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Gavin Sherlock
Gavin Sherlock
Professor of Genetics, Stanford University
Verified email at stanford.edu - Homepage
Title
Cited by
Cited by
Year
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
431982000
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
124982000
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
72332008
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
68012011
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
65381998
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
49042001
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
46012001
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
22312004
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
18582002
A user’s guide to the encyclopedia of DNA elements (ENCODE)
ENCODE Project Consortium
PLoS Biol 9 (4), e1001046, 2011
14432011
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
12142007
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
11852009
GC-content normalization for RNA-Seq data
D Risso, K Schwartz, G Sherlock, S Dudoit
BMC bioinformatics 12 (1), 480, 2011
10652011
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
7612000
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
7422002
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
5962002
The stanford microarray database
G Sherlock, T Hernandez-Boussard, A Kasarskis, G Binkley, JC Matese, ...
Nucleic acids research 29 (1), 152-155, 2001
5852001
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
5611998
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
5272003
Analysis of large-scale gene expression data
G Sherlock
Current opinion in immunology 12 (2), 201-205, 2000
5032000
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
4712002
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
4482017
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
4302015
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
4292003
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
4092005
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
3722017
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
3562008
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
3552015
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
3402008
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
3312008
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
3142014
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
2982013
Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape
DJ Kvitek, G Sherlock
PLoS Genet 7 (4), e1002056, 2011
2942011
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
2842009
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
2752010
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
2662011
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
2642006
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
2552005
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
2472010
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
2422012
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
2352010
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
2322012
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
2242013
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
2222007
Standards for microarray data.
CA Ball, G Sherlock, H Parkinson, P Rocca-Sera, C Brooksbank, ...
Science (New York, NY) 298 (5593), 539, 2002
2142002
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
2072016
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
1922013
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
1902012
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
1852006
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
1822005
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
1592000
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
1582011
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
1542016
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
1542004
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
1522005
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
1422018
TB database 2010: overview and update
JE Galagan, P Sisk, C Stolte, B Weiner, M Koehrsen, F Wymore, ...
Tuberculosis 90 (4), 225-235, 2010
1422010
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
1402010
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
1302008
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
1292013
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
1292003
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
1272009
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
1222013
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
1182009
Analysis of large-scale gene expression data
G Sherlock
Briefings in bioinformatics 2 (4), 350-362, 2001
1182001
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
1152008
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
852010
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
842007
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
821999
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
792001
Ras signaling gets fine-tuned: regulation of multiple pathogenic traits of Candida albicans
DO Inglis, G Sherlock
Eukaryotic cell 12 (10), 1316-1325, 2013
782013
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
752010
Of fish and chips
G Sherlock
Nature Methods 2 (5), 329-330, 2005
712005
Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages
BA Siranosian, FB Tamburini, G Sherlock, AS Bhatt
Nature Communications, 460113, 2020
702020
Funding high-throughput data sharing
CA Ball, G Sherlock, A Brazma
Nature biotechnology 22 (9), 1179-1183, 2004
692004
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
672014
Single nucleotide mapping of trait space reveals Pareto fronts that constrain adaptation
Y Li, DA Petrov, G Sherlock
Nature Ecology & Evolution, 1-13, 2019
632019
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
622012
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
602014
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
602008
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
592019
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
582018
[10] Clustering Microarray Data
J Gollub, G Sherlock
Methods in enzymology 411, 194-213, 2006
582006
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
541994
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
512010
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
472014
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
462016
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
442009
Reply: whole-culture synchronization–effective tools for cell cycle studies
PT Spellman, G Sherlock
TRENDS in Biotechnology 22 (6), 270-273, 2004
442004
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
432012
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
412014
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
412013
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
392013
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
382017
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
372006
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
372004
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
362021
Curation accuracy of model organism databases
IM Keseler, M Skrzypek, D Weerasinghe, AY Chen, C Fulcher, GW Li, ...
Database 2014, bau058, 2014
362014
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