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Bacterial Pangenomics: Methods and Protocols
Paperback
Series: Methods in Molecular Biology, Book 2242
Medical ReferenceOther Animals
ISBN13: 9781071611012
Publisher: Humana
Published: May 7 2022
Pages: 268
Weight: 1.08
Height: 0.59 Width: 7.00 Depth: 10.00
Language: English
Part I: Opportunities from Novel Sequencing Technologies
1. PacBio-Based Protocol for Bacterial Genomes Assembly
Agata Motyka-Pomagruk, Sabina Zoledowska, Michal Kabza, and Ewa Lojkowska
2. The Illumina Sequencing Protocol and the NovaSeq 6000 System
Part II: Pangenomics of Cultured Isolates
3. Comparative Analysis of Core and Accessory Genes in Co-Expression Network
Biliang Zhang, Jian Jiao, Pan Zhang, Wen-Jing Cui, Ziding Zhang, and Chang-Fu Tian
4. Inferring Core Genome Phylogenies for Bacteria
Alexander Keller and Markus J. Ankenbrand
5. Inferring Phylogenomic Relationship of Microbes Using Scalable Alignment-Free Methods
Guillaume Bernard, Timothy G. Stephens, Raúl A. González-Pech, and Cheong Xin Chan
6. Fast Phylogeny Reconstruction from Genomes of Closely Related Microbes
Bernhard Haubold and Fabian Klötzl
7. Comparative Genomics, from the Annotated Genome to Valuable Biological Information: A Case Study
Sabina Zoledowska, Agata Motyka-Pomagruk, Agnieszka Misztak, and Ewa Lojkowska
Part III: Dark Matter Pangenomics
8. Accurate Annotation of Microbial Metagenomic Genes and Identification of Core Sets
Chiara Vanni
9. Metagenomic Assembly: Reconstructing Genomes from Metagenomes
Zhang Wang, Jieliang Liang, Linan Huang, Alessio Mengoni, and Wensheng Shu
10. Genome Recovery, Functional Profiling, and Taxonomic Classification from Metagenomes
Davide Albanese and Claudio Donati
11. Functional Metagenomics for Identification of Antibiotic Resistance Genes (ARGs)
Francesca Di Cesare
12. Host Trait Prediction from High-Resolution Microbial Features
Giovanni Bacci
Part IV: Progresses in Genome-to-Phenome Inference
13. Phylogenetic Methods for Genome-Wide Association Studies in Bacteria
Xavier Didelot
14. Simple, Reliable, and Time-Efficient Manual Annotation of Bacterial Genomes with MAISEN
Mikolaj Dziurzynski, Przemyslaw Decewicz, Karol Ciuchcinski, Adrian Gorecki, and Lukasz Dziewit
Part V: Cookbook for Pangenomics
15. A Compendium of Bioinformatic Tools for Bacterial Pangenomics to Be Used by Wet-Lab Scientists
Camilla Fagorzi and Alice Checcucci
16. A Protocol for Teaching Basic Next Generations Sequencing (NG
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