Gavin James Sherlock - Publications

Stanford University, Palo Alto, CA 
yeast, evolution, genomics

118 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Skrzypek MS, Binkley J, Sherlock G. How to Use the Candida Genome Database. Methods in Molecular Biology (Clifton, N.J.). 2542: 55-69. PMID 36008656 DOI: 10.1007/978-1-0716-2549-1_4  0.75
2022 Choudhary K, Itzkovich Z, Alonso-Perez E, Bishara H, Dunn B, Sherlock G, Kupiec M. S. cerevisiae Cells Can Grow without the Pds5 Cohesin Subunit. Mbio. e0142022. PMID 35708277 DOI: 10.1128/mbio.01420-22  0.742
2022 Sherlock G, Rosamond J. Erratum: Starting to cycle: G1 controls regulating cell division in budding yeast. Microbiology (Reading, England). 168. PMID 35471150 DOI: 10.1099/mic.0.001186  0.735
2021 Aggeli D, Li Y, Sherlock G. Changes in the distribution of fitness effects and adaptive mutational spectra following a single first step towards adaptation. Nature Communications. 12: 5193. PMID 34465770 DOI: 10.1038/s41467-021-25440-7  0.796
2021 Kinnersley M, Schwartz K, Yang DD, Sherlock G, Rosenzweig F. Evolutionary dynamics and structural consequences of de novo beneficial mutations and mutant lineages arising in a constant environment. Bmc Biology. 19: 20. PMID 33541358 DOI: 10.1186/s12915-021-00954-0  0.752
2021 Boyer S, Hérissant L, Sherlock G. Adaptation is influenced by the complexity of environmental change during evolution in a dynamic environment. Plos Genetics. 17: e1009314. PMID 33493203 DOI: 10.1371/journal.pgen.1009314  0.783
2020 Siranosian BA, Tamburini FB, Sherlock G, Bhatt AS. Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages. Nature Communications. 11: 280. PMID 31941900 DOI: 10.1038/S41467-019-14103-3  0.313
2019 Li Y, Petrov DA, Sherlock G. Single nucleotide mapping of trait space reveals Pareto fronts that constrain adaptation. Nature Ecology & Evolution. PMID 31611676 DOI: 10.1038/S41559-019-0993-0  0.395
2019 Jaffe M, Dziulko A, Smith JD, St Onge RP, Levy SF, Sherlock G. Improved discovery of genetic interactions using CRISPRiSeq across multiple environments. Genome Research. PMID 30782640 DOI: 10.1101/Gr.246603.118  0.796
2019 Skrzypek MS, Binkley J, Sherlock G. Using the Candida Genome Database. Methods in Molecular Biology (Clifton, N.J.). 1757: 31-47. PMID 29761455 DOI: 10.1007/978-1-4939-7737-6_3  0.776
2018 Blundell JR, Schwartz K, Francois D, Fisher DS, Sherlock G, Levy SF. The dynamics of adaptive genetic diversity during the early stages of clonal evolution. Nature Ecology & Evolution. PMID 30598529 DOI: 10.1038/S41559-018-0758-1  0.803
2018 Ropars J, Maufrais C, Diogo D, Marcet-Houben M, Perin A, Sertour N, Mosca K, Permal E, Laval G, Bouchier C, Ma L, Schwartz K, Voelz K, May RC, Poulain J, ... ... Sherlock G, et al. Gene flow contributes to diversification of the major fungal pathogen Candida albicans. Nature Communications. 9: 2253. PMID 29884848 DOI: 10.1038/S41467-018-04787-4  0.773
2018 Li Y, Venkataram S, Agarwala A, Dunn B, Petrov DA, Sherlock G, Fisher DS. Hidden Complexity of Yeast Adaptation under Simple Evolutionary Conditions. Current Biology : Cb. PMID 29429618 DOI: 10.1016/J.Cub.2018.01.009  0.751
2018 Aggeli D, Karas VO, Sinnott-Armstrong NA, Varghese V, Shafer RW, Greenleaf WJ, Sherlock G. Diff-seq: A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery. Nucleic Acids Research. PMID 29361139 DOI: 10.1093/Nar/Gky022  0.795
