• R. Starke, K. Oliphant, N. Jehmlich, S. S. Schäpe, T. Sachsenberg, O. Kohlbacher, E. Allen-Vercoe, and M. von Bergen, “Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities,” Journal of Proteomics, p. 103791, 2020.
    [Bibtex] 
    @article{starke2020tracing,
title={Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities},
author={Starke, Robert and Oliphant, Kaitlyn and Jehmlich, Nico and Sch{\"a}pe, Stephanie Serena and Sachsenberg, Timo and Kohlbacher, Oliver and Allen-Vercoe, Emma and von Bergen, Martin},
journal={Journal of Proteomics},
pages={103791},
year={2020},
publisher={Elsevier}
}
  • O. Alka, T. Sachsenberg, L. Bichmann, J. Pfeuffer, H. Weisser, S. Wein, E. Netz, M. Rurik, O. Kohlbacher, and H. Röst, “OpenMS and KNIME for Mass Spectrometry Data Processing,” in Processing Metabolomics and Proteomics Data with Open Software, , 2020, p. 201–231.
    [Bibtex] 
    @incollection{alka2020openms,
title={OpenMS and KNIME for Mass Spectrometry Data Processing},
author={Alka, Oliver and Sachsenberg, Timo and Bichmann, Leon and Pfeuffer, Julianus and Weisser, Hendrik and Wein, Samuel and Netz, Eugen and Rurik, Marc and Kohlbacher, Oliver and R{\"o}st, Hannes},
booktitle={Processing Metabolomics and Proteomics Data with Open Software},
pages={201--231},
year={2020}
}
  • S. Wein, B. Andrews, T. Sachsenberg, H. Santos-Rosa, O. Kohlbacher, T. Kouzarides, B. A. Garcia, and H. Weisser, “A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry,” Nature communications, vol. 11, iss. 1, p. 1–12, 2020.
    [Bibtex] 
    @article{wein2020computational,
title={A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry},
author={Wein, Samuel and Andrews, Byron and Sachsenberg, Timo and Santos-Rosa, Helena and Kohlbacher, Oliver and Kouzarides, Tony and Garcia, Benjamin A and Weisser, Hendrik},
journal={Nature communications},
volume={11},
number={1},
pages={1--12},
year={2020},
publisher={Nature Publishing Group}
}
  • M. Rurik, O. Alka, F. Aicheler, and O. Kohlbacher, “Metabolomics Data Processing Using OpenMS,” in Computational Methods and Data Analysis for Metabolomics, Springer, 2020, p. 49–60.
    [Bibtex] 
    @incollection{rurik2020metabolomics,
title={Metabolomics Data Processing Using OpenMS},
author={Rurik, Marc and Alka, Oliver and Aicheler, Fabian and Kohlbacher, Oliver},
booktitle={Computational Methods and Data Analysis for Metabolomics},
pages={49--60},
year={2020},
publisher={Springer}
}
  • K. Jeong, J. Kim, M. Gaikwad, S. N. Hidayah, L. Heikaus, H. Schlüter, and O. Kohlbacher, “FLASHDeconv: Ultrafast, high-quality feature deconvolution for top-down proteomics,” Cell Systems, vol. 10, iss. 2, p. 213–218, 2020.
    [Bibtex] 
    @article{jeong2020flashdeconv,
title={FLASHDeconv: Ultrafast, high-quality feature deconvolution for top-down proteomics},
author={Jeong, Kyowon and Kim, Jihyung and Gaikwad, Manasi and Hidayah, Siti Nurul and Heikaus, Laura and Schl{\"u}ter, Hartmut and Kohlbacher, Oliver},
journal={Cell Systems},
volume={10},
number={2},
pages={213--218},
year={2020},
publisher={Elsevier}
}
  • L. Bichmann, S. Gupta, G. Rosenberger, L. Kuchenbecker, T. Sachsenberg, P. Ewels, O. Alka, J. Pfeuffer, O. Kohlbacher, and H. Röst, “DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics,” Journal of Proteome Research, 2020.
    [Bibtex] 
    @article{bichmann2020diaproteomics,
title={DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics},
author={Bichmann, Leon and Gupta, Shubham and Rosenberger, George and Kuchenbecker, Leon and Sachsenberg, Timo and Ewels, Phil and Alka, Oliver and Pfeuffer, Julianus and Kohlbacher, Oliver and Röst, Hannes},
journal={Journal of Proteome Research},
year={2020},
publisher={ACS Publications}
}
  • S. Kutuzova, P. Colaianni, H. Rost, T. Sachsenberg, O. Alka, O. Kohlbacher, B. Burla, F. Torta, L. Schrubbers, M. Kristensen, and others, “SmartPeak automates targeted and quantitative metabolomics data processing,” Analytical chemistry, vol. 92, iss. 24, p. 15968–15974, 2020.
