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 Díaz-Viraqué, Gonzalo Greif, Luisa Berná, 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. Köster, 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 Núria Casas-Vila, Anastasia K. Pickford, Harvie P. Portugaliza, Elisabet Tintó-Font, and Alfred Cortés 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 González, Elena Sevilla, Miguel Fernández-García, Alejandro Sánchez-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 Fernández-García, Alejandro Sanchez-Flores, Luis Miguel González, Coral Barbas, Mª Fernanda Rey-Stolle, Elena Sevilla, Antonia García, 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 Cortés Part IV: Genomics of Parasite-Derived Extracellular Vesicles 16. Methods for the Isolation and Study of Exovesicle DNA from Trypanosomatid Parasites Lina María 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.