Gene Ontology: tool for the unification of biology M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, ... Nature genetics 25 (1), 25-29, 2000 | 43198 | 2000 |
Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling AA Alizadeh, MB Eisen, RE Davis, C Ma, IS Lossos, A Rosenwald, ... Nature 403 (6769), 503-511, 2000 | 12498 | 2000 |
Comprehensive genomic characterization defines human glioblastoma genes and core pathways R McLendon, A Friedman, D Bigner, EG Van Meir, DJ Brat, ... Nature 455 (7216), 1061-1068, 2008 | 7233 | 2008 |
Integrated genomic analyses of ovarian carcinoma D Bell, A Berchuck, M Birrer, J Chien, DW Cramer, F Dao, R Dhir, P Disaia, ... Nature Publishing Group 474 (7353), 609-615, 2011 | 6801 | 2011 |
Comprehensive identification of cell cycle–regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization PT Spellman, G Sherlock, MQ Zhang, VR Iyer, K Anders, MB Eisen, ... Molecular biology of the cell 9 (12), 3273-3297, 1998 | 6538 | 1998 |
Minimum information about a microarray experiment (MIAME)—toward standards for microarray data A Brazma, P Hingamp, J Quackenbush, G Sherlock, P Spellman, ... Nature genetics 29 (4), 365-371, 2001 | 4904 | 2001 |
Missing value estimation methods for DNA microarrays O Troyanskaya, M Cantor, G Sherlock, P Brown, T Hastie, R Tibshirani, ... Bioinformatics 17 (6), 520-525, 2001 | 4601 | 2001 |
GO:: TermFinder—open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes EI Boyle, S Weng, J Gollub, H Jin, D Botstein, JM Cherry, G Sherlock Bioinformatics 20 (18), 3710-3715, 2004 | 2231 | 2004 |
Identification of genes periodically expressed in the human cell cycle and their expression in tumors ML Whitfield, G Sherlock, AJ Saldanha, JI Murray, CA Ball, KE Alexander, ... Molecular biology of the cell 13 (6), 1977-2000, 2002 | 1858 | 2002 |
A user’s guide to the encyclopedia of DNA elements (ENCODE) ENCODE Project Consortium PLoS Biol 9 (4), e1001046, 2011 | 1443 | 2011 |
Creating the gene ontology resource: design and implementation M Ashburner, CA Ball, JA Blake, H Butler, JM Cherry, J Corradi, K Dolinski, ... Genome Res 11 (8), 1425–1433, 2001 | 1317* | 2001 |
The prognostic role of a gene signature from tumorigenic breast-cancer cells R Liu, X Wang, GY Chen, P Dalerba, A Gurney, T Hoey, G Sherlock, ... New England Journal of Medicine 356 (3), 217-226, 2007 | 1214 | 2007 |
Evolution of pathogenicity and sexual reproduction in eight Candida genomes G Butler, MD Rasmussen, MF Lin, MAS Santos, S Sakthikumar, CA Munro, ... Nature 459 (7247), 657-662, 2009 | 1185 | 2009 |
GC-content normalization for RNA-Seq data D Risso, K Schwartz, G Sherlock, S Dudoit BMC bioinformatics 12 (1), 480, 2011 | 1065 | 2011 |
A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains N Salama, K Guillemin, TK McDaniel, G Sherlock, L Tompkins, S Falkow Proceedings of the national Academy of Sciences 97 (26), 14668-14673, 2000 | 761 | 2000 |
Molecular characterisation of soft tissue tumours: a gene expression study TO Nielsen, RB West, SC Linn, O Alter, MA Knowling, JX O'Connell, S Zhu, ... The Lancet 359 (9314), 1301-1307, 2002 | 742 | 2002 |
Design and implementation of microarray gene expression markup language (MAGE-ML) PT Spellman, M Miller, J Stewart, C Troup, U Sarkans, S Chervitz, ... Genome biology 3 (9), 1-9, 2002 | 596 | 2002 |
The stanford microarray database G Sherlock, T Hernandez-Boussard, A Kasarskis, G Binkley, JC Matese, ... Nucleic acids research 29 (1), 152-155, 2001 | 585 | 2001 |
Comparison of the complete protein sets of worm and yeast: orthology and divergence SA Chervitz, L Aravind, G Sherlock, CA Ball, EV Koonin, SS Dwight, ... Science 282 (5396), 2022-2028, 1998 | 561 | 1998 |
