Max Planck Institute for Multidisciplinary Sciences

Publications

Journal Article (50)

1.

Journal Article

Cormican, J. A.; Medfai, L.; Wawrzyniuk, M.; Pašen, M.; Afrache, H.; Fourny, C.; Khan, S.; Gneiße, P.; Soh, W. T.; Timelli, A. et al.; Nolfi, E.; Pannekoek, Y.; Cope, A.; Urlaub, H.; Sijts, A. J.A. M.; Mishto, M.; Liepe, J.: PEPSeek-mediated identification of novel epitopes from viral and bacterial pathogens and the impact on host cell immunopeptidomes. Molecular & Cellular Proteomics 24 (4), 100937 (2025)

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Lavdovskaia, E.; Hanitsch, E.; Linden, A.; Pašen, M.; Challa, V.; Horokhovskyi, Y.; Roetschke, H. P.; Nadler, F.; Welp, L.; Steube, E. et al.; Heinrichs, M.; Mai, M. M.-Q.; Urlaub, H.; Liepe, J.; Richter-Dennerlein, R.: A roadmap for ribosome assembly in human mitochondria. Nature Structural & Molecular Biology 31, pp. 1898 - 1908 (2024)

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3.

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Mishto, M.; Takala, I.; Bonfanti, P.; Liepe, J.: Proteasome isoforms in human thymi and mouse models. Immunology Letters 269, 106899 (2024)

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4.

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Jacquet, A.; Soh, W. T.: Spatiotemporal proteolytic susceptibility of allergens: positive or negative effects on the allergic sensitization? Frontiers in Allergy 5, 1426816 (2024)

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5.

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Harasimov, K.; Gorry, R. L.; Welp, L. M.; Penir, S. M.; Horokhovskyi, Y.; Cheng, S.; Takaoka, K.; Stützer, A.; Frombach, A.-S.; Taylor Tavares, A. L. et al.; Raabe, M.; Haag, S.; Saha, D.; Grewe, K.; Schipper, V.; Rizzoli, S. O.; Urlaub, H.; Liepe, J.; Schuh, M.: The maintenance of oocytes in the mammalian ovary involves extreme protein longevity. Nature Cell Biology 26, pp. 1124 - 1138 (2024)

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6.

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Soh, W. T.; Roetschke, H. P.; Cormican, J. A.; Teo, B.F.; Chiam, N. C.; Raabe, M.; Pflanz, R.; Henneberg, F.; Becker, S.; Chari, A. et al.; Liu, H.; Urlaub, H.; Liepe, J.; Mishto, M.: Protein degradation by human 20S proteasomes elucidates the interplay between peptide hydrolysis and splicing. Nature Communications 15 (1), 1147 (2024)

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7.

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Pašen, M.; Boža, V.: Merging of Neural Networks. Neural Processing Letters 56, 8 (2024)

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8.

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Jentoft, I. M. A.; Bäuerlein, F. J.B.; Welp, L. M.; Cooper, B. H.; Petrovic, A.; So, C.; Penir, S. M.; Politi, A. Z.; Horokhovskyi, Y.; Takala, I. et al.; Eckel, H.; Moltrecht, R.; Lenart, P.; Cavazza, T.; Liepe, J.; Brose, N.; Urlaub, H.; Fernández-Busnadiego, R.; Schuh, M.: Mammalian oocytes store proteins for the early embryo on cytoplasmic lattices. Cell 186 (24), pp. 5308 - 5327.e25 (2023)

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9.

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Roetschke, H. P.; Rodriguez-Hernandez, G.; Cormican, J. A.; Yang, X.; Lynham, S.; Mishto, M.; Liepe, J.: InvitroSPI and a large database of proteasome-generated spliced and non-spliced peptides. Scientific Data 10, 18 (2023)

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10.

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Cormican, J. A.; Soh, W. T.; Mishto, M.; Liepe, J.: iBench: A ground truth approach for advanced validation of mass spectrometry identification method. Proteomics 23 (2), 2200271 (2023)

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11.

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Cormican, J. A.; Horokhovskyi, Y.; Soh, W. T.; Mishto, M.; Liepe, J.: inSPIRE: An open-source tool for increased mass spectrometry identification rates using Prosit spectral prediction. Molecular and Cellular Proteomics 21 (12), 100432 (2022)

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12.

