sherlock lab



Publications in PubMed | Google Scholar Profile

Journal Articles

Sherlock group members underlined; postdocs in blue; graduate students in red; undergraduate students in green;
* = equal contribution; ^ = co-corresponding

  1. Li, Y.*, Venkataram, S.*, Agarwala, A.*, Dunn, B., Petrov, D.A.^, Sherlock, G.^, Fisher, D.S.^ (2018). Hidden Complexity of Yeast Adaptation under Simple Evolutionary Conditions. Current Biology 28(4):515-525.e6.
    PubMed

  2. Aggeli, D., Karas, V.O., Sinnott-Armstrong, N.A., Varghese, V., Shafer, R.W., Greenleaf, W.J., Sherlock, G. (2018). Diff-seq: A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery. Nucleic Acids Research, in press.
    PubMed

  3. de Vries et al. (2017). Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biology 18(1), 28.
    PubMed

  4. Sherlock, G. and Petrov, D.A. (2017). Seeking Goldilocks During Evolution of Drug Resistance. PLoS Biology 15(2):e2001872.
    PubMed

  5. Zhu, Y.O., Sherlock, G., Petrov, D.A. (2017). Extremely Rare Polymorphisms in Saccharomyces cerevisiae Allow Inference of the Mutational Spectrum. PLoS Genetics 13(1):e1006455.
    PubMed

  6. Jaffe, M., Sherlock, G. and Levy, S.F. (2017). iSeq: A New Double-Barcode Method for Detecting Dynamic Genetic Interactions in Yeast. G3 7(1):143-153.
    PubMed

  7. Feri, A., Loll-Krippleber, R.*, Commere, P.-H., Maufrais, C., Sertour, N., Schwartz, K., Sherlock, G., Bougnoux, M.-E., d'Enfert, C., and Legrand, M. (2016). Analysis of Repair Mechanisms following an Induced Double-Strand Break Uncovers Recessive Deleterious Alleles in the Candida albicans Diploid Genome. mBio 7(5):e01109-16.
    PubMed

  8. Venkataram, S.*, Dunn, B.*, Li, Y., Agarwala, A., Chang, J., Ebel, E.R., Geiler-Samerotte, K., Herissant, L., Blundell, J.R., Levy, S.F., Fisher, D.S., Sherlock, G.^ and Petrov, D.A.^ (2016). Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast. Cell 166(6):1585-1596.
    PubMed

  9. Zhu, Y.O., Sherlock, G.^ and Petrov, D.A.^ (2016). Whole Genome Analysis of 132 Clinical Saccharomyces cerevisiae Strains Reveals Extensive Ploidy Variation. G3 6(8):2421-34.
    PubMed

  10. Sellis, D., Kvitek, D.J., Dunn, B., Sherlock, G., Petrov, D.A. (2016). Empirical Evidence for Heterozygote Advantage in Adapting Diploid Populations of Saccharomyces cerevisiae. Genetics 203(3), 1401-13.
    PubMed

  11. 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.
    PubMed

  12. 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.
    PubMed PLoS
Genetics

  13. 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.
    PubMed

  14. Rosenzweig, R. and Sherlock, G. (2014). Experimental Evolution: Prospects and Challenges. Genomics 104(6), v-vi.
    PubMed

  15. 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.
    PubMed

  16. 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.
    PubMed

  17. 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.
    PubMed

  18. 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.
    PubMed

  19. 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.
    PubMed PLoS
Genetics

  20. 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.
    PubMed

  21. 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.
    PubMed

  22. 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.
    PubMed

  23. 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.
    PubMed PLoS
Genetics

  24. 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.
    PubMed

  25. 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.
    PubMed

  26. 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.
    PubMed

  27. 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.
    PubMed

  28. Risso, D., Schwartz, K., Sherlock, G. and Dudoit, S. (2011). GC-Content Normalization for RNA-Seq Data. BMC Bioinformatics 12:480.
    PubMedhighly accessed

  29. 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.
    PubMed PLoS Genetics

  30. The Cancer Genome Atlas Research Network (2011). Integrated Genomic Analyses of Ovarian Carcinoma. Nature 474, 609-615.
    PubMed

