Part I: Novel Sequencing and Bioinformatic Pipelines for the Study of Parasite Genomes
1. Nanopore Long Read DNA Sequencing of Protozoan Parasites: Hybrid Genome Assembly of Trypanosoma cruzi
Florencia Diaz-Viraque, Gonzalo Greif, Luisa Berna, and Carlos Robello
2. Chromosomes Conformation Capture Coupled with Next Generation Sequencing (Hi-C) in Plasmodium falciparum
Mohit Gupta, Todd Lenz, and Karine G. Le Roch
3. Sequencing and Reconstructing Helminth Mitochondrial Fenomes Directly from Genomic Next-Generation Sequencing Data
Nikola Palevich and Paul Haydon Maclean
4. Automated Phylogenetic Analysis Using Best Reciprocal BLAST
Erin R. Butterfield, James C. Abbott, and Mark C. Field
Part II: Diagnostic Approaches Using Genomic Tools
5. An Illumina MiSeq-Based Amplicon Sequencing Method for the Detection of Mixed Parasite Infections Using the Blastocystis SSU rRNA Gene as an Example
Jenny G. Maloney, Nadja S. George, Aleksey Molokin, and Monica Santin
6. Giardia duodenalis: Detection by Quantitative Real-Time PCR and Molecular Diversity
Alejandro Dashti, Pamela C. Koester, and David Carmena
Part III: Host-Parasite Interactions: Deciphering Gene Function and Molecular Processes in Parasites
7. Conditional Gene Deletion in Mammalian and Mosquito Stages of Plasmodium berghei Using Dimerizable Cre Recombinase
Priyanka Fernandes, Manon Loubens, Olivier Silvie, and Sylvie Briquet
8. Coupling Auxin-Inducible Degron System with Ultrastructure Expansion Microscopy to Accelerate the Discovery of Gene Function in Toxoplasma gondii
Nicolas Dos Santos Pacheco and Dominique Soldati-Favre
9. Genome-Wide Analysis of RNA-Protein Interactions in Plasmodium falciparum Using eCLIP-Seq
Thomas Hollin, Steven Abel, and Karine G. Le Roch
10. Transcriptional Analysis of Tightly Synchronized Plasmodium falciparum Intraerythrocytic Stages by RT-qPCR
Nuria Casas-Vila, Anastasia K. Pickford, Harvie P. Portugaliza, Elisabet Tinto-Font, and Alfred Cortes
11. Analysis of the Interaction between Plasmodium falciparum-Infected Erythrocytes and Human Endothelial Cells Using a Laminar Flow System, Bioinformatic Tracking and Transcriptome Analysis
Yifan Wu, Philip Bouws, Stephan Lorenzen, Iris Bruchhaus, and Nahla Galal Metwally
12. Integration of Genomic and Transcriptomic Data to Elucidate Molecular Processes in Babesia divergens
Luis Miguel Gonzalez, Elena Sevilla, Miguel Fernandez-Garcia, Alejandro Sanchez-Flores, and Estrella Montero
13. Integration of Functional Genomic, Transcriptomic, and Metabolomic Data to Identify Key Features in Genomic Expression, Metabolites, and Metabolic Pathways of Babesia divergens
Miguel Fernandez-Garcia, Alejandro Sanchez-Flores, Luis Miguel Gonzalez, Coral Barbas, M Fernanda Rey-Stolle, Elena Sevilla, Antonia Garcia, and Estrella Montero
14. Genome Analysis of Programmed DNA Elimination in Parasitic Nematodes
Jianbin Wang
15. Helminth Microbiota Profiling Using Bacterial 16S rRNA Gene Amplicon Sequencing: From Sampling to Sequence Data Mining
Fabio Formenti, Gabriel Rinaldi, Cinzia Cantacessi, and Alba Cortes
Part IV: Genomics of Parasite-Derived Extracellular Vesicles
16. Methods for the Isolation and Study of Exovesicle DNA from Trypanosomatid Parasites
Lina Maria Orrego, Romina Romero, Antonio Osuna, and Luis M. de Pablos
17. Isolation and Analysis of MicroRNAs from Extracellular Vesicles of the Parasitic Model Nematodes Nippostrongylus brasiliensis and Trichuris muris
Ramon M. Eichenberger