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Gavin Sherlock

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Oligonucleotide Array Sequence Analysis

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Gene Expression Profiling

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Fungal Proteins

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TOP 3
Barbara Dunn; Gregory Koniges; Evgueny Kroll; Gianni Liti; Edward J Louis; Terry Paulish; Jeff Piotrowski; Gavin Sherlock; Alison Stanbery; Frank Rosenzweig
Recurrent rearrangement during adaptive evolution in an interspecific yeast hybrid suggests a model for rapid introgression.
Diane O Inglis; Prachi Shah; Martha B Arnaud; Jonathan Binkley; Marek S Skrzypek; Farrell Wymore; Gavin Sherlock
Improved gene ontology annotation for biofilm formation, filamentous growth, and phenotypic switching in Candida albicans.
Liat Avrahami-Moyal; David Engelberg; Gavin Sherlock; Jared W Wenger; Sergei Braun
Turbidostat culture of Saccharomyces cerevisiae W303-1A under selective pressure elicited by ethanol selects for mutations in SSD1 and UTH1.

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All Publications

2013: Barbara Dunn; Gregory Koniges; Evgueny Kroll; Gianni Liti; Edward J Louis; Terry Paulish; Jeff Piotrowski; Gavin Sherlock; Alison Stanbery; Frank Rosenzweig
Recurrent rearrangement during adaptive evolution in an interspecific yeast hybrid suggests a model for rapid introgression.
PLoS genetics 2013;9(3):e1003366.
2013: Diane O Inglis; Prachi Shah; Martha B Arnaud; Jonathan Binkley; Marek S Skrzypek; Farrell Wymore; Gavin Sherlock
Improved gene ontology annotation for biofilm formation, filamentous growth, and phenotypic switching in Candida albicans.
Eukaryotic cell 2013;12(1):101-8.
2012: Liat Avrahami-Moyal; David Engelberg; Gavin Sherlock; Jared W Wenger; Sergei Braun
Turbidostat culture of Saccharomyces cerevisiae W303-1A under selective pressure elicited by ethanol selects for mutations in SSD1 and UTH1.
FEMS yeast research 2012;12(5):521-33.
2012: Katja Schwartz; Barbara Dunn; Jared W Wenger; Gavin Sherlock
APJ1 and GRE3 homologs work in concert to allow growth in xylose in a natural Saccharomyces sensu stricto hybrid yeast.
Genetics 2012;191(2):621-32.
2012: Barbara Dunn; Daniel J Kvitek; Tom Pugh; Chandra Richter; Gavin Sherlock
Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments.
Genome research 2012;22(5):908-24.
2012: Jeff S Piotrowski; Gavin Sherlock; Alison Stanbery; Kami E Chiotti; Barbara Dunn; Evgueny Kroll; Arthur L Kruckeberg; Saisubramanian Nagarajan; Frank Rosenzweig
Different selective pressures lead to different genomic outcomes as newly-formed hybrid yeasts evolve.
BMC evolutionary biology 2012;12():46.
2012: Martha B Arnaud; Stuart R Miyasato; Jonathan Crabtree; Prachi Shah; Clinton Howarth; Gustavo C Cerqueira; Jonathan Binkley; Matt Simison; Farrell Wymore; Diane O Inglis; Marcus Chibucos; Gail Binkley; Joshua Orvis; Gavin Sherlock; Marek S Skrzypek; Jennifer Wortman
The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources.
Nucleic acids research 2012;40(Database issue):D653-9.
2012: Diane O Inglis; Prachi Shah; Farrell Wymore; Jonathan Binkley; Matt Simison; Marek S Skrzypek; Stuart R Miyasato; Martha B Arnaud; Gail Binkley; Gavin Sherlock
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 research 2012;40(Database issue):D667-74.
2011: Jared W Wenger; Gavin Sherlock; Kami Chiotti; Saisubramanian Nagarajan; Jeffrey Piotrowski; Frank Rosenzweig
Hunger artists: yeast adapted to carbon limitation show trade-offs under carbon sufficiency.
PLoS genetics 2011;7(8):e1002202.