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data M Diehn, G Sherlock, G Binkley, H Jin, JC Matese, ... Nucleic acids research 31 (1), 219-223, 2003 | 527 | 2003 |
Analysis of large-scale gene expression data G Sherlock Current opinion in immunology 12 (2), 201-205, 2000 | 503 | 2000 |
Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO) SS Dwight, MA Harris, K Dolinski, CA Ball, G Binkley, KR Christie, DG Fisk, ... Nucleic acids research 30 (1), 69-72, 2002 | 471 | 2002 |
Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus RP de Vries, R Riley, A Wiebenga, G Aguilar-Osorio, S Amillis, ... Genome Biology 18 (1), 28, 2017 | 448 | 2017 |
Quantitative evolutionary dynamics using high-resolution lineage tracking SF Levy, JR Blundell, S Venkataram, DA Petrov, DS Fisher, G Sherlock Nature 519 (7542), 181-186, 2015 | 430 | 2015 |
The Stanford Microarray Database: data access and quality assessment tools J Gollub, CA Ball, G Binkley, J Demeter, DB Finkelstein, JM Hebert, ... Nucleic Acids Research 31 (1), 94-96, 2003 | 429 | 2003 |
A human-curated annotation of the Candida albicans genome BR Braun, M van Het Hoog, C d’Enfert, M Martchenko, J Dungan, A Kuo, ... PLoS Genet 1 (1), 36-57, 2005 | 409 | 2005 |
The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data MS Skrzypek, J Binkley, G Binkley, SR Miyasato, M Simison, G Sherlock Nucleic Acids Research 45 (D1), D592-D596, 2017 | 372 | 2017 |
Isolation and molecular characterization of cancer stem cells in MMTV‐Wnt‐1 murine breast tumors RW Cho, X Wang, M Diehn, K Shedden, GY Chen, G Sherlock, A Gurney, ... Stem cells 26 (2), 364-371, 2008 | 356 | 2008 |
Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions AN Schep, JD Buenrostro, SK Denny, K Schwartz, G Sherlock, ... Genome research 25 (11), 1757-1770, 2015 | 355 | 2015 |
Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus B Dunn, G Sherlock Genome research 18 (10), 1610-1623, 2008 | 340 | 2008 |
Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae KC Kao, G Sherlock Nature genetics 40 (12), 1499-1504, 2008 | 331 | 2008 |
The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations GC Cerqueira, MB Arnaud, DO Inglis, MS Skrzypek, G Binkley, M Simison, ... Nucleic acids research 42 (D1), D705-D710, 2014 | 314 | 2014 |
Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae DO Inglis, J Binkley, MS Skrzypek, MB Arnaud, GC Cerqueira, P Shah, ... BMC microbiology 13 (1), 91, 2013 | 298 | 2013 |
Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape DJ Kvitek, G Sherlock PLoS Genet 7 (4), e1002056, 2011 | 294 | 2011 |
TB database: an integrated platform for tuberculosis research TBK Reddy, R Riley, F Wymore, P Montgomery, D DeCaprio, R Engels, ... Nucleic acids research 37 (suppl 1), D499-D508, 2009 | 284 | 2009 |
Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads J Martin, VM Bruno, Z Fang, X Meng, M Blow, T Zhang, G Sherlock, ... BMC genomics 11 (1), 663, 2010 | 275 | 2010 |
DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer Y Kobayashi, DM Absher, ZG Gulzar, SR Young, JK McKenney, DM Peehl, ... Genome research 21 (7), 1017-1027, 2011 | 266 | 2011 |
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB TF Rayner, P Rocca-Serra, PT Spellman, HC Causton, A Farne, ... Bmc Bioinformatics 7 (1), 489, 2006 | 264 | 2006 |
The Stanford Microarray Database accommodates additional microarray platforms and data formats CA Ball, IAB Awad, J Demeter, J Gollub, JM Hebert, ... Nucleic Acids Research 33 (suppl 1), D580-D582, 2005 | 255 | 2005 |
Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq VM Bruno, Z Wang, SL Marjani, GM Euskirchen, J Martin, G Sherlock, ... Genome research 20 (10), 1451-1458, 2010 | 247 | 2010 |
Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments B Dunn, C Richter, DJ Kvitek, T Pugh, G Sherlock Genome research 22 (5), 908-924, 2012 | 242 | 2012 |
