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Your search keyword '"Aleksander Palkowski"' showing total 8 results
Start Over Author "Aleksander Palkowski" Publisher american association for cancer research (aacr)
8 results on '"Aleksander Palkowski"'

1. Supplementary legends from The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I–Associated Peptides

Author

Javier A. Alfaro, Sachin Kote, Ted R. Hupp, Robin Fahraeus, Kevin Litchfield, David R. Goodlett, Stefan N. Symeonides, Paul M. Brennan, J. Robert O'Neill, Maciej Parys, Maciej Pawlik, Aleksander Palkowski, David J. Harrison, Ajitha Rajan, Håkan Axelson, Catia Pesquita, Fabio Massimo Zanzotto, Christophe Battail, Alexander Laird, Dominika Bedran, Tongjie Wang, Kenneth Weke, Hans-Christof Gasser, and Georges Bedran

Abstract

Legends for Supplementary tables, supplementary figures, and supplementary notes.

Published
2023
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2. Supplementary Table 3 from The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I–Associated Peptides

Author

Javier A. Alfaro, Sachin Kote, Ted R. Hupp, Robin Fahraeus, Kevin Litchfield, David R. Goodlett, Stefan N. Symeonides, Paul M. Brennan, J. Robert O'Neill, Maciej Parys, Maciej Pawlik, Aleksander Palkowski, David J. Harrison, Ajitha Rajan, Håkan Axelson, Catia Pesquita, Fabio Massimo Zanzotto, Christophe Battail, Alexander Laird, Dominika Bedran, Tongjie Wang, Kenneth Weke, Hans-Christof Gasser, and Georges Bedran

Abstract

Annotation of the COD-dipp ncMAPs.

Published
2023
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3. Supplementary Table 2 from The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I–Associated Peptides

Author

Javier A. Alfaro, Sachin Kote, Ted R. Hupp, Robin Fahraeus, Kevin Litchfield, David R. Goodlett, Stefan N. Symeonides, Paul M. Brennan, J. Robert O'Neill, Maciej Parys, Maciej Pawlik, Aleksander Palkowski, David J. Harrison, Ajitha Rajan, Håkan Axelson, Catia Pesquita, Fabio Massimo Zanzotto, Christophe Battail, Alexander Laird, Dominika Bedran, Tongjie Wang, Kenneth Weke, Hans-Christof Gasser, and Georges Bedran

Abstract

Open search peptide-spectrum matches (PSMs) information of serine acetylation, cysteinylation, carbamidomethylation, and cysteine trioxidation.

Published
2023
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4. Supplementary Table 1 from The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I–Associated Peptides

Author

Javier A. Alfaro, Sachin Kote, Ted R. Hupp, Robin Fahraeus, Kevin Litchfield, David R. Goodlett, Stefan N. Symeonides, Paul M. Brennan, J. Robert O'Neill, Maciej Parys, Maciej Pawlik, Aleksander Palkowski, David J. Harrison, Ajitha Rajan, Håkan Axelson, Catia Pesquita, Fabio Massimo Zanzotto, Christophe Battail, Alexander Laird, Dominika Bedran, Tongjie Wang, Kenneth Weke, Hans-Christof Gasser, and Georges Bedran

Abstract

Datasets and samples considered in this study.

Published
2023
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5. Supplementary Table 5 from The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I–Associated Peptides

Author

Javier A. Alfaro, Sachin Kote, Ted R. Hupp, Robin Fahraeus, Kevin Litchfield, David R. Goodlett, Stefan N. Symeonides, Paul M. Brennan, J. Robert O'Neill, Maciej Parys, Maciej Pawlik, Aleksander Palkowski, David J. Harrison, Ajitha Rajan, Håkan Axelson, Catia Pesquita, Fabio Massimo Zanzotto, Christophe Battail, Alexander Laird, Dominika Bedran, Tongjie Wang, Kenneth Weke, Hans-Christof Gasser, and Georges Bedran

Abstract

Mapping of ncMAPs to COSMIC frameshift mutations.

Published
2023
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6. Data from The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I–Associated Peptides

Author

Javier A. Alfaro, Sachin Kote, Ted R. Hupp, Robin Fahraeus, Kevin Litchfield, David R. Goodlett, Stefan N. Symeonides, Paul M. Brennan, J. Robert O'Neill, Maciej Parys, Maciej Pawlik, Aleksander Palkowski, David J. Harrison, Ajitha Rajan, Håkan Axelson, Catia Pesquita, Fabio Massimo Zanzotto, Christophe Battail, Alexander Laird, Dominika Bedran, Tongjie Wang, Kenneth Weke, Hans-Christof Gasser, and Georges Bedran

Abstract

Tumor antigens can emerge through multiple mechanisms, including translation of noncoding genomic regions. This noncanonical category of tumor antigens has recently gained attention; however, our understanding of how they recur within and between cancer types is still in its infancy. Therefore, we developed a proteogenomic pipeline based on deep learning de novo mass spectrometry (MS) to enable the discovery of noncanonical MHC class I–associated peptides (ncMAP) from noncoding regions. Considering that the emergence of tumor antigens can also involve posttranslational modifications (PTM), we included an open search component in our pipeline. Leveraging the wealth of MS-based immunopeptidomics, we analyzed data from 26 MHC class I immunopeptidomic studies across 11 different cancer types. We validated the de novo identified ncMAPs, along with the most abundant PTMs, using spectral matching and controlled their FDR to 1%. The noncanonical presentation appeared to be 5 times enriched for the A03 HLA supertype, with a projected population coverage of 55%. The data reveal an atlas of 8,601 ncMAPs with varying levels of cancer selectivity and suggest 17 cancer-selective ncMAPs as attractive therapeutic targets according to a stringent cutoff. In summary, the combination of the open-source pipeline and the atlas of ncMAPs reported herein could facilitate the identification and screening of ncMAPs as targets for T-cell therapies or vaccine development.

Published
2023
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7. Supplementary figures from The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I–Associated Peptides

Author

Javier A. Alfaro, Sachin Kote, Ted R. Hupp, Robin Fahraeus, Kevin Litchfield, David R. Goodlett, Stefan N. Symeonides, Paul M. Brennan, J. Robert O'Neill, Maciej Parys, Maciej Pawlik, Aleksander Palkowski, David J. Harrison, Ajitha Rajan, Håkan Axelson, Catia Pesquita, Fabio Massimo Zanzotto, Christophe Battail, Alexander Laird, Dominika Bedran, Tongjie Wang, Kenneth Weke, Hans-Christof Gasser, and Georges Bedran

Abstract

Supplementary Figures S1 to S7.

Published
2023
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8. Supplementary notes from The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I–Associated Peptides

Author

Javier A. Alfaro, Sachin Kote, Ted R. Hupp, Robin Fahraeus, Kevin Litchfield, David R. Goodlett, Stefan N. Symeonides, Paul M. Brennan, J. Robert O'Neill, Maciej Parys, Maciej Pawlik, Aleksander Palkowski, David J. Harrison, Ajitha Rajan, Håkan Axelson, Catia Pesquita, Fabio Massimo Zanzotto, Christophe Battail, Alexander Laird, Dominika Bedran, Tongjie Wang, Kenneth Weke, Hans-Christof Gasser, and Georges Bedran

Abstract

Supplementary notes 1 and 2.

Published
2023
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