Description
SPRINGER Plant Bioinformatics Methods And Protocols 3Ed (Hb 2022) by EDWARDS D.
This new edition focuses on applied bioinformatics with specific applications to crops, model and diverse plant species. The scope extends from the genome to the phenome and includes aspects of data management, analysis, visualization, and integration. The methods and approaches found within reflect the increasing use of high performance computing infrastructure to analyze and manage the enormous volume of data being generated by the latest high throughput technologies, the establishment and further maturation of major database systems and repositories, as well as the introduction of new approaches such as machine learning. Written for the highly successful Methods in Molecular Biology series, the chapters include the kind of detailed implementation advice that leads to successful research results. Authoritative and up-to-date, Plant Bioinformatics: Methods and Protocols, Third Edition will aid researchers exploring the broad comparison of species that will drive future plant research, crop breeding, and bioinformatics developments that allow us to understand and manipulate the heritable differences between individuals and populations. Chapters 2, 3, and 26 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com. 1. Using GenBank and SRAEric W. Sayers, Chris O'Sullivan, and Ilene Karsch-Mizrachi2. Scripting Analyses of Genomes in Ensembl PlantsBruno Contreras-Moreira, Guy Naamati, Marc Rosello, James E. Allen, Sarah E. Hunt, Matthieu Muffato, Astrid Gall, and Paul Flicek3. CyVerse for Reproducible Research: RNA-Seq AnalysisJason Williams4. Doing Genetic and Genomic Biology Using the Legume Information System and Associated ResourcesSven Redsun, Sam Hokin, Connor T. Cameron, Alan M. Cleary, Joel Berendzen, Sudhansu Dash, Anne V. Brown, Andrew Wilkey, Jacqueline D. Campbell, Wei Huang, Scott R. Kalberer, Nathan T. Weeks, Steven B. Cannon, and Andrew D. Farmer5. Gramene: A Resource for Comparative Analysis of Plants Genomes and PathwaysMarcela Karey Tello-Ruiz, Pankaj Jaiswal, and Doreen Ware6. CerealsDB: A Whistle-Stop Tour of an Open Access SNP ResourceMark Winfield, Paul Wilkinson, Amanda Burridge, Alexandra Allen, Jane Coghill, Christy Waterfall, Keith Edwards, and Gary Barker7. The Barley and Wheat Pan-GenomesNadia Kamal, Thomas Lux, Murukarthick Jayakodi, Georg Haberer, Heidrun Gundlach, Klaus F.X. Mayer, Martin Mascher, and Manuel Spannagl8. Basics of BashRobyn Anderson9. Pipeline Automation via SnakemakeJakob Petereit10. SciApps: An Automated Platform for Processing and Distribution of Plant Genomics DataLiya Wang, Zhenyuan Lu, Peter Van Buren, and Doreen Ware11. Trimming and Validation of Illumina Short Reads Using Trimmomatic, Trinity Assembly, and Assessment of RNA-Seq DataSteven O. Sewe, Goncalo Silva, Paulo Sicat, Susan E. Seal, and Paul Visendi12. De Novo Assembly of Linked Reads Using Supernova 2.0Paul Visendi13. Applications of Optical Mapping for Plant Genome Assembly and Structural Variation DetectionYuxuan Yuan14. Making a Pangenome Using the Iterative Mapping ApproachCassandria Tay Fernandez15. Construction of Practical Haplotype Graph (PHG) with the Whole Genome Sequence DataPradeep Ruperao, Prasad Gandham, and Abhishek Rathore16. Visualization Tools for Genomic ConservationVenkat Bandi, Carl Gutwin, Jorge Nunez Siri, Eric Neufeld, Andrew Sharpe, and Isobel Parkin17. Annotation of Protein-Coding Genes in Plant GenomesBhavna Hurgobin18. Finding and Characterizing Repeats in Plant GenomesJacques Nicolas, Sebastien Tempel, Anna-Sophie Fiston-Lavier, and Emira Cherif19. Gene Co-Expression Network AnalysisJuan D. Montenegro20. Skim-Based Genotyping by Sequencing Using a Double Haploid Population to Call SNPs, Infer Gene Conversions, and Improve Genome AssembliesPhilipp Emanuel Bayer21. Managing High-Density Genotyping Data with GigwaGuilhem Sempere, Pierre Larmande, and Mathieu Rouard22. Machine Learning for Image Analysis: Leaf Disease SegmentationMonica F. Danilevicz and Philipp E. Bayer23. Analysis of Bisulphite Sequencing Data Using Bismark and DMRcaller to Identify Differentially Methylated RegionsHueyTyng Lee24. Long Intergenic Non-Coding RNA (lincRNA) Discovery from Non-Strand Specific RNA-Seq DataAgnieszka Golicz25. Linkage Disequilibrium Statistics and Block VisualizationJacob Marsh26. Analysis of Small RNA Sequencing Data in PlantsVanika Garg and Rajeev K. Varshney27. Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity KnowledgebasesParul Gupta, Sushma Naithani, Justin Preece, Sunghwan Kim, Tiejun Cheng, Peter D'Eustachio, Justin Elser, Evan E. Bolton, and Pankaj Jaiswal28. AgroLD: A Knowledge Graph Database for Plant Functional GenomicsPierre Larmande, Gildas Tagny Ngompe, Aravind Venkatesan, and Manuel Ruiz