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Research: RNA–DNA sequence differences in Saccharomyces cerevisiae
- Isabel X. Wang,
- Christopher Grunseich,
- Youree G. Chung,
- Hojoong Kwak,
- Girish Ramrattan,
- Zhengwei Zhu,
- and Vivian G. Cheung
Genome Res. November 2016 26: 1544-1554; Published in Advance September 16, 2016, doi:10.1101/gr.207878.116
..., Grunseich Isabel YG Chung Kwak, H Chung, YG Kwak, Hojoong Zhu, Z Wang, IX G Ramrattan Grunseich Cheung Vivian G. Wang Zhu Zhengwei VG Cheung Cheung, V 10.1101/gr.207878.116 genome;gr.207878.116 1549-5469 1088-9051 RNA–DNA sequence differences in Saccharomyces cerevisiae Wang et al. RNA–DNA sequence...
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Research: Unique genetic basis of the distinct antibiotic potency of high acetic acid production in the probiotic yeast Saccharomyces cerevisiae var. boulardii
- Benjamin Offei,
- Paul Vandecruys,
- Stijn De Graeve,
- María R. Foulquié-Moreno,
- and Johan M. Thevelein
Genome Res. September 2019 29: 1478-1494; Published in Advance August 29, 2019, doi:10.1101/gr.243147.118
...obscure. It is considered conspecific with budding yeast Saccharomyces cerevisiae, which is generally used in classical food applications. They have an almost identical sequence, making the genetic basis of probiotic potency in S. boulardii puzzling. We now show that S. boulardii produces at 37°C...
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LETTER: 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,
- and Marc Vidal
Genome Res. August 2008 18: 1294-1303; Published in Advance May 23, 2008, doi:10.1101/gr.076661.108
...genome sequences combined with experimental verifications. Here we reexamine a set of Saccharomyces cerevisiae “orphan” ORFs recently removed from the original ORFeome annotation due to lack of conservation across evolutionarily related yeast species. We show that many orphan ORFs produce detectable...
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Resource: The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen
- Pooja K. Strope,
- Daniel A. Skelly,
- Stanislav G. Kozmin,
- Gayathri Mahadevan,
- Eric A. Stone,
- Paul M. Magwene,
- Fred S. Dietrich,
- and John H. McCusker
Genome Res. May 2015 25: 762-774; Published in Advance April 3, 2015, doi:10.1101/gr.185538.114
...The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen Pooja K. Strope 1 , Daniel A. Skelly 2 , Stanislav G. Kozmin 1 , Gayathri Mahadevan 1...
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RESOURCE: Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae
- Yanhui Hu,
- Andreas Rolfs,
- Bhupinder Bhullar,
- Tellamraju V. S. Murthy,
- Cong Zhu,
- Michael F. Berger,
- Anamaria A. Camargo,
- Fontina Kelley,
- Seamus McCarron,
- Daniel Jepson,
- Aaron Richardson,
- Jacob Raphael,
- Donna Moreira,
- Elena Taycher,
- Dongmei Zuo,
- Stephanie Mohr,
- Michael F. Kane,
- Janice Williamson,
- Andrew Simpson,
- Martha L. Bulyk,
- Edward Harlow,
- Gerald Marsischky,
- Richard D. Kolodner,
- and Joshua LaBaer
Genome Res. April 2007 17: 536-543; Published in Advance February 23, 2007, doi:10.1101/gr.6037607
...of Health Sciences &amp; Technology (HST), Harvard Medical School, Boston, Massachusetts 02115, USA Abstract The availability of an annotated genome sequence for the yeast Saccharomyces cerevisiae has made possible the proteome-scale study of protein function and protein–protein interactions...
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INSIGHT/OUTLOOK: Slip-Sliding the Frame: Programmed −1 Frameshifting on Eukaryotic Transcripts
- Gerald M. Wilson and
- Gary Brewer
Genome Res. May 1, 1999 9: 393-394; doi:10.1101/gr.9.5.393
...an amino acid residue; and (3) translational bypassing, where the translational machinery traverses a gap in the mRNA coding sequence yet yields a single polypeptide chain. Programmed −1 ribosomal frameshift signals are among the most extensively characterized of these translational recoding phenomena (for...
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Research: A genome-wide transcriptome and translatome analysis of Arabidopsis transposons identifies a unique and conserved genome expression strategy for Ty1/Copia retroelements
- Stefan Oberlin,
- Alexis Sarazin,
- Clément Chevalier,
- Olivier Voinnet,
- and Arturo Marí-Ordóñez
Genome Res. September 2017 27: 1549-1562; Published in Advance August 7, 2017, doi:10.1101/gr.220723.117
...diverse translational strategies. Ty1 in Saccharomyces cerevisiae and HIV-1 in human use translational frameshifting owing to GAG and catalytic POL components being encoded in two distinct open reading frames (ORFs). GAG, encoded in the first frame, is optimally translated while ribosomal slipping allows...
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Research: Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus
- Nikolaos Vakirlis,
- Véronique Sarilar,
- Guénola Drillon,
- Aubin Fleiss,
- Nicolas Agier,
- Jean-Philippe Meyniel,
- Lou Blanpain,
- Alessandra Carbone,
- Hugo Devillers,
- Kenny Dubois,
- Alexandre Gillet-Markowska,
- Stéphane Graziani,
- Nguyen Huu-Vang,
- Marion Poirel,
- Cyrielle Reisser,
- Jonathan Schott,
- Joseph Schacherer,
- Ingrid Lafontaine,
- Bertrand Llorente,
- Cécile Neuvéglise,
- and Gilles Fischer
Genome Res. July 2016 26: 918-932; Published in Advance May 31, 2016, doi:10.1101/gr.204420.116
...into an evolutionary framework has only been achieved in a limited number of cases. In yeast, Wolfe and colleagues manually reconstructed the ancestral of Saccharomyces cerevisiae as it was before the WGD event and identified at least 144 structural rearrangements, as well as 124 genes that are present in the actual S...
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RESEARCH: Transposable Elements and Genome Organization: A Comprehensive Survey of Retrotransposons Revealed by the Complete Saccharomyces cerevisiae Genome Sequence
- Jin M. Kim,
- Swathi Vanguri,
- Jef D. Boeke,
- Abram Gabriel,
- and Daniel F. Voytas
Genome Res. May 1, 1998 8: 464-478; doi:10.1101/gr.8.5.464
...Transposable Elements and Genome Organization: A Comprehensive Survey of Retrotransposons Revealed by the Complete Saccharomyces cerevisiae Genome Sequence Jin M. Kim 1 , Swathi Vanguri 2 , Jef D. Boeke 3 , Abram Gabriel 2 , and Daniel F...
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LETTER: Identification of Putative Programmed −1 Ribosomal Frameshift Signals in Large DNA Databases
- Amy B. Hammell,
- Ronald C. Taylor,
- Stuart W. Peltz,
- and Jonathan D. Dinman
Genome Res. May 1, 1999 9: 417-427; doi:10.1101/gr.9.5.417
..., Peltz Amy B, Hammell Dinman, JD Amy Hammell Jonathan Dinman S Peltz 10.1101/gr.9.5.417 genome;9/5/417 1549-5469 1088-9051 Identification of Putative Programmed −1 Ribosomal Frameshift Signals in Large DNA Databases Identification of Putative Programmed −1 Ribosomal Frameshift Signals in Large DNA...

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