2011: Yuya Kobayashi; Jesse K McKenney; Richard M Myers; Donna M Peehl; Devin M Absher; James D Brooks; Zulfiqar G Gulzar; Sarah R Young; Gavin Sherlock
DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer.
Genome research 2011;21(7):1017-27.
2011: Daniel J Kvitek; Gavin Sherlock
Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape.
PLoS genetics 2011;7(4):e1002056.
2011: Davide Risso; Katja Schwartz; Gavin Sherlock; Sandrine Dudoit
GC-content normalization for RNA-Seq data.
BMC bioinformatics 2011;12():480.
2010: Vincent Bruno; Zhong Wang; Sadie L Marjani; Ghia Euskirchen; Jeffrey Martin; Gavin Sherlock; Michael Snyder
Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq.
Genome research 2010;20(10):1451-8.
2010: Ravi Shankar; Helen Parkinson; Tony Burdett; Emma Hastings; Junmin Liu; Michael Miller; Rashmi Srinivasa; Joseph White; Alvis Brazma; Gavin Sherlock; Christian J Stoeckert; Catherine A Ball
Annotare--a tool for annotating high-throughput biomedical investigations and resulting data.
Bioinformatics (Oxford, England) 2010;26(19):2470-1.
2010: Katy C Kao; K Schwartz; 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.
PLoS genetics 2010;6(7):e1001038.
2010: James E Galagan; Peter Sisk; Christian Stolte; Brian Weiner; Michael Koehrsen; Farrell Wymore; T B K Reddy; Jeremy D Zucker; Reinhard Engels; Marcel Gellesch; Jeremy Hubble; Heng Jin; Lisa Larson; Maria Mao; Michael Nitzberg; Jared White; Zachariah K Zachariah; Gavin Sherlock; Catherine A Ball; Gary K Schoolnik
TB database 2010: overview and update.
Tuberculosis (Edinburgh, Scotland) 2010;90(4):225-35.
2010: E H Duval; S L Alves; B Dunn; Gavin Sherlock; Boris U Stambuk
Microarray karyotyping of maltose-fermenting Saccharomyces yeasts with differing maltotriose utilization profiles reveals copy number variation in genes involved in maltose and maltotriose utilization.
Journal of applied microbiology 2010;109(1):248-59.
2010: Jared W Wenger; K Schwartz; Gavin Sherlock
Bulk segregant analysis by high-throughput sequencing reveals a novel xylose utilization gene from Saccharomyces cerevisiae.
PLoS genetics 2010;6(5):e1000942.
2010: Jeffrey Martin; Vincent Bruno; Zhide Fang; Xiandong Meng; Matthew Blow; Tao Zhang; Gavin Sherlock; Michael Snyder; Zhong Wang
Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads.
BMC genomics 2010;11():663.
2010: Marek S Skrzypek; Martha B Arnaud; Maria C Costanzo; Diane O Inglis; Prachi Shah; Gail Binkley; Stuart R Miyasato; Gavin Sherlock
New tools at the Candida Genome Database: biochemical pathways and full-text literature search.
Nucleic acids research 2010;38(Database issue):D428-32.
2010: Martha B Arnaud; Marcus Chibucos; Maria C Costanzo; Jonathan Crabtree; Diane O Inglis; Adil Lotia; Joshua Orvis; Prachi Shah; Marek S Skrzypek; Gail Binkley; Stuart R Miyasato; Jennifer Wortman; Gavin Sherlock
The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community.
Nucleic acids research 2010;38(Database issue):D420-7.
2009: Boris U Stambuk; Barbara Dunn; Sergio L Alves; Eduarda H Duval; Gavin Sherlock
Industrial fuel ethanol yeasts contain adaptive copy number changes in genes involved in vitamin B1 and B6 biosynthesis.
Genome research 2009;19(12):2271-8.
2009: Martha B Arnaud; Maria C Costanzo; Prachi Shah; Marek S Skrzypek; Gavin Sherlock
Gene Ontology and the annotation of pathogen genomes: the case of Candida albicans.
Trends in microbiology 2009;17(7):295-303.
