Searching journal content for articles similar to Tanay et al. 14 (5): 829.

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  1. Research: Tempo and mode of regulatory evolution in Drosophila
    • Joseph D. Coolon,
    • C. Joel McManus,
    • Kraig R. Stevenson,
    • Brenton R. Graveley,
    • and Patricia J. Wittkopp
    Genome Res. May 2014 24: 797-808; Published in Advance February 24, 2014, doi:10.1101/gr.163014.113
    ...selection acting to maintain similar expression levels in the face of new mutations, and has been seen not only in flies, but also in yeast (Tirosh et al. 2009), mice (Goncalves et al. 2012), and plants (Shi et al. 2012).Compensation for cis-regulatory divergence resulting from the fixation of trans...
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  2. Method: A unified model for yeast transcript definition
    • Carl G. de Boer,
    • Harm van Bakel,
    • Kyle Tsui,
    • Joyce Li,
    • Quaid D. Morris,
    • Corey Nislow,
    • Jack F. Greenblatt,
    • and Timothy R. Hughes
    Genome Res. January 2014 24: 154-166; Published in Advance October 29, 2013, doi:10.1101/gr.164327.113
    ...the sequences and factors involved, there has been no global examination of which features are critical to yeast gene identity, and therefore, the problem of how yeast (or any other eukaryote) delineates transcription units remains an open question. Many programs to identify genes in genomic DNA exist (e...
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  3. RESOURCE: An effective model for natural selection in promoters
    • Michael M. Hoffman and
    • Ewan Birney
    Genome Res. May 2010 20: 685-692; Published in Advance March 1, 2010, doi:10.1101/gr.096719.109
    ...analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat Genet 36: 1331–1339. Mustonen V, Kinney J, Callan CG, La¨ssig M. 2008. Energy-dependent fitness: A quantitative model for the evolution of yeast transcription factor binding sites. Proc Natl Acad Sci 105: 12376...
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  4. Research: Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus
    • Eli Rodgers-Melnick,
    • Shrinivasrao P. Mane,
    • Palitha Dharmawardhana,
    • Gancho T. Slavov,
    • Oswald R. Crasta,
    • Steven H. Strauss,
    • Amy M. Brunner,
    • and Stephen P. DiFazio
    Genome Res. January 2012 22: 95-105; Published in Advance October 5, 2011, doi:10.1101/gr.125146.111
    ...retention of WGD pairs while disfavoring the fixation of TD. Indeed, empirical data in yeast and Arabidopsis demonstrate that genes involved in signal transduction and transcription are more likely to be retained following a WGD but less likely to be retained in tandem (Seoighe and Gehring 2004; Davis...
  5. ARTICLE: Extensive low-affinity transcriptional interactions in the yeast genome
    • Amos Tanay
    Genome Res. August 2006 16: 962-972; Published in Advance June 29, 2006, doi:10.1101/gr.5113606
    ...possible weak loci. To test if such selection exists, I used orthologous yeast promoters and developed a conservation score that compares the observed evolutionary changes in the total predicted promoter binding energy to those expected under a neutral model (Methods). The analysis therefore tested...
  6. ARTICLE: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    • Adam Siepel,
    • Gill Bejerano,
    • Jakob S. Pedersen,
    • Angie S. Hinrichs,
    • Minmei Hou,
    • Kate Rosenbloom,
    • Hiram Clawson,
    • John Spieth,
    • LaDeana W. Hillier,
    • Stephen Richards,
    • George M. Weinstock,
    • Richard K. Wilson,
    • Richard A. Gibbs,
    • W. James Kent,
    • Webb Miller,
    • and David Haussler
    Genome Res. August 2005 15: 1034-1050; Published in Advance July 15, 2005, doi:10.1101/gr.3715005
    ...for alignment coverage in coding regions, yielding 56% for the worm data set and 68% for the insects and yeasts. The degree of “smoothing” of the phylo-HMM was also constrained by forcing the expected amount of phylogenetic information (in an information theoretic sense) required to predict a conserved element...
  7. LETTER: Selection-driven transcriptome polymorphism in Escherichia coli/Shigella species
    • Tony Le Gall,
    • Pierre Darlu,
    • Patricia Escobar-Páramo,
    • Bertrand Picard,
    • and Erick Denamur
    Genome Res. February 2005 15: 260-268; doi:10.1101/gr.2405905
    ...difference between trees at 18, and by the corresponding distance matrixes (the probability of incongruence is not rejected at P = 0.18 in the Mantel test). These results argue in favor of convergence in the pattern of global gene expression for Shigella /EIEC, a hallmark for adaptive evolution ( Harvey...
  8. ARTICLE: Genome-wide regulatory complexity in yeast promoters: Separation of functionally conserved and neutral sequence
    • Chen-Shan Chin,
    • Jeffrey H. Chuang,
    • and Hao Li
    Genome Res. February 2005 15: 205-213; Published in Advance January 14, 2005, doi:10.1101/gr.3243305
    ...; Tanay et al. 2004 ). Although a number of transcription factors and binding motifs have been studied in detail, some basic parameters of transcriptional regulation are not known. One important feature that has not been characterized is the amount of functional sequence under purifying selection in yeast...
  9. LETTER: Evolution of the mammalian transcription factor binding repertoire via transposable elements
    • Guillaume Bourque,
    • Bernard Leong,
    • Vinsensius B. Vega,
    • Xi Chen,
    • Yen Ling Lee,
    • Kandhadayar G. Srinivasan,
    • Joon-Lin Chew,
    • Yijun Ruan,
    • Chia-Lin Wei,
    • Huck Hui Ng,
    • and Edison T. Liu
    Genome Res. November 2008 18: 1752-1762; Published in Advance August 5, 2008, doi:10.1101/gr.080663.108
    ...405 : 486 – 489 . ↵ Ihmels, J. , Bergmann, S. , Gerami-Nejad, M. , Yanai, I. , McClellan, M. , Berman, J. , Barkai, N. ( 2005 ) Rewiring of the yeast transcriptional network through the evolution of motif usage . Science 309 : 938 – 940 . ↵ Ivanova, N. , Dobrin, R. , Lu, R. , Kotenko, I. , Levorse, J...
  10. LETTER: cis-Regulatory and Protein Evolution in Orthologous and Duplicate Genes
    • Cristian I. Castillo-Davis,
    • Daniel L. Hartl,
    • and Guillaume Achaz
    Genome Res. August 2004 14: 1530-1536; Published in Advance July 15, 2004, doi:10.1101/gr.2662504
    ...in yeast (using only duplicates) yielded contradictory results; one study argued that expression differences are not correlated with protein evolution ( Wagner 2000 ), whereas more recent work suggests a weak correlation ( Gu et al. 2002 ). However, a recent review ( Wolfe and Li 2003 ) concluded...
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