 (12) pp. 1862-1871.
[DOI][WoS][Pmid][serval:BIB_1C0A054371B1]
 
EasyProt — An easy-to-use graphical platform for proteomics data analysis
Gluck Florent, Hoogland Christine, Antinori Paola, Robin Xavier, Nikitin Frederic, Zufferey Anne, Pasquarello Carla, Fétaud Vanessa, Dayon Loïc, Müller Markus et al., 2013/02. Journal of Proteomics, 79 pp. 146-160.
[DOI][WoS][Pmid][serval:BIB_0F73D585805F]
 
PanelomiX: A threshold-based algorithm to create panels of biomarkers
Robin Xavier, Turck Natacha, Hainard Alexandre, Tiberti Natalia, Lisacek Frédérique, Sanchez Jean-Charles, Müller Markus, 2013. Translational Proteomics, 1 (1) pp. 57-64.
[DOI][serval:BIB_7B41D579B957]
2012
 
Isoelectric point optimization using peptide descriptors and support vector machines
Perez-Riverol Yasset, Audain Enrique, Millan Aleli, Ramos Yassel, Sanchez Aniel, Vizcaíno Juan Antonio, Wang Rui, Müller Markus, Machado Yoan J., Betancourt Lazaro H. et al., 2012/04. Journal of Proteomics, 75 (7) pp. 2269-2274.
[DOI][WoS][Pmid][serval:BIB_86A4C42B9587]
2011
 
pROC: an open-source package for R and S+ to analyze and compare ROC curves
Robin Xavier, Turck Natacha, Hainard Alexandre, Tiberti Natalia, Lisacek Frédérique, Sanchez Jean-Charles, Müller Markus, 2011/12. BMC Bioinformatics, 12 (1).
[DOI][WoS][Pmid][serval:BIB_3892A2943803]
 
Bioinformatics Tools for Detecting Post-Translational Modifications in Mass Spectrometry Data
Palagi Patricia M., Arhné Erik, Müller MarKus, Lisacek Frédérique, 2011/11/28. pp. 463-475 dans Amino Acids, Peptides and Proteins in Organic Chemistry, Wiley-VCH Verlag GmbH & Co. KGaA.
[DOI][serval:BIB_DC9F5C3269B5]
 
An improved method for the construction of decoy peptide MS/MS spectra suitable for the accurate estimation of false discovery rates
Ahrné Erik, Ohta Yuki, Nikitin Frederic, Scherl Alexander, Lisacek Frederique, Müller Markus, 2011/10. PROTEOMICS, 11 (20) pp. 4085-4095.
[DOI][WoS][Pmid][serval:BIB_5E317120F157]
 
In silico analysis of accurate proteomics, complemented by selective isolation of peptides
Perez-Riverol Yasset, Sánchez Aniel, Ramos Yassel, Schmidt Alex, Müller Markus, Betancourt Lázaro, González Luis J., Vera Roberto, Padron Gabriel, Besada Vladimir, 2011/09. Journal of Proteomics, 74 (10) pp. 2071-2082.
[DOI][WoS][Pmid][serval:BIB_5319ACB5CACC]
 
Human hemolysate glycated proteome.
Priego-Capote F., Ramirez-Boo M., Hoogland C., Scherl A., Mueller M., Lisacek F., Sanchez J.C., 2011/07/15. Analytical chemistry, 83 (14) pp. 5673-5680. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_68F402393899]
 
QuickMod: A Tool for Open Modification Spectrum Library Searches
Ahrné Erik, Nikitin Frederic, Lisacek Frederique, Müller Markus, 2011/07. Journal of Proteome Research, 10 (7) pp. 2913-2921.
[DOI][WoS][Pmid][serval:BIB_805BFF39ACB6]
 
Matrix metalloproteinase-9 and intercellular adhesion molecule 1 are powerful staging markers for human African trypanosomiasis : MMP-9 and ICAM-1 for staging of HAT
Hainard Alexandre, Tiberti Natalia, Robin Xavier, Ngoyi Dieudonné M., Matovu Enock, Enyaru John C. K., Müller Markus, Turck Natacha, Ndung'u Joseph M., Lejon Veerle et al., 2011/01. Tropical Medicine & International Health, 16 (1) pp. 119-126.
[DOI][WoS][Pmid][serval:BIB_D45A4BA36DCD]
2010
 
