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Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii
Sophie Brachat, Fred S Dietrich, Sylvia Voegeli, Zhihong Zhang, Larissa Stuart, Anita Lerch, Krista Gates, Tom Gaffney, Peter Philippsen
Genome Biol. 2003; 4(7): R45. Published online 2003 June 25. doi: 10.1186/gb-2003-4-7-r45
PMCID:
PMC193632
Abstract Full Text PDF–270K Supplementary Material

Is Cited by the Following 38 Articles in this Archive:

Axl2 Integrates Polarity Establishment, Maintenance, and Environmental Stress Response in the Filamentous Fungus Ashbya gossypii
Jonathan F. Anker, Amy S. Gladfelter
Eukaryot Cell. 2011 December; 10(12): 1679–1693. doi: 10.1128/EC.05183-11
PMCID:
PMC3232731
Free in PMC on 2012/06/01
Hundreds of putatively functional small open reading frames in Drosophila
Emmanuel Ladoukakis, Vini Pereira, Emile G Magny, Adam Eyre-Walker, Juan Pablo Couso
Genome Biol. 2011; 12(11): R118. Published online 2011 November 25. doi: 10.1186/gb-2011-12-11-r118
PMCID:
PMC3334604
Abstract Full Text PDF–939K Supplementary Material
Direct Iterative Protein Profiling (DIPP) - an Innovative Method for Large-scale Protein Detection Applied to Budding Yeast Mitosis
Régis Lavigne, Emmanuelle Becker, Yuchen Liu, Bertrand Evrard, Aurélie Lardenois, Michael Primig, Charles Pineau
Mol Cell Proteomics. 2012 February; 11(2): M111.012682. Published online 2011 October 13. doi: 10.1074/mcp.M111.012682
PMCID:
PMC3277764
Free in PMC on 2013/02/01
From sequence to function: Insights from natural variation in budding yeasts
Conrad A. Nieduszynski, Gianni Liti
Biochim Biophys Acta. 2011 October; 1810(10): 959–966. doi: 10.1016/j.bbagen.2011.02.004
PMCID:
PMC3271348
Abstract Full Text
Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments
Seán S ÓhÉigeartaigh, David Armisén, Kevin P Byrne, Kenneth H Wolfe
BMC Genomics. 2011; 12: 377. Published online 2011 July 26. doi: 10.1186/1471-2164-12-377
PMCID:
PMC3161974
Abstract Full Text PDF–1.0M Supplementary Material
Genetic Control of Biosynthesis and Transport of Riboflavin and Flavin Nucleotides and Construction of Robust Biotechnological Producers
Charles A. Abbas, Andriy A. Sibirny
Microbiol Mol Biol Rev. 2011 June; 75(2): 321–360. doi: 10.1128/MMBR.00030-10
PMCID:
PMC3122625
Free in PMC on 2012/06/01
Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction
Kechi Fang, Hansheng Zhao, Changyue Sun, Carolyn M C Lam, Suhua Chang, Kunlin Zhang, Gurudutta Panda, Miguel Godinho, Vítor A P Martins dos Santos, Jing Wang
BMC Syst Biol. 2011; 5: 83. Published online 2011 May 25. doi: 10.1186/1752-0509-5-83
PMCID:
PMC3123600
Abstract Full Text PDF–825K Supplementary Material
Structural Mutants of the Spindle Pole Body Cause Distinct Alteration of Cytoplasmic Microtubules and Nuclear Dynamics in Multinucleated Hyphae
Claudia Lang, Sandrine Grava, Mark Finlayson, Rhonda Trimble, Peter Philippsen, Sue L. Jaspersen
Mol Biol Cell. 2010 March 1; 21(5): 753–766. doi: 10.1091/mbc.E09-07-0555
PMCID:
PMC2828962
Abstract Full Text PDF–4.8M Supplementary Material
Polymorphisms in Multiple Genes Contribute to the Spontaneous Mitochondrial Genome Instability of Saccharomyces cerevisiae S288C Strains
Lazar N. Dimitrov, Rachel B. Brem, Leonid Kruglyak, Daniel E. Gottschling
Genetics. 2009 September; 183(1): 365–383. doi: 10.1534/genetics.109.104497
PMCID:
PMC2746160
Abstract Full Text PDF–1.7M
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
Albert Lee, Kasper Daniel Hansen, James Bullard, Sandrine Dudoit, Gavin Sherlock
PLoS Genet. 2008 December; 4(12): e1000299. Published online 2008 December 19. doi: 10.1371/journal.pgen.1000299
PMCID:
PMC2601015
