-
Schep, A.N., Buenrostro, J.D., Denny, S.K., Schwartz, K., Sherlock,
G. and Greenleaf, W.J. (2015). Structured nucleosome
fingerprints enable high-resolution mapping of chromatin architecture
within regulatory regions. Genome Research 25(11), 1757-70.
-
Calderon-Norena, D.M., Gonzalez-Novo, A., Orellana-Munoz, S.,
Gutierrez-Escribano, P., Arnaiz-Pita, Y., Duenas-Santero, E., Suarez,
M.B., Bougnoux, M.E., Del Rey, F., Sherlock, G., d'Enfert, C.,
Correa-Bordes, J. and de Aldana, C.R. (2015). A Single Nucleotide
Polymorphism Uncovers a Novel Function for the Transcription Factor Ace2
during Candida albicans Hyphal Development. PLoS
Genetics 11(4):e1005152.
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Levy, S.F., Blundell, J.R., Venkataram, S., Petrov, D.A., Fisher,
D.S. and Sherlock, G. (2015). Quantitative evolutionary dynamics
using high-resolution lineage tracking. Nature 519, 181-186.
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Rosenzweig, R. and Sherlock, G. (2014). Experimental Evolution:
Prospects and Challenges. Genomics 104(6), v-vi.
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Chiotti, K., Kvitek, D.J., Schmidt, K.,
Koniges, G., Schwartz, K., Donckels, E.A., Rosenzweig,
F.* and Sherlock, G.* (2014). The Valley-of-Death: Reciprocal
sign epistasis constrains adaptive trajectories in a constant, nutrient
limiting environment. Genomics 104(6), 431-437.
-
Kinnersley, M., Wenger, J., Kroll, E., Adams, J., Sherlock, G. and
Rosenzweig, F. (2014). Ex Uno Plures: Clonal Reinforcement Drives
Evolution of a Simple Microbial Community. PLoS Genetics 10(6):e1004430.
-
Muzzey, D., Sherlock, G.* and Weissman, J.S.* (2014). Extensive and
coordinated control of allele-specific expression by both transcription
and translation in Candida albicans. Genome Research 24(6):963-73.
-
Spor, A.*, Kvitek, D.J.*, Nidelet, T., Martin, J., Legrand, J., Dillmann,
C., Bourgais, A., de Vienne, D., Sherlock, G. and Sicard,
D. (2014). Phenotypic and genotypic convergences are influenced by
historical contingency and environment in yeast. Evolution 68(3):772-90.
-
Kvitek, D.J., Sherlock, G. (2013). Whole Genome, Whole Population
Sequencing Reveals That Loss of Signaling Networks Is the Major Adaptive
Strategy in a Constant Environment. PLoS Genetics 9(11):
e1003972.
-
Grant, G.D., Brooks, L., 3rd, Zhang, X., Mahoney, J.M., Martyanov, V.,
Wood, T.A., Sherlock, G., Cheng, C. and Whitfield, M.L. (2013).
Identification of cell cycle-regulated genes periodically expressed in
U2OS cells and their regulation by FOXM1 and E2F transcription
factors. Mol. Biol. Cell 24(23):3634-50.
-
Muzzey, D., Schwartz, K., Weissman, J.S.* and Sherlock, G.* (2013). Assembly of a phased diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure. Genome Biol. 14(9):R97.
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Richter, C.L., Dunn, B., Sherlock, G. and Pugh, T. (2013). Comparative metabolic footprinting of a large number of commercial wine yeast strains in Chardonnay fermentations.
FEMS Yeast Research 13(4):394-410.
-
Dunn, B., Paulish, T., Stanbery, A., Piotrowski, J., Koniges, G.,
Kroll, E., Louis, E.J., Liti, G., Sherlock, G.*, and Rosenzweig,
F.* (2013). Recurrent Rearrangement during Adaptive Evolution in an
Interspecific Yeast Hybrid Suggests a Model for Rapid Introgression.
PLoS Genetics 9(3): e1003366.
-
Piotrowski, J., Nagarajan, S., Kroll, E., Stanbery, A., Chiotti, K.E.,
Kruckeberg, A.L., Dunn, B., Sherlock, G. and Rosenzweig, F. (2012).
Different selective pressures lead to different genomic outcomes as
newly-formed hybrid yeasts evolve. BMC Evolutionary Biology 12:46.