2009: Geraldine Butler; Matthew D Rasmussen; Michael F Lin; Manuel A S Santos; Sharadha Sakthikumar; Carol A Munro; Esther Rheinbay; Manfred Grabherr; Anja Forche; Jennifer L Reedy; Ino Agrafioti; Martha B Arnaud; Steven Bates; Alistair J P Brown; Sascha Brunke; Maria C Costanzo; David A Fitzpatrick; Piet W J de Groot; David Harris; Lois L Hoyer; Bernhard Hube; Frans Klis; Chinnappa Kodira; Nicola Lennard; Mary E Logue; Ronny Martin; Aaron M Neiman; Elissavet Nikolaou; Michael A Quail; Janet Quinn; Maria C Santos; Florian F Schmitzberger; Gavin Sherlock; Prachi Shah; Kevin A T Silverstein; Marek S Skrzypek; David Soll; Rodney Staggs; Ian Stansfield; Michael P H Stumpf; Peter E Sudbery; Thyagarajan Srikantha; Qiandong Zeng; Judith Berman; Matthew Berriman; Joseph Heitman; Neil A R Gow; Michael C Lorenz; Bruce W Birren; Manolis Kellis; Christina A Cuomo
Evolution of pathogenicity and sexual reproduction in eight Candida genomes.
Nature 2009;459(7247):657-62.
2009: Jeremy Hubble; Janos Demeter; Heng Jin; Maria Mao; Michael Nitzberg; T B K Reddy; Farrell Wymore; Zachariah K Zachariah; Gavin Sherlock; Catherine A Ball
Implementation of GenePattern within the Stanford Microarray Database.
Nucleic acids research 2009;37(Database issue):D898-901.
2009: T B K Reddy; Robert Riley; Farrell Wymore; Phillip Montgomery; Dave DeCaprio; Reinhard Engels; Marcel Gellesch; Jeremy Hubble; Dennis Jen; Heng Jin; Michael Koehrsen; Lisa Larson; Maria Mao; Michael Nitzberg; Peter Sisk; Christian Stolte; Brian Weiner; Jared White; Zachariah K Zachariah; Gavin Sherlock; James E Galagan; Catherine A Ball; Gary K Schoolnik
TB database: an integrated platform for tuberculosis research.
Nucleic acids research 2009;37(Database issue):D499-508.
2008: Albert Lee; Kasper Daniel Hansen; James Bullard; Sandrine Dudoit; Gavin Sherlock
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 genetics 2008;4(12):e1000299.
2008: Katy C Kao; Gavin Sherlock
Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae.
Nature genetics 2008;40(12):1499-504.
2008: Peter Karp; Gavin Sherlock; John Alan Gerlt; Ida Sim; Ian Paulsen; Patricia C Babbitt; Keith Laderoute; Lawrence Hunter; Paul Sternberg; John Wooley; Philip Bourne
Changes to NIH grant system may backfire.
Science (New York, N.Y.) 2008;322(5905):1187-8.
2008: Barbara Dunn; Gavin Sherlock
Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus.
Genome research 2008;18(10):1610-23.
2008: Eric W Deutsch; Catherine A Ball; Jules J Berman; G Steven Bova; Alvis Brazma; Roger Bumgarner; David Campbell; Helen C Causton; Jeffrey Christiansen; Fabrice Daian; Delphine Dauga; Duncan R Davidson; Gregory Gimenez; Young Ah Goo; Sean Grimmond; Thorsten Henrich; Bernhard G Herrmann; Michael H Johnson; Martin Korb; Jason C Mills; Asa J Oudes; Helen E Parkinson; Laura E Pascal; Nicolas Pollet; John Quackenbush; Mirana Ramialison; Martin Ringwald; David Salgado; Susanna-Assunta Sansone; Gavin Sherlock; Christian J Stoeckert; Jason Swedlow; Ronald C Taylor; Laura Walashek; Anthony Warford; David George Wilkinson; Yi Zhou; Leonard I Zon; Alvin Y Liu; Lawrence True
Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE).
Nature biotechnology 2008;26(3):305-12.
