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Items: 1 to 50 of 131

1.

Improved discovery of genetic interactions using CRISPRiSeq across multiple environments.

Jaffe M, Dziulko A, Smith JD, St Onge RP, Levy SF, Sherlock G.

Genome Res. 2019 Apr;29(4):668-681. doi: 10.1101/gr.246603.118. Epub 2019 Feb 19.

2.

Acceptability and feasibility of wearing activity monitors in community-dwelling older adults with dementia.

Farina N, Sherlock G, Thomas S, Lowry RG, Banerjee S.

Int J Geriatr Psychiatry. 2019 Apr;34(4):617-624. doi: 10.1002/gps.5064. Epub 2019 Feb 20.

PMID:
30701592
3.

The dynamics of adaptive genetic diversity during the early stages of clonal evolution.

Blundell JR, Schwartz K, Francois D, Fisher DS, Sherlock G, Levy SF.

Nat Ecol Evol. 2019 Feb;3(2):293-301. doi: 10.1038/s41559-018-0758-1. Epub 2018 Dec 31.

PMID:
30598529
4.

Gene flow contributes to diversification of the major fungal pathogen Candida albicans.

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, Battail C, Wincker P, Borman AM, Chowdhary A, Fan S, Kim SH, Le Pape P, Romeo O, Shin JH, Gabaldon T, Sherlock G, Bougnoux ME, d'Enfert C.

Nat Commun. 2018 Jun 8;9(1):2253. doi: 10.1038/s41467-018-04787-4.

5.

Using the Candida Genome Database.

Skrzypek MS, Binkley J, Sherlock G.

Methods Mol Biol. 2018;1757:31-47. doi: 10.1007/978-1-4939-7737-6_3.

6.

Hidden Complexity of Yeast Adaptation under Simple Evolutionary Conditions.

Li Y, Venkataram S, Agarwala A, Dunn B, Petrov DA, Sherlock G, Fisher DS.

Curr Biol. 2018 Feb 19;28(4):515-525.e6. doi: 10.1016/j.cub.2018.01.009. Epub 2018 Feb 8.

7.

Diff-seq: A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery.

Aggeli D, Karas VO, Sinnott-Armstrong NA, Varghese V, Shafer RW, Greenleaf WJ, Sherlock G.

Nucleic Acids Res. 2018 Apr 20;46(7):e42. doi: 10.1093/nar/gky022.

8.

Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus.

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, Cánovas D, Cerqueira GC, Chen F, Chen W, Choi C, Clum A, Dos Santos RA, Damásio AR, Diallinas G, Emri T, Fekete E, Flipphi M, Freyberg S, Gallo A, Gournas C, Habgood R, Hainaut M, Harispe ML, Henrissat B, Hildén KS, Hope R, Hossain A, Karabika E, Karaffa L, Karányi Z, Kraševec N, Kuo A, Kusch H, LaButti K, Lagendijk EL, Lapidus A, Levasseur A, Lindquist E, Lipzen A, Logrieco AF, MacCabe A, Mäkelä MR, Malavazi I, Melin P, Meyer V, Mielnichuk N, Miskei M, Molnár ÁP, Mulé G, Ngan CY, Orejas M, Orosz E, Ouedraogo JP, Overkamp KM, Park HS, Perrone G, Piumi F, Punt PJ, Ram AF, Ramón A, Rauscher S, Record E, Riaño-Pachón DM, Robert V, Röhrig J, Ruller R, Salamov A, Salih NS, Samson RA, Sándor E, Sanguinetti M, Schütze T, Sepčić K, Shelest E, Sherlock G, Sophianopoulou V, Squina FM, Sun H, Susca A, Todd RB, Tsang A, Unkles SE, van de Wiele N, van Rossen-Uffink D, Oliveira JV, Vesth TC, Visser J, Yu JH, Zhou M, Andersen MR, Archer DB, Baker SE, Benoit I, Brakhage AA, Braus GH, Fischer R, Frisvad JC, Goldman GH, Houbraken J, Oakley B, Pócsi I, Scazzocchio C, Seiboth B, vanKuyk PA, Wortman J, Dyer PS, Grigoriev IV.

Genome Biol. 2017 Feb 14;18(1):28. doi: 10.1186/s13059-017-1151-0.

9.

Seeking Goldilocks During Evolution of Drug Resistance.

Sherlock G, Petrov DA.

PLoS Biol. 2017 Feb 3;15(2):e2001872. doi: 10.1371/journal.pbio.2001872. eCollection 2017 Feb.

10.

Extremely Rare Polymorphisms in Saccharomyces cerevisiae Allow Inference of the Mutational Spectrum.

Zhu YO, Sherlock G, Petrov DA.

PLoS Genet. 2017 Jan 3;13(1):e1006455. doi: 10.1371/journal.pgen.1006455. eCollection 2017 Jan.

11.

iSeq: A New Double-Barcode Method for Detecting Dynamic Genetic Interactions in Yeast.

Jaffe M, Sherlock G, Levy SF.

G3 (Bethesda). 2017 Jan 5;7(1):143-153. doi: 10.1534/g3.116.034207.

12.

The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data.

Skrzypek MS, Binkley J, Binkley G, Miyasato SR, Simison M, Sherlock G.

Nucleic Acids Res. 2017 Jan 4;45(D1):D592-D596. doi: 10.1093/nar/gkw924. Epub 2016 Oct 13.

13.

