| Year |
Citation |
Score |
| 2023 |
Li W, Miller D, Liu X, Tosi L, Chkaiban L, Mei H, Hung PH, Parekkadan B, Sherlock G, Levy SF. Arrayed barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries. Biorxiv : the Preprint Server For Biology. PMID 37873145 DOI: 10.1101/2023.10.13.562064 |
0.653 |
|
| 2023 |
Chen V, Johnson MS, Hérissant L, Humphrey PT, Yuan DC, Li Y, Agarwala A, Hoelscher SB, Petrov DA, Desai MM, Sherlock G. Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments. Elife. 12. PMID 37861305 DOI: 10.7554/eLife.92899 |
0.802 |
|
| 2023 |
Muller G, de Godoy VR, Dário MG, Duval EH, Alves-Jr SL, Bücker A, Rosa CA, Dunn B, Sherlock G, Stambuk BU. Improved Sugarcane-Based Fermentation Processes by an Industrial Fuel-Ethanol Yeast Strain. Journal of Fungi (Basel, Switzerland). 9. PMID 37623574 DOI: 10.3390/jof9080803 |
0.731 |
|
| 2023 |
Hays M, Schwartz K, Schmidtke DT, Aggeli D, Sherlock G. Paths to adaptation under fluctuating nitrogen starvation: The spectrum of adaptive mutations in Saccharomyces cerevisiae is shaped by retrotransposons and microhomology-mediated recombination. Plos Genetics. 19: e1010747. PMID 37192196 DOI: 10.1371/journal.pgen.1010747 |
0.81 |
|
| 2023 |
Kruglyak L, Beyer A, Bloom JS, Grossbach J, Lieberman TD, Mancuso CP, Rich MS, Sherlock G, Kaplan CD. Insufficient evidence for non-neutrality of synonymous mutations. Nature. 616: E8-E9. PMID 37076734 DOI: 10.1038/s41586-023-05865-4 |
0.433 |
|
| 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 |
0.748 |
|
| 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 |
0.739 |
|
| 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 |
0.803 |
|
| 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 |
0.753 |
|
| 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 |
0.788 |
|
| 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 |
0.311 |
|
| 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 |
0.407 |
|
| 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 |
0.797 |
|
| 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 |
0.774 |
|
| 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 |
0.807 |
|
| 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 |
0.77 |
|
| 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 |
0.796 |
|
| 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 |
0.337 |
|
| 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 |
0.389 |
|
| 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 |
0.796 |
|
| 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 |
0.766 |
|
| 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 |
0.777 |
|
| 2016 |
Schwartz K, Sherlock G. High-Throughput Yeast Strain Sequencing. Cold Spring Harbor Protocols. 2016: pdb.top077651. PMID 27698244 DOI: 10.1101/Pdb.Top077651 |
0.766 |
|
| 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 |
0.753 |
|
| 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 |
0.797 |
|
| 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 |
0.403 |
|
| 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 |
0.793 |
|
| 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 |
0.774 |
|
| 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 |
0.734 |
|
| 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 |
0.325 |
|
| 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 |
0.698 |
|
| 2015 |
Rosenzweig F, Sherlock G. Experimental evolution: prospects and challenges. Genomics. 104: v-vi. PMID 25496938 DOI: 10.1016/J.Ygeno.2014.11.008 |
0.454 |
|
| 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 |
0.793 |
|
| 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 |
0.803 |
|
| 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 |
0.337 |
|
| 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 |
0.425 |
|
| 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 |
0.41 |
|
| 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 |
0.767 |
|
| 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 |
0.761 |
|
| 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 |
0.814 |
|
| 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 |
0.76 |
|
| 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 |
0.798 |
|
| 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 |
0.342 |
|
| 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 |
0.777 |
|
| 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 |
0.302 |
|
| 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 |
0.768 |
|
| 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 |
0.767 |
|
| 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 |
0.749 |
|
| 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 |
0.756 |
|
| 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 |
0.755 |
|
| 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 |
0.784 |
|
| 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 |
0.79 |
|
| 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 |
0.8 |
|
| 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 |
0.751 |
|
| 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 |
0.77 |
|
| 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 |
0.743 |
|
| 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 |
0.813 |
|
| 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 |
0.814 |
|
| 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 |
0.64 |
|
| 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 |
0.329 |
|
| 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 |
0.353 |
|
| 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 |
0.32 |
|
| 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 |
0.367 |
|
| 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 |
0.808 |
|
| 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 |
0.772 |
|
| 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 |
0.384 |
|
| 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 |
0.416 |
|
| 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 |
0.751 |
|
| 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 |
0.389 |
|
| 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 |
0.386 |
|
| 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 |
0.31 |
|
| 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 |
0.328 |
|
| 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 |
0.536 |
|
| 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 |
0.626 |
|
| 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 |
0.771 |
|
| 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 |
0.311 |
|
| 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 |
0.396 |
|
| 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 |
0.556 |
|
| 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 |
0.304 |
|
| 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 |
0.33 |
|
| 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 |
0.417 |
|
| 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 |
0.6 |
|
| 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 |
0.497 |
|
| 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 |
0.33 |
|
| 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 |
0.435 |
|
| 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 |
0.758 |
|
| 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 |
0.315 |
|
| 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 |
0.414 |
|
| 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 |
0.718 |
|
| 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 |
0.39 |
|
| 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 |
0.525 |
|
| 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 |
0.796 |
|
| 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 |
0.779 |
|
| 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 |
0.537 |
|
| 2004 |
Sherlock G. STARTing to recycle. Nature Genetics. 36: 795-6. PMID 15284848 DOI: 10.1038/Ng0804-795 |
0.328 |
|
| 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 |
0.509 |
|
| 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 |
0.546 |
|
| 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 |
0.59 |
|
| 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 |
0.518 |
|
| 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 |
0.503 |
|
| 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 |
0.583 |
|
| 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 |
0.787 |
|
| 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 |
0.786 |
|
| 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 |
0.315 |
|
| 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 |
0.595 |
|
| 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 |
0.517 |
|
| 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 |
0.602 |
|
| 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 |
0.648 |
|
| 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 |
0.765 |
|
| 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 |
0.579 |
|
| 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 |
0.395 |
|
| 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 |
0.566 |
|
| 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 |
0.723 |
|
| 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 |
0.583 |
|
| 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 |
0.797 |
|
| 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 |
0.787 |
|
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