Jos de Graaf
University of Mainz
11 Papers
38 Citations
Jos de Graaf is an academic researcher from University of Mainz. The author has contributed to research in topics: Exome & Point mutation. The author has an hindex of 8, co-authored 11 publications.
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Papers
Exploiting the mutanome for tumor vaccination
John C. Castle,Sebastian Kreiter,Jan Diekmann,Martin Löwer,Niels van de Roemer,Jos de Graaf,Abderraouf Selmi,Mustafa Diken,Sebastian Boegel,Claudia Paret,Michael Koslowski,Andreas Kuhn,Cedrik M. Britten,Christoph Huber,Özlem Türeci,Ugur Sahin +15 more
TL;DR: The findings provide a comprehensive picture of the mutanome of B16F10 melanoma and offer insight into the extent of the immunogenicity of nonsynonymous base substitution mutations, and argue that the use of deep sequencing to systematically analyze immunogenic mutations may pave the way for individualized immunotherapy of cancer patients.
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Immunomic, genomic and transcriptomic characterization of CT26 colorectal carcinoma
John C. Castle,Martin Loewer,Sebastian Boegel,Jos de Graaf,Christian Bender,Arbel D. Tadmor,Valesca Boisguerin,Thomas Bukur,Patrick Sorn,Claudia Paret,Mustafa Diken,Sebastian Kreiter,Özlem Türeci,Ugur Sahin +13 more
TL;DR: An integrated map of the genome, transcriptome and immunome of an epithelial mouse tumor, the CT26 colon carcinoma cell line, which predicts that CT26 is refractory to anti-EGFR mAbs and sensitive to MEK and MET inhibitors, as have been previously reported.
HLA typing from RNA-Seq sequence reads
Sebastian Boegel,Martin Löwer,Michael K. E. Schäfer,Thomas Bukur,Jos de Graaf,Valesca Boisguerin,Özlem Türeci,Mustafa Diken,John C. Castle,Ugur Sahin +9 more
TL;DR: Because the algorithm uses standard RNA-Seq reads and requires no change to laboratory protocols, it can be used for both existing datasets and future studies, thus adding a new dimension for HLA typing and biomarker studies.
Mutated tumor alleles are expressed according to their DNA frequency.
John C. Castle,Martin Loewer,Sebastian Boegel,Arbel D. Tadmor,Valesca Boisguerin,Jos de Graaf,Claudia Paret,Mustafa Diken,Sebastian Kreiter,Özlem Türeci,Ugur Sahin +10 more
TL;DR: The data strongly suggest that genes are equally transcribed from all alleles, mutated and wild-type, and thus transcribed in proportion to their DNA allele frequency.
Galaxy LIMS for next-generation sequencing
Jelle Scholtalbers,Jasmin Rößler,Patrick Sorn,Jos de Graaf,Valesca Boisguerin,John C. Castle,Ugur Sahin +6 more
TL;DR: A laboratory information management system (LIMS) for a next-generation sequencing (NGS) laboratory within the existing Galaxy platform that provides lab technicians standard and customizable sample information forms, barcoded submission forms, and tracking of input sample quality to aid physical flow cell preparation.
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