Search Results - "yeast"

Impact of systems biology on metabolic engineering

Table of Contents: “…Contents: The biorefinery concept -- The process of metabolic engineering (ME) -- Approaches in systems biology (SB) -- Genome scale metabolic models (GEMs) -- Using SB to design succinic acid production in yeast -- Using SB to compare metabolism of yeast strains -- Using SB to compare penicillin producing in yeast strains -- Inverse metabolic engineering -- Using inverse ME to improve galactose utilization in yeast -- Mechanisms of evolutionary trade-offs.…”
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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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Computational modelling of GPCR signalling dynamics

Table of Contents: “…Contents: GPCRs signalling kinetics can be modelled using simple equations -- Link between computational modelling and pharmacology -- Yeast are excellent system for computational models -- RGS proteins show non-intuitive activity -- Kinetic models of GPCRs can model agonist bias.…”
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