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Items: 28

1.

Proteolytic dynamics of human 20S thymoproteasome.

Kuckelkorn U, Stübler S, Textoris-Taube K, Kilian C, Niewienda A, Henklein P, Janek K, Stumpf MPH, Mishto M, Liepe J.

J Biol Chem. 2019 May 10;294(19):7740-7754. doi: 10.1074/jbc.RA118.007347. Epub 2019 Mar 26.

PMID:
30914481
2.

Untangling Extracellular Proteasome-Osteopontin Circuit Dynamics in Multiple Sclerosis.

Dianzani C, Vecchio D, Clemente N, Chiocchetti A, Martinelli Boneschi F, Galimberti D, Dianzani U, Comi C, Mishto M, Liepe J.

Cells. 2019 Mar 20;8(3). pii: E262. doi: 10.3390/cells8030262.

3.

Mapping the MHC Class I-Spliced Immunopeptidome of Cancer Cells.

Liepe J, Sidney J, Lorenz FKM, Sette A, Mishto M.

Cancer Immunol Res. 2019 Jan;7(1):62-76. doi: 10.1158/2326-6066.CIR-18-0424. Epub 2018 Nov 13.

PMID:
30425108
4.

Why do proteases mess up with antigen presentation by re-shuffling antigen sequences?

Liepe J, Ovaa H, Mishto M.

Curr Opin Immunol. 2018 Jun;52:81-86. doi: 10.1016/j.coi.2018.04.016. Epub 2018 Jun 1. Review.

5.

PEITH(Θ): perfecting experiments with information theory in Python with GPU support.

Dony L, Mackerodt J, Ward S, Filippi S, Stumpf MPH, Liepe J.

Bioinformatics. 2018 Apr 1;34(7):1249-1250. doi: 10.1093/bioinformatics/btx776.

6.

An Unexpected Major Role for Proteasome-Catalyzed Peptide Splicing in Generation of T Cell Epitopes: Is There Relevance for Vaccine Development?

Platteel ACM, Liepe J, van Eden W, Mishto M, Sijts AJAM.

Front Immunol. 2017 Nov 3;8:1441. doi: 10.3389/fimmu.2017.01441. eCollection 2017. Review.

7.

Single Cell Phenotyping Reveals Heterogeneity Among Hematopoietic Stem Cells Following Infection.

MacLean AL, Smith MA, Liepe J, Sim A, Khorshed R, Rashidi NM, Scherf N, Krinner A, Roeder I, Lo Celso C, Stumpf MPH.

Stem Cells. 2017 Nov;35(11):2292-2304. doi: 10.1002/stem.2692. Epub 2017 Sep 24.

8.

Post-Translational Peptide Splicing and T Cell Responses.

Mishto M, Liepe J.

Trends Immunol. 2017 Dec;38(12):904-915. doi: 10.1016/j.it.2017.07.011. Epub 2017 Aug 19. Review.

PMID:
28830734
9.

Multi-level Strategy for Identifying Proteasome-Catalyzed Spliced Epitopes Targeted by CD8+ T Cells during Bacterial Infection.

Platteel ACM, Liepe J, Textoris-Taube K, Keller C, Henklein P, Schalkwijk HH, Cardoso R, Kloetzel PM, Mishto M, Sijts AJAM.

Cell Rep. 2017 Aug 1;20(5):1242-1253. doi: 10.1016/j.celrep.2017.07.026.

10.

Extracellular proteasome-osteopontin circuit regulates cell migration with implications in multiple sclerosis.

Dianzani C, Bellavista E, Liepe J, Verderio C, Martucci M, Santoro A, Chiocchetti A, Gigliotti CL, Boggio E, Ferrara B, Riganti L, Keller C, Janek K, Niewienda A, Fenoglio C, Sorosina M, Cantello R, Kloetzel PM, Stumpf MP, Paul F, Ruprecht K, Galimberti D, Martinelli Boneschi F, Comi C, Dianzani U, Mishto M.

Sci Rep. 2017 Mar 9;7:43718. doi: 10.1038/srep43718.

11.

A large fraction of HLA class I ligands are proteasome-generated spliced peptides.

Liepe J, Marino F, Sidney J, Jeko A, Bunting DE, Sette A, Kloetzel PM, Stumpf MP, Heck AJ, Mishto M.

Science. 2016 Oct 21;354(6310):354-358. Epub 2016 Oct 20.

12.

Accurate Reconstruction of Cell and Particle Tracks from 3D Live Imaging Data.

Liepe J, Sim A, Weavers H, Ward L, Martin P, Stumpf MP.

Cell Syst. 2016 Jul;3(1):102-7. doi: 10.1016/j.cels.2016.06.002. Epub 2016 Jul 21.

13.

Systems Analysis of the Dynamic Inflammatory Response to Tissue Damage Reveals Spatiotemporal Properties of the Wound Attractant Gradient.

Weavers H, Liepe J, Sim A, Wood W, Martin P, Stumpf MPH.

Curr Biol. 2016 Aug 8;26(15):1975-1989. doi: 10.1016/j.cub.2016.06.012. Epub 2016 Jul 14.

14.

