• A. Marcu, L. Bichmann, L. Kuchenbecker, D. J. Kowalewski, L. K. Freudenmann, L. Backert, L. Mühlenbruch, A. Szolek, M. Lübke, P. Wagner, and others, “HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy,” Journal for immunotherapy of cancer, vol. 9, iss. 4, 2021.
    [Bibtex]
    @article{marcu2021hla,
    title={HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy},
    author={Marcu, Ana and Bichmann, Leon and Kuchenbecker, Leon and Kowalewski, Daniel Johannes and Freudenmann, Lena Katharina and Backert, Linus and M{\"u}hlenbruch, Lena and Szolek, Andr{\'a}s and L{\"u}bke, Maren and Wagner, Philipp and others},
    journal={Journal for immunotherapy of cancer},
    volume={9},
    number={4},
    year={2021},
    publisher={BMJ Publishing Group}
    }
  • C. Dai, A. Füllgrabe, J. Pfeuffer, E. Solovyeva, J. Deng, P. Moreno, S. Kamatchinathan, D. J. Kundu, N. George, S. Fexova, and others, “A proteomics sample metadata representation for multiomics integration, and big data analysis,” bioRxiv, 2021.
    [Bibtex]
    @article{dai2021proteomics,
    title={A proteomics sample metadata representation for multiomics integration, and big data analysis},
    author={Dai, Chengxin and F{\"u}llgrabe, Anja and Pfeuffer, Julianus and Solovyeva, Elizaveta and Deng, Jingwen and Moreno, Pablo and Kamatchinathan, Selvakumar and Kundu, Deepti Jaiswal and George, Nancy and Fexova, Silvie and others},
    journal={bioRxiv},
    year={2021},
    publisher={Cold Spring Harbor Laboratory}
    }
  • 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}
    }
  • J. Pfeuffer, T. Sachsenberg, T. M. Dijkstra, O. Serang, K. Reinert, and O. Kohlbacher, “EPIFANY-A method for efficient high-confidence protein inference,” Journal of proteome research, p. 734327, 2019.
    [Bibtex]
    @article{pfeuffer2019epifany,
    title={EPIFANY-A method for efficient high-confidence protein inference},
    author={Pfeuffer, Julianus and Sachsenberg, Timo and Dijkstra, Tjeerd MH and Serang, Oliver and Reinert, Knut and Kohlbacher, Oliver},
    journal={Journal of proteome research},
    pages={734327},
    year={2019},
    publisher={Cold Spring Harbor Laboratory}
    }
  • N. Hulstaert, J. Shofstahl, T. Sachsenberg, M. Walzer, H. Barsnes, L. Martens, and Y. Perez-Riverol, “ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion,” Journal of proteome research, vol. 19, iss. 1, p. 537–542, 2019.
    [Bibtex]
    @article{hulstaert2019thermorawfileparser,
    title={ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion},
    author={Hulstaert, Niels and Shofstahl, Jim and Sachsenberg, Timo and Walzer, Mathias and Barsnes, Harald and Martens, Lennart and Perez-Riverol, Yasset},
    journal={Journal of proteome research},
    volume={19},
    number={1},
    pages={537--542},
    year={2019},
    publisher={ACS Publications}
    }
  • L. Bichmann, A. Nelde, M. Ghosh, L. Heumos, C. Mohr, A. Peltzer, L. Kuchenbecker, T. Sachsenberg, J. S. Walz, S. Stevanović, and others, “MHCquant: Automated and reproducible data analysis for immunopeptidomics,” Journal of proteome research, vol. 18, iss. 11, p. 3876–3884, 2019.
    [Bibtex]
    @article{bichmann2019mhcquant,
    title={MHCquant: Automated and reproducible data analysis for immunopeptidomics},
    author={Bichmann, Leon and Nelde, Annika and Ghosh, Michael and Heumos, Lukas and Mohr, Christopher and Peltzer, Alexander and Kuchenbecker, Leon and Sachsenberg, Timo and Walz, Juliane S and Stevanović, Stefan and others},
    journal={Journal of proteome research},
    volume={18},
    number={11},
    pages={3876--3884},
    year={2019},
    publisher={ACS Publications}
    }
  • M. W. Löffler, C. Mohr, L. Bichmann, L. K. Freudenmann, M. Walzer, C. M. Schroeder, N. Trautwein, F. J. Hilke, R. S. Zinser, L. Mühlenbruch, and others, “Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma,” Genome medicine, vol. 11, iss. 1, p. 28, 2019.
