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M. The · SciRah

Researcher profile · Semantic Scholar

M. The

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M. The — researcher profile on SciRah

h-index: 18
Works: 52
Citations: 1,326

Most-cited papers

Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0
M. The, M. MacCoss, William Stafford Noble, L. Käll
2016Journal of the American Society for Mass Spectrometry424 citations Open access
Semantic Scholar
Decrypting drug actions and protein modifications by dose- and time-resolved proteomics
Jana Zecha, Florian P. Bayer, S. Wiechmann, J. Woortman +33 more
2023Science95 citations Open access
Semantic Scholar
Mass spectrometry-based draft of the mouse proteome
P. Giansanti, Patroklos Samaras, Yangyang Bian, C. Meng +27 more
2022Nature Methods73 citations Open access
Semantic Scholar
ProteomicsDB: toward a FAIR open-source resource for life-science research
Ludwig Lautenbacher, Patroklos Samaras, J. Muller, Andreas Grafberger +11 more
2021Nucleic Acids Res.67 citations Open access
Semantic Scholar
Oktoberfest: Open‐source spectral library generation and rescoring pipeline based on Prosit
Mario Picciani, Wassim Gabriel, Victor Giurcoiu, Omar Shouman +9 more
2023Proteomics63 citations Open access
Semantic Scholar
The one-carbon pool controls mitochondrial energy metabolism via complex I and iron-sulfur clusters
Florian A. Schober, David Moore, I. Atanassov, M. Moedas +17 more
2021Science Advances55 citations Open access
Semantic Scholar
MaRaCluster: A Fragment Rarity Metric for Clustering Fragment Spectra in Shotgun Proteomics.
M. The, L. Käll
2016Journal of Proteome Research46 citations Open access
Semantic Scholar
How to talk about protein‐level false discovery rates in shotgun proteomics
M. The, A. Tasnim, L. Käll
2016Proteomics46 citations Open access
Semantic Scholar
A region‐resolved proteomic map of the human brain enabled by high‐throughput proteomics
Johanna Tüshaus, A. Sakhteman, Severin Lechner, M. The +5 more
2023bioRxiv40 citations Open access
Semantic Scholar
Reanalysis of ProteomicsDB Using an Accurate, Sensitive, and Scalable False Discovery Rate Estimation Approach for Protein Groups
M. The, Patroklos Samaras, B. Kuster, M. Wilhelm
2022Molecular & Cellular Proteomics38 citations Open access
Semantic Scholar
Prosit-TMT: Deep Learning Boosts Identification of TMT-Labeled Peptides.
Wassim Gabriel, M. The, D. Zolg, Florian P. Bayer +12 more
2022Analytical Chemistry38 citations
Semantic Scholar
Identification of 7 000-9 000 Proteins from Cell Lines and Tissues by Single-Shot Microflow LC-MS/MS.
Yang-Yang Bian, M. The, P. Giansanti, J. Mergner +4 more
2021Analytical Chemistry34 citations
Semantic Scholar
CurveCurator: a recalibrated F-statistic to assess, classify, and explore significance of dose–response curves
Florian P. Bayer, Manuel Gander, B. Kuster, M. The
2023bioRxiv32 citations Open access
Semantic Scholar
Integrated Identification and Quantification Error Probabilities for Shotgun Proteomics*
M. The, L. Käll
2018Molecular & Cellular Proteomics29 citations Open access
Semantic Scholar
A Protein Standard That Emulates Homology for the Characterization of Protein Inference Algorithms
M. The, F. Edfors, Yasset Pérez-Riverol, S. Payne +4 more
2017bioRxiv25 citations Open access
Semantic Scholar
Focus on the spectra that matter by clustering of quantification data in shotgun proteomics
M. The, L. Käll
2018Nature Communications22 citations Open access
Semantic Scholar
Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response
Stefanie Höfer, Larissa Frasch, Sarah Brajkovic, K. Putzker +11 more
2024bioRxiv20 citations Open access
Semantic Scholar