2008: Robert W Cho; Xinhao Wang; Maximilian Diehn; Kerby Shedden; Grace Chen; Gavin Sherlock; Austin Gurney; John Lewicki; Michael F Clarke
Isolation and molecular characterization of cancer stem cells in MMTV-Wnt-1 murine breast tumors.
Stem cells (Dayton, Ohio) 2008;26(2):364-71.
2008: Don Maier; Farrell Wymore; Gavin Sherlock; Catherine A Ball
The XBabelPhish MAGE-ML and XML translator.
BMC bioinformatics 2008;9():28.
2008: Robert J Marinelli; Kelli Montgomery; Chih Long Liu; Nigam Shah; Wijan Prapong; Michael Nitzberg; Zachariah K Zachariah; Gavin Sherlock; Yasodha Natkunam; Robert B West; Matt van de Rijn; Patrick O Brown; Catherine A Ball
The Stanford Tissue Microarray Database.
Nucleic acids research 2008;36(Database issue):D871-7.
2007: Rui Liu; Xinhao Wang; Grace Chen; Piero Dalerba; Austin Gurney; Timothy Hoey; Gavin Sherlock; John Lewicki; Kerby Shedden; Michael F Clarke
The prognostic role of a gene signature from tumorigenic breast-cancer cells.
The New England journal of medicine 2007;356(3):217-26.
2007: Catherine C Beauheim; Farrell Wymore; Michael Nitzberg; Zachariah K Zachariah; Heng Jin; J H Pate Skene; Catherine A Ball; Gavin Sherlock
OntologyWidget - a reusable, embeddable widget for easily locating ontology terms.
BMC bioinformatics 2007;8():338.
2007: Janos Demeter; Catherine Beauheim; Jeremy Gollub; Tina Hernandez-Boussard; Heng Jin; Donald Maier; John Matese; Michael Nitzberg; Farrell Wymore; Zachariah K Zachariah; Patrick O Brown; Gavin Sherlock; Catherine A Ball
The Stanford Microarray Database: implementation of new analysis tools and open source release of software.
Nucleic acids research 2007;35(Database issue):D766-70.
2007: Martha B Arnaud; Maria C Costanzo; Marek S Skrzypek; Prachi Shah; Gail Binkley; Christopher Lane; Stuart R Miyasato; Gavin Sherlock
Sequence resources at the Candida Genome Database.
Nucleic acids research 2007;35(Database issue):D452-6.
2006: Gavin Sherlock
Cell cycle: complex evolution.
Nature 2006;443(7111):513-5.
2006: Aslaug Helland; Hilde Johnsen; Caroline Frøyland; Hege B K Landmark; Anna B Saetersdal; Marit Muri Holmen; Turid Gjertsen; Jahn M Nesland; William Ottestad; Stefanie S Jeffrey; Lars O Ottestad; Olag K Rodningen; Gavin Sherlock; Anne-Lise Børresen-Dale
Radiation-induced effects on gene expression: an in vivo study on breast cancer.
Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology 2006;80(2):230-5.
2006: Maria C Costanzo; Martha B Arnaud; Marek S Skrzypek; Gail Binkley; Christopher Lane; Stuart R Miyasato; Gavin Sherlock
The Candida Genome Database: facilitating research on Candida albicans molecular biology.
FEMS yeast research 2006;6(5):671-84.
2006: John Quackenbush; Christian J Stoeckert; Catherine Ball; Alvis Brazma; Robert Gentleman; Wolfgang Huber; Rafael A Irizarry; Marc Salit; Gavin Sherlock; Paul Spellman; Neil Winegarden
Top-down standards will not serve systems biology.
Nature 2006;440(7080):24.
2006: Tim Rayner; Philippe Rocca-Serra; Paul Spellman; Helen C Causton; Anna Farne; Ele Holloway; Rafael A Irizarry; Junmin Liu; Donald S Maier; Michael Miller; Kjell Petersen; John Quackenbush; Gavin Sherlock; Christian J Stoeckert; Joseph White; Patricia L Whetzel; Farrell Wymore; Helen Parkinson; Ugis Sarkans; Catherine A Ball; Alvis Brazma
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.
BMC bioinformatics 2006;7():489.
