Publikationen

Zeitschriftenartikel (44)

1.
Zeitschriftenartikel
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)
2.
Zeitschriftenartikel
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), S. 5308 - 5327.e25 (2023)
3.
Zeitschriftenartikel
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)
4.
Zeitschriftenartikel
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)
5.
Zeitschriftenartikel
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)
6.
Zeitschriftenartikel
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, S. 23771 - 23781 (2022)
7.
Zeitschriftenartikel
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)
8.
Zeitschriftenartikel
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)
9.
Zeitschriftenartikel
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)
10.
Zeitschriftenartikel
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)
11.
Zeitschriftenartikel
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)
12.
Zeitschriftenartikel
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)
13.
Zeitschriftenartikel
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)
14.
Zeitschriftenartikel
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), S. 270 - 283 (2020)
15.
Zeitschriftenartikel
Paul, D.; Stevanovic, D.: Eigenvector-based identification of bipartite subgraphs. Discrete Applied Mathematics 269, S. 146 - 158 (2019)
16.
Zeitschriftenartikel
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, S. 7740 - 7754 (2019)
17.
Zeitschriftenartikel
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)
18.
Zeitschriftenartikel
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), S. 62 - 76 (2019)
19.
Zeitschriftenartikel
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)
20.
Zeitschriftenartikel
Liepe, J.; Ovaa, H.; Mishto, M.: Why do proteases mess up with antigen presentation by re-shuffling antigen sequences? Current Opinion in Immunology 52, S. 81 - 86 (2018)
21.
Zeitschriftenartikel
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), S. 1249 - 1250 (2018)
22.
Zeitschriftenartikel
Mishto, M.; Liepe, J.: Post-translational peptide splicing and T cell responses. Trends in Immunology 38 (12), S. 904 - 915 (2017)
23.
Zeitschriftenartikel
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)
24.
Zeitschriftenartikel
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), S. 2292 - 2304 (2017)
25.
Zeitschriftenartikel
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), S. 1242 - 1253 (2017)
26.
Zeitschriftenartikel
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)
27.
Zeitschriftenartikel
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), S. 354 - 358 (2016)
28.
Zeitschriftenartikel
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), S. 1975 - 1989 (2016)
29.
Zeitschriftenartikel
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), S. 102 - 107 (2016)
30.
Zeitschriftenartikel
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), S. 1109 - 1118 (2016)
31.
Zeitschriftenartikel
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), S. 30417 - 30428 (2015)
32.
Zeitschriftenartikel
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)
33.
Zeitschriftenartikel
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)
34.
Zeitschriftenartikel
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)
35.
Zeitschriftenartikel
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), S. 3508 - 3521 (2014)
36.
Zeitschriftenartikel
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, S. 98 - 108 (2014)
37.
Zeitschriftenartikel
Liepe, J.; Holzhütter, H. G.; Kloetzel, P. M.; Stumpf, M. P.; Mishto, M.: Modelling proteasome and proteasome regulator activities. Biomolecules 4 (2), S. 585 - 599 (2014)
38.
Zeitschriftenartikel
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, S. 439 - 456 (2014)
39.
Zeitschriftenartikel
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)
40.
Zeitschriftenartikel
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), S. 60 - 69 (2013)
41.
Zeitschriftenartikel
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), S. 335 - 345 (2012)
42.
Zeitschriftenartikel
Zhou, Y.; Liepe, J.; Sheng, X.; Stumpf, M. P. H.; Barnes, C.: GPU accelerated biochemical network simulation. Bioinformatics 27 (6), S. 874 - 876 (2011)
43.
Zeitschriftenartikel
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), S. 1797 - 1799 (2010)
44.
Zeitschriftenartikel
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)

Buchkapitel (1)

45.
Buchkapitel
Liepe, J.; Stumpf, M. P. H.: ABC in systems biology. In: Handbook of approximate bayesian computation (Hg. Sisson, S. A.; Fan, Y.; Beaumont, M. A.) (2019)
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