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Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data.

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Title: Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data.
Authors: Bryce-Smith S; UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK., Burri D; Biozentrum, University of Basel, Basel, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland., Gazzara MR; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA., Herrmann CJ; Biozentrum, University of Basel, Basel, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland., Danecka W; Institute for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom., Fitzsimmons CM; Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA., Wan YK; Genome Institute of Singapore, Buona Vista, Singapore.; National University of Singapore, Kent Ridge, Singapore., Zhuang F; Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, USA., Fansler MM; Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell GraduateStudies, New York, NY, USA.; Cancer Biology and Genetics, Sloan-Kettering Institute, MSKCC, New York, NY, USA., Fernández JM; Barcelona Supercomputing Center, Barcelona, Spain.; Spanish National Bioinformatics Institute (INB/ELIXIR-ES)., Ferret M; Barcelona Supercomputing Center, Barcelona, Spain.; Spanish National Bioinformatics Institute (INB/ELIXIR-ES)., Gonzalez-Uriarte A; Barcelona Supercomputing Center, Barcelona, Spain.; Spanish National Bioinformatics Institute (INB/ELIXIR-ES)., Haynes S; Institute for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom., Herdman C; Department of Neurobiology, University of Utah, Utah, USA., Kanitz A; Biozentrum, University of Basel, Basel, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland., Katsantoni M; Biozentrum, University of Basel, Basel, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland., Marini F; Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI) - UniversityMedical Center of the Johannes Gutenberg, University Mainz, Germany., McDonnel E; Leeds Institute for Data Analytics, School of Molecular and Cellular Biology, University of Leeds, United Kingdom., Nicolet B; Department of Hematopoiesis, Sanquin Research, Landsteiner Laboratory, AmsterdamUMC, University of Amsterdam, and Oncode Institute, Amsterdam, The Netherlands., Poon CL; Weill Cornell Medicine, New York, NY, USA., Rot G; Swiss Institute of Bioinformatics, Lausanne, Switzerland.; Institute of Molecular Life Sciences, Zurich, Switzerland., Schärfen L; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven CT, USA., Wu PJ; Center for Plant Molecular Biology (ZMBP), University of Tübingen, Germany., Yoon Y; Department of Microbiology and Molecular Genetics, School of Medicine, University of California Irvine, Irvine, California, USA., Barash Y; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.; Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, USA., Zavolan M; Biozentrum, University of Basel, Basel, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Source: BioRxiv : the preprint server for biology [bioRxiv] 2023 Jun 26. Date of Electronic Publication: 2023 Jun 26.
Publication Type: Preprint; Journal Article
Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE
Database: MEDLINE Ultimate
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  Data: Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data.
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  Data: <searchLink fieldCode="AU" term="%22Bryce-Smith+S%22">Bryce-Smith S</searchLink>; UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK.<br /><searchLink fieldCode="AU" term="%22Burri+D%22">Burri D</searchLink>; Biozentrum, University of Basel, Basel, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Gazzara+MR%22">Gazzara MR</searchLink>; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.<br /><searchLink fieldCode="AU" term="%22Herrmann+CJ%22">Herrmann CJ</searchLink>; Biozentrum, University of Basel, Basel, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Danecka+W%22">Danecka W</searchLink>; Institute for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom.<br /><searchLink fieldCode="AU" term="%22Fitzsimmons+CM%22">Fitzsimmons CM</searchLink>; Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.<br /><searchLink fieldCode="AU" term="%22Wan+YK%22">Wan YK</searchLink>; Genome Institute of Singapore, Buona Vista, Singapore.; National University of Singapore, Kent Ridge, Singapore.<br /><searchLink fieldCode="AU" term="%22Zhuang+F%22">Zhuang F</searchLink>; Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, USA.<br /><searchLink fieldCode="AU" term="%22Fansler+MM%22">Fansler MM</searchLink>; Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell GraduateStudies, New York, NY, USA.; Cancer Biology and Genetics, Sloan-Kettering Institute, MSKCC, New York, NY, USA.<br /><searchLink fieldCode="AU" term="%22Fernández+JM%22">Fernández JM</searchLink>; Barcelona Supercomputing Center, Barcelona, Spain.; Spanish National Bioinformatics Institute (INB/ELIXIR-ES).<br /><searchLink fieldCode="AU" term="%22Ferret+M%22">Ferret M</searchLink>; Barcelona Supercomputing Center, Barcelona, Spain.; Spanish National Bioinformatics Institute (INB/ELIXIR-ES).<br /><searchLink fieldCode="AU" term="%22Gonzalez-Uriarte+A%22">Gonzalez-Uriarte A</searchLink>; Barcelona Supercomputing Center, Barcelona, Spain.; Spanish National Bioinformatics Institute (INB/ELIXIR-ES).<br /><searchLink fieldCode="AU" term="%22Haynes+S%22">Haynes S</searchLink>; Institute for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom.<br /><searchLink fieldCode="AU" term="%22Herdman+C%22">Herdman C</searchLink>; Department of Neurobiology, University of Utah, Utah, USA.<br /><searchLink fieldCode="AU" term="%22Kanitz+A%22">Kanitz A</searchLink>; Biozentrum, University of Basel, Basel, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Katsantoni+M%22">Katsantoni M</searchLink>; Biozentrum, University of Basel, Basel, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Marini+F%22">Marini F</searchLink>; Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI) - UniversityMedical Center of the Johannes Gutenberg, University Mainz, Germany.<br /><searchLink fieldCode="AU" term="%22McDonnel+E%22">McDonnel E</searchLink>; Leeds Institute for Data Analytics, School of Molecular and Cellular Biology, University of Leeds, United Kingdom.<br /><searchLink fieldCode="AU" term="%22Nicolet+B%22">Nicolet B</searchLink>; Department of Hematopoiesis, Sanquin Research, Landsteiner Laboratory, AmsterdamUMC, University of Amsterdam, and Oncode Institute, Amsterdam, The Netherlands.<br /><searchLink fieldCode="AU" term="%22Poon+CL%22">Poon CL</searchLink>; Weill Cornell Medicine, New York, NY, USA.<br /><searchLink fieldCode="AU" term="%22Rot+G%22">Rot G</searchLink>; Swiss Institute of Bioinformatics, Lausanne, Switzerland.; Institute of Molecular Life Sciences, Zurich, Switzerland.<br /><searchLink fieldCode="AU" term="%22Schärfen+L%22">Schärfen L</searchLink>; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven CT, USA.<br /><searchLink fieldCode="AU" term="%22Wu+PJ%22">Wu PJ</searchLink>; Center for Plant Molecular Biology (ZMBP), University of Tübingen, Germany.<br /><searchLink fieldCode="AU" term="%22Yoon+Y%22">Yoon Y</searchLink>; Department of Microbiology and Molecular Genetics, School of Medicine, University of California Irvine, Irvine, California, USA.<br /><searchLink fieldCode="AU" term="%22Barash+Y%22">Barash Y</searchLink>; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.; Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, USA.<br /><searchLink fieldCode="AU" term="%22Zavolan+M%22">Zavolan M</searchLink>; Biozentrum, University of Basel, Basel, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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