Sequence / microRNA
and comparison of yeast species to identify genes and regulatory elements.
discovery and characterization of fly microRNAs using
12 Drosophila genomes.
Systematic discovery of
regulatory motifs in human promoters and 3' UTRs by comparison of several
a comprehensive database of eukaryotic orthologs.
species analysis of microarray expression data.
differences in genome-wide expression data of six organisms.
A gene-coexpression network for global discovery of conserved
4. Periodic gene expression
program of the fission yeast cell cycle.
of transcriptional and post-translational cell-cycle regulation.
analysis reveals a core set of cycling genes.
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
divergence in the fungal response to fluconazole
revealed by soft clustering.
transcriptional regulation has diverged significantly between human and mouse.
transcription factor binding sites across related yeast species.
transcription factors in bacteria have different functions and regulate
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
an evolutionary model of transcription networks.
gene regulatory networks in the preimplantation
embryonic development of three mammalian species.
Conserved patterns of protein interaction in
a tool for alignment of protein interaction networks.
general and robust alignment of multiple large interaction networks.
interaction data reveals degree conservation of hub proteins.
of the human protein interactome and comparison with
yeast, worm and fly interaction datasets.
transfer between genomes: protein-protein interologs
and protein-DNA regulogs.
and rewiring of functional modules revealed by an epistasis
map in fission yeast.
8. Protein complex
evolution does not involve extensive network rewiring.
of phosphoregulation: comparison of phosphorylation patterns across yeast species.
10. Null mutations
in human and mouse orthologs frequently result in
A Scalable Approach for
Discovering Conserved Active Subnetworks across Species.