Abstract Full Text PDF–2.8M Supplementary Material
Revisiting the Saccharomyces cerevisiae predicted ORFeome
Qian-Ru Li, Anne-Ruxandra Carvunis, Haiyuan Yu, Jing-Dong J. Han, Quan Zhong, Nicolas Simonis, Stanley Tam, Tong Hao, Niels J. Klitgord, Denis Dupuy, Danny Mou, Ilan Wapinski, Aviv Regev, David E. Hill, Michael E. Cusick, Marc Vidal
Genome Res. 2008 August; 18(8): 1294–1303. doi: 10.1101/gr.076661.108
PMCID:
PMC2493439
Abstract Full Text PDF–799K
Coa2 Is an Assembly Factor for Yeast Cytochrome c Oxidase Biogenesis That Facilitates the Maturation of Cox1
Fabien Pierrel, Oleh Khalimonchuk, Paul A. Cobine, Megan Bestwick, Dennis R. Winge
Mol Cell Biol. 2008 August; 28(16): 4927–4939. Published online 2008 June 9. doi: 10.1128/MCB.00057-08
PMCID:
PMC2519701
Abstract Full Text PDF–1.5M
Identification of Genes That Function in the Biogenesis and Localization of Small Nucleolar RNAs in Saccharomyces cerevisiae
Hui Qiu, Julia Eifert, Ludivine Wacheul, Marc Thiry, Adam C. Berger, Jelena Jakovljevic, John L. Woolford, Jr., Anita H. Corbett, Denis L. J. Lafontaine, Rebecca M. Terns, Michael P. Terns
Mol Cell Biol. 2008 June; 28(11): 3686–3699. Published online 2008 March 31. doi: 10.1128/MCB.01115-07
PMCID:
PMC2423305
Abstract Full Text PDF–1.3M
Comparative genomics-based investigation of resequencing targets in Vibrio fischeri: Focus on point miscalls and artefactual expansions
Mark J Mandel, Eric V Stabb, Edward G Ruby
BMC Genomics. 2008; 9: 138. Published online 2008 March 25. doi: 10.1186/1471-2164-9-138
PMCID:
PMC2330054
Abstract Full Text PDF–467K Supplementary Material
Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789
Wu Wei, John H. McCusker, Richard W. Hyman, Ted Jones, Ye Ning, Zhiwei Cao, Zhenglong Gu, Dan Bruno, Molly Miranda, Michelle Nguyen, Julie Wilhelmy, Caridad Komp, Raquel Tamse, Xiaojing Wang, Peilin Jia, Philippe Luedi, Peter J. Oefner, Lior David, Fred S. Dietrich, Yixue Li, Ronald W. Davis, Lars M. Steinmetz
Proc Natl Acad Sci U S A. 2007 July 31; 104(31): 12825–12830. Published online 2007 July 25. doi: 10.1073/pnas.0701291104
PMCID:
PMC1933262
Abstract Full Text PDF–1.0M Supplementary Material
Why Are There Still Over 1000 Uncharacterized Yeast Genes?
Lourdes Peña-Castillo, Timothy R. Hughes
Genetics. 2007 May; 176(1): 7–14. doi: 10.1534/genetics.107.074468
PMCID:
PMC1893027
Abstract Full Text PDF–1.4M
Genome-wide identification of spliced introns using a tiling microarray
Zhihong Zhang, Jay R. Hesselberth, Stanley Fields
Genome Res. 2007 April; 17(4): 503–509. doi: 10.1101/gr.6049107
PMCID:
PMC1832097
Abstract Full Text PDF–537K
Ashbya Genome Database 3.0: a cross-species genome and transcriptome browser for yeast biologists
Alexandre Gattiker, Riccarda Rischatsch, Philippe Demougin, Sylvia Voegeli, Fred S Dietrich, Peter Philippsen, Michael Primig
BMC Genomics. 2007; 8: 9. Published online 2007 January 9. doi: 10.1186/1471-2164-8-9
PMCID:
PMC1779777
Abstract Full Text PDF–1.0M
The SH3/PH Domain Protein AgBoi1/2 Collaborates with the Rho-Type GTPase AgRho3 To Prevent Nonpolar Growth at Hyphal Tips of Ashbya gossypii
Philipp Knechtle, Jürgen Wendland, Peter Philippsen
Eukaryot Cell. 2006 October; 5(10): 1635–1647. Published online 2006 September 1. doi: 10.1128/EC.00210-06
PMCID:
PMC1595331
Abstract Full Text PDF–1.4M
Saccharomyces cerevisiae S288C genome annotation: a working hypothesis
Dianna G. Fisk, Catherine A. Ball, Kara Dolinski, Stacia R. Engel, Eurie L. Hong, Laurie Issel-Tarver, Katja Schwartz, Anand Sethuraman, David Botstein, J. Michael Cherry, The Saccharomyces Genome Database Project
Yeast. Author manuscript; available in PMC 2011 February 16.
