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LETTER: 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,
- and Munira A. Basrai
Genome Res. March 2006 16: 365-373; doi:10.1101/gr.4355406
..., M.A., Hieter, P., and Boeke, J.D. 1997 . Small open reading frames: Beautiful needles in the haystack. Genome Res. 7 : 768 –771. ↵ Basrai, M.A., Velculescu, V.E., Kinzler, K.W., and Hieter, P. 1999 . NORF5/HUG1 is a component of the MEC1-mediated checkpoint response to DNA damage and replication...
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LETTER: A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection
- Kousuke Hanada,
- Xu Zhang,
- Justin O. Borevitz,
- Wen-Hsiung Li,
- and Shin-Han Shiu
Genome Res. May 2007 17: 632-640; Published in Advance March 29, 2007, doi:10.1101/gr.5836207
...in the haystack . Genome Res. 7 : 768 – 771 . ↵ Bell, C.J. , Dixon, R.A. , Farmer, A.D. , Flores, R. , Inman, J. , Gonzales, R.A. , Harrison, M.J. , Paiva, N.L. , Scott, A.D. , Weller, J.W. , et al. ( 2001 ) The Medicago Genome Initiative: A model legume database . Nucleic Acids Res. 29 : 114 – 117 . ↵ Bennetzen...
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Perspective: Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship
- Marie A. Brunet,
- Sébastien A. Levesque,
- Darel J. Hunting,
- Alan A. Cohen,
- and Xavier Roucou
Genome Res. May 2018 28: 609-624; Published in Advance April 6, 2018, doi:10.1101/gr.230938.117
...relate phenotypes and genotypes.The now irrefutable existence of “alternative” proteinsRecent work has revealed that s harbor many nonannotated open reading frames (ORFs) (Vanderperre et al. 2011; Bergeron et al. 2013; Anderson et al. 2015; Mouilleron et al. 2016; D'Lima et al. 2017; Plaza et al. 2017...
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Method: An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics
- Ulrich Omasits,
- Adithi R. Varadarajan,
- Michael Schmid,
- Sandra Goetze,
- Damianos Melidis,
- Marc Bourqui,
- Olga Nikolayeva,
- Maxime Québatte,
- Andrea Patrignani,
- Christoph Dehio,
- Juerg E. Frey,
- Mark D. Robinson,
- Bernd Wollscheid,
- and Christian H. Ahrens
Genome Res. December 2017 27: 2083-2095; Published in Advance November 15, 2017, doi:10.1101/gr.218255.116
...repertoire of completely sequenced prokaryotic s. However, large discrepancies among the number of CDSs annotated by different resources, missed functional short open reading frames (sORFs), and overprediction of spurious ORFs represent serious limitations. Our strategy toward accurate and complete...
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Methods: Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations
- Gennifer E. Merrihew,
- Colleen Davis,
- Brent Ewing,
- Gary Williams,
- Lukas Käll,
- Barbara E. Frewen,
- William Stafford Noble,
- Phil Green,
- James H. Thomas,
- and Michael J. MacCoss
Genome Res. October 2008 18: 1660-1669; Published in Advance July 24, 2008, doi:10.1101/gr.077644.108
....A. , Hieter, P. , Boeke, J.D. ( 1997 ) Small open reading frames: Beautiful needles in the haystack . Genome Res. 7 : 768 – 771 . ↵ Brunner, E. , Ahrens, C.H. , Mohanty, S. , Baetschmann, H. , Loevenich, S. , Potthast, F. , Deutsch, E.W. , Panse, C. , de Lichtenberg, U. , Rinner, O. , et al. ( 2007 ) A high...
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LETTER: Parallel Identification of New Genes in Saccharomyces cerevisiae
- Guy Oshiro,
- Lisa M. Wodicka,
- Michael P. Washburn,
- John R. Yates III,
- David J. Lockhart,
- and Elizabeth A. Winzeler
Genome Res. August 1, 2002 12: 1210-1220; doi:10.1101/gr.226802
...mitochondrial F1F0-ATP synthase exists as a dimer: Identification of three dimer-specific subunits. Embo J 17 : 7170 – 7178 . ↵ Basrai M.A. , Hieter P. , Boeke J.D. ( 1997 ) Small open reading frames: Beautiful needles in the haystack. Genome Res. 7 : 768 – 771 . ↵ Basrai M.A. , Velculescu V.E. , Kinzler K...

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