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Re-annotation of protein-coding genes in the genome of saccharomyces cerevisiae based on support vector machines.

Lin D, Yin X, Wang X, Zhou P, Guo FB.

PLoS One. 2013 Jul 10;8(7):e64477. doi: 10.1371/journal.pone.0064477. Print 2013.


Parallel identification of new genes in Saccharomyces cerevisiae.

Oshiro G, Wodicka LM, Washburn MP, Yates JR 3rd, Lockhart DJ, Winzeler EA.

Genome Res. 2002 Aug;12(8):1210-20.


Revisiting the Saccharomyces cerevisiae predicted ORFeome.

Li QR, Carvunis AR, Yu H, Han JD, Zhong Q, Simonis N, Tam S, Hao T, Klitgord NJ, Dupuy D, Mou D, Wapinski I, Regev A, Hill DE, Cusick ME, Vidal M.

Genome Res. 2008 Aug;18(8):1294-303. doi: 10.1101/gr.076661.108. Epub 2008 May 23.


Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas.

King NL, Deutsch EW, Ranish JA, Nesvizhskii AI, Eddes JS, Mallick P, Eng J, Desiere F, Flory M, Martin DB, Kim B, Lee H, Raught B, Aebersold R.

Genome Biol. 2006;7(11):R106.


Saccharomyces cerevisiae S288C genome annotation: a working hypothesis.

Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Cherry JM; Saccharomyces Genome Database Project..

Yeast. 2006 Sep;23(12):857-65.


Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae.

Hurowitz EH, Brown PO.

Genome Biol. 2003;5(1):R2. Epub 2003 Dec 22.


Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii.

Brachat S, Dietrich FS, Voegeli S, Zhang Z, Stuart L, Lerch A, Gates K, Gaffney T, Philippsen P.

Genome Biol. 2003;4(7):R45. Epub 2003 Jun 25.


Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network.

Förster J, Famili I, Fu P, Palsson BØ, Nielsen J.

Genome Res. 2003 Feb;13(2):244-53.


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.


Total number of coding open reading frames in the yeast genome.

Kowalczuk M, Mackiewicz P, Gierlik A, Dudek MR, Cebrat S.

Yeast. 1999 Aug;15(11):1031-4.


How many protein-coding genes are there in the Saccharomyces cerevisiae genome?

Mackiewicz P, Kowalczuk M, Mackiewicz D, Nowicka A, Dudkiewicz M, Laszkiewicz A, Dudek MR, Cebrat S.

Yeast. 2002 May;19(7):619-29.


Small open reading frames: current prediction techniques and future prospect.

Cheng H, Chan WS, Li Z, Wang D, Liu S, Zhou Y.

Curr Protein Pept Sci. 2011 Sep;12(6):503-7. Review.


A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution.

Harrison P, Kumar A, Lan N, Echols N, Snyder M, Gerstein M.

J Mol Biol. 2002 Feb 22;316(3):409-19.


The reference genome sequence of Saccharomyces cerevisiae: then and now.

Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM.

G3 (Bethesda). 2014 Mar 20;4(3):389-98. doi: 10.1534/g3.113.008995.


Origin and properties of non-coding ORFs in the yeast genome.

Mackiewicz P, Kowalczuk M, Gierlik A, Dudek MR, Cebrat S.

Nucleic Acids Res. 1999 Sep 1;27(17):3503-9.


From one to many: expanding the Saccharomyces cerevisiae reference genome panel.

Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM.

Database (Oxford). 2016 Mar 17;2016. pii: baw020. doi: 10.1093/database/baw020. Print 2016.


Whole-genome comparison reveals novel genetic elements that characterize the genome of industrial strains of Saccharomyces cerevisiae.

Borneman AR, Desany BA, Riches D, Affourtit JP, Forgan AH, Pretorius IS, Egholm M, Chambers PJ.

PLoS Genet. 2011 Feb 3;7(2):e1001287. doi: 10.1371/journal.pgen.1001287.


Annotation of unknown yeast ORFs by correlation analysis of microarray data and extensive literature searches.

Pir P, Ulgen KO, Hayes A, Ilsen Onsan Z, Kirdar B, Oliver SG.

Yeast. 2006 May;23(7):553-71.

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