In the advance, online edition of Genome Biology this week, Swiss and American researchers used short read data and tiling arrays to find deletions in Arabidopsis genomes. In the four Arabidopsis strains or accessions they analyzed, the team found several individual deletions that were shared between two or more accessions. That, in turn, prompted them to speculate that some of the variable gene content observed in Arabidopsis might reflect common deletion events.
Johns Hopkins University researcher Akhilesh Pandey and an international group of collaborators describe a public resource of curated human signal transduction pathways called NetPath. The group touted the resource as a tool that will help researchers visualize, process, and work with signaling pathway data gleaned from thousands of published papers. "We anticipate NetPath to become a consolidated resource for human signaling pathways that should enable systems biology approaches," they write.
Michael Ashburner and co-workers discuss ways to retrospectively integrate phenotype ontologies across different species in their methods paper. They provide evidence in favor of using logical definitions to sort out and integrate these ontologies. "We propose a methodology that can be used to add value to existing phenotype ontologies by mapping them to a common reference framework based on existing standard ontologies," they write.
Researchers from the Naval Medical Research Center, the University of Maryland, the University of Florida, 454 Life Sciences, and Emory University report on their work to sequence and characterize the genomes of eight Yersinia species. After getting an average of 25-fold to 42-fold coverage of the genomes, the team was able to compare the genomes of non-invasive and invasive Yersinia species, tease apart relationships between them and gain clues about Yersinia species sequenced in the past.