2006: Jeremy Gollub; Gavin Sherlock
Clustering microarray data.
Methods in enzymology 2006;411():194-213.
2006: Eric W Deutsch; Catherine A Ball; G Steven Bova; Alvis Brazma; Roger Bumgarner; David Campbell; Helen C Causton; Jeff Christiansen; Duncan Davidson; Lillian J Eichner; Young Ah Goo; Sean Grimmond; Thorsten Henrich; Michael H Johnson; Martin Korb; Jason C Mills; Asa Oudes; Helen E Parkinson; Laura E Pascal; John Quackenbush; Mirana Ramialison; Martin Ringwald; Susanna-A Sansone; Gavin Sherlock; Christian J Stoeckert; Jason Swedlow; Ronald C Taylor; Laura Walashek; Yi Zhou; Alvin Y Liu; Lawrence True
Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE).
Omics : a journal of integrative biology 2006;10(2):205-8.
2006: Jeremy Gollub; Catherine A Ball; Gavin Sherlock
The Stanford Microarray Database: a user's guide.
Methods in molecular biology (Clifton, N.J.) 2006;338():191-208.
2006: James A Brown; Gavin Sherlock; Chad L Myers; Nicola M Burrows; Changchun Deng; H Irene Wu; Kelly E McCann; Olga G Troyanskaya; J Martin Brown
Global analysis of gene function in yeast by quantitative phenotypic profiling.
Molecular systems biology 2006;2():2006.0001.
2006: Christian J Stoeckert; Catherine Ball; Alvis Brazma; Ryan Brinkman; Helen C Causton; Liju Fan; Jennifer Fostel; Gilberto Fragoso; Mervi Heiskanen; Frank C P Holstege; Norman Morrison; Helen Parkinson; John Quackenbush; Philippe Rocca-Serra; Susanna-Assunta Sansone; Ugis Sarkans; Gavin Sherlock; Robert Stevens; Chris Taylor; Ronald Taylor; Patricia L Whetzel; Joseph White
Wrestling with SUMO and bio-ontologies.
Nature biotechnology 2006;24(1):21-2; author reply 23.
2005: Burkhard R Braun; Marco van Het Hoog; Christophe d'Enfert; Mikhail Martchenko; Jan Dungan; Alan Kuo; Diane Inglis; M Andrew Uhl; Hervé Hogues; Matthew Berriman; Michael Lorenz; Anastasia Levitin; Ursula Oberholzer; Catherine Bachewich; Doreen Harcus; Anne Marcil; Daniel Dignard; Tatiana Iouk; Rosa Zito; Lionel Frangeul; Fredj Tekaia; Kim Rutherford; edwin wang; Carol A Munro; Steve Bates; Neil A Gow; Lois L Hoyer; Gerwald Köhler; Joachim Morschhäuser; George Newport; Sadri Znaidi; Martine Raymond; Bernard Turcotte; Gavin Sherlock; Maria Costanzo; Jan Ihmels; Judith Berman; Dominique Sanglard; Nina Agabian; Aaron P Mitchell; Alexander D Johnson; Malcolm Whiteway; André Nantel
A human-curated annotation of the Candida albicans genome.
PLoS genetics 2005;1(1):36-57.
2005: Gavin Sherlock; Catherine A Ball
Storage and retrieval of microarray data and open source microarray database software.
Molecular biotechnology 2005;30(3):239-51.
2005: Gavin Sherlock
Of fish and chips.
Nature methods 2005;2(5):329-30.
2005: Barbara Dunn; R Paul Levine; Gavin Sherlock
Microarray karyotyping of commercial wine yeast strains reveals shared, as well as unique, genomic signatures.
BMC genomics 2005;6():53.
2005: Catherine A Ball; Ihab A B Awad; Janos Demeter; Jeremy Gollub; Joan M Hebert; Tina Hernandez-Boussard; Heng Jin; John Matese; Michael Nitzberg; Farrell Wymore; Zachariah K Zachariah; Patrick O Brown; Gavin Sherlock
The Stanford Microarray Database accommodates additional microarray platforms and data formats.