2017 de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G, Amillis S, Uchima CA, Anderluh G, Asadollahi M, Askin M, Barry K, Battaglia E, Bayram Ö, Benocci T, Braus-Stromeyer SA, Caldana C, ... ... Sherlock G, et al. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biology. 18: 28. PMID 28196534 DOI: 10.1186/S13059-017-1151-0  0.37
2017 Sherlock G, Petrov DA. Seeking Goldilocks During Evolution of Drug Resistance. Plos Biology. 15: e2001872. PMID 28158184 DOI: 10.1371/Journal.Pbio.2001872  0.325
2017 Zhu YO, Sherlock G, Petrov DA. Extremely Rare Polymorphisms in Saccharomyces cerevisiae Allow Inference of the Mutational Spectrum. Plos Genetics. 13: e1006455. PMID 28046117 DOI: 10.1371/Journal.Pgen.1006455  0.377
2016 Jaffe M, Sherlock G, Levy SF. iSeq: A New Double-Barcode Method for Detecting Dynamic Genetic Interactions in Yeast. G3 (Bethesda, Md.). PMID 27821633 DOI: 10.1534/G3.116.034207  0.794
2016 Skrzypek MS, Binkley J, Binkley G, Miyasato SR, Simison M, Sherlock G. The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data. Nucleic Acids Research. 45: D592-D596. PMID 27738138 DOI: 10.1093/Nar/Gkw924  0.768
2016 Feri A, Loll-Krippleber R, Commere PH, Maufrais C, Sertour N, Schwartz K, Sherlock G, Bougnoux ME, d'Enfert C, Legrand M. Analysis of Repair Mechanisms following an Induced Double-Strand Break Uncovers Recessive Deleterious Alleles in the Candida albicans Diploid Genome. Mbio. 7. PMID 27729506 DOI: 10.1128/Mbio.01109-16  0.779
2016 Schwartz K, Sherlock G. High-Throughput Yeast Strain Sequencing. Cold Spring Harbor Protocols. 2016: pdb.top077651. PMID 27698244 DOI: 10.1101/Pdb.Top077651  0.769
2016 Schwartz K, Sherlock G. Preparation of Yeast DNA Sequencing Libraries. Cold Spring Harbor Protocols. 2016: pdb.prot088930. PMID 27698239 DOI: 10.1101/Pdb.Prot088930  0.756
2016 Venkataram S, Dunn B, Li Y, Agarwala A, Chang J, Ebel ER, Geiler-Samerotte K, Hérissant L, Blundell JR, Levy SF, Fisher DS, Sherlock G, Petrov DA. Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast. Cell. PMID 27594428 DOI: 10.1016/J.Cell.2016.08.002  0.789
2016 Zhu YO, Sherlock G, Petrov DA. Whole Genome Analysis of 132 Clinical Saccharomyces cerevisiae Strains Reveals Extensive Ploidy Variation. G3 (Bethesda, Md.). PMID 27317778 DOI: 10.1534/G3.116.029397  0.402
2016 Sellis D, Kvitek DJ, Dunn B, Sherlock G, Petrov DA. Empirical Evidence for Heterozygote Advantage in Adapting Diploid Populations of Saccharomyces cerevisiae. Genetics. PMID 27194750 DOI: 10.1534/Genetics.115.185165  0.787
2016 Skrzypek MS, Binkley J, Sherlock G. How to Use the Candida Genome Database. Methods in Molecular Biology (Clifton, N.J.). 1356: 3-15. PMID 26519061 DOI: 10.1007/978-1-4939-3052-4_1  0.776
2015 Schep AN, Buenrostro JD, Denny SK, Schwartz K, Sherlock G, Greenleaf WJ. Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions. Genome Research. PMID 26314830 DOI: 10.1101/Gr.192294.115  0.738
2015 Calderón-Noreña DM, González-Novo A, Orellana-Muñoz S, Gutiérrez-Escribano P, Arnáiz-Pita Y, Dueñas-Santero E, Suárez MB, Bougnoux ME, Del Rey F, Sherlock G, d'Enfert C, Correa-Bordes J, de Aldana CR. A single nucleotide polymorphism uncovers a novel function for the transcription factor Ace2 during Candida albicans hyphal development. Plos Genetics. 11: e1005152. PMID 25875512 DOI: 10.1371/Journal.Pgen.1005152  0.326
2015 Levy SF, Blundell JR, Venkataram S, Petrov DA, Fisher DS, Sherlock G. Quantitative evolutionary dynamics using high-resolution lineage tracking. Nature. 519: 181-6. PMID 25731169 DOI: 10.1038/Nature14279  0.696