Glycation Isotopic Labeling with13C-Reducing Sugars for Quantitative Analysis of Glycated Proteins in Human Plasma
Priego-Capote Feliciano, Scherl Alexander, Müller Markus, Waridel Patrice, Lisacek Frédérique, Sanchez Jean-Charles, 2010/03. Molecular & Cellular Proteomics, 9 (3) pp. 579-592.
[DOI][WoS][Pmid][serval:BIB_0583E7FD6A1B]
 
Unrestricted identification of modified proteins using MS/MS
Ahrné Erik, Müller Markus, Lisacek Frederique, 2010/02. PROTEOMICS, 10 (4) pp. 671-686.
[DOI][WoS][Pmid][serval:BIB_AF639AED27F3]
 
A multiparameter panel method for outcome prediction following aneurysmal subarachnoid hemorrhage
Turck Natacha, Vutskits Laszlo, Sanchez-Pena Paola, Robin Xavier, Hainard Alexandre, Gex-Fabry Marianne, Fouda Catherine, Bassem Hadiji, Mueller Markus, Lisacek Frédérique et al., 2010/01. Intensive Care Medicine, 36 (1) pp. 107-115.
[DOI][WoS][Pmid][serval:BIB_160F9257C1E7]
2009
 
Bioinformatics for protein biomarker panel classification: what is needed to bring biomarker panels intoin vitrodiagnostics?
Robin Xavier, Turck Natacha, Hainard Alexandre, Lisacek Frédérique, Sanchez Jean-Charles, Müller Markus, 2009/12. Expert Review of Proteomics, 6 (6) pp. 675-689.
[DOI][WoS][Pmid][serval:BIB_DFCE8F53A0F2]
 
A Combined CXCL10, CXCL8 and H-FABP Panel for the Staging of Human African Trypanosomiasis Patients
Hainard Alexandre, Tiberti Natalia, Robin Xavier, Lejon Veerle, Ngoyi Dieudonné Mumba, Matovu Enock, Enyaru John Charles, Fouda Catherine, Ndung'u Joseph Mathu, Lisacek Frédérique et al., 2009/06/16. PLoS Neglected Tropical Diseases, 3 (6) pp. e459.
[DOI][WoS][Pmid][serval:BIB_D3ECC68C462A]
 
Analysis of Cell Surface Proteome Changes via Label-free, Quantitative Mass Spectrometry
Schiess Ralph, Mueller Lukas N., Schmidt Alexander, Mueller Markus, Wollscheid Bernd, Aebersold Ruedi, 2009/04. Molecular & Cellular Proteomics, 8 (4) pp. 624-638.
[DOI][WoS][Pmid][serval:BIB_973F1A62C3D1]
 
A simple workflow to increase MS2 identification rate by subsequent spectral library search
Ahrné Erik, Masselot Alexandre, Binz Pierre-Alain, Müller Markus, Lisacek Frederique, 2009/03. PROTEOMICS, 9 (6) pp. 1731-1736.
[DOI][WoS][Pmid][serval:BIB_2541887DA805]
2008
 
An Integrated, Directed Mass Spectrometric Approach for In-depth Characterization of Complex Peptide Mixtures
Schmidt Alexander, Gehlenborg Nils, Bodenmiller Bernd, Mueller Lukas N., Campbell Dave, Mueller Markus, Aebersold Ruedi, Domon Bruno, 2008/11. Molecular & Cellular Proteomics, 7 (11) pp. 2138-2150.
[DOI][WoS][Pmid][serval:BIB_E1746D715EB8]
 
Identification of cross-linked peptides from large sequence databases
Rinner Oliver, Seebacher Jan, Walzthoeni Thomas, Mueller Lukas N, Beck Martin, Schmidt Alexander, Mueller Markus, Aebersold Ruedi, 2008/04. Nature Methods, 5 (4) pp. 315-318.
[DOI][WoS][Pmid][serval:BIB_D2FA79B1C5A4]
 
Quantitative Proteomic Analysis of Protein Complexes : Concurrent Identification of Interactors and Their State of Phosphorylation
Pflieger Delphine, Jünger Martin A., Müller Markus, Rinner Oliver, Lee Hookeun, Gehrig Peter M., Gstaiger Matthias, Aebersold Ruedi, 2008/02. Molecular & Cellular Proteomics, 7 (2) pp. 326-346.
[DOI][WoS][Pmid][serval:BIB_93C9C8D7AFC9]
2007
 
SuperHirn – a novel tool for high resolution LC-MS-based peptide/protein profiling
Mueller Lukas N., Rinner Oliver, Schmidt Alexander, Letarte Simon, Bodenmiller Bernd, Brusniak Mi-Youn, Vitek Olga, Aebersold Ruedi, Müller Markus, 2007/10. PROTEOMICS, 7 (19) pp. 3470-3480.
[DOI][WoS][Pmid][serval:BIB_8DD23655502B]
 
