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Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard.

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Title: Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard.
Authors: Lin YY; Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany., Breuer K; Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany., Weichenhan D; Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany., Lafrenz P; Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany., Sarnataro A; Department of Oncology, KU Leuven, 3000 Leuven, Belgium., Wilk A; Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany., Chepeleva M; Multiomics Data Science Research Group, Department of Cancer Research, Luxembourg Institute of Health, 1445 Strassen, Luxembourg., Mücke O; Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany., Schönung M; Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.; National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, 69120 Heidelberg, Germany., Petermann F; NGS Core Facility, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany., Kensche PR; Omics-IT and Data Management Core Facility (ODCF), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany., Weiser L; Omics-IT and Data Management Core Facility (ODCF), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany., Thommen F; Omics-IT and Data Management Core Facility (ODCF), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany., Giacomelli G; Berlin Institute of Health, University Hospital Charité, 10178 Berlin, Germany., Nordstroem K; Department of EpiGenetics, Saarland University, 66123 Saarbrücken, Germany., Gonzalez-Avalos E; Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA 92037, United States., Merkel A; Bioinformatics Development and Statistical Genomics, Center for Genomic Regulation (CRG), Centro Nacional de Análisis Genómico (CNAG), 08028 Barcelona, Spain.; Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Catalonia, Spain., Kretzmer H; LIFE-Leipzig Research Center for Civilization Diseases, University Leipzig, 04103 Leipzig, Germany.; Max-Planck Institute for Molecular Genetics, 14195 Berlin, Germany., Fischer J; Department for Computer Vision and Machine Learning, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany., Krämer S; Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.; Biomedical Informatics, Data Mining and Data Analytics, Faculty of Applied Computer Science and Medical Faculty, University of Augsburg,86159 Augsburg, Germany.; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany., Iskar M; Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany., Wolf S; NGS Core Facility, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany., Buchhalter I; Omics-IT and Data Management Core Facility (ODCF), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany., Esteller M; Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Catalonia, Spain.; Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain.; Centro de Investigación Biomedica en Red Cancer (CIBERONC), 28029 Madrid, Spain.; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), 08036 Barcelona, Catalonia, Spain., Lawerenz C; Berlin Institute of Health, University Hospital Charité, 10178 Berlin, Germany., Twardziok S; Berlin Institute of Health, University Hospital Charité, 10178 Berlin, Germany., Zapatka M; Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany., Hovestadt V; Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States.; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, United States.; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, United States., Schlesner M; Biomedical Informatics, Data Mining and Data Analytics, Faculty of Applied Computer Science and Medical Faculty, University of Augsburg,86159 Augsburg, Germany., Schulz MH; Institute for Computational Genomic Medicine, Goethe University,60590 Frankfurt-am-Main, Germany.; German Center for Cardiovascular Research, 60590 Frankfurt-am-Mein, Germany., Hoffmann S; LIFE-Leipzig Research Center for Civilization Diseases, University Leipzig, 04103 Leipzig, Germany.; Computational Biology Group, Leibniz Institute on Aging-Fritz Lipmann Institute and Friedrich Schiller, University of Jena, 07745 Jena, Germany., Gerhauser C; Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany., Walter J; Department of EpiGenetics, Saarland University, 66123 Saarbrücken, Germany., Hartmann M; Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.; National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, 69120 Heidelberg, Germany., Lipka DB; Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.; National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, 69120 Heidelberg, Germany.; Faculty of Medicine, Otto-von-Guericke-University,39120 Magdeburg, Germany.; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany., Assenov Y; Department of Mathematics and Technology, RheinAhrCampus Remagen, University of Applied Sciences Koblenz, 53424 Remagen, Germany., Bock C; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.; Institute of Artificial Intelligence, Center for Medical Data Science, Medical University of Vienna,1090 Vienna, Austria., Plass C; Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany., Toth R; Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.; Multiomics Data Science Research Group, Department of Cancer Research, Luxembourg Institute of Health, 1445 Strassen, Luxembourg., Lutsik P; Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.; Department of Oncology, KU Leuven, 3000 Leuven, Belgium.
Source: Nucleic acids research [Nucleic Acids Res] 2025 Oct 14; Vol. 53 (19).
Publication Type: Journal Article
Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE
Database: MEDLINE Ultimate
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