2015 Rosenzweig F, Sherlock G. Experimental evolution: prospects and challenges. Genomics. 104: v-vi. PMID 25496938 DOI: 10.1016/J.Ygeno.2014.11.008  0.444
2014 Chiotti KE, Kvitek DJ, Schmidt KH, Koniges G, Schwartz K, Donckels EA, Rosenzweig F, Sherlock G. The Valley-of-Death: reciprocal sign epistasis constrains adaptive trajectories in a constant, nutrient limiting environment. Genomics. 104: 431-7. PMID 25449178 DOI: 10.1016/J.Ygeno.2014.10.011  0.788
2014 Kinnersley M, Wenger J, Kroll E, Adams J, Sherlock G, Rosenzweig F. Ex uno plures: clonal reinforcement drives evolution of a simple microbial community. Plos Genetics. 10: e1004430. PMID 24968217 DOI: 10.1371/Journal.Pgen.1004430  0.801
2014 Keseler IM, Skrzypek M, Weerasinghe D, Chen AY, Fulcher C, Li GW, Lemmer KC, Mladinich KM, Chow ED, Sherlock G, Karp PD. Curation accuracy of model organism databases. Database : the Journal of Biological Databases and Curation. 2014. PMID 24923819 DOI: 10.1093/Database/Bau058  0.342
2014 Inglis DO, Skrzypek MS, Liaw E, Moktali V, Sherlock G, Stajich JE. Literature-based gene curation and proposed genetic nomenclature for cryptococcus. Eukaryotic Cell. 13: 878-83. PMID 24813190 DOI: 10.1128/Ec.00083-14  0.43
2014 Muzzey D, Sherlock G, Weissman JS. Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans. Genome Research. 24: 963-73. PMID 24732588 DOI: 10.1101/Gr.166322.113  0.335
2014 Hu JC, Sherlock G, Siegele DA, Aleksander SA, Ball CA, Demeter J, Gouni S, Holland TA, Karp PD, Lewis JE, Liles NM, McIntosh BK, Mi H, Muruganujan A, Wymore F, et al. PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. Nucleic Acids Research. 42: D677-84. PMID 24285306 DOI: 10.1093/Nar/Gkt1203  0.416
2014 Cerqueira GC, Arnaud MB, Inglis DO, Skrzypek MS, Binkley G, Simison M, Miyasato SR, Binkley J, Orvis J, Shah P, Wymore F, Sherlock G, Wortman JR. The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. Nucleic Acids Research. 42: D705-10. PMID 24194595 DOI: 10.1093/Nar/Gkt1029  0.769
2014 Binkley J, Arnaud MB, Inglis DO, Skrzypek MS, Shah P, Wymore F, Binkley G, Miyasato SR, Simison M, Sherlock G. The Candida Genome Database: the new homology information page highlights protein similarity and phylogeny. Nucleic Acids Research. 42: D711-6. PMID 24185697 DOI: 10.1093/Nar/Gkt1046  0.762
2014 Spor A, Kvitek DJ, Nidelet T, Martin J, Legrand J, Dillmann C, Bourgais A, de Vienne D, Sherlock G, Sicard D. Phenotypic and genotypic convergences are influenced by historical contingency and environment in yeast. Evolution; International Journal of Organic Evolution. 68: 772-790. PMID 24164389 DOI: 10.1111/Evo.12302  0.809
2014 Kinnersley M, Wenger J, Kroll E, Adams J, Sherlock G, Rosenzweig F. Ex Uno Plures: Clonal Reinforcement Drives Evolution of a Simple Microbial Community Plos Genetics. 10. DOI: 10.1371/journal.pgen.1004430  0.759
2013 Kvitek DJ, Sherlock G. Whole genome, whole population sequencing reveals that loss of signaling networks is the major adaptive strategy in a constant environment. Plos Genetics. 9: e1003972. PMID 24278038 DOI: 10.1371/Journal.Pgen.1003972  0.795
2013 Grant GD, Brooks L, Zhang X, Mahoney JM, Martyanov V, Wood TA, Sherlock G, Cheng C, Whitfield ML. Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors. Molecular Biology of the Cell. 24: 3634-50. PMID 24109597 DOI: 10.1091/Mbc.E13-05-0264  0.348
2013 Muzzey D, Schwartz K, Weissman JS, Sherlock G. Assembly of a phased diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure. Genome Biology. 14: R97. PMID 24025428 DOI: 10.1186/Gb-2013-14-9-R97  0.78