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Gutman, I.; Gutman, R.; Sidney, J.; Chihab, L.; Mishto, M.; Liepe, J.; Chiem, A.; Greenbaum, J.; Yan, Z.; Sette, A. et al.; Koşaloğlu-Yalçın, Z.; Peters, B.: Predicting the Success of Fmoc-Based Peptide Synthesis. ACS Omega 7, pp. 23771 - 23781 (2022)

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13.

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Mishto, M.; Horokhovskyi, Y.; Cormican, J. A.; Yang, X.; Lynham, S.; Urlaub, H.; Liepe, J.: Database search engines and target database features impinge upon the identification of post‐translationally cis‐spliced peptides in HLA class I immunopeptidomes. Proteomics 22 (10), e2100226 (2022)

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14.

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Collin, C. B.; Gebhardt, T.; Golebiewski, M.; Karaderi, T.; Hillemanns, M.; Khan, F. M.; Salehzadeh-Yazdi, A.; Kirschner, M.; Krobitsch, S.; Kuepfer, L.: Computational Models for Clinical Applications in Personalized Medicine—Guidelines and Recommendations for Data Integration and Model Validation. Journal of Personalized Medicine 12 (2), 166 (2022)

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15.

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Mishto, M.; Rodriguez-Hernandez, G.; Neefjes, J.; Urlaub, H.; Liepe, J.: Response: Commentary: An In Silico–In Vitro Pipeline Identifying an HLA-A*02:01+ KRAS G12V+ Spliced Epitope Candidate for a Broad Tumor-Immune Response in Cancer Patients. Frontiers in immunology 12, 679836 (2021)

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16.

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Melacarne, A.; Ferrari, V.; Tiraboschi, L.; Mishto, M.; Liepe, J.; Aralla, M.; Marconato, M.; Lizier, M.; Pozzi, C.; Zeira, O. et al.; Penna, G.; Resigno, M.: Identification of a class of non-conventional ER-stress-response-derived immunogenic peptides. Cell Reports 36 (1), 109312 (2021)

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17.

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Mishto, M.; Mansurkhodzhaev, A.; Rodriguez-Calvo, T.; Liepe, J.: Potential mimicry of viral and pancreatic β cell antigens through non-spliced and cis-spliced zwitter epitope candidates in Type 1 Diabetes. Frontiers in Immunology 12, 656451 (2021)

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18.

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Mansurkhodzhaev, A.; Barbosa, C. R. R.; Mishto, M.; Liepe, J.: Proteasome-generated cis-spliced peptides and their potential role in CD8+ T cell tolerance. Frontiers in Immunology 12, 614276 (2021)

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19.

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Specht, G.; Roetschke, H. P.; Mansurkhodzhaev, A.; Henklein, P.; Textoris-Taube, K.; Urlaub, H.; Mishto, M.; Liepe, J.: Large database for the analysis and prediction of spliced and non-spliced peptide generation by proteasomes. Scientific Data 7, 146 (2020)

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20.

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Textoris‐Taube, K.; Cammann, C.; Henklein, P.; Topfstedt, E.; Ebstein, F.; Henze, S.; Liepe, J.; Zhao, F.; Schadendorf, D.; Dahlmann, B. et al.; Uckert, W.; Paschen, A.; Mishto, M.; Seifert, U.: ER-aminopeptidase 1 determines the processing and presentation of an immunotherapy-relevant melanoma epitope. European Journal of Immunology 50 (2), pp. 270 - 283 (2020)

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21.

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Paul, D.; Stevanovic, D.: Eigenvector-based identification of bipartite subgraphs. Discrete Applied Mathematics 269, pp. 146 - 158 (2019)

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22.

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Kuckelkorn, U.; Stübler, S.; Textoris-Taube, K.; Killian, C.; Niewienda, A.; Henklein, P.; Janek, K.; Stumpf, M. P.; Mishto, M.; Liepe, J.: Proteolytic dynamics of human 20S thymoproteasome. Journal of Biological Chemistry 294, pp. 7740 - 7754 (2019)

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23.

Journal Article

Dianzani, C.; Vecchio, D.; Clemente, N.; Chiocchetti, A.; Boneschi, F. M.; Galimberti, D.; Dianzani, U.; Comi, C.; Mishto, M.; Liepe, J.: Untangling extracellular proteasome-osteopontin circuit dynamics in multiple sclerosis. Cells 8 (3), 262 (2019)

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24.

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Liepe, J.; Sidney, J.; Lorenz, F. K. M.; Sette, A.; Mishto, M.: Mapping the MHC class I spliced immunopeptidome of cancer cells. Cancer Immunology Research 7 (1), pp. 62 - 76 (2019)

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25.

