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How to Use the Candida Genome Database.

Skrzypek MS, Binkley J, Sherlock G.

Methods Mol Biol. 2016;1356:3-15. doi: 10.1007/978-1-4939-3052-4_1.


Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions.

Schep AN, Buenrostro JD, Denny SK, Schwartz K, Sherlock G, Greenleaf WJ.

Genome Res. 2015 Nov;25(11):1757-70. doi: 10.1101/gr.192294.115. Epub 2015 Aug 27.


A single nucleotide polymorphism uncovers a novel function for the transcription factor Ace2 during Candida albicans hyphal development.

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.

PLoS Genet. 2015 Apr 15;11(4):e1005152. doi: 10.1371/journal.pgen.1005152. eCollection 2015 Apr.


Quantitative evolutionary dynamics using high-resolution lineage tracking.

Levy SF, Blundell JR, Venkataram S, Petrov DA, Fisher DS, Sherlock G.

Nature. 2015 Mar 12;519(7542):181-6. doi: 10.1038/nature14279. Epub 2015 Feb 25.


Experimental evolution: prospects and challenges.

Rosenzweig F, Sherlock G.

Genomics. 2014 Dec;104(6 Pt A):v-vi. doi: 10.1016/j.ygeno.2014.11.008. No abstract available.


The Valley-of-Death: reciprocal sign epistasis constrains adaptive trajectories in a constant, nutrient limiting environment.

Chiotti KE, Kvitek DJ, Schmidt KH, Koniges G, Schwartz K, Donckels EA, Rosenzweig F, Sherlock G.

Genomics. 2014 Dec;104(6 Pt A):431-7. doi: 10.1016/j.ygeno.2014.10.011. Epub 2014 Nov 1.


Ex uno plures: clonal reinforcement drives evolution of a simple microbial community.

Kinnersley M, Wenger J, Kroll E, Adams J, Sherlock G, Rosenzweig F.

PLoS Genet. 2014 Jun 26;10(6):e1004430. doi: 10.1371/journal.pgen.1004430. eCollection 2014 Jun.


Curation accuracy of model organism databases.

Keseler IM, Skrzypek M, Weerasinghe D, Chen AY, Fulcher C, Li GW, Lemmer KC, Mladinich KM, Chow ED, Sherlock G, Karp PD.

Database (Oxford). 2014 Jun 12;2014. pii: bau058. doi: 10.1093/database/bau058. Print 2014.


Literature-based gene curation and proposed genetic nomenclature for cryptococcus.

Inglis DO, Skrzypek MS, Liaw E, Moktali V, Sherlock G, Stajich JE.

Eukaryot Cell. 2014 Jul;13(7):878-83. doi: 10.1128/EC.00083-14. Epub 2014 May 9.


Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans.

Muzzey D, Sherlock G, Weissman JS.

Genome Res. 2014 Jun;24(6):963-73. doi: 10.1101/gr.166322.113. Epub 2014 Apr 14.


PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools.

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, Thomas PD, Altman T.

Nucleic Acids Res. 2014 Jan;42(Database issue):D677-84. doi: 10.1093/nar/gkt1203. Epub 2013 Nov 26. Erratum in: Nucleic Acids Res. 2014 Oct 29;42(19):12330.


Whole genome, whole population sequencing reveals that loss of signaling networks is the major adaptive strategy in a constant environment.

Kvitek DJ, Sherlock G.

PLoS Genet. 2013 Nov;9(11):e1003972. doi: 10.1371/journal.pgen.1003972. Epub 2013 Nov 21.


The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations.

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.

Nucleic Acids Res. 2014 Jan;42(Database issue):D705-10. doi: 10.1093/nar/gkt1029. Epub 2013 Nov 4.


The Candida Genome Database: the new homology information page highlights protein similarity and phylogeny.

Binkley J, Arnaud MB, Inglis DO, Skrzypek MS, Shah P, Wymore F, Binkley G, Miyasato SR, Simison M, Sherlock G.

Nucleic Acids Res. 2014 Jan;42(Database issue):D711-6. doi: 10.1093/nar/gkt1046. Epub 2013 Oct 31.


Phenotypic and genotypic convergences are influenced by historical contingency and environment in yeast.

Spor A, Kvitek DJ, Nidelet T, Martin J, Legrand J, Dillmann C, Bourgais A, de Vienne D, Sherlock G, Sicard D.

Evolution. 2014 Mar;68(3):772-90. doi: 10.1111/evo.12302. Epub 2013 Nov 25.


Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors.

Grant GD, Brooks L 3rd, Zhang X, Mahoney JM, Martyanov V, Wood TA, Sherlock G, Cheng C, Whitfield ML.

Mol Biol Cell. 2013 Dec;24(23):3634-50. doi: 10.1091/mbc.E13-05-0264. Epub 2013 Oct 9.


Ras signaling gets fine-tuned: regulation of multiple pathogenic traits of Candida albicans.

Inglis DO, Sherlock G.

Eukaryot Cell. 2013 Oct;12(10):1316-25. doi: 10.1128/EC.00094-13. Epub 2013 Aug 2. Review.


Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae.

Inglis DO, Binkley J, Skrzypek MS, Arnaud MB, Cerqueira GC, Shah P, Wymore F, Wortman JR, Sherlock G.

BMC Microbiol. 2013 Apr 26;13:91. doi: 10.1186/1471-2180-13-91.


Recurrent rearrangement during adaptive evolution in an interspecific yeast hybrid suggests a model for rapid introgression.

Dunn B, Paulish T, Stanbery A, Piotrowski J, Koniges G, Kroll E, Louis EJ, Liti G, Sherlock G, Rosenzweig F.

PLoS Genet. 2013 Mar;9(3):e1003366. doi: 10.1371/journal.pgen.1003366. Epub 2013 Mar 21.

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