Bulk segregant analysis by high-throughput sequencing reveals a novel xylose utilization gene from Saccharomyces cerevisiae JW Wenger, K Schwartz, G Sherlock PLoS Genet 6 (5), e1000942, 2010 | 235 | 2010 |
The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and … DO Inglis, MB Arnaud, J Binkley, P Shah, MS Skrzypek, F Wymore, ... Nucleic acids research 40 (D1), D667-D674, 2012 | 232 | 2012 |
Whole genome, whole population sequencing reveals that loss of signaling networks is the major adaptive strategy in a constant environment DJ Kvitek, G Sherlock PLoS genetics 9 (11), e1003972, 2013 | 224 | 2013 |
The Stanford Microarray Database: implementation of new analysis tools and open source release of software J Demeter, C Beauheim, J Gollub, T Hernandez-Boussard, H Jin, D Maier, ... Nucleic acids research 35 (suppl 1), D766-D770, 2007 | 222 | 2007 |
Standards for microarray data. CA Ball, G Sherlock, H Parkinson, P Rocca-Sera, C Brooksbank, ... Science (New York, NY) 298 (5593), 539, 2002 | 214 | 2002 |
Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast S Venkataram, B Dunn, Y Li, A Agarwala, J Chang, ER Ebel, ... Cell 166 (6), 1585-1596. e22, 2016 | 207 | 2016 |
Identification of cell cycle–regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors GD Grant, L Brooks 3rd, X Zhang, JM Mahoney, V Martyanov, TA Wood, ... Molecular biology of the cell 24 (23), 3634-3650, 2013 | 192 | 2013 |
The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources MB Arnaud, GC Cerqueira, DO Inglis, MS Skrzypek, J Binkley, ... Nucleic acids research 40 (D1), D653-D659, 2012 | 190 | 2012 |
Global analysis of gene function in yeast by quantitative phenotypic profiling JA Brown, G Sherlock, CL Myers, NM Burrows, C Deng, HI Wu, ... Molecular systems biology 2 (1), 2006 | 185 | 2006 |
Microarray karyotyping of commercial wine yeast strains reveals shared, as well as unique, genomic signatures B Dunn, RP Levine, G Sherlock BMC genomics 6 (1), 53, 2005 | 182 | 2005 |
Integrating functional genomic information into the Saccharomyces genome database CA Ball, K Dolinski, SS Dwight, MA Harris, L Issel-Tarver, A Kasarskis, ... Nucleic acids research 28 (1), 77-80, 2000 | 159 | 2000 |
Hunger artists: yeast adapted to carbon limitation show trade-offs under carbon sufficiency JW Wenger, J Piotrowski, S Nagarajan, K Chiotti, G Sherlock, ... PLoS Genet 7 (8), e1002202-e1002202, 2011 | 158 | 2011 |
Whole genome analysis of 132 clinical Saccharomyces cerevisiae strains reveals extensive ploidy variation YO Zhu, G Sherlock, DA Petrov G3: Genes| Genomes| Genetics 6 (8), 2421-2434, 2016 | 154 | 2016 |
Submission of microarray data to public repositories CA Ball, A Brazma, H Causton, S Chervitz, R Edgar, P Hingamp, ... PLoS biology 2 (9), e317, 2004 | 154 | 2004 |
The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information MB Arnaud, MC Costanzo, MS Skrzypek, G Binkley, C Lane, SR Miyasato, ... Nucleic acids research 33 (suppl 1), D358-D363, 2005 | 152 | 2005 |
Gene flow contributes to diversification of the major fungal pathogen Candida albicans J Ropars, C Maufrais, D Diogo, M Marcet-Houben, A Perin, N Sertour, ... Nature communications 9 (1), 2253, 2018 | 142 | 2018 |
TB database 2010: overview and update JE Galagan, P Sisk, C Stolte, B Weiner, M Koehrsen, F Wymore, ... Tuberculosis 90 (4), 225-235, 2010 | 142 | 2010 |
The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community MB Arnaud, MC Chibucos, MC Costanzo, J Crabtree, DO Inglis, A Lotia, ... Nucleic acids research 38 (suppl 1), D420-D427, 2010 | 140 | 2010 |
Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE) EW Deutsch, CA Ball, JJ Berman, GS Bova, A Brazma, RE Bumgarner, ... Nature biotechnology 26 (3), 305-312, 2008 | 130 | 2008 |
