Gavin Sherlock

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
• Global analysis of gene function in yeast by quantitative phenotypic profiling. Brown JA, Sherlock G, Myers CL, Burrows NM, Deng C, Wu HI, McCann KE, Troyanskaya OG, Brown JM. Mol Syst Biol. 2006: 2 2006.0001
• GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G. Bioinformatics. 2004; 20 (18): 3710-5
• Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, Alexander KE, Matese JC, Perou CM, Hurt MM, Brown PO, Botstein D. Mol Biol Cell. 2002; 13 (6): 1977-2000
• Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. Mol Biol Cell. 1998; 9 (12): 3273-97
• New tools at the Candida Genome Database: biochemical pathways and full-text literature search. Skrzypek MS, Arnaud MB, Costanzo MC, Inglis DO, Shah P, Binkley G, Miyasato SR, Sherlock G. Nucleic Acids Res. 2009
• The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community. Arnaud MB, Chibucos MC, Costanzo MC, Crabtree J, Inglis DO, Lotia A, Orvis J, Shah P, Skrzypek MS, Binkley G, Miyasato SR, Wortman JR, Sherlock G. Nucleic Acids Res. 2009
• Gene Ontology and the annotation of pathogen genomes: the case of Candida albicans. Arnaud MB, Costanzo MC, Shah P, Skrzypek MS, Sherlock G. Trends Microbiol. 2009; 17 (7): 295-303
• Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S, Munro CA, Rheinbay E, Grabherr M, Forche A, Reedy JL, Agrafioti I, Arnaud MB, Bates S, Brown AJ, Brunke S, Costanzo MC, Fitzpatrick DA, de Groot PW, Harris D, Hoyer LL, Hube B, Klis FM, Kodira C, Lennard N, Logue ME, Martin R, Neiman AM, Nikolaou E, Quail MA, Quinn J, Santos MC, Schmitzberger FF, Sherlock G, Shah P, Silverstein KA, Skrzypek MS, Soll D, Staggs R, Stansfield I, Stumpf MP, Sudbery PE, Srikantha T, Zeng Q, Berman J, Berriman M, Heitman J, Gow NA, Lorenz MC, Birren BW, Kellis M, Cuomo CA. Nature. 2009; 459 (7247): 657-62
• Implementation of GenePattern within the Stanford Microarray Database. Hubble J, Demeter J, Jin H, Mao M, Nitzberg M, Reddy TB, Wymore F, Zachariah ZK, Sherlock G, Ball CA. Nucleic Acids Res. 2009; 37 (Database issue): D898-901
• TB database: an integrated platform for tuberculosis research. Reddy TB, Riley R, Wymore F, Montgomery P, DeCaprio D, Engels R, Gellesch M, Hubble J, Jen D, Jin H, Koehrsen M, Larson L, Mao M, Nitzberg M, Sisk P, Stolte C, Weiner B, White J, Zachariah ZK, Sherlock G, Galagan JE, Ball CA, Schoolnik GK. Nucleic Acids Res. 2009; 37 (Database issue): D499-508
• The Stanford Tissue Microarray Database. Marinelli RJ, Montgomery K, Liu CL, Shah NH, Prapong W, Nitzberg M, Zachariah ZK, Sherlock GJ, Natkunam Y, West RB, van de Rijn M, Brown PO, Ball CA. Nucleic Acids Res. 2008; 36 (Database issue): D871-7
• Changes to NIH grant system may backfire. Karp PD, Sherlock G, Gerlt JA, Sim I, Paulsen I, Babbitt PC, Laderoute K, Hunter L, Sternberg P, Wooley J, Bourne PE. Science. 2008; 322 (5905): 1187-8
• Isolation and molecular characterization of cancer stem cells in MMTV-Wnt-1 murine breast tumors. Cho RW, Wang X, Diehn M, Shedden K, Chen GY, Sherlock G, Gurney A, Lewicki J, Clarke MF. Stem Cells. 2008; 26 (2): 364-71
• The XBabelPhish MAGE-ML and XML translator. Maier D, Wymore F, Sherlock G, Ball CA. BMC Bioinformatics. 2008: 9 28
• Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Deutsch EW, Ball CA, Berman JJ, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen JH, Daian F, Dauga D, Davidson DR, Gimenez G, Goo YA, Grimmond S, Henrich T, Herrmann BG, Johnson MH, Korb M, Mills JC, Oudes AJ, Parkinson HE, Pascal LE, Pollet N, Quackenbush J, Ramialison M, Ringwald M, Salgado D, Sansone SA, Sherlock G, Stoeckert CJ, Swedlow J, Taylor RC, Walashek L, Warford A, Wilkinson DG, Zhou Y, Zon LI, Liu AY, True LD. Nat Biotechnol. 2008; 26 (3): 305-12
• The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Demeter J, Beauheim C, Gollub J, Hernandez-Boussard T, Jin H, Maier D, Matese JC, Nitzberg M, Wymore F, Zachariah ZK, Brown PO, Sherlock G, Ball CA. Nucleic Acids Res. 2007; 35 (Database issue): D766-70
• Sequence resources at the Candida Genome Database. Arnaud MB, Costanzo MC, Skrzypek MS, Shah P, Binkley G, Lane C, Miyasato SR, Sherlock G. Nucleic Acids Res. 2007; 35 (Database issue): D452-6
• OntologyWidget - a reusable, embeddable widget for easily locating ontology terms. Beauheim CC, Wymore F, Nitzberg M, Zachariah ZK, Jin H, Skene JH, Ball CA, Sherlock G. BMC Bioinformatics. 2007: 8 338
