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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; Department of Neuromuscular Diseases, UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, UCL, London WC1N 3BG, United Kingdom., Burri D; Biozentrum, University of Basel, 4056 Basel, Switzerland.; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland., Gazzara MR; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA., Herrmann CJ; Biozentrum, University of Basel, 4056 Basel, Switzerland.; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland., Danecka W; Institute for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3FF, United Kingdom., Fitzsimmons CM; Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA., Wan YK; Genome Institute of Singapore, Buona Vista, Singapore 138672.; Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge, Singapore 119228., Zhuang F; Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA., Fansler MM; Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Graduate Studies, New York, New York 10065, USA.; Cancer Biology and Genetics, Sloan-Kettering Institute, MSKCC, New York, New York 10065, USA., Fernández JM; Life Sciences Department, Barcelona Supercomputing Center, 08034 Barcelona, Spain.; Spanish National Bioinformatics Institute (INB/ELIXIR-ES), 28029 Madrid, Spain., Ferret M; Life Sciences Department, Barcelona Supercomputing Center, 08034 Barcelona, Spain.; Spanish National Bioinformatics Institute (INB/ELIXIR-ES), 28029 Madrid, Spain., Gonzalez-Uriarte A; Life Sciences Department, Barcelona Supercomputing Center, 08034 Barcelona, Spain.; Spanish National Bioinformatics Institute (INB/ELIXIR-ES), 28029 Madrid, Spain., Haynes S; Institute for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3FF, United Kingdom., Herdman C; Department of Neurobiology, University of Utah, Salt Lake City, Utah 84132, USA., Kanitz A; Biozentrum, University of Basel, 4056 Basel, Switzerland.; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland., Katsantoni M; Biozentrum, University of Basel, 4056 Basel, Switzerland.; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland., Marini F; Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg-University Mainz, 55118 Mainz, Germany., McDonnel E; Leeds Institute for Data Analytics, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9NL, United Kingdom., Nicolet B; Department of Hematopoiesis, Sanquin Research, Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, 1066 CX Amsterdam, The Netherlands.; Oncode Institute, 3521 AL Utrecht, The Netherlands., Poon CL; Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York 10065, USA., Rot G; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.; Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland., Schärfen L; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut 06520, USA., Wu PJ; Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany., Yoon Y; Department of Microbiology and Molecular Genetics, School of Medicine, University of California Irvine, Irvine, California 92617, USA., Barash Y; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA yosephb@upenn.edu mihaela.zavolan@unibas.ch.; Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA., Zavolan M; Biozentrum, University of Basel, 4056 Basel, Switzerland yosephb@upenn.edu mihaela.zavolan@unibas.ch.; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
Source: RNA (New York, N.Y.) [RNA] 2023 Dec; Vol. 29 (12), pp. 1839-1855. Date of Electronic Publication: 2023 Oct 10.
Publication Type: Review; Journal Article
Journal Info: Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9509184 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1469-9001 (Electronic) Linking ISSN: 13558382 NLM ISO Abbreviation: RNA Subsets: MEDLINE
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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>; Department of Neuromuscular Diseases, UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, UCL, London WC1N 3BG, United Kingdom.<br /><searchLink fieldCode="AU" term="%22Burri+D%22">Burri D</searchLink>; Biozentrum, University of Basel, 4056 Basel, Switzerland.; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Gazzara+MR%22">Gazzara MR</searchLink>; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.<br /><searchLink fieldCode="AU" term="%22Herrmann+CJ%22">Herrmann CJ</searchLink>; Biozentrum, University of Basel, 4056 Basel, Switzerland.; Swiss Institute of Bioinformatics, 1015 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 EH9 3FF, 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 20892, USA.<br /><searchLink fieldCode="AU" term="%22Wan+YK%22">Wan YK</searchLink>; Genome Institute of Singapore, Buona Vista, Singapore 138672.; Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge, Singapore 119228.<br /><searchLink fieldCode="AU" term="%22Zhuang+F%22">Zhuang F</searchLink>; Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.<br /><searchLink fieldCode="AU" term="%22Fansler+MM%22">Fansler MM</searchLink>; Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Graduate Studies, New York, New York 10065, USA.; Cancer Biology and Genetics, Sloan-Kettering Institute, MSKCC, New York, New York 10065, USA.<br /><searchLink fieldCode="AU" term="%22Fernández+JM%22">Fernández JM</searchLink>; Life Sciences Department, Barcelona Supercomputing Center, 08034 Barcelona, Spain.; Spanish National Bioinformatics Institute (INB/ELIXIR-ES), 28029 Madrid, Spain.<br /><searchLink fieldCode="AU" term="%22Ferret+M%22">Ferret M</searchLink>; Life Sciences Department, Barcelona Supercomputing Center, 08034 Barcelona, Spain.; Spanish National Bioinformatics Institute (INB/ELIXIR-ES), 28029 Madrid, Spain.<br /><searchLink fieldCode="AU" term="%22Gonzalez-Uriarte+A%22">Gonzalez-Uriarte A</searchLink>; Life Sciences Department, Barcelona Supercomputing Center, 08034 Barcelona, Spain.; Spanish National Bioinformatics Institute (INB/ELIXIR-ES), 28029 Madrid, Spain.<br /><searchLink fieldCode="AU" term="%22Haynes+S%22">Haynes S</searchLink>; Institute for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3FF, United Kingdom.<br /><searchLink fieldCode="AU" term="%22Herdman+C%22">Herdman C</searchLink>; Department of Neurobiology, University of Utah, Salt Lake City, Utah 84132, USA.<br /><searchLink fieldCode="AU" term="%22Kanitz+A%22">Kanitz A</searchLink>; Biozentrum, University of Basel, 4056 Basel, Switzerland.; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Katsantoni+M%22">Katsantoni M</searchLink>; Biozentrum, University of Basel, 4056 Basel, Switzerland.; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Marini+F%22">Marini F</searchLink>; Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg-University Mainz, 55118 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, Leeds LS2 9NL, United Kingdom.<br /><searchLink fieldCode="AU" term="%22Nicolet+B%22">Nicolet B</searchLink>; Department of Hematopoiesis, Sanquin Research, Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, 1066 CX Amsterdam, The Netherlands.; Oncode Institute, 3521 AL Utrecht, The Netherlands.<br /><searchLink fieldCode="AU" term="%22Poon+CL%22">Poon CL</searchLink>; Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York 10065, USA.<br /><searchLink fieldCode="AU" term="%22Rot+G%22">Rot G</searchLink>; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.; Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland.<br /><searchLink fieldCode="AU" term="%22Schärfen+L%22">Schärfen L</searchLink>; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut 06520, USA.<br /><searchLink fieldCode="AU" term="%22Wu+PJ%22">Wu PJ</searchLink>; Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 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 92617, USA.<br /><searchLink fieldCode="AU" term="%22Barash+Y%22">Barash Y</searchLink>; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA yosephb@upenn.edu mihaela.zavolan@unibas.ch.; Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.<br /><searchLink fieldCode="AU" term="%22Zavolan+M%22">Zavolan M</searchLink>; Biozentrum, University of Basel, 4056 Basel, Switzerland yosephb@upenn.edu mihaela.zavolan@unibas.ch.; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
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