  31. 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.
    PubMed PLoS Genetics

  32. 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.
    PubMed

  33. The ENCODE Project Consortium (2011). A User's Guide to the Encyclopedia of DNA Elements (ENCODE). PLoS Biology 9(4): e1001046.
    PubMed

  34. 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.
    PubMedhighly accessed

  35. 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.
    PubMed

  36. 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.
    PubMed PLoS Genetics

  37. 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.
    PubMed PLoS Genetics

  38. 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.
    PubMed

  39. 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.
    PubMed

  40. 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.
    PubMed

  41. 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.
    PubMed PLoS Genetics

  42. 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.
    PubMed

  43. 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.
    PubMed NPR NS

  44. The Cancer Genome Atlas Research Network (2008). Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061-8.
    PubMed

  45. 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.
    PubMed

  46. 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.
    PubMed

  47. Sherlock, G. (2006). Complex Evolution. Nature 443, 513-515.
    PubMed

  48. 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.
    PubMed pdf

  49. 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.
    PubMed pdf

  50. Sherlock, G. (2005). Of fish and chips. Nature Methods 2, 329-330.
    PubMed pdf

  51. 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.
    PubMed pdf website highly accessed

  52. 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.
    PubMed pdf software

  53. Sherlock, G. (2004). STARTing to recycle. Nature Genetics 36, 795-796.
    PubMed pdf

  54. Spellman, P.T. and Sherlock, G. (2004). Reply: Cell Age and Cell Cycle are Unlinked. Trends in Biotechnology 22, 277-8.
    PubMed pdf

  55. Spellman, P.T. and Sherlock, G. (2004). Whole-Culture Synchronization: Effective Tools for Cell Cycle Studies. Trends in Biotechnology 22, 270-3.
    PubMed pdf

  56. 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.
    PubMed pdf website

  57. 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.
    PubMed pdf website comment

  58. 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.
    pdf

  59. Sherlock G. (2001). Analysis of Large Scale Gene Expression Data. Briefings in Bioinformatics 2, 350-362.
    PubMed pdf

  60. 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.
    PubMed pdf software

  61. 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.
    PubMed pdf

  62. 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.
    PubMed pdf website comment comment

  63. Sherlock, G. (2000). Analysis of large-scale expression data. Current Opinion in Immunology 12(2), 201-205.
    PubMed pdf

  64. 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.
    PubMed pdf website

  65. 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.
    PubMed pdf website

  66. 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.
    PubMed pdf

  67. Sherlock, G. and Rosamond, J. (1993). STARTing to Cycle: G1 Controls Regulating Cell Division in Budding Yeast. Journal of General Microbiology 139, 2531-2541.
    PubMed

Databases, Standards and Other Software articles

  1. Skrzypek, M.S., Binkley, J., Binkley, G., Miyasato, S.R., Simison, M. and Sherlock, G. (2017). The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data. Nucleic Acids Res. 45(D1):D592-D596.
    PubMed

  2. Skrzypek, M.S., Binkley, J. and Sherlock, G. (2016). How to Use the Candida Genome Database. Methods Mol Biol. 1356:3-15.
    PubMed

  3. 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.
    PubMed

  4. 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.
    PubMed

  5. 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.
    PubMed

  6. 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.
    PubMed

  7. 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.
    PubMed

  8. 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.
    PubMed

  9. 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.
    PubMed

  10. 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.
    PubMed

  11. 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.
    PubMed

  12. 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.
    PubMed

  13. 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.
    PubMed

  14. 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.
    PubMed

  15. 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.
    PubMed

  16. 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.
    PubMed

  17. 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.
    PubMed

  18. 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.
    PubMed

  19. 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.
    PubMed

  20. 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.
    PubMed

  21. Maier, D., Wymore, F., Sherlock, G. and Ball, C.A. (2008). The XBabelPhish MAGE-ML and XML Translator. BMC Bioinformatics 9:28.
    PubMed pdf

  22. 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.
    PubMed pdf

  23. 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.
    PubMed pdf

  24. 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.
    PubMed pdf

  25. 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.
    PubMed pdf

  26. 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.
    PubMed pdf highly accessed