2013 Inglis DO, Sherlock G. Ras signaling gets fine-tuned: regulation of multiple pathogenic traits of Candida albicans. Eukaryotic Cell. 12: 1316-25. PMID 23913542 DOI: 10.1128/Ec.00094-13  0.303
2013 Inglis DO, Binkley J, Skrzypek MS, Arnaud MB, Cerqueira GC, Shah P, Wymore F, Wortman JR, Sherlock G. Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae. Bmc Microbiology. 13: 91. PMID 23617571 DOI: 10.1186/1471-2180-13-91  0.769
2013 Dunn B, Paulish T, Stanbery A, Piotrowski J, Koniges G, Kroll E, Louis EJ, Liti G, Sherlock G, Rosenzweig F. Recurrent rearrangement during adaptive evolution in an interspecific yeast hybrid suggests a model for rapid introgression. Plos Genetics. 9: e1003366. PMID 23555283 DOI: 10.1371/Journal.Pgen.1003366  0.769
2013 Richter CL, Dunn B, Sherlock G, Pugh T. Comparative metabolic footprinting of a large number of commercial wine yeast strains in Chardonnay fermentations. Fems Yeast Research. 13: 394-410. PMID 23528123 DOI: 10.1111/1567-1364.12046  0.752
2013 Inglis DO, Skrzypek MS, Arnaud MB, Binkley J, Shah P, Wymore F, Sherlock G. Improved gene ontology annotation for biofilm formation, filamentous growth, and phenotypic switching in Candida albicans. Eukaryotic Cell. 12: 101-8. PMID 23143685 DOI: 10.1128/Ec.00238-12  0.758
2012 Piotrowski JS, Nagarajan S, Kroll E, Stanbery A, Chiotti KE, Kruckeberg AL, Dunn B, Sherlock G, Rosenzweig F. Different selective pressures lead to different genomic outcomes as newly-formed hybrid yeasts evolve. Bmc Evolutionary Biology. 12: 46. PMID 22471618 DOI: 10.1186/1471-2148-12-46  0.757
2012 Avrahami-Moyal L, Engelberg D, Wenger JW, Sherlock G, Braun S. Turbidostat culture of Saccharomyces cerevisiae W303-1A under selective pressure elicited by ethanol selects for mutations in SSD1 and UTH1 Fems Yeast Research. 12: 521-533. PMID 22443114 DOI: 10.1111/J.1567-1364.2012.00803.X  0.78
2012 Schwartz K, Wenger JW, Dunn B, Sherlock G. APJ1 and GRE3 homologs work in concert to allow growth in xylose in a natural Saccharomyces sensu stricto hybrid yeast. Genetics. 191: 621-32. PMID 22426884 DOI: 10.1534/Genetics.112.140053  0.789
2012 Dunn B, Richter C, Kvitek DJ, Pugh T, Sherlock G. 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: 908-24. PMID 22369888 DOI: 10.1101/Gr.130310.111  0.799
2012 Arnaud MB, Cerqueira GC, Inglis DO, Skrzypek MS, Binkley J, Chibucos MC, Crabtree J, Howarth C, Orvis J, Shah P, Wymore F, Binkley G, Miyasato SR, Simison M, Sherlock G, et al. The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources. Nucleic Acids Research. 40: D653-9. PMID 22080559 DOI: 10.1093/Nar/Gkr875  0.752
2012 Inglis DO, Arnaud MB, Binkley J, Shah P, Skrzypek MS, Wymore F, Binkley G, Miyasato SR, Simison M, Sherlock G. 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. PMID 22064862 DOI: 10.1093/Nar/Gkr945  0.772
2011 Risso D, Schwartz K, Sherlock G, Dudoit S. GC-content normalization for RNA-Seq data. Bmc Bioinformatics. 12: 480. PMID 22177264 DOI: 10.1186/1471-2105-12-480  0.747
2011 Wenger JW, Piotrowski J, Nagarajan S, Chiotti K, Sherlock G, Rosenzweig F. Hunger artists: yeast adapted to carbon limitation show trade-offs under carbon sufficiency. Plos Genetics. 7: e1002202. PMID 21829391 DOI: 10.1371/Journal.Pgen.1002202  0.808
2011 Kvitek DJ, Sherlock G. Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape. Plos Genetics. 7: e1002056. PMID 21552329 DOI: 10.1371/Journal.Pgen.1002056  0.808