-
Avrahami-Moyal, L., Engelberg, D., Wenger, J.W., Sherlock, G. and
Braun, S. (2012). Turbidostat Culture of Saccharomyces cerevisiae
W303-1A under Selective Pressure Elicited by Ethanol Selects for Mutations
in SSD1 and UTH1.
FEMS Yeast Res. 12(5):521-33.
-
Schwartz, K.*, Wenger, J.W.*, Dunn, B. and Sherlock, G. (2012). APJ1
and GRE3 Homologs Work in Concert to Allow Growth in Xylose in a Natural
Saccharomyces sensu stricto Hybrid Yeast.
Genetics 191(2):621-32.
-
Dunn, B., Richter, C., Kvitek, D.J., Pugh, T. and Sherlock,
G. (2012). 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 22(5):908-24.
-
Risso, D., Schwartz, K., Sherlock, G. and Dudoit, S. (2011).
GC-Content Normalization for RNA-Seq Data. BMC
Bioinformatics 12:480.
-
Wenger, J.W., Piotrowski, J., Nagarajan, S., Chiotti, K., Sherlock,
G.,*, and Rosenzweig, F.* (2011). Hunger Artists: Yeast Adapted to
Carbon Limitation Show Trade-Offs under Carbon Sufficiency. PLoS
Genet 7(8): e1002202.
-
The Cancer Genome Atlas Research Network (2011). Integrated
Genomic Analyses of Ovarian Carcinoma. Nature 474,
609-615.
-
Kvitek, D.J. and Sherlock, G. (2011). Reciprocal Sign Epistasis between
Frequently Experimentally Evolved Adaptive Mutations Causes a Rugged
Fitness Landscape. PLoS Genet 7(4): e1002056.
-
Kobayashi, Y., Absher, D.M., Gulzar, Z.G., Young, S.R., McKenney,
J.K., Peehl, D.M., Brooks, J.D., Myers, R.M. and Sherlock, G.
(2011). DNA methylation profiling reveals novel biomarkers and
important roles for DNA methyltransferases in prostate
cancer. Genome Research 21, 1017-1027.
-
The ENCODE Project Consortium (2011). A User's Guide to the
Encyclopedia of DNA Elements (ENCODE). PLoS
Biology 9(4): e1001046.
-
Martin, J., Bruno, V.M., Fang, Z., Meng, X., Blow, M., Zhang, T.,
Sherlock, G., Snyder, M. and Wang, Z. (2010). Rnnotator: an
automated de novo transcriptome assembly pipeline from stranded
RNA-Seq reads. BMC Genomics 11, 663.
-
Bruno, V.M., Wang, Z., Marjani, S.L., Euskirchen, G.M., Martin, J.,
Sherlock, G. and Snyder, M. (2010). Comprehensive annotation of
the transcriptome of the human fungal pathogen Candida albicans using
RNA-seq. Genome Research 20, 1451-1458.
-
Kao, K.C., Schwartz, K., Sherlock, G. (2010). 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 6(7), e1001038.
-
Wenger, J.W., Schwartz, K. and Sherlock, G. (2010). Bulk
Segregant Analysis by High-Throughput Sequencing Reveals a Novel
Xylose Utilization Gene from Saccharomyces cerevisiae. PLoS
Genetics 6(5):e1000942.
-
Duval, E.H., Alves Jr., S.L., Dunn, B., Sherlock, G. and Stambuk,
B.U. (2010). 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 109, 248 - 259.
-
Stambuk, B.U., Dunn, B., Alves, S.L. Jr., Duval, E.H., Sherlock,
G. (2009). Industrial fuel ethanol yeasts contain adaptive copy
number changes in genes involved in vitamin B1 and B6
biosynthesis. Genome Research 19, 2271-2278.
