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List of works by Gavin Sherlock

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

scientific article

A guide to microarray experiments-an open letter to the scientific journals

scientific article published in The Lancet

A human-curated annotation of the Candida albicans genome

scientific article

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

scientific article

A single nucleotide polymorphism uncovers a novel function for the transcription factor Ace2 during Candida albicans hyphal development.

scientific article published on 15 April 2015

A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains

scientific article published in December 2000

APJ1 and GRE3 homologs work in concert to allow growth in xylose in a natural Saccharomyces sensu stricto hybrid yeast

scientific article

Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages

scientific article published on 15 January 2020

Adaptation is influenced by the complexity of environmental change during evolution in a dynamic environment

scientific article published on 25 January 2021

An open letter on microarray data from the MGED Society

scientific article published on November 2004

Analysis of Repair Mechanisms following an Induced Double-Strand Break Uncovers Recessive Deleterious Alleles in the Candida albicans Diploid Genome

scientific article published on 11 October 2016

Analysis of large-scale gene expression data

scientific article

Analysis of large-scale gene expression data

article

Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments

scientific article published on 27 February 2012

Annotare--a tool for annotating high-throughput biomedical investigations and resulting data

scientific article

Assembly of a phased diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure

scientific article published on January 2013

Author Correction: Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages

scientific article published on 31 January 2020

Bulk segregant analysis by high-throughput sequencing reveals a novel xylose utilization gene from Saccharomyces cerevisiae

scientific article (publication date: 13 May 2010)

Caryoscope: an Open Source Java application for viewing microarray data in a genomic context

scientific article

Cell cycle: complex evolution

scientific article

Changes in the distribution of fitness effects and adaptive mutational spectra following a single first step towards adaptation

scientific article published on 31 August 2021

Changes to NIH Grant System May Backfire

scientific article

Clustering microarray data

scientific article

Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus.

scientific article

Comparative metabolic footprinting of a large number of commercial wine yeast strains in Chardonnay fermentations

scientific article

Comparison of the complete protein sets of worm and yeast: orthology and divergence

scientific article

Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae

scientific article

Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq

scientific article

Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization

scientific article

Curation accuracy of model organism databases

scientific article

DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer

scientific article published on 26 April 2011

Design and implementation of microarray gene expression markup language (MAGE-ML)

scientific article

Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast

scientific article published on 27 August 2016

Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE).

scientific article published on January 2006

Different selective pressures lead to different genomic outcomes as newly-formed hybrid yeasts evolve

scientific article

Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling

scientific article (publication date: 3 February 2000)

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

scientific article

Ex uno plures: clonal reinforcement drives evolution of a simple microbial community

scientific article

Experimental evolution: prospects and challenges

scientific article published on December 2014

Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans

scientific article

Extremely Rare Polymorphisms in Saccharomyces cerevisiae Allow Inference of the Mutational Spectrum

scientific article

Final words: cell age and cell cycle are unlinked

scientific article published in June 2004

Funding high-throughput data sharing

scientific article

GC-content normalization for RNA-Seq data

scientific article

GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes

scientific article (publication date: 12 December 2004)

Gene Ontology and the annotation of pathogen genomes: the case of Candida albicans

scientific article published on 03 July 2009

Gene flow contributes to diversification of the major fungal pathogen Candida albicans

scientific article

Gene ontology: tool for the unification of biology

scientific article

GeneXplorer: an interactive web application for microarray data visualization and analysis

scientific article

Global analysis of gene function in yeast by quantitative phenotypic profiling

scientific article

Heterozygote Advantage Is a Common Outcome of Adaptation in Saccharomyces cerevisiae.

scientific article published on 18 May 2016

High-Throughput Yeast Strain Sequencing

scientific article

Hunger artists: yeast adapted to carbon limitation show trade-offs under carbon sufficiency

scientific article

Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors

scientific article published on 09 October 2013

Identification of genes periodically expressed in the human cell cycle and their expression in tumors

scientific article (publication date: June 2002)

Implementation of GenePattern within the Stanford Microarray Database.

scientific article published on 25 October 2008

Improved discovery of genetic interactions using CRISPRiSeq across multiple environments

scientific article published on 19 February 2019

Improved gene ontology annotation for biofilm formation, filamentous growth, and phenotypic switching in Candida albicans

scientific article published on 9 November 2012

Industrial fuel ethanol yeasts contain adaptive copy number changes in genes involved in vitamin B1 and B6 biosynthesis

scientific article (publication date: December 2009)