• The prognostic role of a gene signature from tumorigenic breast-cancer cells. Liu R, Wang X, Chen GY, Dalerba P, Gurney A, Hoey T, Sherlock G, Lewicki J, Shedden K, Clarke MF. N Engl J Med. 2007; 356 (3): 217-26
• Cell cycle: complex evolution. Sherlock G, Nature. 2006; 443 (7111): 513-5
• A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A. BMC Bioinformatics. 2006: 7 489
• Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). Deutsch EW, Ball CA, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen J, Davidson D, Eichner LJ, Goo YA, Grimmond S, Henrich T, Johnson MH, Korb M, Mills JC, Oudes A, Parkinson HE, Pascal LE, Quackenbush J, Ramialison M, Ringwald M, Sansone SA, Sherlock G, Stoeckert CJ, Swedlow J, Taylor RC, Walashek L, Zhou Y, Liu AY, True LD. OMICS. 2006; 10 (2): 205-8
• Top-down standards will not serve systems biology. Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, Huber W, Irizarry R, Salit M, Sherlock G, Spellman P, Winegarden N. Nature. 2006; 440 (7080): 24
• Clustering microarray data. Gollub J, Sherlock G. Methods Enzymol. 2006: 411 194-213
• Radiation-induced effects on gene expression: an in vivo study on breast cancer. Helland A, Johnsen H, Frøyland C, Landmark HB, Saetersdal AB, Holmen MM, Gjertsen T, Nesland JM, Ottestad W, Jeffrey SS, Ottestad LO, Rodningen OK, Sherlock G, Børresen-Dale AL. Radiother Oncol. 2006; 80 (2): 230-5
• The Stanford Microarray Database: a user's guide. Gollub J, Ball CA, Sherlock G. Methods Mol Biol. 2006: 338 191-208
• Wrestling with SUMO and bio-ontologies. Stoeckert C, Ball C, Brazma A, Brinkman R, Causton H, Fan L, Fostel J, Fragoso G, Heiskanen M, Holstege F, Morrison N, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Sarkans U, Sherlock G, Stevens R, Taylor C, Taylor R, Whetzel P, White J. Nat Biotechnol. 2006; 24 (1): 21-2; author reply 23
• The Candida Genome Database: facilitating research on Candida albicans molecular biology. Costanzo MC, Arnaud MB, Skrzypek MS, Binkley G, Lane C, Miyasato SR, Sherlock G. FEMS Yeast Res. 2006; 6 (5): 671-84
• The Stanford Microarray Database accommodates additional microarray platforms and data formats. Ball CA, Awad IA, Demeter J, Gollub J, Hebert JM, Hernandez-Boussard T, Jin H, Matese JC, Nitzberg M, Wymore F, Zachariah ZK, Brown PO, Sherlock G. Nucleic Acids Res. 2005; 33 (Database issue): D580-2
• The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information. Arnaud MB, Costanzo MC, Skrzypek MS, Binkley G, Lane C, Miyasato SR, Sherlock G. Nucleic Acids Res. 2005; 33 (Database issue): D358-63
• Microarray karyotyping of commercial wine yeast strains reveals shared, as well as unique, genomic signatures. Dunn B, Levine RP, Sherlock G. BMC Genomics. 2005; 6 (1): 53
• Of fish and chips. Sherlock G, Nat Methods. 2005; 2 (5): 329-30
• Storage and retrieval of microarray data and open source microarray database software. Sherlock G, Ball CA. Mol Biotechnol. 2005; 30 (3): 239-51
• A human-curated annotation of the Candida albicans genome. Braun BR, van Het Hoog M, d'Enfert C, Martchenko M, Dungan J, Kuo A, Inglis DO, Uhl MA, Hogues H, Berriman M, Lorenz M, Levitin A, Oberholzer U, Bachewich C, Harcus D, Marcil A, Dignard D, Iouk T, Zito R, Frangeul L, Tekaia F, Rutherford K, Wang E, Munro CA, Bates S, Gow NA, Hoyer LL, Köhler G, Morschhäuser J, Newport G, Znaidi S, Raymond M, Turcotte B, Sherlock G, Costanzo M, Ihmels J, Berman J, Sanglard D, Agabian N, Mitchell AP, Johnson AD, Whiteway M, Nantel A. PLoS Genet. 2005; 1 (1): 36-57
• Caryoscope: an Open Source Java application for viewing microarray data in a genomic context. Awad IA, Rees CA, Hernandez-Boussard T, Ball CA, Sherlock G. BMC Bioinformatics. 2004: 5 151
• An open letter on microarray data from the MGED Society. Ball C, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Icahn C, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N. Microbiology. 2004; 150 (Pt 11): 3522-4
• Funding high-throughput data sharing. Ball CA, Sherlock G, Brazma A. Nat Biotechnol. 2004; 22 (9): 1179-83
• Reply: whole-culture synchronization - effective tools for cell cycle studies. Spellman PT, Sherlock G. Trends Biotechnol. 2004; 22 (6): 270-3
• Final words: cell age and cell cycle are unlinked. Spellman PT, Sherlock G. Trends Biotechnol. 2004; 22 (6): 277-8
