Publications of Isabell Bludau

Strauss, M. T.; Bludau, I.; Zeng, W.-F.; Voytik, E.; Ammar, C.; Schessner, J. P.; Ilango, R.; Gill, M.; Meier, F.; Willems, S. et al.; Mann, M.: AlphaPept: A modern and open framework for MS-based proteomics. Nature Communications 15 (1), 2168 (2024)

Hansen, F. M.; Kremer, L. S.; Karayel, O.; Bludau, I.; Larsson, N.-G.; Kühl, I.; Mann, M.: Mitochondrial phosphoproteomes are functionally specialized across tissues. Life Science Alliance 7, e202302147 (2024)

Michaelis, A. C.; Brunner, A.-D.; Zwiebel, M.; Meier, F.; Strauss, M. T.; Bludau, I.; Mann, M.: The social and structural architecture of the yeast protein interactome. Nature 624 (7990), pp. 192 - 200 (2023)

Thielert, M.; Itang, E. C. M.; Ammar, C.; Rosenberger, F. A.; Bludau, I.; Schweizer, L.; Nordmann, T. M.; Skowronek, P.; Wahle, M.; Zeng, W.-F. et al.; Zhou, X.-X.; Brunner, A.-D.; Richter, S.; Levesque, M. P.; Theis, F. J.; Steger, M.; Mann, M.: Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel. Molecular Systems Biology 19 (9), e1150 (2023)

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)

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 (5), pp. 1520 - 1536 (2023)

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 (3), pp. 681 - 696 (2023)

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 & Cellular Proteomics 22 (2), 100485 (2023)

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)

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)

Schessner, J. P.; Voytik, E.; Bludau, I.: A practical guide to interpreting and generating bottom-up proteomics data visualizations. Proteomics 22 (8), e2100103 (2022)

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)

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)

Bludau, I.: Discovery-versus hypothesis-driven detection of protein-protein interactions and complexes. International Journal of Molecular Sciences 22 (9), 4450 (2021)

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)

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)

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)

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)

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)

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)