Assembly of a phased diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure D Muzzey, K Schwartz, JS Weissman, G Sherlock Genome Biol 14 (9), R97, 2013 | 129 | 2013 |
The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD) PJ Killion, G Sherlock, VR Iyer Bmc Bioinformatics 4 (1), 32, 2003 | 129 | 2003 |
Implementation of genepattern within the stanford microarray database J Hubble, J Demeter, H Jin, M Mao, M Nitzberg, TBK Reddy, F Wymore, ... Nucleic acids research 37 (suppl 1), D898-D901, 2009 | 127 | 2009 |
Recurrent rearrangement during adaptive evolution in an interspecific yeast hybrid suggests a model for rapid introgression B Dunn, T Paulish, A Stanbery, J Piotrowski, G Koniges, E Kroll, EJ Louis, ... PLoS Genet 9 (3), e1003366, 2013 | 122 | 2013 |
Industrial fuel ethanol yeasts contain adaptive copy number changes in genes involved in vitamin B1 and B6 biosynthesis BU Stambuk, B Dunn, SL Alves, EH Duval, G Sherlock Genome research 19 (12), 2271-2278, 2009 | 118 | 2009 |
Analysis of large-scale gene expression data G Sherlock Briefings in bioinformatics 2 (4), 350-362, 2001 | 118 | 2001 |
The Stanford tissue microarray database RJ Marinelli, K Montgomery, CL Liu, NH Shah, W Prapong, M Nitzberg, ... Nucleic acids research 36 (suppl 1), D871-D877, 2008 | 115 | 2008 |
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 KC Kao, K Schwartz, G Sherlock PLoS Genet 6 (7), e1001038, 2010 | 85 | 2010 |
Sequence resources at the Candida genome database MB Arnaud, MC Costanzo, MS Skrzypek, P Shah, G Binkley, C Lane, ... Nucleic acids research 35 (suppl 1), D452-D456, 2007 | 84 | 2007 |
Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure SA Chervitz, ET Hester, CA Ball, K Dolinski, SS Dwight, MA Harris, ... Nucleic acids research 27 (1), 74-78, 1999 | 82 | 1999 |
Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data CA Ball, H Jin, G Sherlock, S Weng, JC Matese, R Andrada, G Binkley, ... Nucleic acids research 29 (1), 80-81, 2001 | 79 | 2001 |
Ras signaling gets fine-tuned: regulation of multiple pathogenic traits of Candida albicans DO Inglis, G Sherlock Eukaryotic cell 12 (10), 1316-1325, 2013 | 78 | 2013 |
New tools at the Candida Genome Database: biochemical pathways and full-text literature search MS Skrzypek, MB Arnaud, MC Costanzo, DO Inglis, P Shah, G Binkley, ... Nucleic acids research 38 (suppl 1), D428-D432, 2010 | 75 | 2010 |
Of fish and chips G Sherlock Nature Methods 2 (5), 329-330, 2005 | 71 | 2005 |
Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages BA Siranosian, FB Tamburini, G Sherlock, AS Bhatt Nature Communications, 460113, 2020 | 70 | 2020 |
Funding high-throughput data sharing CA Ball, G Sherlock, A Brazma Nature biotechnology 22 (9), 1179-1183, 2004 | 69 | 2004 |
Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans D Muzzey, G Sherlock, JS Weissman Genome research 24 (6), 963-973, 2014 | 67 | 2014 |
Single nucleotide mapping of trait space reveals Pareto fronts that constrain adaptation Y Li, DA Petrov, G Sherlock Nature Ecology & Evolution, 1-13, 2019 | 63 | 2019 |
Different selective pressures lead to different genomic outcomes as newly-formed hybrid yeasts evolve JS Piotrowski, S Nagarajan, E Kroll, A Stanbery, KE Chiotti, ... BMC evolutionary biology 12 (1), 46, 2012 | 62 | 2012 |
Phenotypic and genotypic convergences are influenced by historical contingency and environment in yeast A Spor, DJ Kvitek, T Nidelet, J Martin, J Legrand, C Dillmann, A Bourgais, ... Evolution 68 (3), 772-790, 2014 | 60 | 2014 |
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 A Lee, KD Hansen, J Bullard, S Dudoit, G Sherlock PLoS Genet 4 (12), e1000299, 2008 | 60 | 2008 |
The dynamics of adaptive genetic diversity during the early stages of clonal evolution JR Blundell, K Schwartz, D Francois, DS Fisher, G Sherlock, SF Levy Nature ecology & evolution 3 (2), 293-301, 2019 | 59 | 2019 |
