MPG.eBooks - Table of Contents: Computational methods in analysis of gene regulation and protein interactions

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Bibliographic Details
Main Author:	Shamir, Ron
Format:	eBook
Language:	English
Published:	London Henry Stewart Talks 2012, 2012
Series:	Protein homeostasis : folding proteins and maintaining the protein-protein interaction networks
Subjects:	Computational Biology Computational Biology / Methods Systems Biology Protein Interaction Mapping Algorithms Protein-protein Interactions / Data Processing Biological Models Proteomics Gene Regulatory Networks
Online Access:	https://hstalks.com/bs/2219 https://hstalks.com/bs/p/641
Collection:	Henry Stewart Talks - Collection details see MPG.ReNa

Table of Contents:

Finding regulatory motifs
Finding motifs using target sets of promoters
Problem definition
The Amadeus motif finding algorithm
Architecture, benchmark results and global analysis
Finding transcriptional programs and their regulatory motifs
Problem definition
The Allegro software for recovering transcriptional program
Results on yeast osmotic shock expression profiles
Recovering microRNA binding motifs from 3' UTRs using stem cell expression profiles
Discovering a novel motif pair in C. elegans
Utilizing network information
Using expression and protein interaction data
Problem definition and the Matisse algorithm
Demonstration of Matisse on yeast osmotic shock data
Comparison of Matisse to other algorithms
Demonstration of Matisse on human stem cell data
The pluripotency network
Using expression and protein interaction data with interaction confidence
The Cezanne algorithm
DNA damage response in yeast