Publications
Journal Article (43)
1.
Journal Article
Mammalian oocytes store proteins for the early embryo on cytoplasmic lattices. Cell (2023)
2.
Journal Article
10, 18 (2023)
InvitroSPI and a large database of proteasome-generated spliced and non-spliced peptides. Scientific Data 3.
Journal Article
23 (2), 2200271 (2023)
iBench: A ground truth approach for advanced validation of mass spectrometry identification method. Proteomics 4.
Journal Article
21 (12), 100432 (2022)
inSPIRE: An open-source tool for increased mass spectrometry identification rates using Prosit spectral prediction. Molecular and Cellular Proteomics 5.
Journal Article
7, pp. 23771 - 23781 (2022)
Predicting the Success of Fmoc-Based Peptide Synthesis. ACS Omega 6.
Journal Article
22 (10), e2100226 (2022)
Database search engines and target database features impinge upon the identification of post‐translationally cis‐spliced peptides in HLA class I immunopeptidomes. Proteomics 7.
Journal Article
12 (2), 166 (2022)
Computational Models for Clinical Applications in Personalized Medicine—Guidelines and Recommendations for Data Integration and Model Validation. Journal of Personalized Medicine 8.
Journal Article
12, 679836 (2021)
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 9.
Journal Article
36 (1), 109312 (2021)
Identification of a class of non-conventional ER-stress-response-derived immunogenic peptides. Cell Reports 10.
Journal Article
12, 656451 (2021)
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 11.
Journal Article
12, 614276 (2021)
Proteasome-generated cis-spliced peptides and their potential role in CD8+ T cell tolerance. Frontiers in Immunology 12.
Journal Article
7, 146 (2020)
Large database for the analysis and prediction of spliced and non-spliced peptide generation by proteasomes. Scientific Data 13.
Journal Article
50 (2), pp. 270 - 283 (2020)
ER-aminopeptidase 1 determines the processing and presentation of an immunotherapy-relevant melanoma epitope. European Journal of Immunology 14.
Journal Article
269, pp. 146 - 158 (2019)
Eigenvector-based identification of bipartite subgraphs. Discrete Applied Mathematics 15.
Journal Article
294, pp. 7740 - 7754 (2019)
Proteolytic dynamics of human 20S thymoproteasome. Journal of Biological Chemistry 16.
Journal Article
8 (3), 262 (2019)
Untangling extracellular proteasome-osteopontin circuit dynamics in multiple sclerosis. Cells 17.
Journal Article
7 (1), pp. 62 - 76 (2019)
Mapping the MHC class I spliced immunopeptidome of cancer cells. Cancer Immunology Research 18.
Journal Article
10, 2572 (2019)
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 19.
Journal Article
52, pp. 81 - 86 (2018)
Why do proteases mess up with antigen presentation by re-shuffling antigen sequences? Current Opinion in Immunology 20.
Journal Article
34 (7), pp. 1249 - 1250 (2018)
PEITH(Θ) - perfecting experiments with information theory in python with GPU support. Bioinformatics 21.
Journal Article
38 (12), pp. 904 - 915 (2017)
Post-translational peptide splicing and T cell responses. Trends in Immunology 22.
Journal Article
8, 1441 (2017)
An unexpected major role for proteasome-catalyzed peptide splicing in generation of T cell epitopes: Is there relevance for vaccine development? Frontiers in Immunology 23.
Journal Article
35 (11), pp. 2292 - 2304 (2017)
Single cell phenotyping reveals heterogeneity among haematopoietic stem cells following infection. Stem Cells 24.
Journal Article
20 (5), pp. 1242 - 1253 (2017)
Multi-level strategy for identifying proteasome-catalyzed spliced epitopes targeted by CD8+ T cells during bacterial infection. Cell Reports 25.
Journal Article
7, 43718 (2017)
Extracellular proteasome-osteopontin circuit regulates cell migration with implications in multiple sclerosis. Scientific Reports 26.
Journal Article
354 (6310), pp. 354 - 358 (2016)
A large fraction of HLA class I ligands are proteasome-generated spliced peptides. Science 27.
Journal Article
26 (15), pp. 1975 - 1989 (2016)
Systems analysis of the dynamic inflammatory response to tissue damage reveals spatiotemporal properties of the wound attractant gradient. Current Biology 28.
Journal Article
3 (1), pp. 102 - 107 (2016)
Accurate reconstruction of cell and particle tracks from 3D live imaging data. Cell Systems 29.
Journal Article
46 (5), pp. 1109 - 1118 (2016)
CD8(+) T cells of Listeria monocytogenes-infected mice recognize both linear and spliced proteasome products. European Journal of Immunology 30.
Journal Article
290 (51), pp. 30417 - 30428 (2015)
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 31.
Journal Article
12 (6), 066001 (2015)
Inference of random walk models to describe leukocyte migration. Physical Biology 32.
Journal Article
4, e07545 (2015)
Quantitative time-resolved analysis reveals intricate, differential regulation of standard- and immuno-proteasomes. eLife 33.
Journal Article
91 (4), 042115 (2015)
Goldstein-Kac telegraph processes with random speeds: Path probabilities, likelihoods, and reported Lévy flights. Physical Review E 34.
Journal Article
44 (12), pp. 3508 - 3521 (2014)
Proteasome isoforms exhibit only quantitative differences in cleavage and epitope generation. European Journal of Immunology 35.
Journal Article
35, pp. 98 - 108 (2014)
Information theory and signal transduction systems: From molecular information processing to network inference. Seminars in Cell and Developmental Biology 36.
Journal Article
4 (2), pp. 585 - 599 (2014)
Modelling proteasome and proteasome regulator activities. Biomolecules 37.
Journal Article
9, pp. 439 - 456 (2014)
A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation. Nature Protocols 38.
Journal Article
9 (1), e1002888 (2013)
Maximizing the information content of experiments in systems biology. PLoS Computational Biology 39.
Journal Article
91 (1), pp. 60 - 69 (2013)
P38 and JNK have opposing effects on persistence of in vivo leukocyte migration in zebrafish. Immunology and Cell Biology 40.
Journal Article
4 (3), pp. 335 - 345 (2012)
Calibrating spatio-temporal models of leukocyte dynamics against in vivo live-imaging data using approximate Bayesian computation. Integrative Biology 41.
Journal Article
27 (6), pp. 874 - 876 (2011)
GPU accelerated biochemical network simulation. Bioinformatics 42.
Journal Article
26 (14), pp. 1797 - 1799 (2010)
ABC-SysBio-approximate Bayesian computation in Python with GPU support. Bioinformatics 43.
Journal Article
6 (6), e1000830 (2010)
The 20S proteasome splicing activity discovered by SpliceMet. PLoS Computational Biology Book Chapter (1)
44.
Book Chapter
ABC in systems biology. In: Handbook of approximate bayesian computation (Eds. Sisson, S. A.; Fan, Y.; Beaumont, M. A.) (2019)