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Items: 1 to 20 of 113

1.

High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome.

Liti G, Nguyen Ba AN, Blythe M, Müller CA, Bergström A, Cubillos FA, Dafhnis-Calas F, Khoshraftar S, Malla S, Mehta N, Siow CC, Warringer J, Moses AM, Louis EJ, Nieduszynski CA.

BMC Genomics. 2013 Jan 31;14:69. doi: 10.1186/1471-2164-14-69.

2.

A Comprehensive Analysis of Transcript-Supported De Novo Genes in Saccharomyces sensu stricto Yeasts.

Lu TC, Leu JY, Lin WC.

Mol Biol Evol. 2017 Nov 1;34(11):2823-2838. doi: 10.1093/molbev/msx210.

3.

Genome-wide identification of replication origins in yeast by comparative genomics.

Nieduszynski CA, Knox Y, Donaldson AD.

Genes Dev. 2006 Jul 15;20(14):1874-9.

4.

Saccharomyces cerevisiae: gene annotation and genome variability, state of the art through comparative genomics.

Louis E.

Methods Mol Biol. 2011;759:31-40. doi: 10.1007/978-1-61779-173-4_2.

PMID:
21863479
5.

The Saccharomyces cerevisiae W303-K6001 cross-platform genome sequence: insights into ancestry and physiology of a laboratory mutt.

Ralser M, Kuhl H, Ralser M, Werber M, Lehrach H, Breitenbach M, Timmermann B.

Open Biol. 2012 Aug;2(8):120093. doi: 10.1098/rsob.120093.

6.

Sequencing and comparison of yeast species to identify genes and regulatory elements.

Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES.

Nature. 2003 May 15;423(6937):241-54.

PMID:
12748633
7.

Reference-guided de novo assembly approach improves genome reconstruction for related species.

Lischer HEL, Shimizu KK.

BMC Bioinformatics. 2017 Nov 10;18(1):474. doi: 10.1186/s12859-017-1911-6.

8.

A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach.

Proux-Wéra E, Armisén D, Byrne KP, Wolfe KH.

BMC Bioinformatics. 2012 Sep 17;13:237. doi: 10.1186/1471-2105-13-237.

9.

From sequence mapping to genome assemblies.

Otto TD.

Methods Mol Biol. 2015;1201:19-50. doi: 10.1007/978-1-4939-1438-8_2.

PMID:
25388106
10.

A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes.

Bratcher HB, Corton C, Jolley KA, Parkhill J, Maiden MC.

BMC Genomics. 2014 Dec 18;15:1138. doi: 10.1186/1471-2164-15-1138.

11.

Transposon fingerprinting using low coverage whole genome shotgun sequencing in cacao (Theobroma cacao L.) and related species.

Sveinsson S, Gill N, Kane NC, Cronk Q.

BMC Genomics. 2013 Jul 24;14:502. doi: 10.1186/1471-2164-14-502.

12.

Saccharomyces Genome Database: the genomics resource of budding yeast.

Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED.

Nucleic Acids Res. 2012 Jan;40(Database issue):D700-5. doi: 10.1093/nar/gkr1029. Epub 2011 Nov 21.

13.

Detection of replication origins using comparative genomics and recombinational ARS assay.

Nieduszynski CA, Donaldson AD.

Methods Mol Biol. 2009;521:295-313. doi: 10.1007/978-1-60327-815-7_16.

PMID:
19563113
14.

Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of de novo assemblers.

Amin S, Prentis PJ, Gilding EK, Pavasovic A.

BMC Res Notes. 2014 Aug 1;7:488. doi: 10.1186/1756-0500-7-488.

15.

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer.

Istace B, Friedrich A, d'Agata L, Faye S, Payen E, Beluche O, Caradec C, Davidas S, Cruaud C, Liti G, Lemainque A, Engelen S, Wincker P, Schacherer J, Aury JM.

Gigascience. 2017 Feb 1;6(2):1-13. doi: 10.1093/gigascience/giw018.

16.

Population genomics of domestic and wild yeasts.

Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, Tsai IJ, Bergman CM, Bensasson D, O'Kelly MJ, van Oudenaarden A, Barton DB, Bailes E, Nguyen AN, Jones M, Quail MA, Goodhead I, Sims S, Smith F, Blomberg A, Durbin R, Louis EJ.

Nature. 2009 Mar 19;458(7236):337-41. doi: 10.1038/nature07743. Epub 2009 Feb 11.

17.

A new system for comparative functional genomics of Saccharomyces yeasts.

Caudy AA, Guan Y, Jia Y, Hansen C, DeSevo C, Hayes AP, Agee J, Alvarez-Dominguez JR, Arellano H, Barrett D, Bauerle C, Bisaria N, Bradley PH, Breunig JS, Bush E, Cappel D, Capra E, Chen W, Clore J, Combs PA, Doucette C, Demuren O, Fellowes P, Freeman S, Frenkel E, Gadala-Maria D, Gawande R, Glass D, Grossberg S, Gupta A, Hammonds-Odie L, Hoisos A, Hsi J, Hsu YH, Inukai S, Karczewski KJ, Ke X, Kojima M, Leachman S, Lieber D, Liebowitz A, Liu J, Liu Y, Martin T, Mena J, Mendoza R, Myhrvold C, Millian C, Pfau S, Raj S, Rich M, Rokicki J, Rounds W, Salazar M, Salesi M, Sharma R, Silverman S, Singer C, Sinha S, Staller M, Stern P, Tang H, Weeks S, Weidmann M, Wolf A, Young C, Yuan J, Crutchfield C, McClean M, Murphy CT, Llinás M, Botstein D, Troyanskaya OG, Dunham MJ.

Genetics. 2013 Sep;195(1):275-87. doi: 10.1534/genetics.113.152918. Epub 2013 Jul 12.

18.
19.

Comparative genomic hybridization provides new insights into the molecular taxonomy of the Saccharomyces sensu stricto complex.

Edwards-Ingram LC, Gent ME, Hoyle DC, Hayes A, Stateva LI, Oliver SG.

Genome Res. 2004 Jun;14(6):1043-51.

20.

A high-definition view of functional genetic variation from natural yeast genomes.

Bergström A, Simpson JT, Salinas F, Barré B, Parts L, Zia A, Nguyen Ba AN, Moses AM, Louis EJ, Mustonen V, Warringer J, Durbin R, Liti G.

Mol Biol Evol. 2014 Apr;31(4):872-88. doi: 10.1093/molbev/msu037. Epub 2014 Jan 14.

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