    [Bibtex] 
    @article{kutuzova2020smartpeak,
title={SmartPeak automates targeted and quantitative metabolomics data processing},
author={Kutuzova, Svetlana and Colaianni, Pasquale and Rost, Hannes and Sachsenberg, Timo and Alka, Oliver and Kohlbacher, Oliver and Burla, Bo and Torta, Federico and Schrubbers, Lars and Kristensen, Mette and others},
journal={Analytical chemistry},
volume={92},
number={24},
pages={15968--15974},
year={2020},
publisher={ACS Publications}
}
  • A. Stützer, L. M. Welp, M. Raabe, T. Sachsenberg, C. Kappert, A. Wulf, A. M. Lau, S. David, A. Chernev, K. Kramer, and others, “Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry,” Nature communications, vol. 11, iss. 1, p. 1–12, 2020.
    [Bibtex] 
    @article{stutzer2020analysis,
title={Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry},
author={St{\"u}tzer, Alexandra and Welp, Luisa M and Raabe, Monika and Sachsenberg, Timo and Kappert, Christin and Wulf, Alexander and Lau, Andy M and David, Stefan-Sebastian and Chernev, Aleksandar and Kramer, Katharina and others},
journal={Nature communications},
volume={11},
number={1},
pages={1--12},
year={2020},
publisher={Nature Publishing Group}
}
  • E. Netz, T. M. Dijkstra, T. Sachsenberg, L. Zimmermann, M. Walzer, T. Monecke, R. Ficner, O. Dybkov, H. Urlaub, and O. Kohlbacher, “OpenPepXL: An open-source tool for sensitive identification of cross-linked peptides in XL-MS,” Molecular & Cellular Proteomics, vol. 19, iss. 12, p. 2157–2168, 2020.
    [Bibtex] 
    @article{netz2020openpepxl,
title={OpenPepXL: An open-source tool for sensitive identification of cross-linked peptides in XL-MS},
author={Netz, Eugen and Dijkstra, Tjeerd MH and Sachsenberg, Timo and Zimmermann, Lukas and Walzer, Mathias and Monecke, Thomas and Ficner, Ralf and Dybkov, Olexandr and Urlaub, Henning and Kohlbacher, Oliver},
journal={Molecular \& Cellular Proteomics},
volume={19},
number={12},
pages={2157--2168},
year={2020},
publisher={ASBMB}
}
  • L. Nothias, D. Petras, R. Schmid, K. Dührkop, J. Rainer, A. Sarvepalli, I. Protsyuk, M. Ernst, H. Tsugawa, M. Fleischauer, and others, “Feature-based molecular networking in the GNPS analysis environment,” Nature methods, vol. 17, iss. 9, p. 905–908, 2020.
    [Bibtex] 
    @article{nothias2020feature,
title={Feature-based molecular networking in the GNPS analysis environment},
author={Nothias, Louis-F{\'e}lix and Petras, Daniel and Schmid, Robin and D{\"u}hrkop, Kai and Rainer, Johannes and Sarvepalli, Abinesh and Protsyuk, Ivan and Ernst, Madeleine and Tsugawa, Hiroshi and Fleischauer, Markus and others},
journal={Nature methods},
volume={17},
number={9},
pages={905--908},
year={2020},
publisher={Nature Publishing Group}
}
  • T. Scheidt, O. Alka, H. Gonczarowska-Jorge, W. Gruber, F. Rathje, M. Dell’Aica, M. Rurik, O. Kohlbacher, R. P. Zahedi, F. Aberger, and others, “Phosphoproteomics of short-term hedgehog signaling in human medulloblastoma cells,” Cell Communication and Signaling, vol. 18, iss. 1, p. 1–18, 2020.
    [Bibtex] 
    @article{scheidt2020phosphoproteomics,
title={Phosphoproteomics of short-term hedgehog signaling in human medulloblastoma cells},
author={Scheidt, Tamara and Alka, Oliver and Gonczarowska-Jorge, Humberto and Gruber, Wolfgang and Rathje, Florian and Dell’Aica, Margherita and Rurik, Marc and Kohlbacher, Oliver and Zahedi, Ren{\'e} P and Aberger, Fritz and others},
journal={Cell Communication and Signaling},
volume={18},
number={1},
pages={1--18},
year={2020},
publisher={BioMed Central}
}