This book constitutes the thoroughly refereed post-proceedings of the RECOMB 2004 Satellite Workshop on Regulatory Genomics, RRG 2004, held in San Diego, CA, USA in March 2004.
The 10 revised full papers presented were carefully reviewed and improved for inclusion in the book. The papers address a broad variety of aspects of regulatory genomics including classification, functional module detection, proteonomics, sampling, kernel methods, TF binding motifs, gene expression data analysis, regulatory network model learning, RNA regulatory sequence motifs, DNA regulatory sequence motifs, parameter landscape analysis, and biological network regulation.
Author(s): Manuel Middendorf, Anshul Kundaje, Chris Wiggins, Yoav Freund (auth.), Eleazar Eskin, Christopher Workman (eds.)
Series: Lecture Notes in Computer Science 3318 : Lecture Notes in Bioinformatics
Edition: 1
Publisher: Springer-Verlag Berlin Heidelberg
Year: 2005
Language: English
Pages: 116
Tags: Algorithm Analysis and Problem Complexity; Discrete Mathematics in Computer Science; Data Structures; Database Management; Bioinformatics; Computer Appl. in Life Sciences
Front Matter....Pages -
Predicting Genetic Regulatory Response Using Classification: Yeast Stress Response....Pages 1-13
Detecting Functional Modules of Transcription Factor Binding Sites in the Human Genome....Pages 14-21
Fishing for Proteins in the Pacific Northwest....Pages 22-29
PhyloGibbs: A Gibbs Sampler Incorporating Phylogenetic Information....Pages 30-41
Application of Kernel Method to Reveal Subtypes of TF Binding Motifs....Pages 42-51
Learning Regulatory Network Models that Represent Regulator States and Roles....Pages 52-64
Using Expression Data to Discover RNA and DNA Regulatory Sequence Motifs....Pages 65-78
Parameter Landscape Analysis for Common Motif Discovery Programs....Pages 79-87
Inferring Cis-region Hierarchies from Patterns in Time-Course Gene Expression Data....Pages 88-97
Modeling and Analysis of Heterogeneous Regulation in Biological Networks....Pages 98-113
Back Matter....Pages -