Analysis of Repair Mechanisms following an Induced Double-Strand Break Uncovers Recessive Deleterious Alleles in the Candida albicans Diploid Genome.

Feri A, Loll-Krippleber R, Commere PH, Maufrais C, Sertour N, Schwartz K, Sherlock G, Bougnoux ME, d'Enfert C, Legrand M.

MBio. 2016 Oct 11;7(5). pii: e01109-16. doi: 10.1128/mBio.01109-16.

14.

High-Throughput Yeast Strain Sequencing.

Schwartz K, Sherlock G.

Cold Spring Harb Protoc. 2016 Oct 3;2016(10). doi: 10.1101/pdb.top077651. Review.

PMID:
27698244
15.

Preparation of Yeast DNA Sequencing Libraries.

Schwartz K, Sherlock G.

Cold Spring Harb Protoc. 2016 Oct 3;2016(10). doi: 10.1101/pdb.prot088930.

PMID:
27698239
16.

Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast.

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.

Cell. 2016 Sep 8;166(6):1585-1596.e22. doi: 10.1016/j.cell.2016.08.002. Epub 2016 Sep 1.

17.

Whole Genome Analysis of 132 Clinical Saccharomyces cerevisiae Strains Reveals Extensive Ploidy Variation.

Zhu YO, Sherlock G, Petrov DA.

G3 (Bethesda). 2016 Aug 9;6(8):2421-34. doi: 10.1534/g3.116.029397.

18.

Heterozygote Advantage Is a Common Outcome of Adaptation in Saccharomyces cerevisiae.

Sellis D, Kvitek DJ, Dunn B, Sherlock G, Petrov DA.

Genetics. 2016 Jul;203(3):1401-13. doi: 10.1534/genetics.115.185165. Epub 2016 May 18.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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):772-790. doi: 10.1111/evo.12302. Epub 2013 Nov 25.

34.

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.

36.

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.

37.

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.

38.

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.

39.

Comparative metabolic footprinting of a large number of commercial wine yeast strains in Chardonnay fermentations.

Richter CL, Dunn B, Sherlock G, Pugh T.

FEMS Yeast Res. 2013 Jun;13(4):394-410. doi: 10.1111/1567-1364.12046. Epub 2013 Apr 12.

40.

Improved gene ontology annotation for biofilm formation, filamentous growth, and phenotypic switching in Candida albicans.

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

Eukaryot Cell. 2013 Jan;12(1):101-8. doi: 10.1128/EC.00238-12. Epub 2012 Nov 9.

41.

Different selective pressures lead to different genomic outcomes as newly-formed hybrid yeasts evolve.

Piotrowski JS, Nagarajan S, Kroll E, Stanbery A, Chiotti KE, Kruckeberg AL, Dunn B, Sherlock G, Rosenzweig F.

BMC Evol Biol. 2012 Apr 2;12:46. doi: 10.1186/1471-2148-12-46.

42.

Turbidostat culture of Saccharomyces cerevisiae W303-1A under selective pressure elicited by ethanol selects for mutations in SSD1 and UTH1.

Avrahami-Moyal L, Engelberg D, Wenger JW, Sherlock G, Braun S.

FEMS Yeast Res. 2012 Aug;12(5):521-33. doi: 10.1111/j.1567-1364.2012.00803.x. Epub 2012 Apr 23.

43.

APJ1 and GRE3 homologs work in concert to allow growth in xylose in a natural Saccharomyces sensu stricto hybrid yeast.

Schwartz K, Wenger JW, Dunn B, Sherlock G.

Genetics. 2012 Jun;191(2):621-32. doi: 10.1534/genetics.112.140053. Epub 2012 Mar 16.

44.

Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments.

Dunn B, Richter C, Kvitek DJ, Pugh T, Sherlock G.

Genome Res. 2012 May;22(5):908-24. doi: 10.1101/gr.130310.111. Epub 2012 Feb 27.

45.

GC-content normalization for RNA-Seq data.

Risso D, Schwartz K, Sherlock G, Dudoit S.

BMC Bioinformatics. 2011 Dec 17;12:480. doi: 10.1186/1471-2105-12-480.

46.

The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources.

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, Wortman JR.

Nucleic Acids Res. 2012 Jan;40(Database issue):D653-9. doi: 10.1093/nar/gkr875. Epub 2011 Nov 12.

47.

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.

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

Nucleic Acids Res. 2012 Jan;40(Database issue):D667-74. doi: 10.1093/nar/gkr945. Epub 2011 Nov 7.

48.

Hunger artists: yeast adapted to carbon limitation show trade-offs under carbon sufficiency.

Wenger JW, Piotrowski J, Nagarajan S, Chiotti K, Sherlock G, Rosenzweig F.

PLoS Genet. 2011 Aug;7(8):e1002202. doi: 10.1371/journal.pgen.1002202. Epub 2011 Aug 4.

49.

Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape.

Kvitek DJ, Sherlock G.

PLoS Genet. 2011 Apr;7(4):e1002056. doi: 10.1371/journal.pgen.1002056. Epub 2011 Apr 28.

50.

DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer.

Kobayashi Y, Absher DM, Gulzar ZG, Young SR, McKenney JK, Peehl DM, Brooks JD, Myers RM, Sherlock G.

Genome Res. 2011 Jul;21(7):1017-27. doi: 10.1101/gr.119487.110. Epub 2011 Apr 26.

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