Integrating functional genomic information into the Saccharomyces genome database

scientific article

Isolation and molecular characterization of cancer stem cells in MMTV-Wnt-1 murine breast tumors

scientific article published in November 2007

Literature-based gene curation and proposed genetic nomenclature for cryptococcus

scientific article

Microarray databases: storage and retrieval of microarray data

scientific article

Microarray karyotyping of commercial wine yeast strains reveals shared, as well as unique, genomic signatures

scientific article

Microarray karyotyping of maltose-fermenting Saccharomyces yeasts with differing maltotriose utilization profiles reveals copy number variation in genes involved in maltose and maltotriose utilization.

scientific article published on 18 December 2009

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

scientific article (publication date: December 2001)

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)

scientific article

Missing value estimation methods for DNA microarrays

scientific article (publication date: June 2001)

Molecular characterisation of soft tissue tumours: a gene expression study

scientific article published in The Lancet

Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae

scientific article published on December 2008

Molecular cloning and analysis of CDC28 and cyclin homologues from the human fungal pathogen Candida albicans

scientific article published in December 1994

New tools at the Candida Genome Database: biochemical pathways and full-text literature search

scientific article

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

scientific article

Of fish and chips

scientific article published in May 2005

OntologyWidget - a reusable, embeddable widget for easily locating ontology terms

scientific article

Phenotypic and genotypic convergences are influenced by historical contingency and environment in yeast

scientific article

PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools.

scientific article

Preparation of Yeast DNA Sequencing Libraries

scientific article

Quantitative evolutionary dynamics using high-resolution lineage tracking

scientific article

Radiation-induced effects on gene expression: an in vivo study on breast cancer

scientific article

Ras Signaling Gets Fine-Tuned: Regulation of Multiple Pathogenic Traits of Candida albicans ⬇️

scientific article published on 02 August 2013

Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape

scientific article

Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus

scientific article

Recurrent rearrangement during adaptive evolution in an interspecific yeast hybrid suggests a model for rapid introgression

scientific article

Reply: whole-culture synchronization - effective tools for cell cycle studies

scientific article

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

scientific article

STARTing to recycle

Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)

scientific article

Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data

scientific article

Seeking Goldilocks During Evolution of Drug Resistance

scientific article

Sequence resources at the Candida Genome Database

scientific article

Single nucleotide mapping of trait space reveals Pareto fronts that constrain adaptation

scientific article published on 14 October 2019

Standards for microarray data

scientific article

Standards for microarray data: an open letter

scientific article

Starting to cycle: G1 controls regulating cell division in budding yeast

scientific article

Storage and retrieval of microarray data and open source microarray database software

scientific article

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

scientific article

Submission of microarray data to public repositories

scientific article

TB database 2010: overview and update

scientific article

TB database: an integrated platform for tuberculosis research

scientific article published on 03 October 2008

The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources

scientific article published on 12 November 2011

The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community

scientific article

The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations

scientific article

The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information

scientific article

The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data

scientific article

The Candida Genome Database: facilitating research on Candida albicans molecular biology

scientific article published on August 2006

The Candida Genome Database: the new homology information page highlights protein similarity and phylogeny

scientific article published on 31 October 2013

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

scientific article

The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD)

scientific article

The Stanford Microarray Database

scientific article

The Stanford Microarray Database accommodates additional microarray platforms and data formats

scientific article

The Stanford Microarray Database: a user's guide

scientific article published on January 2006

The Stanford Microarray Database: implementation of new analysis tools and open source release of software

scientific article published on 20 December 2006

The Stanford Tissue Microarray Database

scientific article

The Valley-of-Death: reciprocal sign epistasis constrains adaptive trajectories in a constant, nutrient limiting environment

scientific article

The XBabelPhish MAGE-ML and XML translator

scientific article

The dynamics of adaptive genetic diversity during the early stages of clonal evolution

scientific article published on 31 December 2018

The prognostic role of a gene signature from tumorigenic breast-cancer cells

scientific article

The underlying principles of scientific publication.

scientific article published in November 2002

Top-down standards will not serve systems biology

scientific article published in Nature

Turbidostat culture of Saccharomyces cerevisiae W303-1A under selective pressure elicited by ethanol selects for mutations in SSD1 and UTH1

scientific article published on 23 April 2012

Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure

scientific article

What are Microarrays?

Whole Genome Analysis of 132 Clinical Saccharomyces cerevisiae Strains Reveals Extensive Ploidy Variation

scientific article published on 17 June 2016

Whole genome, whole population sequencing reveals that loss of signaling networks is the major adaptive strategy in a constant environment

scientific article

Wrestling with SUMO and bio-ontologies

scientific article

iSeq: A New Double-Barcode Method for Detecting Dynamic Genetic Interactions in Yeast

scientific article

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