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Parasite Genomics Protocols, Second Edition expands upon the previous edition with current, detailed methodologies that have been adapted to research parasites in the post genomic era. With new chapters on parasite studies, helminth pathogens, and protocols for undertaking other large-scale 'omics' methodologies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and practical, Parasite Genomics Protocols, Second Edition offers a wide-ranging collection of diverse methods and protocols for further study into these unique organisms.

Parasite Genomics Protocols

1. The Eukaryotic Pathogen Databases: A Functional Genomic Resource Integrating Data from of Human and Veterinary Parasites

Omar S. Harb and David S. Roos

2. From Sequence Mapping to Genome Assemblies

Thomas D. Otto

3. Sequencing and Annotation of Mitochondrial Genomes from Individual Parasitic Helminths

Aaron R. Jex, D. Timothy Littlewood, and Robin B. Gasser

4. A Beginners Guide to Estimating the Non-synonymous to Synonymous Rate Ratio of all Protein-coding Genes in a Genome

Daniel C. Jeffares, Bartlomiej Tomiczek,Victor Sojo, and Mario dos Reis

5. Exploiting Genetic Variation to Discover Genes Involved in Important Disease Phenotypes

Paul Capewell, Anneli Cooper, Caroline Clucas, Willie Weir, Heli Vaikkinen, Liam Morrison, Andy Tait, and Annette MacLeod

6. Identification and Analysis of Ingi-Related Retroposons in the Trypanosomatid Genomes

Frédéric Bringaud, Matthew Rogers, and Elodie Ghedin

7. Approaches for Studying mRNA Decay Mediated by SIDER2 Retroposons in Leishmania

Barbara Papadopoulou, Michaela Müller-McNicoll, and Prasad K. Padmanabhan

8. Gene Suppression in Schistosomes using RNAi

Akram A. Da'dara and Patrick J. Skelly

9. Construction of Trypanosoma brucei Illumina RNA-Seq Libraries Enriched for Transcript Ends

Nikolay G. Kolev, Elisabetta Ullu and Christian Tschudi

10. Techniques to Study Epigenetic Control and the Epigenome in Parasites

Sheila C. Nardelli, Li-Min Ting, and Kami Kim

11. The Genome-wide Identification of Promoter Regions in Toxoplasma gondii

Junya Yamagish and Yutaka Suzuki

12. RNA-seq Approaches for Determining mRNA Abundance in Leishmania

Andrew Haydock, Monica Terrao, Aarthi Sekar, Gowthaman Ramasamy, Loren Baugh, and Peter J. Myler

13. Protein Microarrays for Parasite Antigen Discovery

Patrick Driguez, Denise L Doolan, Douglas M Molina, Alex Loukas, Angela Trieu, Phil L Felgner, and Donald P McManus

14. A Transposon-based Tool for Transformation and Mutagenesis in Trypanosomatid Protozoa

Jeziel D. Damasceno, Stephen M. Beverley, and Luiz R. O. Tosi

15. Separation of Basic Proteins from Leishmania using a combination of Free Flow Electrophoresis (FFE) and 2D Electrophoresis (2-DE) under Basic Conditions

Marie-Christine Brotherton, Gina Racine, and Marc Ouellette

16. Proteomic Analysis of Post Translational Modifications using iTRAQ in Leishmania

Dan Zilberstein

17. Large Scale Differential Proteome Analysis in Plasmodium falciparum under Drug Treatment

Judith Helena Prieto, Elisabeth Fisher, Sasa Koncarevic, John Yates, and Katja Becker

18. Use of ¹³C Stable Isotope Labelling for Pathway and Metabolic Flux Analysis in Leishmania Parasites

Eleanor C. Saunders, David P. de Souza, Jennifer M. Chambers, Milica Ng, James Pyke, and Malcolm J. McConville

19. Molecular Genotyping of Trypanosoma cruzi for Lineage Assignment and Population Genetics

Louisa A. Messenger, Matthew Yeo, Michael D. Lewis, Martin S. Llewellyn, and Michael A. Miles

20. Screening Leishmania donovani Complex-specific Genes Required for Visceral Disease

Wen-Wei Zhang and Greg Matlashewski