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Mishto, M.; Mansurkhodzhaev, A.; Ying, G.; Bitra, A.; Cordfunke, R. A.; Henze, S.; Paul, D.; Sidney, J.; Urlaub, H.; Neefjes, J. et al.; Sette, A.; Zajonc, D. M.; Liepe, J.: An in silico-in vitro pipeline identifying an HLA-A^*02:01⁺ KRAS G12V⁺ spliced epitope candidate for a broad tumor-immune response in cancer patients. Frontiers in Immunology 10, 2572 (2019)

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26.

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Liepe, J.; Ovaa, H.; Mishto, M.: Why do proteases mess up with antigen presentation by re-shuffling antigen sequences? Current Opinion in Immunology 52, pp. 81 - 86 (2018)

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27.

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Dony, L.; Mackerodt, J.; Ward, S.; Filippi, S.; Stumpf, M. P. H.; Liepe, J.: PEITH(Θ) - perfecting experiments with information theory in python with GPU support. Bioinformatics 34 (7), pp. 1249 - 1250 (2018)

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28.

Journal Article

Mishto, M.; Liepe, J.: Post-translational peptide splicing and T cell responses. Trends in Immunology 38 (12), pp. 904 - 915 (2017)

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29.

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Platteel, A. C. M.; Liepe, J.; van Eden, W.; Mishto, M.; Sijts, A. J. A. M.: An unexpected major role for proteasome-catalyzed peptide splicing in generation of T cell epitopes: Is there relevance for vaccine development? Frontiers in Immunology 8, 1441 (2017)

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30.

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MacLean, A. L.; Smith, M. A.; Liepe, J.; Sim, A.; Khorshed, R.; Rashidi, N. M.; Scherf, N.; Kinner, A.; Roeder, I.; Lo Celso, C. et al.; Stumpf, M. P. H.: Single cell phenotyping reveals heterogeneity among haematopoietic stem cells following infection. Stem Cells 35 (11), pp. 2292 - 2304 (2017)

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31.

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Platteel, A. C. M.; Liepe, J.; Textoris-Taube, K.; Keller, C.; Henklein, P.; Schalkwijk, H. H.; Cardoso, R.; Kloetzel, P. M.; Mishto, M.; Sijts, A. J. A. M.: Multi-level strategy for identifying proteasome-catalyzed spliced epitopes targeted by CD8⁺ T cells during bacterial infection. Cell Reports 20 (5), pp. 1242 - 1253 (2017)

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32.

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Dianzani, C.; Bellavista, E.; Liepe, J.; Verderio, C.; Martucci, M.; Santoro, A.; Chiocchetti, A.; Gigliotti, C. L.; Boggio, E.; Ferrara, B. et al.; Riganti, L.; Keller, C.; Janek, K.; Niewienda, A.; Fenoglio, C.; Sorosina, M.; Cantello, R.; Kloetzel, P. M.; Stumpf, M. P. H.; Paul, F.; Ruprecht, K.; Galimberti, D.; Boneschi, F. M.; Comi, C.; Dianzani, U.; Mishto, M.: Extracellular proteasome-osteopontin circuit regulates cell migration with implications in multiple sclerosis. Scientific Reports 7, 43718 (2017)

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33.

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Liepe, J.; Marino, F.; Sidney, J.; Jeko, A.; Bunting, D. E.; Sette, A.; Kloetzel, P. M.; Stumpf, M.l. P. H.; Heck, A. J. R.; Mishto, M.: A large fraction of HLA class I ligands are proteasome-generated spliced peptides. Science 354 (6310), pp. 354 - 358 (2016)

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34.

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Weavers, H.; Liepe, J.; Sim, A.; Wood, W.; Martin, P.-; Stumpf, M. P. H.: Systems analysis of the dynamic inflammatory response to tissue damage reveals spatiotemporal properties of the wound attractant gradient. Current Biology 26 (15), pp. 1975 - 1989 (2016)

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35.

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Liepe, J.; Sim, A.; Weavers, H.; Ward, L.; Martin, P.; Stump, M. P. H.: Accurate reconstruction of cell and particle tracks from 3D live imaging data. Cell Systems 3 (1), pp. 102 - 107 (2016)

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36.

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Platteel, A. C. M.; Mishto, M.; Textoris-Taube, K.; Keller, C.; Liepe, J.; Busch, D. H.; Kloetzel, P. M.; Sijts, A. J. A. M.: CD8(⁺) T cells of Listeria monocytogenes-infected mice recognize both linear and spliced proteasome products. European Journal of Immunology 46 (5), pp. 1109 - 1118 (2016)

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37.