    [Bibtex]
    @article{loffler2019multi,
    title={Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma},
    author={L{\"o}ffler, Markus W and Mohr, Christopher and Bichmann, Leon and Freudenmann, Lena Katharina and Walzer, Mathias and Schroeder, Christopher M and Trautwein, Nico and Hilke, Franz J and Zinser, Raphael S and M{\"u}hlenbruch, Lena and others},
    journal={Genome medicine},
    volume={11},
    number={1},
    pages={28},
    year={2019},
    publisher={BioMed Central}
    }
  • A. Marcu, L. Bichmann, L. Kuchenbecker, L. Backert, D. J. Kowalewski, L. K. Freudenmann, M. W. Löffler, M. Lübke, J. S. Walz, J. Velz, and others, “The HLA Ligand Atlas. A resource of natural HLA ligands presented on benign tissues,” BioRxiv, p. 778944, 2019.
    [Bibtex]
    @article{marcu2019hla,
    title={The HLA Ligand Atlas. A resource of natural HLA ligands presented on benign tissues},
    author={Marcu, Ana and Bichmann, Leon and Kuchenbecker, Leon and Backert, Linus and Kowalewski, Daniel J and Freudenmann, Lena Katharina and L{\"o}ffler, Markus W and L{\"u}bke, Maren and Walz, Juliane S and Velz, Julia and others},
    journal={BioRxiv},
    pages={778944},
    year={2019},
    publisher={Cold Spring Harbor Laboratory}
    }
  • B. Gruening, O. Sallou, P. Moreno, F. da Veiga Leprevost, H. Ménager, D. S{o}ndergaard, H. Röst, T. Sachsenberg, B. O’Connor, F. Madeira, and others, “Recommendations for the packaging and containerizing of bioinformatics software,” F1000Research, vol. 7, 2018.
    [Bibtex]
    @article{gruening2018recommendations,
    title={Recommendations for the packaging and containerizing of bioinformatics software},
    author={Gruening, Bjorn and Sallou, Olivier and Moreno, Pablo and da Veiga Leprevost, Felipe and M{\'e}nager, Herv{\'e} and S{\o}ndergaard, Dan and R{\"o}st, Hannes and Sachsenberg, Timo and O'Connor, Brian and Madeira, F{\'a}bio and others},
    journal={F1000Research},
    volume={7},
    year={2018}
    }
  • A. Kahles, K. Lehmann, N. C. Toussaint, M. Hüser, S. G. Stark, T. Sachsenberg, O. Stegle, O. Kohlbacher, C. Sander, S. J. Caesar-Johnson, and others, “Comprehensive analysis of alternative splicing across tumors from 8,705 patients,” Cancer cell, vol. 34, iss. 2, p. 211–224, 2018.
    [Bibtex]
    @article{kahles2018comprehensive,
    title={Comprehensive analysis of alternative splicing across tumors from 8,705 patients},
    author={Kahles, Andr{\'e} and Lehmann, Kjong-Van and Toussaint, Nora C and H{\"u}ser, Matthias and Stark, Stefan G and Sachsenberg, Timo and Stegle, Oliver and Kohlbacher, Oliver and Sander, Chris and Caesar-Johnson, Samantha J and others},
    journal={Cancer cell},
    volume={34},
    number={2},
    pages={211--224},
    year={2018},
    publisher={Elsevier}
    }
  • J. A. Vizcaíno, G. Mayer, S. R. Perkins, H. Barsnes, M. Vaudel, Y. Perez-Riverol, T. Ternent, J. Uszkoreit, M. Eisenacher, L. Fischer, and others, “The mzIdentML data standard version 1.2, supporting advances in proteome informatics,” Molecular & Cellular Proteomics, p. mcp–M117, 2017.
