1. Studying Circadian Rhythm and Sleep Using Genetic Screens in Drosophila Sofia Axelrod, Lino Saez and Michael W. Young 2. Dissecting the Mechanisms of the Clock in Neurospora Jennifer Hurley, Jennifer J. Loros and Jay C. Dunlap 3. High Throughput and Quantitative Approaches for Measuring Circadian Rhythms in Cyanobacteria Using Bioluminescence Ryan K. Shultzaberger, Mark L. Paddock, Takeo Katsuki, Ralph J. Greenspan and Susan S. Golden 4. Using Circadian Entrainment to Find Cryptic Clocks Zheng Eelderink-Chen, Maria Olmedo, Jasper Bosman and Martha Merrow 5. Wavelet-based Analysis of Circ adian Behavioral Rhythms Tanya L. Leise 6. Genetic Analysis of Drosophila Circadian Behavior in Semi-Natural Conditions Edward W Green, Emma K O'Callaghan, Mirko Pegoraro, J Douglas Armstrong, Rodolfo Costa3 and Charalambos P Kyriacou 7. Methods to Study Molecular Mechanisms of the Neurospora Circadian Clock Joonseok Cha, Mian Zhou, and Yi Liu 8. Detecting KaiC Phosphorylation Rhythms of the Cyanobacterial Circadian Oscillator in Vitro and in Vivo Yong-Ick Kim, Joseph S. Boyd, Javier Espinosa, and Susan S. Golden 9. The Role of Casein Kinase I in the Drosophila Circadian Clock Jeffrey L. Price, Jin-Yuan Fan, Andrew Keightley and John C. Means 10. Purification and Analysis of PERIOD Protein Complexes of the Mammalian Circadian Clock Jin Young Kim, Pieter Bas Kwak, Michael Gebert, Hao A. Duong and Charles J. Weitz 11. Best Practices for Fluorescence Microscopy of the Cyanobacterial Circadian Clock Susan E. Cohen, Marcella L. Erb, Joe Pogliano and Susan S. Golden 12. Structural and Biophysical Methods to Analyze Clock Function and Mechanism Martin Egli 13. Identification of Small Molecule Modulators of the Circadian Clock Tsuyoshi Hirota and Steve A. Kay 14. ChIP-Seq and RNA-Seq Methods to Study Circadian Control of Transcription in Mammals Joseph S. Takahashi, Vivek Kumar , Prachi Nakashe, Nobuya Koike, Hung-Chung Huang, Carla B. Green, and Tae-Kyung Kim 15. Chipping away at the Drosophila Clock Jian Zhou, Wangjie Yu and Paul E. Hardin 16. Considerations for RNA-seq Analysis of Circadian Rhythms Jiajia Li, Gregory R Grant, John B Hogenesch and Michael E Hughes 17. RNA-Seq Profiling of Small Numbers of Drosophila Neurons Katharine Abruzzi, Xiao Chen, Emi Nagoshi, Abby Zadina, and Michael Rosbash 18. Analysis of Circadian Regulation of Poly(A) Tail Length Shihoko Kojima and Carla B. Green 19. Sample Preparation for Phosphoproteomic Analysis of Circadian Time Series in Arabidopsis Thaliana Johanna Krahmer, Matthew M Hindle, Sarah F Martin, Thierry Le Bihan and Andrew J Millar