Published in final edited form as: Yeast. 2006 September; 23(12): 857–865. doi: 10.1002/yea.1400
PMCID:
PMC3040122
Abstract Full Text PDF–122K
Yeast homolog of a cancer-testis antigen defines a new transcription complex
Elena Kisseleva-Romanova, Raffaele Lopreiato, Agnès Baudin-Baillieu, Jean-Claude Rousselle, Laila Ilan, Kay Hofmann, Abdelkader Namane, Carl Mann, Domenico Libri
EMBO J. 2006 August 9; 25(15): 3576–3585. Published online 2006 July 27. doi: 10.1038/sj.emboj.7601235
PMCID:
PMC1538566
Abstract Full Text PDF–216K Supplementary Material
Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae
James P. Kastenmayer, Li Ni, Angela Chu, Lauren E. Kitchen, Wei-Chun Au, Hui Yang, Carole D. Carter, David Wheeler, Ronald W. Davis, Jef D. Boeke, Michael A. Snyder, Munira A. Basrai
Genome Res. 2006 March; 16(3): 365–373. doi: 10.1101/gr.4355406
PMCID:
PMC1415214
Abstract Full Text PDF–466K
Global analysis of gene function in yeast by quantitative phenotypic profiling
James A Brown, Gavin Sherlock, Chad L Myers, Nicola M Burrows, Changchun Deng, H Irene Wu, Kelly E McCann, Olga G Troyanskaya, J Martin Brown
Mol Syst Biol. 2006; 2: 2006.0001. Published online 2006 January 17. doi: 10.1038/msb4100043
PMCID:
PMC1681475
Abstract Full Text PDF–322K Supplementary Material
Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome
Jodi E. Hirschman, Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Eurie L. Hong, Michael S. Livstone, Robert Nash, Julie Park, Rose Oughtred, Marek Skrzypek, Barry Starr, Chandra L. Theesfeld, Jennifer Williams, Rey Andrada, Gail Binkley, Qing Dong, Christopher Lane, Stuart Miyasato, Anand Sethuraman, Mark Schroeder, Mayank K. Thanawala, Shuai Weng, Kara Dolinski, David Botstein, J. Michael Cherry
Nucleic Acids Res. 2006 January 1; 34(Database issue): D442–D445. Published online 2005 December 28. doi: 10.1093/nar/gkj117
PMCID:
PMC1347479
Abstract Full Text PDF–283K
Interactions of the Yeast SF3b Splicing Factor
Qiang Wang, Jin He, Bert Lynn, Brian C. Rymond
Mol Cell Biol. 2005 December; 25(24): 10745–10754. doi: 10.1128/MCB.25.24.10745-10754.2005
PMCID:
PMC1316957
Abstract Full Text PDF–381K Supplementary Material
Defining Genes in the Genome of the Hyperthermophilic Archaeon Pyrococcus furiosus: Implications for All Microbial Genomes
Farris L. Poole, II, Brian A. Gerwe, Robert C. Hopkins, Gerrit J. Schut, Michael V. Weinberg, Francis E. Jenney, Jr., Michael W. W. Adams
J Bacteriol. 2005 November; 187(21): 7325–7332. doi: 10.1128/JB.187.21.7325-7332.2005
PMCID:
PMC1272981
Abstract Full Text PDF–127K Supplementary Material
Identification of programmed translational -1 frameshifting sites in the genome of Saccharomyces cerevisiae
Michaël Bekaert, Hugues Richard, Bernard Prum, Jean-Pierre Rousset
Genome Res. 2005 October; 15(10): 1411–1420. doi: 10.1101/gr.4258005
Retraction in:
Genome Res. 2006 August; 16(8): 1074.
PMCID:
PMC1240084
Abstract Full Text Retraction
Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes
Stephan Steigele, Kay Nieselt
Nucleic Acids Res. 2005; 33(16): 5034–5044. Published online 2005 September 7. doi: 10.1093/nar/gki804
PMCID:
PMC1201330
Abstract Full Text PDF–420K Supplementary Material
Evidence for abundant transcription of non-coding regions in the Saccharomyces cerevisiae genome
Moshe Havilio, Erez Y Levanon, Galia Lerman, Martin Kupiec, Eli Eisenberg
BMC Genomics. 2005; 6: 93. Published online 2005 June 16. doi: 10.1186/1471-2164-6-93
PMCID:
PMC1181813
Abstract Full Text PDF–397K Supplementary Material
Mapping of transcription start sites in Saccharomyces cerevisiae using 5′ SAGE
Zhihong Zhang, Fred S. Dietrich
Nucleic Acids Res. 2005; 33(9): 2838–2851. Published online 2005 May 19. doi: 10.1093/nar/gki583
PMCID:
PMC1131933
Abstract Full Text PDF–730K Supplementary Material
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