Assigned Readings

Chromatin Structure

Pokholok et al. Cell, 2005. Genome-wide map of nucleosome acetylation and methylation in yeast.

Yuan et al. Science, 2005. Genome-scale identification of nucleosome positions in S. cerevisiae.

RNA Regulation

Lim et al. Nature, 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs.

Sood et al. PNAS, 2006. Cell-type-specific signatures of microRNAs on target mRNA expression.

John et al. PLoS Biology, 2004. Human microRNA targets.

Foat et al. PNAS, 2005. Profiling condition-specific, genome-wide regulation of mRNA stability in yeast.

Protein - Protein Interactions

Yeger-Lotem et al. PNAS 2004. Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction.

Zhang et al. J Biol. 2004. Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network.

Jansen et al. Science 2003. A Bayesian networks approach for predicting protein-protein interactions from genomic data.

Lee et al. Science 2004. A Probabilistic Functional Network of Yeast Genes.

Sharan et al. PNAS 2005. Conserved patterns of protein interaction in multiple species.

Jensen et al. Nature 2006. Co-evolution of transcriptional and post-transcriptional cell-cycle regulation.

Han et al. Nature Biotechnology 2005. Effect of sampling on topology predictions of protein-protein interaction networks."

Han et al. Nature 2004. Evidence for dynamically organized modularity in the yeast protein-protein interaction network.

Gavin et al. Nature 2006. Proteome survey reveals intrinsic modularity in genetic networks.

Krogan et al. Nature 2006. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.

Jaimovich et al. JCB 2006. Towards an integrated protein-protein interaction network: a relational Markov network approach.

Metabolic Networks

Duarte et al. Genome Research 2004. Reconstruction and validation of Saccharomyces cerevisia iND750, a fully compartmentalized genome-scale metabolic model.

Fong and Palsson. Nature Genetics 2004. Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes.

Shlomi et al. PNAS 2005. Regulatory on/off minimization of metabolic flux changes after genetic perturbations.

Covert et al. Journal of Theoretical Biology 2001. Regulation of gene expression in flux balance models of metaboism.

Edwards et al. Nature Biotechnology 2001. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data.

Timothy Allen and Bernhard Palsson. Contraint-based Modeling: Part I. Biological Constraints, Network Reconstruction, and FBA.

Bilu et al. PLoS Computational Biology 2006. Conservation of Expression and Sequence of Metabolic Genes is Reflected by Activity Across Metabolic States.

Fong et al. Genome Research 2005. Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states.

Almaas et al. Nature 2004. Global organization of metabolic fluxes in the bacterium Escherichia coli.

Almaas et al. PLoS Computational Biology 2005. The activity reaction core and plasticity of metabolic networks .

Kharchenko et al. BMC Bioinformatics 2006. Identifying metabolic enzymes with multiple types of association evidence .

Ihmels et al. Nature Biotechnology 2003. Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae .

Zaslaver et al. Nature Genetics 2004. Just-in-time transcriptional program in metabolic pathways .

Phenotype

Kelley and Ideker. Nature Biotechnology 2005. Systematic interpretation of genetic interactions using protein networks .

Zhang et al. Journal of Biology 2005. Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network.

Workman et al. Science 2006. A systems approach to mapping DNA damage response pathways.

Segre et al. Nature Genetics 2004. Modular epistasis in yeast metabolism.