High-Density Sequencing Applications in Microbial Molecular Genetics

1. Characterizing the Role of Exoribonucleases in the Control of Microbial Gene Expression: Differential RNA-SeqVânia Pobre and Cecília M. Arraiano2. Conformational Studies of Bacterial Chromosomes by High-Throughput Sequencing MethodsVirginia S. Lioy and Frédéric Boccard3. Large-Scale Measurement of mRNA Degradation in Escherichia coli: To Delay or Not to DelaySandrine Laguerre, Ignacio González, Sébastien Nouaille, Annick Moisan, Nathalie Villa-Vialaneix, Christine Gaspin, Marie Bouvier, Agamemnon J. Carpousis, Muriel Cocaign-Bousquet and Laurence Girbal4. FASTBAC-Seq: Functional AnalysiS of Toxin-Antitoxin Systems in BACteria by Deep SequencingSara Masachis, Nicolas J. Tourasse, Sandrine Chabas, Olivier Bouchez and Fabien Darfeuille5. The Challenges of Genome-Wide Studies in a Unicellular Eukaryote With Two Nuclear GenomesSandra Duharcourt and Linda Sperling6. CLIP-Seq in Bacteria: Global Recognition Patterns of Bacterial RNA-Binding ProteinsLiis Andresen and Erik Holmqvist7. High-Resolution Profiling of NMD Targets in YeastFeng He, Alper Celik, Richard Baker and Allan Jacobson8. Generation of a Metagenomics Proximity Ligation 3C Library of a Mammalian Gut MicrobiotaThéo Foutel-Rodier, Agnès Thierry, Romain Koszul and Martial Marbouty9. Genome-Wide Mapping of Yeast Retrotransposon Integration Target SitesAnastasia Barkova, Amna Asif-Laidin and Pascale Lesage10. Genome-Wide Quantitation of Protein Synthesis Rates in BacteriaGrace E. Johnson and Gene-Wei Li11. On the Prowl: An In Vivo Method to Identify RNA Partners of a sRNAMarie-Claude Carrier, Claire Morin and Eric Massé12. Analysis of Bacterial Transcription by "Massively Systematic Transcript End Readout," MASTERIrina O. Vvedenskaya, Seth R. Goldman and Bryce E. Nickels13. Transcriptomic Approaches for Studying Quorum Sensing in Vibrio choleraeRoman Herzog and Kai Papenfort14. In Vitro Study of the Major Bacillus subtilis Ribonucleases Y and JLiliana Mora, Saravuth Ngo, Soumaya Laalami and Harald Putzer15. Mapping 5'-Ends and Their Phosphorylation State With EMOTE, TSS-EMOTE, and nEMOTEPeter Redder16. MS2-Affinity Purification Coupled With RNA Sequencing Approach in the Human Pathogen Staphylococcus aureusDavid Lalaouna, Emma Desgranges, Isabelle Caldelari and Stefano Marzi17. Noncoding RNAs in Archaea: Genome-Wide Identification and Functional ClassificationAnne Buddeweg, Michael Daume, Lennart Randau and Ruth A. Schmitz18. Methodology for Ribosome Profiling of Key Stages of the Caulobacter crescentus Cell CycleJames R. Aretakis, Nadra Al-Husini and Jared M. Schrader19. Transcriptome-Wide Analysis of Protein-RNA and RNA-RNA Interactions in Pathogenic BacteriaJai J. Tree, Kenn Gerdes and David Tollervey20. Profiling RNA Polymerase II Phosphorylation Genome-Wide in Fission YeastTea Kecman, Dong-Hyuk Heo and Lidia Vasiljeva21. Toward Cell Type-Specific In Vivo Dual RNA-SeqLutz Frönicke, Denise N. Bronner, Mariana X. Byndloss, Bridget McLaughlin, Andreas J. Bäumler and Alexander J. Westermann22. Genomic Analysis of DNA Double-Strand Break Repair in Escherichia coliA.M. Mahedi Hasan, Benura Azeroglu and David R.F. Leach