Genboree News:

« NIH Epigenomics Roadmap Initiative hosted by Genboree »   The Epigenomics Data Analysis and Coordination Center (EDACC), a key component of the NIH Epigenomics Roadmap Initiative, will be hosted by Genboree.

« The Cancer Genome Atlas »  The Cancer Genome Atlas (TCGA) project has adopted Genboree for target selection, PCR assay design, quarterly reporting, and mutation capture. For more information, please refer to this PowerPoint® file.

« Sea Urchin »  The Sea Urchin genome has been published, and its sequence and annotations are now available! You can read more and access the database at The HGSC Sea Urchin site . That database is linked to Genboree, so you can view the annotations in context (example).

« Rhesus »  The Rhesus Macaque genome (rheMac2) is now available as a genomic template within Genboree. A public database contains assembly- and gene-related tracks, as well as BAC-mappings by end sequences and PGI, and fosmid end mappings.

« H.s. Chr3 »  The Human Chr 3 Nature publication is now available. Annotations developed and used during the curation effort have been published in Genboree, and many of the figures and tables are linked to the Genboree database.

« H.s. Chr12 »  A project page for the Human Chr12 Nature publication has been created. The public Genboree database contains annotations from the curation effort.

« Cows »  We mapped contigs from the preliminary cow genome assembly onto human using Pash. The cow contig mappings are available through Genboree.

BRL News:

« Genome Portrait of MCF-7 in NYT, Genome Res. »  
A map of breakpoints in the MCF-7 breast cancer cell line made by BRL grad student Oliver A. Hampton is featured in The New York Times ("The Chaos Inside a Cancer Cell") and is published in Genome Research (Hampton et al., 2008).

« Pash »  A new version of Pash, 2.0, has been released! It improves mapping accuracy in the presence of indels, increases speed by up to a factor of 3 over the previous version, and provides the option of refining Pash anchorings by performing banded alignment. Contributed by Pash's main developer, Cristian Coarfa. Please see the license and download page to acquire the new version.

« Genomic Triangulation »  Our paper Human-Specific Changes of Genome Structure Detected by Genomic Triangulation as well our contributions to the Evolutionary and Biomedical Insights from the Rhesus Macaque Genome paper have been published. Data used in the ancestral reconstructions, including genome pairwise comparisons, BAC mappings, fosmid mappings, and markers, as well as the reconstructions themselves and detected breakpoints are available through Genboree.

« Pash »  A new version of Pash has been released! Improvements in usage, dependencies, accuracy, scratch space, and small-query mapping; also, the introduction of new scoring methods. Contributed by Pash's main developer, Cristian Coarfa. Please see the license and download page to acquire the new version.

« H.s. Chr3 & Chr12 »  The Human Chr 3 & 12 Nature articles have been published. Figure 2 in both papers were contributed by Alan Harris. See the Genboree news items for more information and links.

« Gap Map »  We applied the Gap Map concept to the Rhesus-Human Comparative Linkage Map.

« Rhesus »  Our integrated comparative map of rhesus, chimp, and human includes matepair chains, contigs, and our latest mappings of 16,495 Rhesus BACs to the Human genome using the PGI method.

Note: The rhesus PGI paper has been published in Genome Research!

« Sequencing »  We have developed the Tagamizer program to parse and identify short sequence tags present in a sequencing read. The Tagamizer program is now available for download.