Key Documents
Curriculum Vitae available Online
Gavin Sherlock
- Assistant Professor (Research), Genetics
- Member, Cancer Center
Contact Information
- Academic Offices
Personal Information Email sherlock@genome.stanford.edu Tel (650) 498-6012
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
- B.Sc., Manchester University Genetics (1991)
- Ph.D., Manchester University Molecular Biology (1994)
Graduate & Fellowship Program Affiliations
Web Site Links
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, and also provide various tools for exploring these data.
5. The Aspergillus Genome Database (http://www.aspgd.org/)
There are a number of sequenced Aspergillus species, which include pathogens (A. fumigatus), a genetic model (A. nidulans) and industrially relevant strains (e.g. A. oryzae). We have created a database to house curated data from these species, and in collaboration with Jennifer Wortman's group at the University of Maryland, are working to improve annotation across all the genomes using a comparative genomics pipeline.
6. The Tuberculosis Database (http://www.tbdb.org/)
In collaboration with James Galagan's group, we have built a database containing both curated information for M. tuberculosis, as well as genomic and high throughput experimental data, with various tools for navigating and exploring these data.
Publications
- Genome Res. 2009;
- Genome Res. 2008; (10): 1610-23
- Nat Genet. 2008; (12): 1499-504
- PLoS Genet. 2008; (12): e1000299
- Nature. 2008; (7216): 1061-8
- Mol Syst Biol. 2006; 2006.0001
- Bioinformatics. 2004; (18): 3710-5
- Mol Biol Cell. 2002; (6): 1977-2000
- Mol Biol Cell. 1998; (12): 3273-97
- Nucleic Acids Res. 2009;
- Nucleic Acids Res. 2009;
- Trends Microbiol. 2009; (7): 295-303
- Nature. 2009; (7247): 657-62
- Nucleic Acids Res. 2009; (Database issue): D898-901
- Nucleic Acids Res. 2009; (Database issue): D499-508
- Nucleic Acids Res. 2008; (Database issue): D871-7
- Science. 2008; (5905): 1187-8
- Stem Cells. 2008; (2): 364-71
- BMC Bioinformatics. 2008; 28
- Nat Biotechnol. 2008; (3): 305-12
- Nucleic Acids Res. 2007; (Database issue): D766-70
- Nucleic Acids Res. 2007; (Database issue): D452-6
- BMC Bioinformatics. 2007; 338
- N Engl J Med. 2007; (3): 217-26
- Nature. 2006; (7111): 513-5
- BMC Bioinformatics. 2006; 489
- OMICS. 2006; (2): 205-8
- Nature. 2006; (7080): 24
- Methods Enzymol. 2006; 194-213
- Radiother Oncol. 2006; (2): 230-5
- Methods Mol Biol. 2006; 191-208
- Nat Biotechnol. 2006; (1): 21-2; author reply 23
- FEMS Yeast Res. 2006; (5): 671-84
- Nucleic Acids Res. 2005; (Database issue): D580-2
- Nucleic Acids Res. 2005; (Database issue): D358-63
- BMC Genomics. 2005; (1): 53
- Nat Methods. 2005; (5): 329-30
- Mol Biotechnol. 2005; (3): 239-51
- PLoS Genet. 2005; (1): 36-57
- BMC Bioinformatics. 2004; 151
- Microbiology. 2004; (Pt 11): 3522-4
- Nat Biotechnol. 2004; (9): 1179-83
- Trends Biotechnol. 2004; (6): 270-3
- Trends Biotechnol. 2004; (6): 277-8
- Nat Genet. 2004; (8): 795-6
- BMC Bioinformatics. 2004; 141
- Environ Health Perspect. 2004; (12): A666-7
- PLoS Biol. 2004; (9): E317
- BMC Bioinformatics. 2003; 32
- Methods Mol Biol. 2003; 235-48
- Nucleic Acids Res. 2003; (1): 219-23
- Nucleic Acids Res. 2003; (1): 94-6
- Genome Biol. 2002; (9): RESEARCH0046
- Science. 2002; (5593): 539
- Bioinformatics. 2002; (11): 1409
- Lancet. 2002; (9314): 1301-7
- Nucleic Acids Res. 2002; (1): 69-72
- Nat Genet. 2001; (4): 365-71
- Bioinformatics. 2001; (6): 520-5
- Brief Bioinform. 2001; (4): 350-62
- Genome Res. 2001; (8): 1425-33
- Nucleic Acids Res. 2001; (1): 80-1
- Nucleic Acids Res. 2001; (1): 152-5
- Proc Natl Acad Sci U S A. 2000; (26): 14668-73
- Nucleic Acids Res. 2000; (1): 77-80
- Nat Genet. 2000; (1): 25-9
- Nature. 2000; (6769): 503-11
- Curr Opin Immunol. 2000; (2): 201-5
- Nucleic Acids Res. 1999; (1): 74-8
- Science. 1998; (5396): 2022-8
- Mol Gen Genet. 1994; (6): 716-23
- J Gen Microbiol. 1993; (11): 2531-41