The origins of genome complexity

Lynch, Michael, Conery, John S.·2003·Science

Cited by (1,002)

Items 801–900 of 1,002

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    Andrew H. Paterson, X. Wang, Haibao Tang, T. H. Lee · 2012 · Springer eBooks
  2. Endogenous Mechanisms for the Origins of Spliceosomal Introns
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  3. GENOMICS IN THE LIGHT OF EVOLUTIONARY TRANSITIONS
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  4. Position of the Final Intron in Full-Length Transcripts: Determined by NMD?
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  9. Density dependent expression of a diatom retrotransposon
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  10. A Dynamic Mobile DNA Family in the Yeast Mitochondrial Genome
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  18. Gene Transfer and the Reconstruction of Life’s Early History from Genomic Data
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  22. Within-population genome size variation is mediated by multiple genomic elements that segregate independently during meiosis
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  89. Rates and Patterns of Mutation in Tandem Repetitive DNA in Six Independent Lineages of Chlamydomonas reinhardtii
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  90. ΦX174 Attenuation by Whole-Genome Codon Deoptimization
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  92. Mutation Rates: How Low Can You Go?
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  93. Duplicate gene enrichment and expression pattern diversification in multicellularity
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  94. Tropical Africa as a cradle for horizontal transfers of transposable elements between species of the genera Drosophila and Zaprionus
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  95. Variation in gene duplicates with low synonymous divergence in Saccharomyces cerevisiae relative to Caenorhabditis elegans
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  98. Interconversion of Germline-Limited and Somatic DNA in a Scrambled Gene
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  99. Polymorphix: a sequence polymorphism database
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