CD8(+) T cells of Listeria monocytogenes-infected mice recognize both linear and spliced proteasome products.

Platteel AC, Mishto M, Textoris-Taube K, Keller C, Liepe J, Busch DH, Kloetzel PM, Sijts AJ.

Eur J Immunol. 2016 May;46(5):1109-18. doi: 10.1002/eji.201545989. Epub 2016 Mar 16.

15.

The T210M Substitution in the HLA-a*02:01 gp100 Epitope Strongly Affects Overall Proteasomal Cleavage Site Usage and Antigen Processing.

Textoris-Taube K, Keller C, Liepe J, Henklein P, Sidney J, Sette A, Kloetzel PM, Mishto M.

J Biol Chem. 2015 Dec 18;290(51):30417-28. doi: 10.1074/jbc.M115.695189. Epub 2015 Oct 27.

16.

Inference of random walk models to describe leukocyte migration.

Jones PJ, Sim A, Taylor HB, Bugeon L, Dallman MJ, Pereira B, Stumpf MP, Liepe J.

Phys Biol. 2015 Sep 25;12(6):066001. doi: 10.1088/1478-3975/12/6/066001.

17.

Quantitative time-resolved analysis reveals intricate, differential regulation of standard- and immuno-proteasomes.

Liepe J, Holzhütter HG, Bellavista E, Kloetzel PM, Stumpf MP, Mishto M.

Elife. 2015 Sep 22;4:e07545. doi: 10.7554/eLife.07545.

18.

Goldstein-Kac telegraph processes with random speeds: Path probabilities, likelihoods, and reported Lévy flights.

Sim A, Liepe J, Stumpf MP.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Apr;91(4):042115. Epub 2015 Apr 15.

PMID:
25974447
19.

Proteasome isoforms exhibit only quantitative differences in cleavage and epitope generation.

Mishto M, Liepe J, Textoris-Taube K, Keller C, Henklein P, Weberruß M, Dahlmann B, Enenkel C, Voigt A, Kuckelkorn U, Stumpf MP, Kloetzel PM.

Eur J Immunol. 2014 Dec;44(12):3508-21. doi: 10.1002/eji.201444902. Epub 2014 Nov 20.

20.

Modelling proteasome and proteasome regulator activities.

Liepe J, Holzhütter HG, Kloetzel PM, Stumpf MP, Mishto M.

Biomolecules. 2014 Jun 20;4(2):585-99. doi: 10.3390/biom4020585. Review.

21.

Information theory and signal transduction systems: from molecular information processing to network inference.

Mc Mahon SS, Sim A, Filippi S, Johnson R, Liepe J, Smith D, Stumpf MP.

Semin Cell Dev Biol. 2014 Nov;35:98-108. doi: 10.1016/j.semcdb.2014.06.011. Epub 2014 Jun 19. Review.

PMID:
24953199
22.

A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation.

Liepe J, Kirk P, Filippi S, Toni T, Barnes CP, Stumpf MP.

Nat Protoc. 2014 Feb;9(2):439-56. doi: 10.1038/nprot.2014.025. Epub 2014 Jan 23.

23.

Maximizing the information content of experiments in systems biology.

Liepe J, Filippi S, Komorowski M, Stumpf MP.

PLoS Comput Biol. 2013;9(1):e1002888. doi: 10.1371/journal.pcbi.1002888. Epub 2013 Jan 31.

24.

P38 and JNK have opposing effects on persistence of in vivo leukocyte migration in zebrafish.

Taylor HB, Liepe J, Barthen C, Bugeon L, Huvet M, Kirk PD, Brown SB, Lamb JR, Stumpf MP, Dallman MJ.

Immunol Cell Biol. 2013 Jan;91(1):60-9. doi: 10.1038/icb.2012.57. Epub 2012 Nov 20.

25.

Calibrating spatio-temporal models of leukocyte dynamics against in vivo live-imaging data using approximate Bayesian computation.

Liepe J, Taylor H, Barnes CP, Huvet M, Bugeon L, Thorne T, Lamb JR, Dallman MJ, Stumpf MPH.

Integr Biol (Camb). 2012 Mar;4(3):335-345. doi: 10.1039/c2ib00175f. Epub 2012 Feb 10.

26.

GPU accelerated biochemical network simulation.

Zhou Y, Liepe J, Sheng X, Stumpf MP, Barnes C.

Bioinformatics. 2011 Mar 15;27(6):874-6. doi: 10.1093/bioinformatics/btr015. Epub 2011 Jan 11.

27.

The 20S proteasome splicing activity discovered by SpliceMet.

Liepe J, Mishto M, Textoris-Taube K, Janek K, Keller C, Henklein P, Kloetzel PM, Zaikin A.

PLoS Comput Biol. 2010 Jun 24;6(6):e1000830. doi: 10.1371/journal.pcbi.1000830.

28.

ABC-SysBio--approximate Bayesian computation in Python with GPU support.

Liepe J, Barnes C, Cule E, Erguler K, Kirk P, Toni T, Stumpf MP.

Bioinformatics. 2010 Jul 15;26(14):1797-9. doi: 10.1093/bioinformatics/btq278.

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