Search

Your search keyword '"Sorn, Patrick"' showing total 17 results
Start Over Author "Sorn, Patrick"
17 results on '"Sorn, Patrick"'

3. Prediction of tumor-specific splicing from somatic mutations as a source of neoantigen candidates

Author

Lang, Franziska, primary, Sorn, Patrick, additional, Suchan, Martin, additional, Henrich, Alina, additional, Albrecht, Christian, additional, Köhl, Nina, additional, Beicht, Aline, additional, Riesgo-Ferreiro, Pablo, additional, Holtsträter, Christoph, additional, Schrörs, Barbara, additional, Weber, David, additional, Löwer, Martin, additional, Sahin, Ugur, additional, and Ibn-Salem, Jonas, additional

Published
2024
Full Text
View/download PDF

9. Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer

Author

Sahin, Ugur, Derhovanessian, Evelyna, Miller, Matthias, Kloke, Bjrn-Philipp, Simon, Petra, Lwer, Martin, Bukur, Valesca, Tadmor, Arbel D., Luxemburger, Ulrich, Schrrs, Barbara, Omokoko, Tana, Vormehr, Mathias, Albrecht, Christian, Paruzynski, Anna, Kuhn, Andreas N., Buck, Janina, Heesch, Sandra, Schreeb, Katharina H., Mller, Felicitas, Ortseifer, Inga, Vogler, Isabel, Godehardt, Eva, Attig, Sebastian, Rae, Richard, Breitkreuz, Andrea, Tolliver, Claudia, Suchan, Martin, Martic, Goran, Hohberger, Alexander, Sorn, Patrick, Diekmann, Jan, Ciesla, Janko, Waksmann, Olga, Brck, Alexandra-Kemmer, Witt, Meike, Zillgen, Martina, Rothermel, Andree, Kasemann, Barbara, Langer, David, Bolte, Stefanie, Diken, Mustafa, Kreiter, Sebastian, Nemecek, Romina, Gebhardt, Christoffer, Grabbe, Stephan, Hller, Christoph, Utikal, Jochen, Huber, Christoph, Loquai, Carmen, and Treci, zlem

Subjects
Precision medicine -- Methods, Mutation -- Health aspects, Cancer -- Genetic aspects -- Prevention, RNA -- Health aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Ugur Sahin (corresponding author) [1, 2, 3]; Evelyna Derhovanessian [1]; Matthias Miller [1]; Bjrn-Philipp Kloke [1]; Petra Simon [1]; Martin Lwer [2]; Valesca Bukur [1, 2]; Arbel D. Tadmor [...]

Published
2017
Full Text
View/download PDF

11. OXPHOS remodeling in high-grade prostate cancer involves mtDNA mutations and increased succinate oxidation

Author

Schöpf, Bernd, primary, Weissensteiner, Hansi, additional, Schäfer, Georg, additional, Fazzini, Federica, additional, Charoentong, Pornpimol, additional, Naschberger, Andreas, additional, Rupp, Bernhard, additional, Fendt, Liane, additional, Bukur, Valesca, additional, Giese, Irina, additional, Sorn, Patrick, additional, Sant’Anna-Silva, Ana Carolina, additional, Iglesias-Gonzalez, Javier, additional, Sahin, Ugur, additional, Kronenberg, Florian, additional, Gnaiger, Erich, additional, and Klocker, Helmut, additional

Published
2020
Full Text
View/download PDF

12. Additional file 2: of HLA and proteasome expression body map

Author

Boegel, Sebastian, LĂśwer, Martin, Bukur, Thomas, Sorn, Patrick, Castle, John, and Ugur Sahin

Abstract

Figure S1. HLA Class I (A) and II (B) expression body map including anatomical substructures. Figure S2. Immunological characterization of brain samples. Figure S3. Locus specific expression of classical HLA class I (A) and class II (B) genes across all examined tissues. Figure S4. Expression body map of the non-classical HLA Class I genes. (A) HLA-E transcripts are ubiquitously expressed in all tissues. Figure S5. Expression of constitutive proteasome versus immunoproteasome normalized with TPM. Figure S6. Correlation analysis of CIITA and HLA expression. Figure S7. Expression of constitutive proteasome, Immunoproteasome and its inducing cytokines. Figure S8. Expression of TAP1, TAP2 and PSMB9. (PPTX 5223Â kb)

Published
2018
Full Text
View/download PDF

14. ArtiFuse—computational validation of fusion gene detection tools without relying on simulated reads.

Author

Sorn, Patrick, Holtsträter, Christoph, Löwer, Martin, Sahin, Ugur, and Weber, David

Subjects
*GENE fusion, *RNA sequencing, *SOURCE code, *CANCER, *ASSET management accounts
Abstract

Motivation Gene fusions are an important class of transcriptional variants that can influence cancer development and can be predicted from RNA sequencing (RNA-seq) data by multiple existing tools. However, the real-world performance of these tools is unclear due to the lack of known positive and negative events, especially with regard to fusion genes in individual samples. Often simulated reads are used, but these cannot account for all technical biases in RNA-seq data generated from real samples. Results Here, we present ArtiFuse, a novel approach that simulates fusion genes by sequence modification to the genomic reference, and therefore, can be applied to any RNA-seq dataset without the need for any simulated reads. We demonstrate our approach on eight RNA-seq datasets for three fusion gene prediction tools: average recall values peak for all three tools between 0.4 and 0.56 for high-quality and high-coverage datasets. As ArtiFuse affords total control over involved genes and breakpoint position, we also assessed performance with regard to gene-related properties, showing a drop-in recall value for low-expressed genes in high-coverage samples and genes with co-expressed paralogues. Overall tool performance assessed from ArtiFusions is lower compared to previously reported estimates on simulated reads. Due to the use of real RNA-seq datasets, we believe that ArtiFuse provides a more realistic benchmark that can be used to develop more accurate fusion gene prediction tools for application in clinical settings. Availability and implementation ArtiFuse is implemented in Python. The source code and documentation are available at https://github.com/TRON-Bioinformatics/ArtiFusion. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Published
2020
Full Text
View/download PDF

15. Additional file 2: Figure S1. of TCLP: an online cancer cell line catalogue integrating HLA type, predicted neo-epitopes, virus and gene expression

Author

Scholtalbers, Jelle, Boegel, Sebastian, Bukur, Thomas, Byl, Marius, Goerges, Sebastian, Sorn, Patrick, Loewer, Martin, Ugur Sahin, and Castle, John

Subjects
virus diseases, digestive system diseases
Abstract

Virus identification. HBV is expressed in the liver carcinoma cell line PLC/PRF/5. (PPTX 180 kb)

Published
2015
Full Text
View/download PDF

17. Immunomic, genomic and transcriptomic characterization of CT26 colorectal carcinoma

Author

Castle, John C, primary, Loewer, Martin, additional, Boegel, Sebastian, additional, de Graaf, Jos, additional, Bender, Christian, additional, Tadmor, Arbel D, additional, Boisguerin, Valesca, additional, Bukur, Thomas, additional, Sorn, Patrick, additional, Paret, Claudia, additional, Diken, Mustafa, additional, Kreiter, Sebastian, additional, Türeci, Özlem, additional, and Sahin, Ugur, additional

Published
2014
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results