2011 Kobayashi Y, Absher DM, Gulzar ZG, Young SR, McKenney JK, Peehl DM, Brooks JD, Myers RM, Sherlock G. DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer. Genome Research. 21: 1017-27. PMID 21521786 DOI: 10.1101/Gr.119487.110  0.65
2010 Martin J, Bruno VM, Fang Z, Meng X, Blow M, Zhang T, Sherlock G, Snyder M, Wang Z. Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads. Bmc Genomics. 11: 663. PMID 21106091 DOI: 10.1186/1471-2164-11-663  0.333
2010 Bruno VM, Wang Z, Marjani SL, Euskirchen GM, Martin J, Sherlock G, Snyder M. Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq. Genome Research. 20: 1451-8. PMID 20810668 DOI: 10.1101/Gr.109553.110  0.356
2010 Shankar R, Parkinson H, Burdett T, Hastings E, Liu J, Miller M, Srinivasa R, White J, Brazma A, Sherlock G, Stoeckert CJ, Ball CA. Annotare--a tool for annotating high-throughput biomedical investigations and resulting data. Bioinformatics (Oxford, England). 26: 2470-1. PMID 20733062 DOI: 10.1093/Bioinformatics/Btq462  0.324
2010 Kao KC, Schwartz K, Sherlock G. 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: e1001038. PMID 20686707 DOI: 10.1371/Journal.Pgen.1001038  0.799
2010 Galagan JE, Sisk P, Stolte C, Weiner B, Koehrsen M, Wymore F, Reddy TB, Zucker JD, Engels R, Gellesch M, Hubble J, Jin H, Larson L, Mao M, Nitzberg M, ... ... Sherlock G, et al. TB database 2010: overview and update. Tuberculosis (Edinburgh, Scotland). 90: 225-35. PMID 20488753 DOI: 10.1016/J.Tube.2010.03.010  0.373
2010 Wenger JW, Schwartz K, Sherlock G. Bulk segregant analysis by high-throughput sequencing reveals a novel xylose utilization gene from Saccharomyces cerevisiae. Plos Genetics. 6: e1000942. PMID 20485559 DOI: 10.1371/Journal.Pgen.1000942  0.807
2010 Duval EH, Alves SL, Dunn B, Sherlock G, Stambuk BU. 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: 248-59. PMID 20070441 DOI: 10.1111/J.1365-2672.2009.04656.X  0.775
2010 Skrzypek MS, Arnaud MB, Costanzo MC, Inglis DO, Shah P, Binkley G, Miyasato SR, Sherlock G. New tools at the Candida Genome Database: biochemical pathways and full-text literature search. Nucleic Acids Research. 38: D428-32. PMID 19808938 DOI: 10.1093/Nar/Gkp836  0.39
2010 Arnaud MB, Chibucos MC, Costanzo MC, Crabtree J, Inglis DO, Lotia A, Orvis J, Shah P, Skrzypek MS, Binkley G, Miyasato SR, Wortman JR, Sherlock G. The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community. Nucleic Acids Research. 38: D420-7. PMID 19773420 DOI: 10.1093/Nar/Gkp751  0.42
2009 Stambuk BU, Dunn B, Alves SL, Duval EH, Sherlock G. Industrial fuel ethanol yeasts contain adaptive copy number changes in genes involved in vitamin B1 and B6 biosynthesis. Genome Research. 19: 2271-8. PMID 19897511 DOI: 10.1101/Gr.094276.109  0.753
2009 Arnaud MB, Costanzo MC, Shah P, Skrzypek MS, Sherlock G. Gene Ontology and the annotation of pathogen genomes: the case of Candida albicans. Trends in Microbiology. 17: 295-303. PMID 19577928 DOI: 10.1016/J.Tim.2009.04.007  0.393
2009 Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S, Munro CA, Rheinbay E, Grabherr M, Forche A, Reedy JL, Agrafioti I, Arnaud MB, Bates S, Brown AJ, Brunke S, ... ... Sherlock G, et al. Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature. 459: 657-62. PMID 19465905 DOI: 10.1038/Nature08064  0.389
2009 Hubble J, Demeter J, Jin H, Mao M, Nitzberg M, Reddy TB, Wymore F, Zachariah ZK, Sherlock G, Ball CA. Implementation of GenePattern within the Stanford Microarray Database. Nucleic Acids Research. 37: D898-901. PMID 18953035 DOI: 10.1093/Nar/Gkn786  0.315