-
Butler, G., Rasmussen, M.D., Lin, M.F., Santos, M.A., Sakthikumar,
S., Munro, C.A., Rheinbay, E., Grabherr, M., Forche, A., Reedy, J.L.,
Agrafioti, I., Arnaud, M.B., Bates, S., Brown, A.J., Brunke, S.,
Costanzo, M.C., Fitzpatrick, D.A., de Groot, P.W., Harris, D., Hoyer,
L.L., Hube, B., Klis, F.M., Kodira, C., Lennard, N., Logue, M.E.,
Martin, R., Neiman, A.M., Nikolaou, E., Quail, M.A., Quinn, J.,
Santos, M.C., Schmitzberger, F.F., Sherlock, G., Shah, P.,
Silverstein, K.A., Skrzypek, M.S., Soll, D., Staggs, R., Stansfield,
I., Stumpf, M.P., Sudbery, P.E., Srikantha, T., Zeng, Q., Berman, J.,
Berriman, M., Heitman, J., Gow, N.A., Lorenz, M.C., Birren, B.W.,
Kellis, M., Cuomo, C.A. (2009). Evolution of pathogenicity and
sexual reproduction in eight Candida genomes. Nature
459, 657-662.
-
Lee, A., Hansen, K.D., Bullard, J., Dudoit, S. and Sherlock,
G. (2008). 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 Genet
4(12): e1000299.
-
Kao, K.C. and Sherlock, G. (2008). Molecular characterization
of clonal interference during adaptive evolution in asexual
populations of Saccharomyces cerevisiae. Nature
Genetics 40, 1499 - 1504.
-
Dunn, B. and Sherlock, G. (2008). Reconstruction of the genome
origins and evolution of the hybrid lager yeast Saccharomyces
pastorianus. Genome Research 18, 1610-1623.
-
The Cancer Genome Atlas Research Network (2008). Comprehensive
genomic characterization defines human glioblastoma genes and core
pathways. Nature 455, 1061-8.
-
Cho, R.W., Wang, X., Diehn, M., Shedden, K., Chen, G.Y., Sherlock,
G., Gurney, A., Lewicki, J. and Clarke, M.F. (2008). Isolation and
Molecular Characterization of Cancer Stem Cells in MMTV-Wnt-1 Murine
Breast Tumors. Stem Cells 26(2), 364-371.
-
Liu, R., Wang, X., Chen, G.Y., Dalerba, P., Gurney, A., Hoey, T.,
Sherlock, G., Lewicki, J., Shedden, K. and Clarke, M.F. (2007).
The Prognostic Role of a Gene Signature from Tumorigenic Breast-Cancer
Cells. N Engl J Med. 356(3):217-226.
-
Sherlock, G. (2006). Complex Evolution. Nature
443, 513-515.
-
Helland, S., Johnsen, H., Froyland, C., Landmark, H.B., Saetersdal,
A.B., Holmen, M.M., Gjertsen, T., Nesland, J.M., Ottestad, W.,
Jeffrey, S.S., Ottestad, L.O., Rodningen, O.K., Sherlock, G. and
Borresen-Dale, A.L. (2006). Radiation-induced effects on gene
expression: An in vivo study on breast cancer.
Radiother. Oncol. 80, 230-235.
-
Brown, J.A., Sherlock, G., Myers, C.L., Burrows, N.M.,
Deng, C., Wu, H.I., McCann, K.E., Troyanskaya, O.G. and Brown,
J.M. (2006). Global analysis of gene function in yeast by
quantitative phenotypic profiling. Molecular Systems Biology 2:2006.0001.
-
Sherlock, G. (2005). Of fish and chips. Nature Methods
2, 329-330.
-
Dunn, B., Levine, R.P. and Sherlock, G. (2005). Microarray
karyotyping of commercial wine yeast strains reveals shared, as well
as unique, genomic signatures. BMC Genomics 6:53.
-
Boyle, E.I., Weng, S., Gollub, J., Jin, H., Botstein, D., Cherry,
J.M. and Sherlock, G. (2004). GO::TermFinder - open source
software for accessing Gene Ontology information and finding
significantly enriched Gene Ontology terms associated with a list of
genes. Bioinformatics 20, 3710-3715.
-
Sherlock, G. (2004). STARTing to recycle.
Nature Genetics 36, 795-796.
-
Spellman, P.T. and Sherlock, G. (2004). Reply: Cell Age and Cell
Cycle are Unlinked. Trends in Biotechnology 22, 277-8.
-
Spellman, P.T. and Sherlock, G. (2004). Whole-Culture
Synchronization: Effective Tools for Cell Cycle Studies. Trends in
Biotechnology 22, 270-3.
-
Whitfield, M.L., Sherlock, G., Saldanha, A., Murray, J.I., Ball, C.A.,
Alexander, K.E., Matese, J.C., Perou, C.M., Hurt, M.M., Brown, P.O.,
and Botstein, D. (2002). Identification of Genes Periodically
Expressed in the Human Cell Cycle and Their Expression in Tumors.