An integrated mass spectrometric and computational framework for the analysis of protein interaction networks
Rinner Oliver, Mueller Lukas N., Hubálek Martin, Müller Markus, Gstaiger Matthias, Aebersold Ruedi, 2007/03. Nature Biotechnology, 25 (3) pp. 345-352.
[DOI][WoS][Pmid][serval:BIB_A6D1C48A5317]
 
Reproducible isolation of distinct, overlapping segments of the phosphoproteome
Bodenmiller Bernd, Mueller Lukas N, Mueller Markus, Domon Bruno, Aebersold Ruedi, 2007/03. Nature Methods, 4 (3) pp. 231-237.
[DOI][WoS][Pmid][serval:BIB_011C052EA8CB]
 
Tandem mass spectrometry protein identification on a PC grid.
Zosso D., Podvinec M., Müller M., Aebersold R., Peitsch M.C., Schwede T., 2007. pp. 3-12 dans From Genes to Personalized HealthCare: Grid Solutions for the Life Sciences, IOS Press.
[Pmid][serval:BIB_DEBB25C28609]
2006
 
Processing and classification of protein mass spectra
Hilario Melanie, Kalousis Alexandros, Pellegrini Christian, Müller Markus, 2006/05. Mass Spectrometry Reviews, 25 (3) pp. 409-449.
[DOI][WoS][Pmid][serval:BIB_3635E7192BB6]
 
Automated protein identification by tandem mass spectrometry: Issues and strategies
Hernandez Patricia, Müller Markus, Appel Ron D., 2006/03. Mass Spectrometry Reviews, 25 (2) pp. 235-254.
[DOI][WoS][Pmid][serval:BIB_E20EB6F0FB2F]
2004
 
The molecular scanner: concept and developments
Binz Pierre-Alain, Müller Markus, Hoogland Christine, Zimmermann Catherine, Pasquarello Carla, Corthals Garry, Sanchez Jean-Charles, Hochstrasser Denis F, Appel Ron D, 2004/02. Current Opinion in Biotechnology, 15 (1) pp. 17-23.
[DOI][WoS][Pmid][serval:BIB_4280BCF139E6]
2003
 
Machine learning approaches to lung cancer prediction from mass spectra
Hilario Melanie, Kalousis Alexandros, Müller Markus, Pellegrini Christian, 2003/09. PROTEOMICS, 3 (9) pp. 1716-1719.
[DOI][WoS][Pmid][serval:BIB_1A2729C12414]
2002
 
Molecular scanner experiment with human plasma: Improving protein identification by using intensity distributions of matching peptide masses
Müller Markus, Gras Robin, Binz Pierre-Alain, Hochstrasser Denis F., Appel Ron D., 2002/10. PROTEOMICS, 2 (10) pp. 1413-1425.
[DOI][Pmid][serval:BIB_85D838B99663]
 
Visualization and analysis of molecular scanner peptide mass spectra
Müller Markus, Gras Robin, Appel Ron D., Bienvenut Willy V., Hochstrasser Denis F., 2002/03. Journal of the American Society for Mass Spectrometry, 13 (3) pp. 221-231.
[DOI][Pmid][serval:BIB_C0186CA7DE3D]
2001
 
Computational aspects of protein identification by mass spectrometry.
Gras R., Müller M., 2001/12. Current opinion in molecular therapeutics, 3 (6) pp. 526-532. Peer-reviewed.
[WoS][Pmid][serval:BIB_F08872BC5206]
1999
 
Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection
Gras Robin, Müller Markus, Gasteiger Elisabeth, Gay Steven, Binz Pierre-Alain, Bienvenut William, Hoogland Christine, Sanchez Jean-Charles, Bairoch Amos, Hochstrasser Denis F. et al., 1999/12/01. Electrophoresis, 20 (18) pp. 3535-3550.
[DOI][Pmid][serval:BIB_ED57AFD74D67]
 
A Molecular Scanner To Automate Proteomic Research and To Display Proteome Images
Binz Pierre-Alain, Müller Markus, Walther Daniel, Bienvenut Willy V., Gras Robin, Hoogland Christine, Bouchet Gérard, Gasteiger Elisabeth, Fabbretti Roberto, Gay Steven et al., 1999/11. Analytical Chemistry, 71 (21) pp. 4981-4988.
[DOI][WoS][Pmid][serval:BIB_36057DB72583]
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