Gavin Sherlock
Publications
- Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments. Genome Res. 2012; (5): 908-24
- DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer. Genome Res. 2011; (7): 1017-27
- Hunger artists: yeast adapted to carbon limitation show trade-offs under carbon sufficiency. PLoS Genet. 2011; (8): e1002202
- Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape. PLoS Genet. 2011; (4): e1002056
- A genome-wide analysis reveals no nuclear dobzhansky-muller pairs of determinants of speciation between S. cerevisiae and S. paradoxus, but suggests more complex incompatibilities. PLoS Genet. 2010; (7): e1001038
- Bulk segregant analysis by high-throughput sequencing reveals a novel xylose utilization gene from Saccharomyces cerevisiae. PLoS Genet. 2010; (5): e1000942
- Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae. Nat Genet. 2008; (12): 1499-504
- Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus. Genome Res. 2008; (10): 1610-23
- GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics. 2004; (18): 3710-5
- Comparative metabolic footprinting of a large number of commercial wine yeast strains in Chardonnay fermentations. FEMS Yeast Res. 2013; (4): 394-410
- Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae. BMC Microbiol. 2013; (1): 91
- Improved gene ontology annotation for biofilm formation, filamentous growth, and phenotypic switching in Candida albicans. Eukaryot Cell. 2013; (1): 101-8
- Recurrent rearrangement during adaptive evolution in an interspecific yeast hybrid suggests a model for rapid introgression. PLoS Genet. 2013; (3): e1003366
- APJ1 and GRE3 homologs work in concert to allow growth in xylose in a natural Saccharomyces sensu stricto hybrid yeast. Genetics. 2012; (2): 621-32
- Different selective pressures lead to different genomic outcomes as newly-formed hybrid yeasts evolve. BMC Evol Biol. 2012: 46
- The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources. Nucleic Acids Res. 2012; (Database issue): D653-9
- The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata. Nucleic Acids Res. 2012; (Database issue): D667-74
- Turbidostat culture of Saccharomyces cerevisiae W303-1A under selective pressure elicited by ethanol selects for mutations in SSD1 and UTH1. FEMS Yeast Res. 2012; (5): 521-33
- GC-content normalization for RNA-Seq data. BMC Bioinformatics. 2011: 480
- Integrated genomic analyses of ovarian carcinoma. Nature. 2011; (7353): 609-15
- Annotare--a tool for annotating high-throughput biomedical investigations and resulting data. Bioinformatics. 2010; (19): 2470-1
- Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq. Genome Res. 2010; (10): 1451-8
- Microarray karyotyping of maltose-fermenting Saccharomyces yeasts with differing maltotriose utilization profiles reveals copy number variation in genes involved in maltose and maltotriose utilization. J Appl Microbiol. 2010; (1): 248-59
- New tools at the Candida Genome Database: biochemical pathways and full-text literature search. Nucleic Acids Res. 2010; (Database issue): D428-32
- Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads. BMC Genomics. 2010: 663
- TB database 2010: overview and update. Tuberculosis (Edinb). 2010; (4): 225-35
- The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community. Nucleic Acids Res. 2010; (Database issue): D420-7
- Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature. 2009; (7247): 657-62
- Gene Ontology and the annotation of pathogen genomes: the case of Candida albicans. Trends Microbiol. 2009; (7): 295-303
- Implementation of GenePattern within the Stanford Microarray Database. Nucleic Acids Res. 2009; (Database issue): D898-901
- Industrial fuel ethanol yeasts contain adaptive copy number changes in genes involved in vitamin B1 and B6 biosynthesis. Genome Res. 2009; (12): 2271-8
- TB database: an integrated platform for tuberculosis research. Nucleic Acids Res. 2009; (Database issue): D499-508
- Changes to NIH grant system may backfire. Science. 2008; (5905): 1187-8
- Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008; (7216): 1061-8
- Isolation and molecular characterization of cancer stem cells in MMTV-Wnt-1 murine breast tumors. Stem Cells. 2008; (2): 364-71
- Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nat Biotechnol. 2008; (3): 305-12
- 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. PLoS Genet. 2008; (12): e1000299
- The Stanford Tissue Microarray Database. Nucleic Acids Res. 2008; (Database issue): D871-7
- The XBabelPhish MAGE-ML and XML translator. BMC Bioinformatics. 2008: 28
- OntologyWidget - a reusable, embeddable widget for easily locating ontology terms. BMC Bioinformatics. 2007: 338
- Sequence resources at the Candida Genome Database. Nucleic Acids Res. 2007; (Database issue): D452-6