Nucleic acids research 2005;33(Database issue):D580-2.
2005: Martha B Arnaud; Maria C Costanzo; Marek S Skrzypek; Gail Binkley; Christopher Lane; Stuart R Miyasato; Gavin Sherlock
The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information.
Nucleic acids research 2005;33(Database issue):D358-63.
2004: Elizabeth I Boyle; Shuai Weng; Jeremy Gollub; Heng Jin; David Botstein; J Michael Cherry; Gavin Sherlock
GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes.
Bioinformatics (Oxford, England) 2004;20(18):3710-5.
2004: Catherine Ball; Alvis Brazma; Helen C Causton; Steve Chervitz; Ron Edgar; Pascal Hingamp; John Matese; Carl Icahn; Helen Parkinson; John Quackenbush; Martin Ringwald; Susanna-Assunta Sansone; Gavin Sherlock; Paul Spellman; Christian J Stoeckert; Yoshio Tateno; Ronald Taylor; Joseph White; Neil Winegarden
An open letter on microarray data from the MGED Society.
Microbiology (Reading, England) 2004;150(Pt 11):3522-4.
2004: Ihab A B Awad; Christian A Rees; Tina Hernandez-Boussard; Catherine A Ball; Gavin Sherlock
Caryoscope: an Open Source Java application for viewing microarray data in a genomic context.
BMC bioinformatics 2004;5():151.
2004: Christian A Rees; Janos Demeter; John Matese; David Botstein; Gavin Sherlock
GeneXplorer: an interactive web application for microarray data visualization and analysis.
BMC bioinformatics 2004;5():141.
2004: Catherine A Ball; Alvis Brazma; Helen C Causton; Steve Chervitz; Ron Edgar; Pascal Hingamp; John Matese; Helen Parkinson; John Quackenbush; Martin Ringwald; Susanna-Assunta Sansone; Gavin Sherlock; Paul Spellman; Christian J Stoeckert; Yoshio Tateno; Ronald Taylor; Joseph White; Neil Winegarden
Submission of microarray data to public repositories.
PLoS biology 2004;2(9):E317.
2004: Catherine A Ball; Gavin Sherlock; Alvis Brazma
Funding high-throughput data sharing.
Nature biotechnology 2004;22(9):1179-83.
2004: Catherine Ball; Alvis Brazma; Helen C Causton; Steve Chervitz; Ron Edgar; Pascal Hingamp; John Matese; Helen Parkinson; John Quackenbush; Martin Ringwald; Susanna-Assunta Sansone; Gavin Sherlock; Paul Spellman; Christian J Stoeckert; Yoshio Tateno; Ronald Taylor; Joseph White; Neil Winegarden
Standards for microarray data: an open letter.
Environmental health perspectives 2004;112(12):A666-7.
2004: Gavin Sherlock
STARTing to recycle.
Nature genetics 2004;36(8):795-6.
2004: Paul Spellman; Gavin Sherlock
Final words: cell age and cell cycle are unlinked.
Trends in biotechnology 2004;22(6):277-8.
2004: Paul Spellman; Gavin Sherlock
Reply: whole-culture synchronization - effective tools for cell cycle studies.
Trends in biotechnology 2004;22(6):270-3.
2003: Patrick J Killion; Gavin Sherlock; Vishwanath R Iyer
The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD).
BMC bioinformatics 2003;4():32.
2003: Gavin Sherlock; Catherine A Ball
Microarray databases: storage and retrieval of microarray data.
Methods in molecular biology (Clifton, N.J.) 2003;224():235-48.
2003: Maximilian Diehn; Gavin Sherlock; Gail Binkley; Heng Jin; John Matese; Tina Hernandez-Boussard; Christian A Rees; J Michael Cherry; David Botstein; Patrick O Brown; Ash A Alizadeh
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.
Nucleic acids research 2003;31(1):219-23.
2003: Jeremy Gollub; Catherine A Ball; Gail Binkley; Janos Demeter; David B Finkelstein; Joan M Hebert; Tina Hernandez-Boussard; Heng Jin; Miroslava Kaloper; John Matese; Mark Schroeder; Patrick O Brown; David Botstein; Gavin Sherlock
The Stanford Microarray Database: data access and quality assessment tools.
