Gavin Sherlock

Administrative Appointments

• Internal Advisory Board, PharmGKB (2003 - 2005)
• Steering Committee, NINDS/NIMH Microarray Consortium (2003 - 2009)
• Advisory Board, TAIR (2002 - 2004)
• Board of Directors, MGED (2002 - present)

Honors and Awards

• Army Breast Cancer Research Fellowship, Department of Defence (1997-1998)
• Cold Spring Harbor Fellowship, Cold Spring Harbor Laboratory (1996-1997)
• Prize Studentship, The Wellcome Trust (1991-1994)
• John Buckley Entrance Scholarship for Science, Manchester University (1988-1991)

Professional Education

Graduate & Fellowship Program Affiliations

• Biomedical Informatics
• Genetics

Web Site Links

• Sherlock Lab Home Page

Research Interests

1. Evolution and the Adpative Landscape

When yeast are evolved under various selective pressures in a chemostat, mutations that arise and provide an adaptive advantage will expand within the population. We are using high throughput sequencing to determine the identity of such mutations, as well as to understand the dynamics of the mutations within the populations, and the interactions between the mutations (such as epistasis).

2. Genome Annotation by Transcriptome Sequencing

The set of genes in a sequenced genome has typically been defined using various prediction criteria (such as ORFs capable of encoding a protein > 100 amino acids), coupled with experimental data, such as transposon mutagenesis and EST sequencing. The availability of high throughput sequencing now allows full transcriptome sequencing to better annotate the transcribed regions of the genome, and we are applying this to various yeasts.

3. The Stanford Microarray Database (http://smd.stanford.edu/microarray/)

The Stanford Microarray Database (SMD) serves all on campus microarray researchers, and allows them to share their experimental data with each other and off-site collaborators. It is the largest academic microarray database in the world, and makes available more public data than any other microarray database. Our current projects for development of SMD include the incorporation of controlled vocabularies for the annotation of experiments and gene products, the addition of tools for quality assessment and control, and the implementation of new tools for data analysis.

4. The Candida Genome Database (http://www.candidagenome.org/)

Candida albicans is the most important human fungal pathogen. We have created a curated resource for the Candida albicans research community, that was built on the existing infrastructure of the Saccharomyces Genome Database. We curate gene names, gene ontology terms and phenotypes from the literature,...

Publications

• Industrial fuel ethanol yeasts contain adaptive copy number changes in genes involved in vitamin B1 and B6 biosynthesis. Stambuk BU, Dunn B, Alves SL, Duval EH, Sherlock G. Genome Res. 2009
• Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus. Dunn B, Sherlock G. Genome Res. 2008; 18 (10): 1610-23
• Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae. Kao KC, Sherlock G. Nat Genet. 2008; 40 (12): 1499-504
• Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species. Lee A, Hansen KD, Bullard J, Dudoit S, Sherlock G. PLoS Genet. 2008; 4 (12): e1000299
• Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008; 455 (7216): 1061-8