- The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res. 2007; (Database issue): D766-70
- The prognostic role of a gene signature from tumorigenic breast-cancer cells. N Engl J Med. 2007; (3): 217-26
- A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics. 2006: 489
- Cell cycle: complex evolution. Nature. 2006; (7111): 513-5
- Clustering microarray data. Methods Enzymol. 2006: 194-213
- Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). OMICS. 2006; (2): 205-8
- Global analysis of gene function in yeast by quantitative phenotypic profiling. Mol Syst Biol. 2006: 2006.0001
- Radiation-induced effects on gene expression: an in vivo study on breast cancer. Radiother Oncol. 2006; (2): 230-5
- The Candida Genome Database: facilitating research on Candida albicans molecular biology. FEMS Yeast Res. 2006; (5): 671-84
- The Stanford Microarray Database: a user's guide. Methods Mol Biol. 2006: 191-208
- Top-down standards will not serve systems biology. Nature. 2006; (7080): 24
- Wrestling with SUMO and bio-ontologies. Nat Biotechnol. 2006; (1): 21-2; author reply 23
- A human-curated annotation of the Candida albicans genome. PLoS Genet. 2005; (1): 36-57
- Microarray karyotyping of commercial wine yeast strains reveals shared, as well as unique, genomic signatures. BMC Genomics. 2005: 53
- Of fish and chips. Nat Methods. 2005; (5): 329-30
- Storage and retrieval of microarray data and open source microarray database software. Mol Biotechnol. 2005; (3): 239-51
- The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information. Nucleic Acids Res. 2005; (Database issue): D358-63
- The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res. 2005; (Database issue): D580-2
- An open letter on microarray data from the MGED Society. Microbiology. 2004; (Pt 11): 3522-4
- Caryoscope: an Open Source Java application for viewing microarray data in a genomic context. BMC Bioinformatics. 2004: 151
- Final words: cell age and cell cycle are unlinked. Trends Biotechnol. 2004; (6): 277-8
- Funding high-throughput data sharing. Nat Biotechnol. 2004; (9): 1179-83
- GeneXplorer: an interactive web application for microarray data visualization and analysis. BMC Bioinformatics. 2004: 141
- Reply: whole-culture synchronization - effective tools for cell cycle studies. Trends Biotechnol. 2004; (6): 270-3
- STARTing to recycle. Nat Genet. 2004; (8): 795-6
- Standards for microarray data: an open letter. Environ Health Perspect. 2004; (12): A666-7
- Submission of microarray data to public repositories. PLoS Biol. 2004; (9): E317
- Microarray databases: storage and retrieval of microarray data. Methods Mol Biol. 2003: 235-48
- SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res. 2003; (1): 219-23
- The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD). BMC Bioinformatics. 2003: 32
- The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res. 2003; (1): 94-6
- Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol. 2002; (9): RESEARCH0046
- Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell. 2002; (6): 1977-2000
- Molecular characterisation of soft tissue tumours: a gene expression study. Lancet. 2002; (9314): 1301-7
- Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002; (1): 69-72
- Standards for microarray data. Science. 2002; (5593): 539
- The underlying principles of scientific publication. Bioinformatics. 2002; (11): 1409
- Analysis of large-scale gene expression data. Brief Bioinform. 2001; (4): 350-62
- Creating the gene ontology resource: design and implementation. Genome Res. 2001; (8): 1425-33
- Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001; (4): 365-71
- Missing value estimation methods for DNA microarrays. Bioinformatics. 2001; (6): 520-5
- Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001; (1): 80-1
- The Stanford Microarray Database. Nucleic Acids Res. 2001; (1): 152-5
- A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc Natl Acad Sci U S A. 2000; (26): 14668-73
- Analysis of large-scale gene expression data. Curr Opin Immunol. 2000; (2): 201-5
- Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000; (6769): 503-11
- Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; (1): 25-9
- Integrating functional genomic information into the Saccharomyces genome database. Nucleic Acids Res. 2000; (1): 77-80
- Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. Nucleic Acids Res. 1999; (1): 74-8
- Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science. 1998; (5396): 2022-8
- Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell. 1998; (12): 3273-97
- Molecular cloning and analysis of CDC28 and cyclin homologues from the human fungal pathogen Candida albicans. Mol Gen Genet. 1994; (6): 716-23
- Starting to cycle: G1 controls regulating cell division in budding yeast. J Gen Microbiol. 1993; (11): 2531-41