    [Bibtex]
    @article{vizcaino2017mzidentml,
    title={The mzIdentML data standard version 1.2, supporting advances in proteome informatics},
    author={Vizca{\'i}no, Juan Antonio and Mayer, Gerhard and Perkins, Simon R and Barsnes, Harald and Vaudel, Marc and Perez-Riverol, Yasset and Ternent, Tobias and Uszkoreit, Julian and Eisenacher, Martin and Fischer, Lutz and others},
    journal={Molecular \& Cellular Proteomics},
    pages={mcp--M117},
    year={2017},
    publisher={ASBMB}
    }
  • E. Audain, J. Uszkoreit, T. Sachsenberg, J. Pfeuffer, X. Liang, H. Hermjakob, A. Sanchez, M. Eisenacher, K. Reinert, D. L. Tabb, and others, “In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics,” Journal of proteomics, vol. 150, p. 170–182, 2017.
    [Bibtex]
    @article{audain2017depth,
    title={In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics},
    author={Audain, Enrique and Uszkoreit, Julian and Sachsenberg, Timo and Pfeuffer, Julianus and Liang, Xiao and Hermjakob, Henning and Sanchez, Aniel and Eisenacher, Martin and Reinert, Knut and Tabb, David L and others},
    journal={Journal of proteomics},
    volume={150},
    pages={170--182},
    year={2017},
    publisher={Elsevier}
    }
  • H. L. Röst, R. Aebersold, and O. T. Schubert, “Automated SWATH data analysis using targeted extraction of ion chromatograms,” Proteomics: Methods and Protocols, p. 289–307, 2017.
    [Bibtex]
    @article{rost2017automated,
    title={Automated SWATH data analysis using targeted extraction of ion chromatograms},
    author={R{\"o}st, Hannes L and Aebersold, Ruedi and Schubert, Olga T},
    journal={Proteomics: Methods and Protocols},
    pages={289--307},
    year={2017},
    publisher={Springer New York}
    }
  • F. da Veiga Leprevost, B. A. Grüning, S. Alves Aflitos, H. L. Röst, J. Uszkoreit, H. Barsnes, M. Vaudel, P. Moreno, L. Gatto, J. Weber, and others, “BioContainers: an open-source and community-driven framework for software standardization,” Bioinformatics, p. btx192, 2017.
    [Bibtex]
    @article{da2017biocontainers,
    title={BioContainers: an open-source and community-driven framework for software standardization},
    author={da Veiga Leprevost, Felipe and Gr{\"u}ning, Bj{\"o}rn A and Alves Aflitos, Saulo and R{\"o}st, Hannes L and Uszkoreit, Julian and Barsnes, Harald and Vaudel, Marc and Moreno, Pablo and Gatto, Laurent and Weber, Jonas and others},
    journal={Bioinformatics},
    pages={btx192},
    year={2017},
    publisher={Oxford University Press}
    }
  • [DOI] H. Weisser and J. S. Choudhary, “Targeted feature detection for data-dependent shotgun proteomics,” Journal of Proteome Research, 2017.
    [Bibtex]
    @article{weisser2017targeted,
    title={Targeted feature detection for data-dependent shotgun proteomics},
    author={Weisser, Hendrik and Choudhary, Jyoti S},
    journal={Journal of Proteome Research},
    year={2017},
    publisher={ACS Publications},
    doi={10.1021/acs.jproteome.7b00248}
    }
  • [DOI] J. Pfeuffer, T. Sachsenberg, O. Alka, M. Walzer, A. Fillbrunn, L. Nilse, O. Schilling, K. Reinert, and O. Kohlbacher, “OpenMS – A platform for reproducible analysis of mass spectrometry data,” Journal of Biotechnology, 2017.
    [Bibtex]
    @article{pfeuffer2017denbi,
    title = "OpenMS – A platform for reproducible analysis of mass spectrometry data",
    journal = "Journal of Biotechnology",
    volume = "",
    number = "",
    pages = "",
    year = "2017",
    note = "",
    issn = "0168-1656",
    doi = "10.1016/j.jbiotec.2017.05.016",
    url = "http://www.sciencedirect.com/science/article/pii/S0168165617302511",
    author = "Julianus Pfeuffer and Timo Sachsenberg and Oliver Alka and Mathias Walzer and Alexander Fillbrunn and Lars Nilse and Oliver Schilling and Knut Reinert and Oliver Kohlbacher"
    }
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