Molecular Biology of the Cell 13, 1977-2000.
-
Nielsen, T.O., West, R.B., Linn, S.C., Alter, O., Knowling, M.A.,
J.X., Zhu, S., Fero, M., Sherlock, G., Pollack, J.R., Brown, P.O.,
Botstein, D., and van de Rijn, M. (2002). Molecular characterisation
of soft tissue tumours: a gene expression study. The Lancet
359, 1301-07.
-
Tibshirani, R., Hastie, T., Narashimhan, B., Eisen, M., Sherlock, G.,
Brown, P. and Botstein, D. (2002). Exploratory screening of genes and
clusters from microarray experiments. Statistica Sinica 12,
47-49.
-
Sherlock G. (2001). Analysis of Large Scale Gene Expression Data.
Briefings in Bioinformatics 2, 350-362.
-
Troyanskaya O., Cantor, M., Sherlock G., Brown P.O., Hastie T.,
Tibshirani R., Botstein B., and Altman, R.B. (2001). Missing value
estimation methods for DNA microarrays. Bioinformatics 17,
520-525.
-
Salama, N., Guillemin, K., McDaniel, T.K., Sherlock, G., Tompkins,
L. and Falkow, S. (2000). A Whole Genome Microarray Reveals Genetic
Diversity Among Helicobacter pylori Strains. Proceedings of the
National Academy of Science USA 97, 14668-14673.
-
Alizadeh, A.A, Eisen, M.B., Davis, R.E, Ma, C., Lossos, I.S.,
Rosenwald, A., Boldrick, J.C., Sabet, H., Tran, T., Yu, X., Powell,
J.I., Yang, L., Marti, G.E., Moore, T., Hudson, J., Lu, L., Lewis,
D.B., Tibshirani, R., Sherlock, G., Chan, W.C., Greiner, T.C.,
Weisenburger, D.D., Armitage, J.O., Warnke, R., Levy, R., Wilson, W.,
Grever, M.R., Byrd, J.C., Botstein, D., Brown, P.O., and Staudt,
L.M. (2000). Distinct types of diffuse large B-cell lymphoma
identified by gene expression profiling. Nature 403, 503-511.
-
Sherlock, G. (2000). Analysis of large-scale expression data.
Current Opinion in Immunology 12(2), 201-205.
-
Spellman, P.T.*, Sherlock, G.*, Zhang, M.Q., Iyer, V.R., Anders,
K., Eisen, M.B., Brown, P.O., Botstein, D., and B. Futcher (1998).
Comprehensive Identification of Cell Cycle-regulated Genes of the
Yeast Saccharomyces cerevisiae by Microarray Hybridization.
Molecular Biology of the Cell 9, 3273-3297.
*=joint first authors.
-
Chervitz, S.A., Aravind, L., Sherlock, G., Ball, C.A., Koonin, E.V.,
Dwight, S.S., Harris, M.A., Dolinski, K., Mohr, S., Smith, T., Weng,
S., Cherry, J.M., and Botstein, D. (1998). Comparison of the Complete
Protein Sets of Worm and Yeast: Orthology and Divergence. Science
282, 2022-2028.
-
Sherlock, G., Bahman, A.M., Mahal, A., Shieh, J.-C., Ferreira, M., and
Rosamond, J. (1994). Molecular cloning and analysis of CDC28 and
cyclin homologues from the human fungal pathogen Candida albicans.
Mol. Gen. Genet. 245, 716-723.
-
Sherlock, G. and Rosamond, J. (1993). STARTing to Cycle: G1
Controls Regulating Cell Division in Budding Yeast. Journal of
General Microbiology 139, 2531-2541.
|
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Skrzypek, M.S., Binkley, J., Sherlock, G. (2016). How to Use the Candida
Genome Database. Methods Mol Biol. 1356:3-15.
-
Keseler, I.M., Skrzypek, M., Weerasinghe, D., Chen, A.Y., Fulcher, C., Li, G.W., Lemmer,
K.C., Mladinich, K.M., Chow, E.D., Sherlock, G. and Karp, P.D. (2014). Curation accuracy
of model organism databases. Database bau058.
-
Inglis, D.O., Skrzypek, M.S., Liaw, E., Moktali, V., Sherlock, G. and
Stajich, J.E. (2014). Literature-based gene curation and a proposed
genetic nomenclature for Cryptococcus. Eukaryotic Cell 13(7):878-83.
