(as subset of) Cross species papers

Sequence / microRNA

1. Sequencing and comparison of yeast species to identify genes and regulatory elements.

2. Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes.

3. Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals.

4. Inparanoid: a comprehensive database of eukaryotic orthologs.

Expression

1. Cross species analysis of microarray expression data.

2. Similarities and differences in genome-wide expression data of six organisms.

3. A gene-coexpression network for global discovery of conserved genetic modules.

4. Periodic gene expression program of the fission yeast cell cycle.

5. Co-evolution of transcriptional and post-translational cell-cycle regulation.

6. Combined analysis reveals a core set of cycling genes.

7. A genetic signature of interspecies variations in gene expression.

8. A gene atlas of the mouse and human protein-encoding transcriptomes.

9. Assessing the conservation of mammalian gene expression using high-density exon arrays.

10. Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering.

Regulation

1. Tissue-specific transcriptional regulation has diverged significantly between human and mouse.

2. Divergence of transcription factor binding sites across related yeast species.

3. Orthologous transcription factors in bacteria have different functions and regulate different genes.

4. Alignment and Prediction of cis-Regulatory Modules Based on a Probabilistic Model of Evolution.

5. Cross-species de novo identification of cis-regulatory modules with GibbsModule: Application to gene regulation in embryonic stem cells.

6. Towards an evolutionary model of transcription networks.

7. Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species.

Interactions

1. Conserved patterns of protein interaction in multiple species.

2. PathBLAST: a tool for alignment of protein interaction networks.

3. Graemlin: general and robust alignment of multiple large interaction networks.

4. High throughput interaction data reveals degree conservation of hub proteins.

5. Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets.

6. Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.

7. Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast.

8. Protein complex evolution does not involve extensive network rewiring.

9. Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species.

10. Null mutations in human and mouse orthologs frequently result in different phenotypes.

11. A Scalable Approach for Discovering Conserved Active Subnetworks across Species.