2009 Reddy TB, Riley R, Wymore F, Montgomery P, DeCaprio D, Engels R, Gellesch M, Hubble J, Jen D, Jin H, Koehrsen M, Larson L, Mao M, Nitzberg M, Sisk P, ... ... Sherlock G, et al. TB database: an integrated platform for tuberculosis research. Nucleic Acids Research. 37: D499-508. PMID 18835847 DOI: 10.1093/Nar/Gkn652  0.333
2008 Lee A, Hansen KD, Bullard J, Dudoit S, Sherlock G. 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 Genetics. 4: e1000299. PMID 19096707 DOI: 10.1371/Journal.Pgen.1000299  0.545
2008 Kao KC, Sherlock G. Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae. Nature Genetics. 40: 1499-504. PMID 19029899 DOI: 10.1038/Ng.280  0.618
2008 Dunn B, Sherlock G. Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus. Genome Research. 18: 1610-23. PMID 18787083 DOI: 10.1101/Gr.076075.108  0.774
2007 Beauheim CC, Wymore F, Nitzberg M, Zachariah ZK, Jin H, Skene JH, Ball CA, Sherlock G. OntologyWidget - a reusable, embeddable widget for easily locating ontology terms. Bmc Bioinformatics. 8: 338. PMID 17854506 DOI: 10.1186/1471-2105-8-338  0.314
2007 Arnaud MB, Costanzo MC, Skrzypek MS, Shah P, Binkley G, Lane C, Miyasato SR, Sherlock G. Sequence resources at the Candida Genome Database. Nucleic Acids Research. 35: D452-6. PMID 17090582 DOI: 10.1093/Nar/Gkl899  0.401
2006 Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ, White J, et al. A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. Bmc Bioinformatics. 7: 489. PMID 17087822 DOI: 10.1186/1471-2105-7-489  0.563
2006 Deutsch EW, Ball CA, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen J, Davidson D, Eichner LJ, Goo YA, Grimmond S, Henrich T, Johnson MH, Korb M, ... ... Sherlock G, et al. Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). Omics : a Journal of Integrative Biology. 10: 205-8. PMID 16901227 DOI: 10.1089/Omi.2006.10.205  0.31
2006 Gollub J, Ball CA, Sherlock G. The Stanford Microarray Database: a user's guide. Methods in Molecular Biology (Clifton, N.J.). 338: 191-208. PMID 16888360 DOI: 10.1385/1-59745-097-9:191  0.335
2006 Costanzo MC, Arnaud MB, Skrzypek MS, Binkley G, Lane C, Miyasato SR, Sherlock G. The Candida Genome Database: facilitating research on Candida albicans molecular biology. Fems Yeast Research. 6: 671-84. PMID 16879419 DOI: 10.1111/J.1567-1364.2006.00074.X  0.424
2006 Brown JA, Sherlock G, Myers CL, Burrows NM, Deng C, Wu HI, McCann KE, Troyanskaya OG, Brown JM. Global analysis of gene function in yeast by quantitative phenotypic profiling. Molecular Systems Biology. 2: 2006.0001. PMID 16738548 DOI: 10.1038/Msb4100043  0.605
2006 Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, Huber W, Irizarry R, Salit M, Sherlock G, Spellman P, Winegarden N. Top-down standards will not serve systems biology. Nature. 440: 24. PMID 16511469 DOI: 10.1038/440024A  0.501
2006 Sherlock G, Ball CA. Storage and retrieval of microarray data and open source microarray database software. Molecular Biotechnology. 30: 239-51. PMID 15988049 DOI: 10.1385/Mb:30:3:239  0.336
2005 Braun BR, van Het Hoog M, d'Enfert C, Martchenko M, Dungan J, Kuo A, Inglis DO, Uhl MA, Hogues H, Berriman M, Lorenz M, Levitin A, Oberholzer U, Bachewich C, Harcus D, ... ... Sherlock G, et al. A human-curated annotation of the Candida albicans genome. Plos Genetics. 1: 36-57. PMID 16103911 DOI: 10.1371/Journal.Pgen.0010001  0.438