-
Hu, J.C., Sherlock, G., Siegele, D.A., Aleksander, S.A., Ball, C.A.,
Demeter, J., Gouni, S., Holland, T.A., Karp, P.D., Lewis, J.E., Liles,
N.M., McIntosh, B.K., Mi, H., Muruganujan, A., Wymore, F. and Thomas,
P.D. (2014). PortEco: a resource for exploring bacterial biology
through high-throughput data and analysis tools. Nucleic Acids
Research 42(1):D677-84.
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Cerqueira, G.C., Arnaud, M.B., Inglis, D.O., Skrzypek, M.S., Binkley,
G., Simison, M., Miyasato, S.R., Binkley, J., Orvis, J., Shah, P.,
Wymore, F., Sherlock, G. and Wortman, J.R. (2014).
The Aspergillus genome database: multispecies curation and
incorporation of RNA-Seq data to improve structural gene
annotations. Nucleic Acids Research 42(1):D705-10.
-
Binkley, J., Arnaud, M.B., Inglis, D.O., Skrzypek, M.S., Shah, P.,
Wymore, F., Binkley, G., Miyasato, S.R., Simison, M. and
Sherlock. G. (2014). The Candida Genome Database: The new
homology information page highlights protein similarity and
phylogeny. Nucleic Acids Research 42(1):D711-6.
-
Inglis, D.O. and Sherlock, G. (2013). Ras signaling gets
fine-tuned: regulation of multiple pathogenic traits of Candida
albicans. Eukaryotic Cell 12(10), 1316-25.
-
Inglis, D.O., Binkley, J., Skrzypek, M.S., Arnaud, M.B., Cerqueira,
G.C., Shah, P., Wymore, F., Wortman, J.R. and Sherlock, G. (2013).
Comprehensive annotation of secondary metabolite biosynthetic genes and
gene clusters of Aspergillus
nidulans, A. fumigatus, A. niger
and A. oryzae. BMC Microbiol. 13(1), 91.
-
Inglis, D.O., Skrzypek, M.S., Arnaud, M.B., Binkley, J., Shah, P., Wymore, F. and Sherlock, G. (2013). Improved Gene Ontology annotation for biofilm formation, filamentous growth and phenotypic switching in Candida albicans. Eukaryotic Cell 12(1), 101.
-
Arnaud, M.B., Cerqueira, G.C., Inglis, D.O., Skrzypek, M.S., Binkley,
J., Chibucos, M.C., Crabtree, J., Howarth, C., Orvis, J., Shah, P.,
Wymore, F., Binkley, G., Miyasato, S.R., Simison, M., Sherlock, G. and
Wortman, J.R. (2012). The Aspergillus Genome Database (AspGD): recent
developments in comprehensive multispecies curation, comparative genomics
and community resources. Nucleic Acids Research 40:D653-9.
-
Inglis, D.O., Arnaud, M.B., Binkley, J., Shah, P., Skrzypek, M.S.,
Wymore, F., Binkley, G., Miyasato, S.R., Simison, M. and Sherlock,
G. (2012). 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 40:D667-74.
-
Shankar, R., Parkinson, H., Burdett, T., Hastings, E., Liu, J.,
Miller, M., Srinivasa, R., White, J., Brazma, A., Sherlock, G.,
Stoeckert, C.J. Jr., and Ball, C.A. (2010). Annotare - a tool
for annotating high-throughput biomedical investigations and
resulting data. Bioinformatics 26, 2470-1.
-
Galagan, J.E., Sisk, P., Stolte, C., Weiner, B., Koehrsen, M.,
Wymore, F., Reddy, T.B., Engels, R., Gellesch, M., Hubble, J., Jin,
H., Larson, L., Mao, M., Nitzberg, M., White, J., Zachariah, Z.K.,
Sherlock, G., Ball, C.A. and Schoolnik, G.K. (2010). TB
database 2010: Overview and update.
Tuberculosis (Edinb). 90, 225-235.
-
Skrzypek, M.S., Arnaud, M.B., Costanzo, M.C., Inglis, D.O., Shah,
P., Binkley, G., Miyasato, S.R., Sherlock, G. (2010). New tools
at the Candida Genome Database: biochemical pathways and full-text
literature search. Nucleic Acids Res. 38, D428-32.
