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A first course in systems biology / by Voit, Eberhard O.

Table of Contents: “…chapter 1 Biological Systems -- chapter 2 Introduction to Mathematical Modeling -- chapter 3 Static Network Models -- chapter 4 The Mathematics of Biological Systems -- chapter 5 Parameter Estimation -- chapter 6 Gene Systems -- chapter 7 Protein Systems -- chapter 8 Metabolic Systems -- chapter 9 Signaling Systems -- chapter 10 Population Systems -- chapter 11 Integrative Analysis of Genome, Protein, and Metabolite Data: A Case Study in Yeast -- chapter 12 Physiological Modeling: The Heart as an Example -- chapter 13 Systems Biology in Medicine and Drug Development -- chapter 14 Design of Biological Systems -- chapter 15 Emerging Topics in Systems Biology.…”
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Computational methods in analysis of gene regulation and protein interactions

Table of Contents: “…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.…”
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Protein networks and analysis of global gene expression

Table of Contents: “…Contents: A paradigm shift: from databases of protein sequences to protein interactions -- Technologies for measuring interactions -- Chromatin immunoprecipitation (ChIP) -- Yeast Two Hybrid (Y2H) technology -- Mass spectrometry based approaches -- Methods for querying protein networks with gene expression profiles -- Systematic validation of protein network models using gene deletions -- Cytoscape open-source software for network modeling and visualization -- Methods for network comparison across species -- Application to discover conserved protein complexes among the networks of yeast, worm, fly and Plasmodium -- Methods for querying protein networks to explain genetic (synthetic lethal) interactions -- Future directions: how network queries will enable systems biology.…”
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