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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
..., J.R. , Jr. , Dawson, E.P. , Rushing, K.L. , Jackson, C.H. , Lockshon, D. , Conover, D. , Lanciault, C. , Harris, J.R. , Simmons, S.J. , Rothstein, R. , et al. ( 1997 ) The complete set of predicted genes from Saccharomyces cerevisiae in a readily usable form . Genome Res. 7 : 1169 – 1173 . ↵ Hughes...
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Methods: Finding friends and enemies in an enemies-only network: A graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions
- Yan Qi,
- Yasir Suhail,
- Yu-yi Lin,
- Jef D. Boeke,
- and Joel S. Bader
Genome Res. December 2008 18: 1991-2004; Published in Advance October 2, 2008, doi:10.1101/gr.077693.108
...). These methods have achieved success in analyzing the accruing genetic interaction data sets. Most analysis of the genetic interaction network has focused on pathway inference; predicting genetic interactions from genetic interactions has received less attention. Previous methods with good performance have...
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Methods: Predicting essential genes in fungal genomes
- Michael Seringhaus,
- Alberto Paccanaro,
- Anthony Borneman,
- Michael Snyder,
- and Mark Gerstein
Genome Res. September 2006 16: 1126-1135; Published in Advance August 9, 2006, doi:10.1101/gr.5144106
...: In this window In a new window Table 1. Homology comparison of S. mikatae and S. cerevisiae The S. mikatae contains 7047 putative ORFs, of which a subset of 3939 was ultimately usable by our predictive technique (see Methods). The complete set of S. mikatae ORF sequences was queried against the S. cerevisiae...
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Research: Diversification and collapse of a telomere elongation mechanism
- Bastien Saint-Leandre,
- Son C. Nguyen,
- and Mia T. Levine
Genome Res. June 2019 29: 920-931; Published in Advance May 28, 2019, doi:10.1101/gr.245001.118
...conducted a final refinement step for each complete gag and RT domain by mapping raw reads to our set of telomeric retrotransposon candidates. These raw reads came from Illumina-based short-read sequence databases generated independently of the Sanger and 454 reads used to build the consensus sequences...
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Methods: Forcing interactions as a genetic screen to identify proteins that exert a defined activity
- Michael DeVit,
- Paul J. Cullen,
- Margaret Branson,
- George F. Sprague, Jr.,
- and Stanley Fields
Genome Res. April 2005 15: 560-565; doi:10.1101/gr.3259905
.... The complete set of predicted genes from Saccharomyces cerevisiae in a readily usable form. Genome Res. 7 : 1169 -1173. ↵ Huh, W.K., Falvo, J.V., Gerke, L.C., Carroll, A.S., Howson, R.W., Weissman, J.S., and O'Shea, E.K. 2003 . Global analysis of protein localization in budding yeast. Nature 425 : 686 -691...
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METHODS: Judging the Quality of Gene Expression-Based Clustering Methods Using Gene Annotation
- Francis D. Gibbons and
- Frederick P. Roth
Genome Res. October 1, 2002 12: 1574-1581; doi:10.1101/gr.397002
...this table: In this window In a new window Table 1. Four Data Sets Analyzed, Representing Both Affymetrix- and Two-Color cDNA Microarrays, Cell Cycle and Non-Cell Cycle Data Sets The Cho data set consists of 15 time points covering two complete cell cycles, and collected in a non-ratio format ( Cho et al...
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Methods: A Strategy for Constructing Large Protein Interaction Maps Using the Yeast Two-Hybrid System:Regulated Expression Arrays and Two-Phase Mating
- Jinhui Zhong,
- Huamei Zhang,
- Clement A. Stanyon,
- Gerard Tromp,
- and Russell L. Finley, Jr.
Genome Res. December 2003 13: 2691-2699; Published in Advance January 1, 2003, doi:10.1101/gr.1134603
...defined sets of proteins ( Fromont-Racine et al. 2000 ; Walhout et al. 2000 ; Drees et al. 2001 ), and a few studies have set out to map the interactions among proteins encoded by a , including -wide screens for T7 bacteriophage, vaccinia virus, Helicobacter pylori , and the yeast Saccharomyces cerevisiae...
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Methods: Fosmid-Based Physical Mapping of the Histoplasma capsulatum Genome
- Vincent Magrini,
- Wesley C. Warren,
- John Wallis,
- William E. Goldman,
- Jian Xu,
- Elaine R. Mardis,
- and John D. McPherson
Genome Res. August 2004 14: 1603-1609; doi:10.1101/gr.2361404
...sets in a map-assisted whole- shotgun approach, we can resolve the difference between the predicted and assembled size of H. capsulatum G217B. In this study, successive modifications of the PCAP WGS assembly were used to incorporate more of the shotgun reads. The initial PCAP WGS assembly includes 75...
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Insight/Outlook: Academia-Industry Collaboration: An Integral Element for Building “Omic” Resources
- David E. Hill,
- Michael A. Brasch,
- Anthony A. del Campo,
- Lynn Doucette-Stamm,
- James I. Garrels,
- Judith Glaven,
- James L. Hartley,
- James R. Hudson, Jr.,
- Troy Moore,
- and Marc Vidal
Genome Res. October 15, 2004 14: 2010-2014; doi:10.1101/gr.2771404
....H., Lockshon, D., Conover, D., Lanciault, C., Harris, J.R., Simmons, S.J., Rothstein, R., et al. 1997 . The complete set of predicted genes from Saccharomyces cerevisiae in a readily usable form. Genome Res. 7 : 1169 -1173. ↵ Ideker, T., Galitski, T., and Hood, L. 2001 . A new approach to decoding life...
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ARTICLE: Systematic Management and Analysis of Yeast Gene Expression Data
- John Aach,
- Wayne Rindone,
- and George M. Church
Genome Res. April 1, 2000 10: 431-445; doi:10.1101/gr.10.4.431
...(Fig. 2 b, step 2) which presents information fields and Measures available on the database for the selected data sets, and the user chooses the ones he or she wishes to see. Here, the user has asked to see the information field SGDID ( Saccharomyces Genome Database identifier) ( Cherry et al. 1999...

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