Evaluation of disposable trap column nanoLC-FAIMS-MS/MS for the proteomic analysis of FFPE tissue
S. Eckert, Yun-Chien Chang, Florian P. Bayer, M. The +3 more
2021Journal of Proteome Research20 citations Open access
Semantic Scholar
Uncertainty estimation of predictions of peptides' chromatographic retention times in shotgun proteomics
Heydar Maboudi Afkham, Xuan-Bing Qiu, M. The, L. Käll
2016Bioinform.18 citations
Semantic Scholar
PTMNavigator: interactive visualization of differentially regulated post-translational modifications in cellular signaling pathways
Julian Müller, Florian P. Bayer, M. Wilhelm, Maximilian G. Schuh +2 more
2024bioRxiv17 citations Open access
Semantic Scholar
Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics.
Yun-Chien Chang, Christian Gnann, Raphael R. Steimbach, Florian P. Bayer +9 more
2024Cell Reports17 citations Open access
Semantic Scholar
SIMSI-Transfer: Software-Assisted Reduction of Missing Values in Phosphoproteomic and Proteomic Isobaric Labeling Data Using Tandem Mass Spectrum Clustering
Firas Hamood, Florian P. Bayer, M. Wilhelm, B. Kuster +1 more
2022Molecular & Cellular Proteomics17 citations Open access
Semantic Scholar
Towards routine proteome profiling of FFPE tissue: insights from a 1,220-case pan-cancer study
Johanna Tüshaus, S. Eckert, Marius Schliemann, Yuxiang Zhou +19 more
2024EMBO Journal14 citations Open access
Semantic Scholar
Illuminating phenotypic drug responses of sarcoma cells to kinase inhibitors by phosphoproteomics
Chien-Yun Lee, M. The, Chen Meng, Florian P. Bayer +9 more
2023Molecular Systems Biology14 citations Open access
Semantic Scholar
Speeding up Percolator
John T. Halloran, Hantian Zhang, Kaan Kara, Cédric Renggli +5 more
2019Journal of Proteome Research8 citations Open access
Semantic Scholar
Response to "Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra".
J. Griss, Yasset Pérez-Riverol, M. The, L. Käll +1 more
2018Journal of Proteome Research8 citations
Semantic Scholar
Proteome Informatics Research Group ( iPRG ) 2016 Study : Inferring Proteoforms from Bottom-up Proteomics Data
Joon-Yong Lee, Hyungwon Choi, C. Colangelo, Darryl L. Davis +9 more
20188 citations
Semantic Scholar
Proteomic analyses identify targets, pathways, and cellular consequences of oncogenic KRAS signaling.
Nicole Kabella, Florian P. Bayer, Konstantinos Stamatiou, Miriam Abele +14 more
2025Science Signaling7 citations Open access
Semantic Scholar
Triqler for Protein Summarization of Data from Data-Independent Acquisition Mass Spectrometry
P. Truong, M. The, L. Käll
2023Journal of Proteome Research7 citations Open access
Semantic Scholar
Triqler for MaxQuant: Enhancing Results from MaxQuant by Bayesian Error Propagation and Integration
M. The, L. Käll
2021Journal of Proteome Research6 citations Open access
Semantic Scholar
Therapeutic implications of phosphoproteomics in molecular cancer diagnostics.
Annika Schneider, J. Woortman, C. Jensen, A. Sakhteman +16 more
2024Journal of Clinical Oncology4 citations
Semantic Scholar
Computational Approaches for Pathway‐Centric Analysis of Protein Post‐Translational Modifications
Julian Müller, B. Kuster, M. The
2025Proteomics3 citations Open access
Semantic Scholar
Multi-layered molecular profiling informs the diagnosis and targeted therapy of desmoplastic small round cell tumor
Marcus Renner, M. Oleś, N. Paramasivam, C. Heilig +42 more
2026Nature Communications2 citations Open access
Semantic Scholar
Mapping drug mechanisms with ProteomicsDB: unified omics and cell sensitivity data at scale
Mario Picciani, Armin Soleymaniniya, Julian Müller, Amirhossein Sakhteman +11 more
2025Nucleic Acids Research2 citations Open access
Semantic Scholar