-
Arnaud, M.B., Chibucos, M.C., Costanzo, M.C., Crabtree, J., Inglis,
D.O., Lotia, A., Orvis, J., Shah, P., Skrzypek, M.S., Binkley, G.,
Miyasato, S.R., Wortman, J.R., Sherlock, G. (2010).
The Aspergillus Genome Database, a curated comparative genomics
resource for gene, protein and sequence information for the
Aspergillus research community. Nucleic Acids Res. 38, D420-7.
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Arnaud, M.B., Costanzo, M.C., Shah, P., Skrzypek, M.S., Sherlock,
G. (2009). Gene Ontology and the annotation of pathogen genomes:
the case of Candida albicans. Trends in Microbiology
17(7), 295-303.
-
Hubble, J., Demeter, J., Jin, H., Mao, M., Nitzberg, M., Reddy,
T.B., Wymore, F., Zachariah, Z.K., Sherlock, G. and Ball,
C.A. (2009). Implementation of GenePattern within the Stanford
Microarray Database. Nucleic Acids Res. 37, D898-D901.
-
Reddy, T.B., 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, Z.K., Sherlock, G., Galagan, J.E., Ball, C.A.,
Schoolnik, G.K. (2009). TB database: an integrated platform for
tuberculosis research. Nucleic Acids Res. 37, D499-D508.
-
Deutsch, E.W., Ball, C.A., Berman, J.J., Bova, G.S., Brazma, A.,
Bumgarner, R.E., Campbell, D., Causton, H.C., Christiansen, J.H.,
Daian, F., Dauga, D., Davidson, D.R., Gimenez, G., Goo, Y.A.,
Grimmond, S., Henrich, T., Herrmann, B.G., Johnson, M.H., Korb, M.,
Mills, J.C., Oudes, A.J., Parkinson, H.E., Pascal, L.E., Pollet, N.,
Quackenbush, J., Ramialison, M., Ringwald, M., Salgado, D., Sansone,
S.A., Sherlock, G., Stoeckert, C.J. Jr., Swedlow, J., Taylor, R.C.,
Walashek, L., Warford, A., Wilkinson, D.G., Zhou, Y., Zon, L.I., Liu,
A.Y. and True, L.D. (2008). Minimum information specification for
in situ hybridization and immunohistochemistry experiments
(MISFISHIE). Nature Biotechnology 26(3), 305-12.
-
Maier, D., Wymore, F., Sherlock, G. and Ball, C.A. (2008). The
XBabelPhish MAGE-ML and XML Translator. BMC Bioinformatics 9:28.
-
Marinelli, R.J., Montgomery, K., Liu, C.L., Shah, N.H., Prapong,
W., Nitzberg, M., Zachariah, Z.K., Sherlock, G.J., Natkunam, Y., West,
R.B., Rijn, M.V., Brown, P.O. and Ball, C.A. (2008). The Stanford
Tissue Microarray Database. Nucleic Acids Res. 36, D871-7.
-
Beauheim, C.C., Wymore, F., Nitzberg, M., Zachariah, Z.K., Jin, H.,
Skene, J.H.P., Ball, C.A. and Sherlock, G. (2007). OntologyWidget -
a reusable, embeddable widget for easily locating ontology terms.
BMC Bioinformatics 8(1), 338.
-
Demeter, J., Beauheim, C., Gollub, J., Hernandez-Boussard, T., Jin,
H., Maier, D., Matese, J.C., Nitzberg, M., Wymore, F., Zachariah,
Z.K., Brown, P.O., Sherlock, G. and Ball, C.A. (2007). The
Stanford Microarray Database: implementation of new analysis tools and
open source release of software. Nucleic Acids Res. 35,
D766-D770.
-
Arnaud, M.B., Costanzo, M.C., Skrzypek, M.S., Shah, P., Binkley,
G., Lane, C., Miyasato, S.R. and Sherlock, G. (2007). Sequence
resources at the Candida Genome Database. Nucleic Acids
Res. 35, D452-D456.
-
Rayner, T.F., Rocca-Serra, P., Spellman, P.T., Causton, H.C.,
Farne, A., Holloway, E., Irizarry, R.A., Liu, J., Maier, D.S., Miller,
M., Petersen, K., Quackenbush, J., Sherlock, G., Stoeckert, C.J. Jr.,
White, J., Whetzel, P.L., Wymore, F., Parkinson, H., Sarkans, U.,
Ball, C.A. and Brazma, A. (2006). A simple spreadsheet-based,
MIAME-supportive format for microarray data: MAGE-TAB. BMC
Bioinformatics 7(1):489.