Hidden Complexity of Yeast Adaptation under Simple Evolutionary Conditions Y Li, S Venkataram, A Agarwala, B Dunn, DA Petrov, G Sherlock, ... Current Biology 28 (4), 515-525. e6, 2018 | 58 | 2018 |
[10] Clustering Microarray Data J Gollub, G Sherlock Methods in enzymology 411, 194-213, 2006 | 58 | 2006 |
Molecular cloning and analysis of CDC28 and cyclin homologues from the human fungal pathogen Candida albicans G Sherlock, AM Bahman, A Mahal, JC Shieh, M Ferreira, J Rosamond Molecular and General Genetics MGG 245 (6), 716-723, 1994 | 54 | 1994 |
Microarray karyotyping of maltose‐fermenting Saccharomyces yeasts with differing maltotriose utilization profiles reveals copy number variation in genes involved in maltose and … EH Duval, SL Alves Jr, B Dunn, G Sherlock, BU Stambuk Journal of applied microbiology 109 (1), 248-259, 2010 | 51 | 2010 |
The underlying principles of scientific publication. CA Ball, G Sherlock, H Parkinson, P Rocca-Sera, C Brooksbank, ... Bioinformatics (Oxford, England) 18 (11), 1409, 2002 | 48* | 2002 |
Ex uno plures: clonal reinforcement drives evolution of a simple microbial community M Kinnersley, J Wenger, E Kroll, J Adams, G Sherlock, F Rosenzweig PLoS genetics 10 (6), e1004430, 2014 | 47 | 2014 |
Heterozygote advantage is a common outcome of adaptation in Saccharomyces cerevisiae D Sellis, DJ Kvitek, B Dunn, G Sherlock, DA Petrov Genetics 203 (3), 1401-1413, 2016 | 46 | 2016 |
Gene Ontology and the annotation of pathogen genomes: the case of Candida albicans MB Arnaud, MC Costanzo, P Shah, MS Skrzypek, G Sherlock Trends in microbiology 17 (7), 295-303, 2009 | 44 | 2009 |
Reply: whole-culture synchronization–effective tools for cell cycle studies PT Spellman, G Sherlock TRENDS in Biotechnology 22 (6), 270-273, 2004 | 44 | 2004 |
Turbidostat culture of Saccharomyces cerevisiae W303‐1A under selective pressure elicited by ethanol selects for mutations in SSD1 and UTH1 L Avrahami‐Moyal, D Engelberg, J Wenger, G Sherlock, S Braun FEMS yeast research 12 (5), 521-533, 2012 | 43 | 2012 |
The Candida Genome Database: the new homology information page highlights protein similarity and phylogeny J Binkley, MB Arnaud, DO Inglis, MS Skrzypek, P Shah, F Wymore, ... Nucleic acids research 42 (D1), D711-D716, 2014 | 41 | 2014 |
Comparative metabolic footprinting of a large number of commercial wine yeast strains in Chardonnay fermentations CL Richter, B Dunn, G Sherlock, T Pugh FEMS yeast research 13 (4), 394-410, 2013 | 41 | 2013 |
Improved gene ontology annotation for biofilm formation, filamentous growth, and phenotypic switching in Candida albicans DO Inglis, MS Skrzypek, MB Arnaud, J Binkley, P Shah, F Wymore, ... Eukaryotic cell 12 (1), 101-108, 2013 | 39 | 2013 |
iSeq: A New Double-Barcode Method for Detecting Dynamic Genetic Interactions in Yeast M Jaffe, G Sherlock, SF Levy G3: Genes| Genomes| Genetics 7 (1), 143-153, 2017 | 38 | 2017 |
Radiation-induced effects on gene expression: an in vivo study on breast cancer Å Helland, H Johnsen, C Frøyland, HBK Landmark, AB Sætersdal, ... Radiotherapy and oncology 80 (2), 230-235, 2006 | 37 | 2006 |
Caryoscope: an Open Source Java application for viewing microarray data in a genomic context IAB Awad, CA Rees, T Hernandez-Boussard, CA Ball, G Sherlock BMC bioinformatics 5 (1), 151, 2004 | 37 | 2004 |
Adaptation is influenced by the complexity of environmental change during evolution in a dynamic environment S Boyer, L Hérissant, G Sherlock PLoS genetics 17 (1), e1009314, 2021 | 36 | 2021 |
Curation accuracy of model organism databases IM Keseler, M Skrzypek, D Weerasinghe, AY Chen, C Fulcher, GW Li, ... Database 2014, bau058, 2014 | 36 | 2014 |