Part I Experimental Analysis of Signalling in Gene Regulatory Networks

1. Global Estimation of mRNA Stability in Yeast

Julia Marín-Navarro, Alexandra Jauhiainen, Joaquín Moreno, Paula Alepuz, José E. Pérez-Ortín, and Per Sunnerhagen

2. Genomic-wide Methods to Evaluate Transcription Rates in Yeast

José García-Martínez, Vicent Pelechano, and José E. Pérez-Ortín

3. Construction of Cis-regulatory Input Functions of Yeast Promoters

Prasuna Ratna and Attila Becskei

4. Luminescence as a Continuous Real-Time Reporter of Promoter Activity in Yeast Undergoing Respiratory Oscillations or Cell Division Rhythms

J. Brian Robertson and Carl Hirschie Johnson

5. Linearizer Gene Circuits with Negative Feedback Regulation

Dmitry Nevozhay, Rhys M. Adams, and Gábor Balázsi

6. Measuring In vivo Signaling Kinetics in a Mitogen-activated Kinase Pathway using Dynamic Input Stimulation

Megan N. McClean, Pascal Hersen, and Sharad Ramanathan

Part II Mathematical Modelling of Network Behavior

7. Stochastic Analysis of Gene Expression

Xiu-Deng Zheng and Yi Tao

8. Studying Adaptation and Homeostatic Behaviors of Kinetic Networks by using MATLAB

Tormod Drengstig, Thomas Kjosmoen, and Peter Ruoff

9. Biochemical Systems Analysis of Signaling Pathways to Understand Fungal Pathogenicity

Jacqueline Garcia, Kellie J. Sims, John H. Schwacke, and Maurizio Del Poeta

10. Clustering Change Patterns Using Fourier Transformation with Time-course Gene Expression Data

Jaehee Kim

Part III Analysis of Network Behaviour by Quantitative Genetics

11. Finding Modulators of Stochasticity Levels by Quantitative Genetics

Steffen Fehrmann and Gaël Yvert

12. Functional Mapping of Expression Quantitative Trait Loci That Regulate Oscillatory Gene Expression

Arthur Berg, Ning Li, Chunfa Tong, Zhong Wang, Scott A. Berceli, and Rongling Wu

Part IV Examination of Network Behaviour in Related Yeast Species

13. Evolutionary Aspects of a Genetic Network: Studying the Lactose/Galactose Regulon of Kluyveromyces lactis

Alexander Anders and Karin D. Breunig

14. Analysis of Subtelomeric Silencing in Candida glabrata

Alejandro Juárez-Reyes, Alejandro De Las Peñas, and Irene Castaño

15. Morphological and Molecular Genetic Analysis of Epigenetic Switching of the Human Fungal Pathogen Candida albicans

Denes Hnisz, Michael Tscherner, and Karl Kuchler

16. Quantitation of Cellular Components in Cryptococcus neoformans for System Biology Analysis

Arpita Singh, Asfia Qureshi, and Maurizio Del Poeta