Nucleic acids research 2003;31(1):94-6.
2002: Catherine A Ball; Gavin Sherlock; Helen Parkinson; Philippe Rocca-Sera; Catherine Brooksbank; Helen C Causton; Duccio Cavalieri; Terry Gaasterland; Pascal Hingamp; Frank C P Holstege; Martin Ringwald; Paul Spellman; Christian J Stoeckert; Jason E Stewart; Ronald Taylor; Alvis Brazma; John Quackenbush
The underlying principles of scientific publication.
Bioinformatics (Oxford, England) 2002;18(11):1409.
2002: Catherine A Ball; Gavin Sherlock; Helen Parkinson; Philippe Rocca-Sera; Catherine Brooksbank; Helen C Causton; Duccio Cavalieri; Terry Gaasterland; Pascal Hingamp; Frank C P Holstege; Martin Ringwald; Paul Spellman; Christian J Stoeckert; Jason E Stewart; Ronald Taylor; Alvis Brazma; John Quackenbush
Standards for microarray data.
Science (New York, N.Y.) 2002;298(5593):539.
2002: Paul Spellman; Michael Miller; Jason Stewart; Charles Troup; Ugis Sarkans; Steve Chervitz; Derek Bernhart; Gavin Sherlock; Catherine Ball; Marc Lepage; Marcin Swiatek; W L Marks; Jason Goncalves; Scott Markel; Daniel Iordan; Mohammadreza Shojatalab; Angel Pizarro; Joe White; Robert Hubley; Eric Deutsch; Martin Senger; Bruce Aronow; Alan Robinson; Doug Bassett; Christian J Stoeckert; Alvis Brazma
Design and implementation of microarray gene expression markup language (MAGE-ML).
Genome biology 2002;3(9):RESEARCH0046.
2002: Michael L Whitfield; Gavin Sherlock; Alok J Saldanha; John I Murray; Catherine A Ball; Karen E Alexander; John Matese; Charles M Perou; Myra M Hurt; Patrick O Brown; David Botstein
Identification of genes periodically expressed in the human cell cycle and their expression in tumors.
Molecular biology of the cell 2002;13(6):1977-2000.
2002: Torsten O Nielsen; Robert B West; Sabine C Linn; Orly Alter; Margaret A Knowling; John X O'Connell; Shirley Zhu; Michael Fero; Gavin Sherlock; Jonathan R Pollack; Patrick O Brown; David Botstein; Matt van de Rijn
Molecular characterisation of soft tissue tumours: a gene expression study.
Lancet 2002;359(9314):1301-7.
2002: Selina S Dwight; Midori A Harris; Kara Dolinski; Catherine A Ball; Gail Binkley; Karen R Christie; Dianna G Fisk; Laurie Issel-Tarver; Mark Schroeder; Gavin Sherlock; Anand Sethuraman; Shuai Weng; David Botstein; J Michael Cherry
Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO).
Nucleic acids research 2002;30(1):69-72.
2001: Gavin Sherlock
Analysis of large-scale gene expression data.
Briefings in bioinformatics 2001;2(4):350-62.
2001: Alvis Brazma; Pascal Hingamp; John Quackenbush; Gavin Sherlock; Paul Spellman; Christian J Stoeckert; J Aach; W Ansorge; Catherine A Ball; Helen C Causton; Terry Gaasterland; P Glenisson; Frank C P Holstege; I F Kim; V Markowitz; John Matese; Helen Parkinson; Alan Robinson; Ugis Sarkans; S Schulze-Kremer; J Stewart; R Taylor; Jaak Vilo; Martin Vingron
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.
Nature genetics 2001;29(4):365-71.
2001: Olga G Troyanskaya; M Cantor; Gavin Sherlock; P Brown; Trevor Hastie; Robert Tibshirani; David Botstein; Russ B Altman
Missing value estimation methods for DNA microarrays.
Bioinformatics (Oxford, England) 2001;17(6):520-5.