  27. 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 Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). OMICS: A Journal of Integrative Biology 10, 205-208.
    PubMed pdf

  28. 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.
    PubMed journal

  29. 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.
    PubMed pdf

  30. Sherlock, G. and Ball, C.A. (2005). Storage and Retrieval of Microarray Data and Open Source Microarray Database Software. Molecular Biotechnology 30, 239-52.
    PubMed

  31. 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.
    PubMed pdf

  32. 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.
    PubMed pdf website

  33. 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.
    PubMed pdf website

  34. 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.
    PubMed pdf software

  35. 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.
    PubMed pdf software

  36. Ball, C.A., Sherlock, G. and Brazma, A. (2004). Funding high-throughput data sharing. Nature Biotechnology 22, 1179-1183.
    PubMed pdf

  37. 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.
    PubMed pdf website highly accessed

  38. 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.
    PubMed pdf website

  39. 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.
    PubMed pdf website

  40. 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.
    PubMed pdf website

  41. 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.
    PubMed pdf website

  42. 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.
    PubMed pdf website comment

  43. 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.
    PubMed pdf website

  44. 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.
    PubMed pdf website

  45. 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.
    PubMed pdf website

  46. 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.
    PubMed pdf website

  47. 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.
    PubMed pdf website

  48. 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 similarities and structure. Nucleic Acids Research 27, 74-78.
    PubMed pdf website


Book Chapters

  1. Schwartz, K. and Sherlock, G. (2016). High Throughput Yeast Strain Sequencing. Cold Spring Harb Protoc; doi:10.1101/pdb.top077651
    PubMed

  2. Schwartz, K. and Sherlock, G. (2016). Preparation of Yeast DNA Sequencing Libraries. Cold Spring Harb Protoc; doi:10.1101/pdb.prot088930
    PubMed

  3. Kinnersley, M., Wenger, J.W., Sherlock, G. and Rosenzweig, F.R. (2011). Rapid Evolution of Simple Microbial Communities in the Laboratory. In Evolutionary Biology - Concepts, Biodiversity, Macroevolution and Genome Evolution, Ed. by P. Pontarotti. Springer Press.

  4. Rosenzweig, F. and Sherlock, G. (2009). Through a Glass, Clearly: Experimental Evolution as a Window on Adaptive Genome Evolution. In EXPERIMENTAL EVOLUTION: Concepts, Methods, and Applications of Selection Experiments, Eds. T. Garland, Jr. and M. R. Rose. University of California Press.

  5. Skrzypek, M.S., Arnaud, M.B., Costanzo, M.C. and Sherlock, G. (2007). Candida albicans Genomics Resources and Tools. In Candida: Comparative and Functional Genomics. Ed. by C. d'Enfert and B. Hube. Caister Academic Press.

  6. Ball, C.A. and Sherlock, G. (2007). What Are Microarrays? In Bioinformatics for Geneticists: A Bioinformatics Primer for the Analysis of Genetic Data, 2nd edition. Ed. by M.R. Barnes. Wiley.

  7. Gollub, J. and Sherlock, G. (2006). Clustering Microarray Data. In: Methods In Enzymology, volume 411 : DNA Microarrays, Part B. Databases and Statistics. Ed. by A. Kimmel and B. Oliver. Academic Press, pp 194-213.
    PubMed

  8. Gollub, J., Ball, C.A. and Sherlock, G. (2006). The Stanford Microarray Database: A User's Guide. In: Gene Mapping, Discovery, and Expression Ed. by Minou Bina. Humana Press, NJ., pp 191-208.
    PubMed

  9. Ball, C.A. and Sherlock, G. (2006). Microarray Data: Annotation, Storage, Retrieval and Communication. In: Handbook of Computational Molecular Biology. Ed. by S. Aluru. Chapman & Hall/CRC Press, FL.

  10. Sherlock, G. and Spellman, P.T. (2005). Seven Years of Yeast Microarray Analysis. In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Ed. by M.J. Dunn, L.B. Jorde, P.F.R. Little, and S. Subramaniam. John Wiley & Sons, Inc, New Jersey.

