All Publications


  • Outreach and online training services at the Saccharomyces Genome Database DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION MacPherson, K. A., Starr, B., Wong, E. D., Dalusag, K. S., Hellerstedt, S. T., Lang, O., Nash, R. S., Skrzypek, M. S., Engel, S. R., Cherry, J. M. 2017

    Abstract

    The Saccharomyces Genome Database (SGD; www.yeastgenome.org ), the primary genetics and genomics resource for the budding yeast S. cerevisiae , provides free public access to expertly curated information about the yeast genome and its gene products. As the central hub for the yeast research community, SGD engages in a variety of social outreach efforts to inform our users about new developments, promote collaboration, increase public awareness of the importance of yeast to biomedical research, and facilitate scientific discovery. Here we describe these various outreach methods, from networking at scientific conferences to the use of online media such as blog posts and webinars, and include our perspectives on the benefits provided by outreach activities for model organism databases.http://www.yeastgenome.org.

    View details for DOI 10.1093/database/bax002

    View details for Web of Science ID 000397529600002

    View details for PubMedID 28365719

  • The Saccharomyces Genome Database Variant Viewer. Nucleic acids research Sheppard, T. K., Hitz, B. C., Engel, S. R., Song, G., Balakrishnan, R., Binkley, G., Costanzo, M. C., Dalusag, K. S., Demeter, J., Hellerstedt, S. T., Karra, K., Nash, R. S., Paskov, K. M., Skrzypek, M. S., Weng, S., Wong, E. D., Cherry, J. M. 2016; 44 (D1): D698-702

    Abstract

    The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. In recent years, we have moved toward increased representation of sequence variation and allelic differences within S. cerevisiae. The publication of numerous additional genomes has motivated the creation of new tools for their annotation and analysis. Here we present the Variant Viewer: a dynamic open-source web application for the visualization of genomic and proteomic differences. Multiple sequence alignments have been constructed across high quality genome sequences from 11 different S. cerevisiae strains and stored in the SGD. The alignments and summaries are encoded in JSON and used to create a two-tiered dynamic view of the budding yeast pan-genome, available at http://www.yeastgenome.org/variant-viewer.

    View details for DOI 10.1093/nar/gkv1250

    View details for PubMedID 26578556

    View details for PubMedCentralID PMC4702884

  • Integration of new alternative reference strain genome sequences into the Saccharomyces genome database. Database : the journal of biological databases and curation Song, G., Balakrishnan, R., Binkley, G., Costanzo, M. C., Dalusag, K., Demeter, J., Engel, S., Hellerstedt, S. T., Karra, K., Hitz, B. C., Nash, R. S., Paskov, K., Sheppard, T., Skrzypek, M., Weng, S., Wong, E., Michael Cherry, J. 2016; 2016

    Abstract

    The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. To provide a wider scope of genetic and phenotypic variation in yeast, the genome sequences and their corresponding annotations from 11 alternative S. cerevisiae reference strains have been integrated into SGD. Genomic and protein sequence information for genes from these strains are now available on the Sequence and Protein tab of the corresponding Locus Summary pages. We illustrate how these genome sequences can be utilized to aid our understanding of strain-specific functional and phenotypic differences.Database URL: www.yeastgenome.org.

    View details for DOI 10.1093/database/baw074

    View details for PubMedID 27252399

    View details for PubMedCentralID PMC4888754