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

Autor: 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.

Publikováno v: RNA (New York, N.Y.) [RNA] 2023 Dec; Vol. 29 (12), pp. 1839-1855. Date of Electronic Publication: 2023 Oct 10.

The Translatome Map: RNC-Seq vs. Ribo-Seq for Profiling of HBE, A549, and MCF-7 Cell Lines.

Autor: Kozlova, Anna¹ (AUTHOR) lapd@ibmc.msk.ru, Sarygina, Elizaveta¹ (AUTHOR), Ilgisonis, Ekaterina¹ (AUTHOR) ilgisonis.ev@gmail.com, Tarbeeva, Svetlana¹ (AUTHOR), Ponomarenko, Elena¹ (AUTHOR)

Publikováno v: International Journal of Molecular Sciences. Oct2024, Vol. 25 Issue 20, p10970. 14p.

Long Non-Coding RNAs, Nuclear Receptors and Their Cross-Talks in Cancer—Implications and Perspectives.

Autor: Tiwari, Prabha¹ (AUTHOR) prabhatiwari@keio.jp, Tripathi, Lokesh P.^2,3 (AUTHOR) prabhatiwari@keio.jp

Publikováno v: Cancers. Aug2024, Vol. 16 Issue 16, p2920. 21p.

sRNAfrag: a pipeline and suite of tools to analyze fragmentation in small RNA sequencing data.

Autor: Nakatsu, Ken^1,2 (AUTHOR), Jijiwa, Mayumi² (AUTHOR), Khadka, Vedbar² (AUTHOR), Nasu, Masaki² (AUTHOR), Deng, Youping² (AUTHOR) dengy@hawaii.edu

Publikováno v: Briefings in Bioinformatics. Jan2024, Vol. 25 Issue 1, p1-15. 15p.

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