Publications of T Sachsenberg

Chandel, S.; Bhattacharya, A.; Gautam, A.; Zeng, W.; Alka, O.; Sachsenberg, T.; Gupta, G.; Narang, R.; Ravichandiran, V.; Singh, R.: Investigation of the anti-cancer potential of epoxyazadiradione in neuroblastoma: experimental assays and molecular analysis. Journal of Biomolecular Structure and Dynamics 42 (21), pp. 11377 - 11395 (2024)

Kleiner, M.; Kouris, A.; Violette, M.; D’Angelo, G.; Liu, Y.; Korenek, A.; Tolić, N.; Sachsenberg, T.; McCalder, J.; Lipton, M. et al.; Strous, M.: Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes. Microbiome 11 (1), 24 (2023)

Netz, E.; Dijkstra, T.; Sachsenberg, T.; Zimmermann, L.; Walzer, M.; Monecke, T.; Ficner, R.; Dybkiv, O.; Urlaub, H.; Kohlbacher, O.: OpenPepXL: An open-source tool for sensitive identification of cross-linked peptides in XL-MS. Molecular and Cellular Proteomics 19 (12), pp. 2157 - 2168 (2020)

Stützer, A.; Welp, L.; Raabe, M.; Sachsenberg, T.; Kappert, C.; Wulf, A.; Lau, A.; David, S.-S.; Chernev, A.; Kramer, K. et al.; Politis, A.; Kohlbacher, O.; Fischle, W.; Urlaub, H.: Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry. Nature Communications 11, 5250, p. 1 (2020)

Starke, R.; Oliphant, K.; Jehmlich, N.; Schäpe, S.; Sachsenberg, T.; Kohlbacher, O.; Allen-Vercoe, E.; von Bergen, M.: Corrigendum to Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities. Journal of Proteomics 224, 103829 (2020)

Starke, R.; Oliphant, K.; Jehmlich, N.; Schäpe, S.; Sachsenberg, T.; Kohlbacher, O.; Allen-Vercoe, E.; von Bergen, M.: Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities. Journal of Proteomics 222, 103791 (2020)

Pfeuffer, J.; Sachsenberg, T.; Dijkstra, T.; Serang, O.; Reinert, K.; Kohlbacher, O.: EPIFANY: A Method for Efficient High-Confidence Protein Inference. Journal of Proteome Research 19 (3), pp. 1060 - 1072 (2020)

Wein, S.; Andrews, B.; Sachsenberg, T.; Santos-Rosa, H.; Kohlbacher, O.; Kouzarides, T.; Garcia, B.; Weisser, H.: A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry. Nature Communications 11, 926 (2020)

Bichmann, L.; Nelde, A.; Ghosh, M.; Heumos, L.; Mohr, C.; Peltzer, A.; Kuchenbecker, L.; Sachsenberg, T.; Walz, J.; Stevanović, S. et al.; Rammensee, H.-G.; Kohlbacher, O.: MHCquant: Automated and Reproducible Data Analysis for Immunopeptidomics. Journal of Proteome Research 18 (11), pp. 3876 - 3884 (2019)

Kahles, A.; Lehmann, K.-V.; Toussaint, N.; Hüser, M.; Sachsenberg, T.; Stegle, O.; Kohlbacher, O.; Sander, C.; Cancer Genome Atlas Research Network; Rätsch, G.: Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients. Cancer Cell 34 (2), pp. 211 - 224 (2018)

Flett, F.; Sachsenberg, T.; Kohlbacher, O.; Mackay, C.; Interthal, H.: Differential Enzymatic O-16/O-18 Labeling for the Detection of Cross-Linked Nucleic Acid-Protein Heteroconjugates. Analytical Chemistry 89 (21), pp. 11208 - 11213 (2017)

Pfeuffer, J.; Sachsenberg, T.; Alka, O.; Walzer, M.; Fillbrunn, A.; Nilse, L.; Schilling, O.; Reinert, K.; Kohlbacher, O.: OpenMS: A platform for reproducible analysis of mass spectrometry data. Journal of Biotechnology 261, pp. 142 - 148 (2017)

Audain, E.; Uszkoreit, J.; Sachsenberg, T.; Pfeuffer, J.; Liang, X.; Hermjakob, H.; Sanchez, A.; Eisenacher, M.; Reinert, K.; Tabb, D. et al.; Kohlbacher, O.; Perez-Riverol, Y.: In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics. Journal of Proteomics 150, pp. 170 - 182 (2017)

Veit, J.; Sachsenberg, T.; Chernev, A.; Aicheler, F.; Urlaub, H.; Kohlbacher, O.: LFQProfiler and RNP(xl): Open-Source Tools for Label-Free Quantification and Protein-RNA Cross-Linking Integrated into Proteome Discoverer. Journal of Proteome Research 15 (9), pp. 3441 - 3448 (2016)

Röst, H.; Sachsenberg, T.; Aiche, S.; Bielow, C.; Weisser, H.; Aicheler, F.; Andreotti, S.; Ehrlich, H.-C.; Gutenbrunner, P.; Kenar, E. et al.; Liang, X.; Nahnsen, S.; Nilse, L.; Pfeuffer, J.; Rosenberger, G.; Rurik, M.; Schmitt, U.; Veit, J.; Walzer, M.; Woijnar, D.; Wolski, W.; Schilling, O.; Choudhary, J.; Malmström, L.; Aebersold, R.; Reinert, K.; Kohlbacher, O.: OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nature Methods 13 (9), pp. 741 - 748 (2016)

Zaman, U.; Richter, F.; Hofele, R.; Kramer, K.; Sachsenberg, T.; Kohlbacher, O.; Lenz, C.; Urlaub, H.: Dithiothreitol (DTT) acts as a specific, UV-inducible cross-linker in elucidation of protein-RNA interactions. Molecular and Cellular Proteomics 14 (12), pp. 3196 - 3210 (2015)

Sharma, K.; Hrle, A.; Kramer, K.; Sachsenberg, T.; Staals, R.; Randau, L.; Marchfelder, A.; van der Oost, J.; Kohlbacher, O.; Conti, E. et al.; Urlaub, H.: Analysis of protein–RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry. Methods 89, pp. 138 - 148 (2015)

Kramer, K.; Sachsenberg, T.; Beckmann, B.; Qamar, S.; Boon, K.; Hentze, M.; Kohlbacher, O.; Urlaub, H.: Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins. Nature Methods 11 (10), pp. 1064 - 1070 (2014)

Laubinger, S.; Zeller, G.; Henz, S.; Buechel, S.; Sachsenberg, T.; Wang, J.-W.; Rätsch, G.; Weigel, D.: Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome. Proceedings of the National Academy of Sciences of the United States of America 107 (41), pp. 17466 - 17573 (2010)

Zeller, G.; Henz, S.; Widmer, C.; Sachsenberg, T.; Rätsch, G.; Weigel, D.; Laubinger, S.: Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays. The Plant Journal 58 (6), pp. 1068 - 1082 (2009)