Preface...
Table of Contents...
Contributing Authors...
1. From Genes to Networks: Characterizing Gene-Regulatory Interactions in Plants
Kerstin Kaufmann and Dijun Chen
Part I Experimental Approaches to Study Plant Gene-Regulatory Networks
2. Inducible Promoter Systems for Gene Perturbation Experiments in Arabidopsis
Bennett Thomson, Emmanuelle Graciet, and Frank Wellmer
3. Cell Type-Specific Gene Expression Profiling Using Fluorescence-Activated Nuclear Sorting
Daniel Slane and Martin Bayer
4. Characterization of Cell Type-Specific DNA Binding Sites of Plant Transcription Factors using Chromatin Immunoprecipitation
On Sun Lau
5. Yeast One and Two Hybrid High-Throughput Screenings using Arrayed Libraries
Rocio Sanchez-Montesino and Luis Onate-Sanchez
6. SELEX-Seq: A Method to Determine DNA-Binding Specificities of Plant Transcription Factors
Cezary Smaczniak, Gerco C. Angenent and Kerstin Kaufmann
7. Analysis of a Plant Transcriptional Regulatory Network using Transient Expression Systems
Sara Diaz-Trivino, Yuchen Long, Ben Scheres, and Ikram Blilou
8. Analysis of In Vivo Chromatin and Protein Interactions of Arabidopsis Transcript Elongation Factors
Alexander Pfab, Wojciech Antosz, Philipp Holzinger, Astrid Bruckmann, Joachim Griesenbeck, and Klaus D. Grasser
9. Characterization of Mediator Complex and its Associated Proteins from Rice
Subhasis Samanta and Jitendra Kumar Thakur
10. DNase I SIM: A Simplified In-Nucleus Method for DNase I Hypersensitive Site Sequencing
Sergei A. Filichkin and Molly Megraw
11. In Situ Hi-C Library Preparation for Plants to Study their Three-Dimensional Chromatin Interactions on a Genome-Wide Scale
Chang Liu
12. Multiplexed Transcriptional Activation or Repression in Plants using CRISPR-dCas9 Based Systems
Levi G. Lowder, Joseph W. Paul III, and Yiping Qi
13. Generation of dTALEs and Libraries of Synthetic TALE-Activated Promoters for Engineering of Gene Regulatory Networks in Plants
Tom Schreiber and Alain Tissier
Part II Computational Approaches to Study Plant Gene-Regulatory Networks
14. Design of Knowledge Bases for Plant Gene Regulatory Networks
Eric Mukundi, Fabio Gomez-Cano, Wilberforce Zachary Ouma, and Erich Grotewold
15. AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species
Tak Lee and Insuk Lee
16. Integration of Genome-Wide TF Binding and Gene Expression Data to Characterize Gene Regulatory Networks in Plant Development
Dijun Chen and Kerstin Kaufmann
17. Predicting Transcription Factor-Binding Sites and their Cognate Transcription Factors using Gene Expression Data
Chun-Ping Yu and Wen-Hsiung Li
18. Computational Approaches to Study Gene Regulatory Networks
Nooshin Omranian and Zoran Nikoloski
19. Boolean Dynamic Modeling Approaches to Study Plant Gene Regulatory Networks: Integration, Validation and Prediction
J. Davila-Velderrain, J.C. Martinez-Garcia, and R.E. Alvarez Buylla
20. ODE-Based Modeling of Complex Regulatory Circuits
Daniel D. Seaton
21. Inferring Gene Regulatory Networks in the Arabidopsis Root using a Dynamic Bayesian Network Approach
Maria Angels de Luis Balaguer and Rosangela Sozzani