  11. Sherlock, G. and Ball, C.A. (2003). Microarray Databases: Storage and Retrieval of Microarray Data. In: Functional Genomics : Methods and Protocols. Ed. by M.J. Brownstein and A. Khodursky. Humana Press, NJ., pp 235-248.
    PubMed

  12. Matese, J.C., Ball, C.A., Binkley, G., Gollub, J., Hernandez-Boussard, T., Hebert, J., Jin, H., Kaloper, M., Brown, P.O., Botstein, D. and Sherlock, G. (2002). SMD - The Stanford Microarray Database. In: Analysing Gene Expression. Ed. by S. Lorkowski and P. Kullen. Wiley-VCH, Weinheim. pp 845-847.

  13. Ball, C.A., Sherlock,G.J., Dolinski, K., Binkley, G., Dwight, S.S., Issel-Tarver, L., Schroeder, M., Weng, S., Botstein, D. and Cherry, J.M. (2002). SGD - The Saccharomyces Genome Database and its Expression Connection. In: Analysing Gene Expression. Ed. by S. Lorkowski and P. Kullen. Wiley-VCH, Weinheim. p 845.

  14. Ball, C.A. and Sherlock, G. (2002). LIMS, databases and data management. In: DNA Arrays. Ed. by D. Bowtell and J. Sambrook. Cold Spring Harbor Laboratory Press, NY. pp 552-568.

MGED Letters

  1. Quackenbush, J., Stoeckert, C., Ball, C. Brazma, A., Gentleman, R., Huber, W., Irizarry, R., Salit, M., Sherlock, G., Spellman, P. and Winegarden, N. (2006). Top-down standards will not serve systems biology. Nature 440, 24.
    PubMed pdf

  2. Microarray Gene Expression Data (MGED) Society (2004). An open letter on microarray data from the MGED Society. Int J Syst Evol Microbiol. 54, 1917-8.
    PubMed pdf

  3. Microarray Gene Expression Data (MGED) Society (2004). An open letter on microarray data from the MGED Society. Microbiology 150, 3522-3524.
    PubMed pdf

  4. Ball, C, Brazma, A., Causton, H., Chervitz, S., Edgar, R., Hingamp, P., Matese, J.C., Parkinson, H., Quackenbush, J., Ringwald, M., Sansone, A., Sherlock, G., Spellman, P., Stoeckert, C., Tateno, Y., Taylor, R., White, J. and Winegarden, N. (2004). 112-12 correspondence: standards for microarray data: an open letter. Environmental Health Perspectives 112, A666.
    PubMed pdf

  5. Ball, C.A., Brazma, A., Causton, H., Chervitz, S., Edgar, R., Hingamp, P., Matese, J.C., Parkinson, H., Quackenbush, J., Ringwald, M., Sansone, A., Sherlock, G., Spellman, P., Stoeckert, C., Tateno, Y., Taylor, R., White, J. and Winegarden, N. (2004). Submission of Microarray Data to Public Repositories. PLoS Biol 2(9): 1276-1277.
    PubMed pdf

  6. Ball, C.A., Sherlock, G., Parkinson, H., Rocca-Sera, P., Brooksbank, C., Causton, H.C., Cavalieri, D., Gaasterland, T., Hingamp, P., Holstege, F. et al. (2002). A guide to microarray experiments - an open letter to the scientific journals. The Lancet 360, 1019-1019.
    PubMed pdf

  7. Ball, C.A., Sherlock, G., Parkinson, H., Rocca-Sera, P., Brooksbank, C., Causton, H.C., Cavalieri, D., Gaasterland, T., Hingamp, P., Holstege, F. et al. (2002). Standards for microarray data. Science 298, 539.
    PubMed pdf

  8. Ball, C.A., Sherlock, G., Parkinson, H., Rocca-Sera, P., Brooksbank, C., Causton, H.C., Cavalieri, D., Gaasterland, T., Hingamp, P., Holstege, F. et al. (2002). The underlying principles of scientific publication. Bioinformatics 18, 1409.
    PubMed pdf