News
A preview of PomBase, the new model organism database for the fission yeast Schizosaccharomyces pombe, has been announced to the S. pombe community for testing and feedback. For more on PomBase, see the NAR Database Issue paper (PubMed abstract) or contact the PomBase staff.
A paper describing PomBase has been published online will be included in the 2012 Database Issue of Nucleic Acids Research. Abstract and open access full text are available.
A paper describing the major findings of the Schizosaccharomyces Comparative Genome Project was published today in Science Express and reported changes are included in GeneDB.
Further details are described in the pombe mailing list posts:
Further information on the pombe mailing list.
Further details are available on the pombe mailing list.
The analysis of the fission yeast deletion collection is now published online in Nature Biotechnology.
Funding was awarded by the Wellcome Trust for a fission yeast Model Organism Database, Pombase.
Fission yeast is one of the 12 key organisms of the reference genomes project. The goal of this project is to completely annotate twelve reference genomes so that those annotations may be used to effectively seed the automatic annotation efforts of other genome.
GeneDB (S. pombe) now uses the latest update to Pfam, release 24.0 and 88.5% of fission yeast proteins now contain a match to at least one Pfam domain (increased from 83% in version 23).
The fission yeast genome and annotation dataset is now available as part of Ensembl Fungi.
GeneDB is now using Version 23 of the Pfam protein family database. A total of 4154 (83%) S. pombe proteins now have at least one Pfam domain or family assignment (compared to 76% for S. cerevisiae), the highest percentage coverage for any eukaryote.
S. pombe GeneDB now includes "deep links" to the Biological General Repository for Interaction Datasets (BioGRID) interaction datasets from the 'Database Cross References' section of the individual Gene Pages.
Dynamic repertoire of the fission yeast transcriptome reveals: 94% of the genome is transcribed; extensive variation in different stages and conditions; global and condition-specific coupling between splicing efficiency and transcription; confirms the majority of introns; refines ~75 gene structures; identifies 453 new transcripts 26 of which were predicted to code for proteins.
The h- mating type region has been provided by Xavier Marsellach and Lorena Aguilar.
Baumann and Zakian labs identify elusive telomerase RNA (PMID:18157152 and PMID:18157149)
Wellcome Trust Advanced Course 'Genome-wide approaches with fission yeast' held in Hinxton.
4th International Fission Yeast Meeting held in Copenhagen.
GeneDB representation of the fission yeast data moved from contigs to chromosomes. See the pombelist archive for details.
The October issue of the journal Yeast is a fission yeast special issue containing 13 articles and reviews commissioned as a result of the European Fission Yeast Meeting, which are FREE to download.
The first fission yeast whole proteome localization study is now published: Matsuyama A. et al (2006): ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe. Nat Biotech 24, 841-7.
The fission yeast database survey is now closed. You can view the survey results here.
The European Fission Yeast Meeting (16th-18th March 2006) and The Fission Yeast Bioinformatics workshop (15th - 16th Mar 2006) both took place at the Wellcome Trust Genome Campus in Hinxton (Cambridge, UK).
Comparative Genomics of Eukaryotic Microorganisms:
Eukaryotic Genome Evolution, Approaches with Yeasts and Fungi
This conference took place from 12th-17th November 2005 in Sant Feliu de Guixols, Spain. Full details can be found here.
Second East Coast Regional pombe Meeting
This meeting took place from November 11-13, 2005 in Miami Beach, Florida.
A project to record published genetic and physical interactions is underway with Mike Tyers and the GRID group at Toronto.
The meeting was held at UC San Diego on August 24-29, 2004.
This issue of Methods includes 11 papers for fission yeast protocols including DNA damage checkpoint assays, cell wall analysis, TAP, nuclear envelope integrity assays, GFP imaging, TS mutant creation and plasmid use and construction. See Methods or click here for details of the papers including PMIDs.
Correlations Between Gene Expression and Gene Conservation in Fission Yeast. Mata J, Bahler J. Genome Res. 2003 Nov 12 PMID:14613978
FELINES: a utility for extracting and examining EST-defined introns and exons. Drabenstot SD et al Nucleic Acids Res. 2003 Nov 15;31(22):e141. PMID:14602934
Genome-wide distribution of DNA replication origins at A+T-rich islands in Schizosaccharomyces pombe. Segurado M, De Luis A, Antequera F. EMBO Rep. 2003 Nov;4(11):1048-53. Epub 2003 Oct 17. PMID:14566325
Retrotransposons and their recognition of pol II promoters: a comprehensive survey... Bowen NJ et al Genome Res. 2003 Sep;13(9):1984-97. PMID:12952871
Egel, R., Copenhagen, Denmark (Ed.) The Molecular Biology of Schizosaccharomyces pombe Genetics, Genomics and Beyond ISBN:3-540-00693-1
Decottignies A, Sanchez-Perez I, Nurse P Genome Res. 2003 Mar;13(3):399-406. PMID:12618370
Chen D, Toone WM, Mata J, Lyne R, Burns G, Kivinen K, Brazma A, Jones N, Bähler J. Mol Biol Cell. 2003 Jan;14(1):214-29. www.ncbi.nlm.nih.gov/pubmed?term=12529438http://www.ncbi.nlm.nih.gov/pubmed?term=12529438