• STARTing to recycle. Sherlock G, Nat Genet. 2004; 36 (8): 795-6
• GeneXplorer: an interactive web application for microarray data visualization and analysis. Rees CA, Demeter J, Matese JC, Botstein D, Sherlock G. BMC Bioinformatics. 2004: 5 141
• Standards for microarray data: an open letter. Ball C, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N. Environ Health Perspect. 2004; 112 (12): A666-7
• Submission of microarray data to public repositories. Ball CA, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N. PLoS Biol. 2004; 2 (9): E317
• The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD). Killion PJ, Sherlock G, Iyer VR. BMC Bioinformatics. 2003: 4 32
• Microarray databases: storage and retrieval of microarray data. Sherlock G, Ball CA. Methods Mol Biol. 2003: 224 235-48
• SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Diehn M, Sherlock G, Binkley G, Jin H, Matese JC, Hernandez-Boussard T, Rees CA, Cherry JM, Botstein D, Brown PO, Alizadeh AA. Nucleic Acids Res. 2003; 31 (1): 219-23
• The Stanford Microarray Database: data access and quality assessment tools. Gollub J, Ball CA, Binkley G, Demeter J, Finkelstein DB, Hebert JM, Hernandez-Boussard T, Jin H, Kaloper M, Matese JC, Schroeder M, Brown PO, Botstein D, Sherlock G. Nucleic Acids Res. 2003; 31 (1): 94-6
• Design and implementation of microarray gene expression markup language (MAGE-ML). Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, Shojatalab M, Pizarro A, White J, Hubley R, Deutsch E, Senger M, Aronow BJ, Robinson A, Bassett D, Stoeckert CJ, Brazma A. Genome Biol. 2002; 3 (9): RESEARCH0046
• Standards for microarray data. Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ, Stewart JE, Taylor R, Brazma A, Quackenbush J. Science. 2002; 298 (5593): 539
• The underlying principles of scientific publication. Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ, Stewart JE, Taylor R, Brazma A, Quackenbush J. Bioinformatics. 2002; 18 (11): 1409
• Molecular characterisation of soft tissue tumours: a gene expression study. Nielsen TO, West RB, Linn SC, Alter O, Knowling MA, O'Connell JX, Zhu S, Fero M, Sherlock G, Pollack JR, Brown PO, Botstein D, van de Rijn M. Lancet. 2002; 359 (9314): 1301-7
• Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. Nucleic Acids Res. 2002; 30 (1): 69-72
• Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M. Nat Genet. 2001; 29 (4): 365-71
• Missing value estimation methods for DNA microarrays. Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB. Bioinformatics. 2001; 17 (6): 520-5
• Analysis of large-scale gene expression data. Sherlock G, Brief Bioinform. 2001; 2 (4): 350-62
• Creating the gene ontology resource: design and implementation. Genome Res. 2001; 11 (8): 1425-33
• Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. Nucleic Acids Res. 2001; 29 (1): 80-1
• The Stanford Microarray Database. Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper M, Weng S, Jin H, Ball CA, Eisen MB, Spellman PT, Brown PO, Botstein D, Cherry JM. Nucleic Acids Res. 2001; 29 (1): 152-5
• A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Salama N, Guillemin K, McDaniel TK, Sherlock G, Tompkins L, Falkow S. Proc Natl Acad Sci U S A. 2000; 97 (26): 14668-73
• Integrating functional genomic information into the Saccharomyces genome database. Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res. 2000; 28 (1): 77-80
• Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Nat Genet. 2000; 25 (1): 25-9
• Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, Staudt LM. Nature. 2000; 403 (6769): 503-11
• Analysis of large-scale gene expression data. Sherlock G, Curr Opin Immunol. 2000; 12 (2): 201-5
• Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock G, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res. 1999; 27 (1): 74-8
• Comparison of the complete protein sets of worm and yeast: orthology and divergence. Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science. 1998; 282 (5396): 2022-8
• Molecular cloning and analysis of CDC28 and cyclin homologues from the human fungal pathogen Candida albicans. Sherlock G, Bahman AM, Mahal A, Shieh JC, Ferreira M, Rosamond J. Mol Gen Genet. 1994; 245 (6): 716-23
• Starting to cycle: G1 controls regulating cell division in budding yeast. Sherlock G, Rosamond J. J Gen Microbiol. 1993; 139 (11): 2531-41