2005 Dunn B, Levine RP, Sherlock G. Microarray karyotyping of commercial wine yeast strains reveals shared, as well as unique, genomic signatures. Bmc Genomics. 6: 53. PMID 15833139 DOI: 10.1186/1471-2164-6-53  0.761
2005 Ball CA, Awad IA, Demeter J, Gollub J, Hebert JM, Hernandez-Boussard T, Jin H, Matese JC, Nitzberg M, Wymore F, Zachariah ZK, Brown PO, Sherlock G. The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Research. 33: D580-2. PMID 15608265 DOI: 10.1093/Nar/Gki006  0.32
2005 Arnaud MB, Costanzo MC, Skrzypek MS, Binkley G, Lane C, Miyasato SR, Sherlock G. The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information. Nucleic Acids Research. 33: D358-63. PMID 15608216 DOI: 10.1093/Nar/Gki003  0.419
2004 Ball C, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Icahn C, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, et al. An open letter on microarray data from the MGED Society. Microbiology (Reading, England). 150: 3522-4. PMID 15528642 DOI: 10.1099/mic.0.27637-0  0.72
2004 Awad IAB, Rees CA, Hernandez-Boussard T, Ball CA, Sherlock G. Caryoscope: An Open Source Java application for viewing microarray data in a genomic context Bmc Bioinformatics. 5: 151-151. PMID 15488149 DOI: 10.1186/1471-2105-5-151  0.395
2004 Rees CA, Demeter J, Matese JC, Botstein D, Sherlock G. GeneXplorer: an interactive web application for microarray data visualization and analysis. Bmc Bioinformatics. 5: 141. PMID 15458579 DOI: 10.1186/1471-2105-5-141  0.529
2004 Ball C, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, et al. Standards for microarray data: an open letter. Environmental Health Perspectives. 112: A666-7. PMID 15345376 DOI: 10.1289/Ehp.112-1277123  0.798
2004 Ball CA, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, et al. Submission of microarray data to public repositories. Plos Biology. 2: E317. PMID 15340489 DOI: 10.1371/Journal.Pbio.0020317  0.78
2004 Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G. GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics (Oxford, England). 20: 3710-5. PMID 15297299 DOI: 10.1093/Bioinformatics/Bth456  0.54
2004 Sherlock G. STARTing to recycle. Nature Genetics. 36: 795-6. PMID 15284848 DOI: 10.1038/Ng0804-795  0.333
2004 Spellman PT, Sherlock G. Final words: cell age and cell cycle are unlinked. Trends in Biotechnology. 22: 277-8. PMID 15158055 DOI: 10.1016/J.Tibtech.2004.04.012  0.514
2004 Spellman PT, Sherlock G. Reply: whole-culture synchronization - effective tools for cell cycle studies. Trends in Biotechnology. 22: 270-3. PMID 15158053 DOI: 10.1016/J.Tibtech.2004.04.010  0.551
2003 Diehn M, Sherlock G, Binkley G, Jin H, Matese JC, Hernandez-Boussard T, Rees CA, Cherry JM, Botstein D, Brown PO, Alizadeh AA. SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Research. 31: 219-23. PMID 12519986 DOI: 10.1093/Nar/Gkg014  0.593
2003 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. The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Research. 31: 94-6. PMID 12519956 DOI: 10.1093/Nar/Gkg078  0.523
2002 Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ, Stewart JE, Taylor R, et al. The underlying principles of scientific publication. Bioinformatics (Oxford, England). 18: 1409. PMID 12424109 DOI: 10.1093/Bioinformatics/18.11.1409  0.507
2002 Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ, Stewart JE, Taylor R, et al. Standards for microarray data. Science (New York, N.Y.). 298: 539. PMID 12387284 DOI: 10.1126/Science.298.5593.539B  0.59