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Textoris-Taube, K.; Keller, C.; Liepe, J.; Henklein, P.; Sidney, J.; Sette, A.; Kloetzel, P. M.; Mishto, M.: The T210M substitution in the HLA-a*02:01 gp100 epitope strongly affects overall proteasomal cleavage site usage and antigen processing. Journal of Biological Chemistry 290 (51), pp. 30417 - 30428 (2015)

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38.

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Jones, P. J. M.; Sim, A.; Taylor, H. B.; Bugeon, L.; Dallman, M. J.; Pereira, B.; Stumpf, M. P. H.; Liepe, J.: Inference of random walk models to describe leukocyte migration. Physical Biology 12 (6), 066001 (2015)

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39.

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Liepe, J.; Holzhütter, H. G.; Bellavista, E.; Kloetzel, P. M.; Stumpf, M. P. H.; Mishto, M.: Quantitative time-resolved analysis reveals intricate, differential regulation of standard- and immuno-proteasomes. eLife 4, e07545 (2015)

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40.

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Sim, A.; Liepe, J.; Stumpf, M. P.: Goldstein-Kac telegraph processes with random speeds: Path probabilities, likelihoods, and reported Lévy flights. Physical Review E 91 (4), 042115 (2015)

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41.

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Mishto, M.; Liepe, J.; Textoris-Taube, K.; Keller, C.; Henklein, P.; Weberruss, M.; Dahlmann, B.; Enenkel, C.; Voigt, A.; Kuckelkorn, U. et al.; Stumpf, M. P. H.; Kloetzel, P. M.: Proteasome isoforms exhibit only quantitative differences in cleavage and epitope generation. European Journal of Immunology 44 (12), pp. 3508 - 3521 (2014)

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42.

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McMahon, S. S.; Sim, A.; Filippi, S.; Johnson, R.; Liepe, J.; Smith, D.; Stumpf, M. P. H.: Information theory and signal transduction systems: From molecular information processing to network inference. Seminars in Cell and Developmental Biology 35, pp. 98 - 108 (2014)

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43.

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Liepe, J.; Holzhütter, H. G.; Kloetzel, P. M.; Stumpf, M. P.; Mishto, M.: Modelling proteasome and proteasome regulator activities. Biomolecules 4 (2), pp. 585 - 599 (2014)

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44.

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Liepe, J.; Kirk, P.; Filippi, S.; Toni, T.; Barnes, C. P.; Stumpf, M. P. H.: A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation. Nature Protocols 9, pp. 439 - 456 (2014)

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45.

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Liepe, J.; Filippi, S.; Komorowski, M.; Stumpf, M. P. H.: Maximizing the information content of experiments in systems biology. PLoS Computational Biology 9 (1), e1002888 (2013)

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46.

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Taylor, H. B.; Liepe, J.; Barthen, C.; Bugeon, L.; Huvet, M.; Kirk, P. D. W.; Brown, S. B.; Lamb, J. R.; Stumpf, M. P. H.; Dallman, M. J.: P38 and JNK have opposing effects on persistence of in vivo leukocyte migration in zebrafish. Immunology and Cell Biology 91 (1), pp. 60 - 69 (2013)

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47.

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Liepe, J.; Taylor, H.; Barnes, C. P.; Huvet, M.; Bugeon, L.; Thorne, T.; Lamb, J. R.; Dallman, M. J.; Stumpf, M. P. H.: Calibrating spatio-temporal models of leukocyte dynamics against in vivo live-imaging data using approximate Bayesian computation. Integrative Biology 4 (3), pp. 335 - 345 (2012)

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48.

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Zhou, Y.; Liepe, J.; Sheng, X.; Stumpf, M. P. H.; Barnes, C.: GPU accelerated biochemical network simulation. Bioinformatics 27 (6), pp. 874 - 876 (2011)

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49.

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Liepe, J.; Barnes, C.; Cule, E.; Erguler, K.; Kirk, P.; Toni, T.; Stumpf, M. P. H.: ABC-SysBio-approximate Bayesian computation in Python with GPU support. Bioinformatics 26 (14), pp. 1797 - 1799 (2010)

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50.

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Liepe, J.; Mishto, M.; Textoris-Taube, K.; Janek, K.; Keller, C.; Henklein, P.; Kloetzel, P. M.; Zaikin, A.: The 20S proteasome splicing activity discovered by SpliceMet. PLoS Computational Biology 6 (6), e1000830 (2010)

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