-
Deutsch, E.W., Ball, C.A., Bova, G.S., Brazma, A., Bumgarner, R.E.,
Campbell, D., Causton, H.C., Christiansen, J., Davidson, D., Eichner,
L.J., Goo, Y.A., Grimmond, S., Henrich, T., Johnson, M.H., Korb, M.,
Mills, J.C., Oudes, A., Parkinson, H.E., Pascal, L.E., Quackenbush,
J., Ramialison, M., Ringwald, M., Sansone, S.A., Sherlock, G.,
Stoeckert, Jr., C.J., Swedlow, J., Taylor, R.C., Walashek, L., Zhou,
Y., Liu, A.Y. and True, L.D. (2006). Minimum Information
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Experiments (MISFISHIE). OMICS: A Journal of Integrative Biology 10,
205-208.
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Costanzo, M.C., Arnaud, M.B., Skrzypek, M.S., Binkley, G., Lane,
C., Miyasato, S.R. and Sherlock, G. (2006). The Candida Genome
Database: Facilitating research on Candida albicans molecular
biology. FEMS Yeast Research 6, 671-684.
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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, S.A., Sarkans, U., Sherlock, G., Stevens, R., Taylor, C.,
Taylor, R., Whetzel, P. and White, J. (2006). Wrestling with SUMO
and bio-ontologies. Nature Biotechnology 24, 21-2.
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Sherlock, G. and Ball, C.A. (2005). Storage and Retrieval of
Microarray Data and Open Source Microarray Database
Software. Molecular Biotechnology 30, 239-52.
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Braun, B.R., van het Hoog, M., d'Enfert, C., Martchenko, M.,
Dungan, J., Kuo, A., Inglis, D.O., Uhl, M.A., 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, C.A., Bates, S., Gow, N.A.,
Hoyer, L.L., Kohler, G., Morschhauser, J., Newport, G., Znaidi, S.,
Raymond, M., Turcotte, B., Sherlock, G., Costanzo, M., Ihmels, J.,
Berman, J., Sanglard, D., Agabian, N., Mitchell, A.P., Johnson, A.D.,
Whiteway, M., and Nantel, A. (2005). A Human-Curated Annotation
of the Candida albicans Genome. PLoS Genetics
1(1):e1.
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Ball, C.A., Awad, I.A.B, Demeter, J., Gollub, J., Hebert, J.,
Hernandez-Boussard, T., Jin, H., Matese, J.C., Nitzberg, M., Wymore,
F., Zachariah, Z., Brown, P.O. and Sherlock, G. (2005). The Stanford
Microarray Database accommodates additional microarray platforms and
data formats. Nucleic Acids Research 33, D580-D582.
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Arnaud, M.B., Costanzo, M.C., Skrzypek, M.S., Binkley, G., Lane, C.,
Miyasato, S.R. and Sherlock, G. (2005). The Candida Genome
Database (CGD), a community resource for Candida albicans gene
and protein information. Nucleic Acids Research 33,
D358-D363.
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Awad, I.A.B, Rees, C.A., Hernandez-Boussard, T., Ball, C.A. and
Sherlock, G. (2004). Caryoscope: An Open Source Java Application for
Viewing Microarray Data in a Genomic Context. BMC
Bioinformatics 5:151.
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Rees, C.A., Demeter, J., Matese, J.C., Botstein, D. and Sherlock,
G. (2004). GeneXplorer: an interactive web application for microarray
data visualization and analysis. BMC Bioinformatics
5:41.
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Ball, C.A., Sherlock, G. and Brazma, A. (2004). Funding
high-throughput data sharing. Nature Biotechnology 22,
1179-1183.
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Killion, P., Sherlock, G. and Iyer, V.R. (2003). The Longhorn Array
Database (LAD): An Open-Source, MIAME compliant implementation of the
Stanford Microarray Database (SMD). BMC Bioinformatics
4:32.
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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. (2003). The Stanford Microarray Database:
data access and quality assessment tools. Nucleic Acids
Res. 31, 94-6.