Chemical proteomics decrypts the kinases that shape the dynamic human phosphoproteome
Florian P. Bayer, Julian Müller, Nicole Kabella, Miriam Abele +8 more
2025bioRxiv2 citations Open access
Semantic Scholar
Proceedings of the EuBIC-MS developers meeting 2023.
P. Beltrao, Tim Van Den Bossch, R. Gabriels, Tanja Holstein +18 more
2024Journal of Proteomics2 citations Open access
Semantic Scholar
Prospective pan-cancer phosphoproteomics at clinical scale extends therapeutic options in precision oncology
Annika Schneider, Julia Wortmann, C. Jensen, Leonardo Estrada Duenas +70 more
2026bioRxiv1 citations Open access
Semantic Scholar
TOPAS: phosphoproteome data analysis and decision support platform for molecular tumor boards
C. Jensen, Amirhossein Sakhteman, Firas Hamood, Annika Schneider +11 more
2026bioRxiv1 citations Open access
Semantic Scholar
Illuminating oncogenic KRAS signaling by multi-dimensional chemical proteomics
Nicole Kabella, Florian P. Bayer, Konstantinos Stamatiou, Miriam Abele +14 more
2025bioRxiv1 citations Open access
Semantic Scholar
Deep Learning-Assisted Analysis of Immunopeptidomics Data.
Wassim Gabriel, Mario Picciani, M. The, M. Wilhelm
2024Methods in molecular biology1 citations
Semantic Scholar
Towards routine proteome profiling of FFPE tissue: Insights from a 1,200 case pan-cancer study
Johanna Tüshaus, S. Eckert, Marius Fraefel, Yuxiang Zhou +17 more
2024bioRxiv1 citations Open access
Semantic Scholar
Integrating identification and quantification uncertainty for differential protein abundance analysis with Triqler
M. The, L. Käll
2020bioRxiv1 citations Open access
Semantic Scholar
Statistical and machine learning methods to analyze large-scale mass spectrometry data
M. The
20181 citations
Semantic Scholar
Abstract 1028: A tumor-agnostic YAP/TAZ score predicts TEAD inhibitor sensitivity independent of Hippo alterations
Michael Wegert-Verhoeven, Mathea Fransisca, Sylvia Martin, Attila Jády +42 more
2026Cancer Research0 citations
Semantic Scholar
ProSIMSIt: The Best of Both Worlds in Data-Driven Rescoring and Identification Transfer
Firas Hamood, Wassim Gabriel, Pia Pfeiffer, B. Kuster +2 more
2025Journal of Proteome Research0 citations Open access
Semantic Scholar
Abstract 6373: From genotype to phenotype: Adding phosphoproteomic analysis to molecularly-guided therapy recommendation in Cancer of Unknown Primary (CUP)
M. Werner, T. Mundt, Annika Schneider, Waqar Hussain +36 more
2025Cancer Research0 citations
Semantic Scholar
SWAPS: A Modular Deep-Learning Empowered Peptide Identity Propagation Framework Beyond Match-Between-Run
Zixuan Xiao, Johanna Tüshaus, B. Kuster, M. The +1 more
2025Journal of Proteome Research0 citations Open access
Semantic Scholar
CurveCurator: Decrypting drugs by identifying relevant concentration-response curves in large-scale screens
M. The, Florian P. Bayer, Manuel Gander, B. Kuster
2024CurveCurator: Decrypting drugs by identifying relevant concentration-response curves in large-scale screens0 citations Open access
Semantic Scholar
AI-Assisted Processing Pipeline to Boost Protein Isoform Detection.
M. The, Mario Picciani, C. Jensen, Wassim Gabriel +2 more
2024Methods in molecular biology0 citations
Semantic Scholar
Enhancing treatment recommendations in precision oncology with proteomics and phosphoproteomics data
C. Jensen, Annika Schneider, M. The, A. Sakhteman +11 more
2023Enhancing treatment recommendations in precision oncology with proteomics and phosphoproteomics data0 citations Open access
Semantic Scholar

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Florian P. Bayer×17
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L. Käll×14
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