2001: Gavin Sherlock; Tina Hernandez-Boussard; A Kasarskis; Gail Binkley; John Matese; Selina S Dwight; Miroslava Kaloper; Shuai Weng; Heng Jin; Catherine A Ball; Michael B Eisen; Paul Spellman; Patrick O Brown; David Botstein; J Michael Cherry
The Stanford Microarray Database.
Nucleic acids research 2001;29(1):152-5.
2001: Catherine A Ball; Heng Jin; Gavin Sherlock; Shuai Weng; John Matese; Rey Andrada; Gail Binkley; Kara Dolinski; Selina S Dwight; Midori A Harris; Laurie Issel-Tarver; Mark Schroeder; David Botstein; J Michael Cherry
Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data.
Nucleic acids research 2001;29(1):80-1.
2000: Nina R Salama; Karen Guillemin; TK McDaniel; Gavin Sherlock; Lucy S Tompkins; Stanley Falkow
A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(26):14668-73.
2000: Michael Ashburner; Catherine A Ball; Judith A Blake; David Botstein; H Butler; J Michael Cherry; Allan Peter Davis; Kara Dolinski; Selina S Dwight; Janan T Eppig; Midori A Harris; David P Hill; Laurie Issel-Tarver; A Kasarskis; S Lewis; John Matese; Joel E Richardson; Martin Ringwald; G M Rubin; Gavin Sherlock
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
Nature genetics 2000;25(1):25-9.
2000: Gavin Sherlock
Analysis of large-scale gene expression data.
Current opinion in immunology 2000;12(2):201-5.
2000: A A Alizadeh; M B Eisen; R E Davis; C Ma; Izidore S Lossos; A Rosenwald; J C Boldrick; H Sabet; T Tran; X Yu; J I Powell; L Yang; G E Marti; T Moore; J Hudson; L Lu; D B Lewis; R Tibshirani; Gavin Sherlock; W C Chan; T C Greiner; D D Weisenburger; J O Armitage; R Warnke; Ronald Levy; W Wilson; M R Grever; J C Byrd; D Botstein; P O Brown; L M Staudt
Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling.
Nature 2000;403(6769):503-11.
2000: Catherine A Ball; Kara Dolinski; Selina S Dwight; Midori A Harris; Laurie Issel-Tarver; A Kasarskis; C R Scafe; Gavin Sherlock; Gail Binkley; Heng Jin; Miroslava Kaloper; S D Orr; Mark Schroeder; Shuai Weng; Y Zhu; David Botstein; J Michael Cherry
Integrating functional genomic information into the Saccharomyces genome database.
Nucleic acids research 2000;28(1):77-80.
1999: Steve Chervitz; E T Hester; Catherine A Ball; Kara Dolinski; Selina S Dwight; Midori A Harris; G Juvik; A Malekian; S Roberts; T Roe; C Scafe; Mark Schroeder; Gavin Sherlock; Shuai Weng; Y Zhu; J Michael Cherry; David Botstein
Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure.
Nucleic acids research 1999;27(1):74-8.
1998: Steve Chervitz; L Aravind; Gavin Sherlock; Catherine A Ball; E V Koonin; Selina S Dwight; Midori A Harris; Kara Dolinski; S Mohr; T Smith; Shuai Weng; J Michael Cherry; David Botstein
Comparison of the complete protein sets of worm and yeast: orthology and divergence.
Science (New York, N.Y.) 1998;282(5396):2022-8.
1998: Paul Spellman; Gavin Sherlock; M Q Zhang; Vishwanath R Iyer; K Anders; Michael B Eisen; Patrick O Brown; David Botstein; Bruce Futcher
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.
Molecular biology of the cell 1998;9(12):3273-97.
1994: Gavin Sherlock; A M Bahman; A Mahal; J C Shieh; Miguel Godinho Ferreira; JD Rosamond
Molecular cloning and analysis of CDC28 and cyclin homologues from the human fungal pathogen Candida albicans.
Molecular & general genetics : MGG 1994;245(6):716-23.
1993: Gavin Sherlock; JD Rosamond
Starting to cycle: G1 controls regulating cell division in budding yeast.
Journal of general microbiology 1993;139(11):2531-41.