Publications of Isabell Bludau

Journal Article (18)

Journal Article
Krismer, E.; Bludau, I.; Strauss, M. T.; Mann, M.: AlphaPeptStats: an open-source Python package for automated and scalable statistical analysis of mass spectrometry-based proteomics. Bioinformatics 39 (8), btad461 (2023)
Journal Article
Bludau, I.; Nicod, C.; Martelli, C.; Xue, P.; Heusel, M.; Fossati, A.; Uliana, F.; Frommelt, F.; Aebersold, R.; Collins, B. C.: Rapid Profiling of Protein Complex Reorganization in Perturbed Systems. Journal of Proteome Research 22, pp. 1520 - 1536 (2023)
Journal Article
Neely, B. A.; Dorfer, V.; Martens, L.; Bludau, I.; Bouwmeester, R.; Degroeve, S.; Deutsch, E. W.; Gessulat, S.; Kaell, L.; Palczynski, P. et al.; Payne, S. H.; Rehfeldt, T. G.; Schmidt, T.; Schwaemmle, V.; Uszkoreit, J.; Vizcaino, J. A.; Wilhelm, M.; Palmblad, M.: Toward an Integrated Machine Learning Model of a Proteomics Experiment. Journal of Proteome Research 22, pp. 681 - 696 (2023)
Journal Article
Samant, R. S.; Batista, S.; Larance, M.; Ozer, B.; Milton, C. I.; Bludau, I.; Wu, E.; Biggins, L.; Andrews, S.; Hervieu, A. et al.; Johnston, H. E.; Al-Lazikhani, B.; Lamond, A. I.; Clarke, P. A.; Workman, P.: Native Size-Exclusion Chromatography-Based Mass Spectrometry Reveals New Components of the Early Heat Shock Protein 90 Inhibition Response Among Limited Global Changes. Molecular and Cellular Proteomics 22 (2), 100485 (2023)
Journal Article
Zeng, W.-F.; Zhou, X.-X.; Willems, S.; Ammar, C.; Wahle, M.; Bludau, I.; Voytik, E.; Strauss, M. T.; Mann, M.: AlphaPeptDeep: a modular deep learning framework to predict peptide properties for proteomics. Nature Communications 13 (1), 7238 (2022)
Journal Article
Bludau, I.; Willems, S.; Zeng, W.-F.; Strauss, M. T.; Hansen, F. M.; Tanzer, M. C.; Karayel, O.; Schulman, B. A.; Mann, M.: The structural context of posttranslational modifications at a proteome-wide scale. PLoS Biology 20 (5), e3001636 (2022)
Journal Article
Grossbach, J.; Gillet, L.; Clement-Ziza, M.; Schmalohr, C. L.; Schubert, O. T.; Schuetter, M.; Mawer, J. S. P.; Barnes, C. A.; Bludau, I.; Weith, M. et al.; Tessarz, P.; Graef, M.; Aebersold, R.; Beyer, A.: The impact of genomic variation on protein phosphorylation states and regulatory networks. Molecular Systems Biology 18 (5), e10712 (2022)
Journal Article
Schessner, J. P.; Voytik, E.; Bludau, I.: A practical guide to interpreting and generating bottom-up proteomics data visualizations. Proteomics, e2100103 (2022)
Journal Article
Voytik, E.; Bludau, I.; Willems, S.; Hansen, F. M.; Brunner, A.-D.; Strauss, M. T.; Mann, M.: AlphaMap: an open-source Python package for the visual annotation of proteomics data with sequence-specific knowledge. Bioinformatics 38 (3), pp. 849 - 852 (2022)
Journal Article
Bludau, I.; Frank, M.; Doerig, C.; Cai, Y.; Heusel, M.; Rosenberger, G.; Picotti, P.; Collins, B. C.; Rost, H.; Aebersold, R.: Systematic detection of functional proteoform groups from bottom-up proteomic datasets. Nature Communications 12 (1), 3810 (2021)
Journal Article
Fossati, A.; Li, C.; Uliana, F.; Wendt, F.; Frommelt, F.; Sykacek, P.; Heusel, M.; Hallal, M.; Bludau, I.; Capraz, T. et al.; Xue, P.; Song, J.; Wollscheid, B.; Purcell, A. W.; Gstaiger, M.; Aebersold, R.: PCprophet: a framework for protein complex prediction and differential analysis using proteomic data. Nature Methods 18 (5), pp. 520 - 527 (2021)
Journal Article
Hansen, F. M.; Tanzer, M. C.; Brüning, F.; Bludau, I.; Stafford, C.; Schulman, B. A.; Robles, M. S.; Karayel, O.; Mann, M.: Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology. Nature Communications 12 (1), 254 (2021)
Journal Article
Tanzer, M. C.; Bludau, I.; Stafford, C. A.; Hornung, V.; Mann, M.: Phosphoproteome profiling uncovers a key role for CDKs in TNF signaling. Nature Communications 12 (1), 6053 (2021)
Journal Article
Bludau, I.; Aebersold, R.: Proteomic and interactomic insights into the molecular basis of cell functional diversity. Nature Reviews Molecular Cell Biology 21 (6), pp. 327 - 340 (2020)
Journal Article
Bludau, I.; Aebersold, R.: Proteomic and interactomic insights into the molecular basis of cell functional diversity. NATURE REVIEWS MOLECULAR CELL BIOLOGY 21, pp. 327 - 340 (2020)
Journal Article
Bludau, I.; Heusel, M.; Frank, M.; Rosenberger, G.; Hafen, R.; Banaei-Esfahani, A.; van Drogen, A.; Collins, B. C.; Gstaiger, M.; Aebersold, R.: Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes. Nature Protocols 15 (8), pp. 2341 - 2386 (2020)
Journal Article
Karayel, Ö.; Xu, P.; Bludau, I.; Velan Bhoopalan, S.; Yao, Y.; Ana Rita, F.C.; Santos, A.; Schulman, B. A.; Alpi, A. F.; Weiss, M.J. et al.; Mann, M.: Integrative proteomics reveals principles of dynamic phosphosignaling networks in human erythropoiesis. Molecular Systems Biology 16 (12), e9813 (2020)
Journal Article
Meier, F.; Brunner, A.-D.; Frank, M.; Ha, A.; Bludau, I.; Voytik, E.; Kaspar-Schoenefeld, S.; Lubeck, M.; Raether, O.; Bache, N. et al.; Aebersold, R.; Collins, B.C.; Röst, H.L.; Mann, M.: diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition. Nature Methods 17 (12), pp. 1229 - 1236 (2020)

Review Article (1)

Review Article
Bludau, I.: Discovery-Versus Hypothesis-Driven Detection of Protein-Protein Interactions and Complexes. (2021)
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