• Publications
  • Influence
Drift-barrier hypothesis and mutation-rate evolution
Mutation dictates the tempo and mode of evolution, and like all traits, the mutation rate is subject to evolutionary modification. Here, we report refined estimates of the mutation rate for aExpand
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A proposed superfamily of transposase genes: transposon-like elements in ciliated protozoa and a common "D35E" motif.
The transposon-like elements TBE1, Tec1, and Tec2 of hypotrichous ciliated protozoa appear to encode a protein that belongs to the IS630-Tc1 family of transposases. The Anabaena IS895 transposaseExpand
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A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes
  • Y. Ye, T. Doak
  • Biology, Computer Science
  • PLoS Comput. Biol.
  • 1 August 2009
We developed a parsimony approach, called MinPath (Minimal set of Pathways), for biological pathway reconstructions using protein family predictions, which yields a more conservative, yet more faithful, estimation of the biological pathways for a query dataset. Expand
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RNA-mediated epigenetic programming of a genome-rearrangement pathway
Genome-wide DNA rearrangements occur in many eukaryotes but are most exaggerated in ciliates, making them ideal model systems for epigenetic phenomena. During development of the somatic macronucleus,Expand
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The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development
Programmed DNA rearrangements in the single-celled eukaryote Oxytricha trifallax completely rewire its germline into a somatic nucleus during development. This elaborate, RNA-mediated pathwayExpand
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Extraordinary genome stability in the ciliate Paramecium tetraurelia
Mutation plays a central role in all evolutionary processes and is also the basis of genetic disorders. Established base-substitution mutation rates in eukaryotes range between ∼5 × 10−10 and 5 ×Expand
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STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq
Motivation Fusion genes created by genomic rearrangements can be potent drivers of tumorigenesis. However, accurate identification of functionally fusion genes from genomic sequencing requires wholeExpand
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Developmental precise excision of Oxytricha trifallax telomere‐bearing elements and formation of circles closed by a copy of the flanking target duplication.
The 4.1 kbp TBE1 elements of Oxytricha fallax and Oxytricha trifallax are deduced to transpose into a centrisymmetric target, CAnTG, and to duplicate the central AnT. Despite conserved C(A4C4)2Expand
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The Spontaneous Mutation Rate in the Fission Yeast Schizosaccharomyces pombe
The rate at which new mutations arise in the genome is a key factor in the evolution and adaptation of species. Here we describe the rate and spectrum of spontaneous mutations for the fission yeastExpand
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The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes
With more chromosomes than any other sequenced genome, the macronuclear genome of Oxytricha trifallax has a unique and complex architecture, including alternative fragmentation and predominantlyExpand
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