MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant whole-genome bisulfite sequencing data.

Autor: Hüther P; Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria.; LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Martinsried, Germany., Hagmann J; Computomics GmbH, 72072 Tübingen, Germany., Nunn A; ecSeq Bioinformatics GmbH, 04103 Leipzig, Germany.; Department of Computer Science, Leipzig University, 04107 Leipzig, Germany., Kakoulidou I; Department of Plant Sciences, Technical University of Munich, 85354 Freising, Germany., Pisupati R; Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria., Langenberger D; ecSeq Bioinformatics GmbH, 04103 Leipzig, Germany., Weigel D; Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany., Johannes F; Department of Plant Sciences, Technical University of Munich, 85354 Freising, Germany.; Institute for Advanced Study, Technical University of Munich, 85748 Garching, Germany., Schultheiss SJ; Computomics GmbH, 72072 Tübingen, Germany., Becker C; Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria.; LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Martinsried, Germany.

Publikováno v: Quantitative plant biology [Quant Plant Biol] 2022 Sep 26; Vol. 3, pp. e19. Date of Electronic Publication: 2022 Sep 26 (Print Publication: 2022).

Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates.

Autor: Nunn A; ecSeq Bioinformatics GmbH, Leipzig, Germany.; Department of Computer Science, Leipzig University, Leipzig, Germany., Rodríguez-Arévalo I; Genetics, Faculty of Biology, Ludwig Maximilians University, Martinsried, Germany.; Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC), Vienna, Austria., Tandukar Z; Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, USA., Frels K; Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, USA.; Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA., Contreras-Garrido A; Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany., Carbonell-Bejerano P; Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany., Zhang P; Institut de Recherche pour le Développement, UMR232 DIADE, Montpellier, France.; Laboratory of Plant Genome and Development, University of Perpignan, Perpignan, France., Ramos Cruz D; Genetics, Faculty of Biology, Ludwig Maximilians University, Martinsried, Germany.; Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC), Vienna, Austria., Jandrasits K; Genetics, Faculty of Biology, Ludwig Maximilians University, Martinsried, Germany.; Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC), Vienna, Austria., Lanz C; Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany., Brusa A; Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, USA., Mirouze M; Institut de Recherche pour le Développement, UMR232 DIADE, Montpellier, France.; Laboratory of Plant Genome and Development, University of Perpignan, Perpignan, France., Dorn K; Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA.; USDA-ARS, Soil Management and Sugarbeet Research, Fort Collins, CO, USA., Galbraith DW; BIO5 Institute, Arizona Cancer Center, Department of Biomedical Engineering, University of Arizona, School of Plant Sciences, Tucson, AZ, USA., Jarvis BA; School of Biological Sciences, Illinois State University, Normal, IL, USA., Sedbrook JC; School of Biological Sciences, Illinois State University, Normal, IL, USA., Wyse DL; Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, USA., Otto C; ecSeq Bioinformatics GmbH, Leipzig, Germany., Langenberger D; ecSeq Bioinformatics GmbH, Leipzig, Germany., Stadler PF; Department of Computer Science, Leipzig University, Leipzig, Germany.; Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany., Weigel D; Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany., Marks MD; Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA., Anderson JA; Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, USA., Becker C; Genetics, Faculty of Biology, Ludwig Maximilians University, Martinsried, Germany.; Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC), Vienna, Austria., Chopra R; Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, USA.; Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA.

Publikováno v: Plant biotechnology journal [Plant Biotechnol J] 2022 May; Vol. 20 (5), pp. 944-963. Date of Electronic Publication: 2022 Feb 06.

Erratum to: Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis.

Autor: Nunn A; ecSeq Bioinformatics GmbH, Sternwartenstraße 29, 04103, Saxony, Germany.; Institut für Informatik, Universität Leipzig, Härtelstraße 16-18, 04107, Saxony, Germany., Otto C; ecSeq Bioinformatics GmbH, Sternwartenstraße 29, 04103, Saxony, Germany., Stadler PF; Institut für Informatik, Universität Leipzig, Härtelstraße 16-18, 04107, Saxony, Germany., Langenberger D; ecSeq Bioinformatics GmbH, Leipzig, Germany.

Publikováno v: Briefings in bioinformatics [Brief Bioinform] 2021 Sep 02; Vol. 22 (5).

The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline.

Autor: Can SN; Plant Cell Biology, Department of Biology, University of Marburg, 35043 Marburg, Germany., Nunn A; ecSeq Bioinformatics GmbH, 04103 Leipzig, Germany.; Bioinformatics Group, Department of Computer Science, University of Leipzig, 04107 Leipzig, Germany., Galanti D; Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076 Tübingen, Germany., Langenberger D; ecSeq Bioinformatics GmbH, 04103 Leipzig, Germany., Becker C; Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.; Genetics, Faculty of Biology, Ludwig-Maximilians-University München, 82152 Martinsried, Germany., Volmer K; Department of Forest Genetic Resources, Nordwestdeutsche Forstliche Versuchsanstalt (NW-FVA), 37079 Göttingen, Germany., Heer K; Conservation Biology, Department of Biology, University of Marburg, 35043 Marburg, Germany.; Plant Ecology and Geobotany, Department of Biology, University of Marburg, 35043 Marburg, Germany., Opgenoorth L; Centre for Biological Signaling Studies (BIOSS), University of Freiburg, 79104 Freiburg, Germany., Fernandez-Pozo N; Plant Cell Biology, Department of Biology, University of Marburg, 35043 Marburg, Germany., Rensing SA; Plant Cell Biology, Department of Biology, University of Marburg, 35043 Marburg, Germany.; Centre for Biological Signaling Studies (BIOSS), University of Freiburg, 79104 Freiburg, Germany.; SYNMIKRO Center for Synthetic Microbiology, University of Marburg, 35043 Marburg, Germany.

Publikováno v: Epigenomes [Epigenomes] 2021 May 04; Vol. 5 (2). Date of Electronic Publication: 2021 May 04.

Comparison and benchmark of deep learning methods for non-coding RNA classification.

Autor: Creux, Constance^1,2 (AUTHOR), Zehraoui, Farida¹ (AUTHOR), Radvanyi, François² (AUTHOR), Tahi, Fariza¹ (AUTHOR) fariza.tahi@univ-evry.fr

Publikováno v: PLoS Computational Biology. 9/12/2024, Vol. 20 Issue 9, p1-21. 21p.