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Diehn, M., Sherlock, G., Binkley, G., Jin, H., Matese, J.C.,
Hernandez-Boussard, T., Rees, C.A., Cherry, J.M., Botstein, D., Brown,
P.O., and Alizadeh, A.A. (2003). SOURCE: A Unified Genomic Resource
of Functional Annotations, Ontologies, and Gene Expression Data.
Nucleic Acids Research 31, 219-23.
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Spellman, P.T., Miller, M., Stewart, J., Troup, C., Sarkans, U.,
Chervitz, C., Bernhart, D., Sherlock, G., Ball, C., Lepage, M.,
Swiatek, M., Marks, W.L., Goncalves, J., Markel, S., Iordan, D.,
Shojatalab, M., Pizzaro, A., White, J., Hubley, R., Deutsch, E.,
Senger, M., Arnow, B.J., Robinson, A., Bassett, D., Stoeckert, C., and
Brazma, A. (2002). Design and Implementation of Microarray Gene
Expression Markup Language (MAGE-ML). Genome Biology 3(9):RESEARCH0046.
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Dwight, SS, Harris, MA, Dolinski, K., Ball, C.A., Binkley, G.,
Christie, K.R., Fisk, D.G., Issel-Tarver, L., Schroeder, M., Sherlock,
G., Sethuraman, A., Weng, S., Botstein, D., and Cherry, J.M. (2002).
Saccharomyces Genome Database (SGD) provides secondary gene
annotation using the Gene Ontology (GO).
Nucleic Acids Research 30, 69-72.
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Brazma, A., Hingamp, P., Quackenbush, Q., Sherlock, G., Spellman, P.,
Stoeckert, C., Ansorge, W., Ball, C.A., Causton, H., Glenison, P.,
Holstege, F., Kim, I.F., Markowitz, V., Matese, J.C., Robinson, A.,
Stewart, J., Taylor, R. and Vingron, M. (2001). Minimum Information
About a Microarray Experiment - MIAME - towards Standards
for Microarray Data. Nature Genetics 29, 365-371.
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The Gene Ontology Consortium (2001). Creating the Gene Ontology Resource:
Design and Implementation. Genome Research 11, 1425-1433.
Alphabetical list of authors: Ashburner, M., Ball, C.A., Blake, J.A.,
Butler, H., Cherry, J.M., Corradi, J., Dolinski, K., Eppig, J.T.,
Harris, M., Hill, D.P., Lewis, S., Marshall, B., Mungall, C., Reiser,
L., Rhee, S., Richardson, J.E., Richter, J., Ringwald, M., Rubin,
G.M., Sherlock, G., Yoon, J.
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Sherlock G., Hernandez-Boussard, T., Kasarskis, A., Binkley, G.,
Matese, J.C., Dwight, S.S., Kaloper, M., Weng, S., Jin, H., Ball,
C.A., Eisen, M.B., Spellman, P.T., Brown, P.O., Botstein, D. and
Cherry, J.M. (2001). The Stanford Microarray Database.
Nucleic Acids Research 29, 152-155.
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Ball, C.A., Jin, H., Sherlock, G., Weng, S., Matese, J.C., Andrada,
R. Binkley, G., Dolinski, K., Dwight S.S, Harris, M.A., Issel-Tarver,
L., Schroeder, M., Botstein, D. and Cherry, J.M. (2001).
Saccharomyces Genome Database provides tools to survey gene
expression and functional analysis data. Nucleic Acids
Research 29, 80-81.
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The Gene Ontology Consortium (2000). Gene Ontology: tool for the
unification of biology. Nature Genetics 25, 25-29.
Alphabetical list of authors: Ashburner, M., Ball, C.A., Blake, J.A.,
Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K.,
Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L.,
Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald,
M., Rubin, G.M., Sherlock, G.
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Ball, C.A., Dolinski, K., Dwight, S.S., Harris, M.A., Issel-Tarver,
L., Kasarskis, A., Scafe, C.R., Sherlock, G., Binkley, G., Jin, H.,
Kaloper, M., Orr, S.D., Schroeder, M., Weng, S., Zhu, Y., Botstein,
D., and Cherry, J.M. (2000). Integrating functional genomic
information into the Saccharomyces Genome Database.
Nucleic Acids Research 28, 77-80.
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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., Zhu, SWY, Cherry, JM, and Botstein, D (1999). Using the
Saccharomyces Genome Database (SGD) for analysis of protein
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