2002 Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, et al. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biology. 3: RESEARCH0046. PMID 12225585 DOI: 10.1186/Gb-2002-3-9-Research0046  0.789
2002 Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, Alexander KE, Matese JC, Perou CM, Hurt MM, Brown PO, Botstein D. Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Molecular Biology of the Cell. 13: 1977-2000. PMID 12058064 DOI: 10.1091/Mbc.02-02-0030  0.787
2002 Nielsen TO, West RB, Linn SC, Alter O, Knowling MA, O'Connell JX, Zhu S, Fero M, Sherlock G, Pollack JR, Brown PO, Botstein D, van de Rijn M. Molecular characterisation of soft tissue tumours: a gene expression study. Lancet (London, England). 359: 1301-7. PMID 11965276 DOI: 10.1016/S0140-6736(02)08270-3  0.735
2002 Sherlock G. Analysis of large-scale gene expression data. Briefings in Bioinformatics. 2: 350-62. PMID 11808747 DOI: 10.1093/Bib/2.4.350  0.321
2002 Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Research. 30: 69-72. PMID 11752257 DOI: 10.1093/Nar/30.1.69  0.598
2002 Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Jr CJS, Stewart JE, Taylor R, et al. A guide to microarray experiments-an open letter to the scientific journals The Lancet. 360: 1019. DOI: 10.1016/S0140-6736(02)11100-7  0.523
2001 Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nature Genetics. 29: 365-71. PMID 11726920 DOI: 10.1038/Ng1201-365  0.609
2001 Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB. Missing value estimation methods for DNA microarrays Bioinformatics. 17: 520-525. PMID 11395428 DOI: 10.1093/Bioinformatics/17.6.520  0.652
2001 Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper M, Weng S, Jin H, Ball CA, Eisen MB, Spellman PT, Brown PO, Botstein D, Cherry JM. The Stanford Microarray Database. Nucleic Acids Research. 29: 152-5. PMID 11125075 DOI: 10.1093/Nar/29.1.152  0.768
2001 Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. Saccharomyces genome database provides tools to survey gene expression and functional analysis data Nucleic Acids Research. 29: 80-81. PMID 11125055 DOI: 10.1093/Nar/29.1.80  0.582
2000 Salama N, Guillemin K, McDaniel TK, Sherlock G, Tompkins L, Falkow S. A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proceedings of the National Academy of Sciences of the United States of America. 97: 14668-73. PMID 11121067 DOI: 10.1073/Pnas.97.26.14668  0.398
2000 Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, ... ... Sherlock G, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics. 25: 25-9. PMID 10802651 DOI: 10.1038/75556  0.569
2000 Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J, ... ... Sherlock G, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 403: 503-11. PMID 10676951 DOI: 10.1038/35000501  0.725
2000 Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, et al. Integrating functional genomic information into the Saccharomyces Genome Database Nucleic Acids Research. 28: 77-80. PMID 10592186 DOI: 10.1093/Nar/28.1.77  0.587
1999 Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock G, Weng S, Zhu Y, et al. Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. Nucleic Acids Research. 27: 74-8. PMID 9847146 DOI: 10.1093/Nar/27.1.74  0.798
1998 Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science (New York, N.Y.). 282: 2022-8. PMID 9851918 DOI: 10.1126/Science.282.5396.2022  0.779
1998 Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell. 9: 3273-97. PMID 9843569 DOI: 10.1091/Mbc.9.12.3273  0.789
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