7 Result(s)
within
Tim Massingham
English
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Article
Open AccessError-correcting properties of the SOLiD Exact Call Chemistry
The Exact Call Chemistry for the SOLiD Next-Generation Sequencing platform augments the two-base-encoding chemistry with an additional round of ligation, using an alternative set of probes, that allows some mi...
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Article
Open AccessAll Your Base: a fast and accurate probabilistic approach to base calling
The accuracy of base calls produced by Illumina sequencers is adversely affected by several processes, with laser cross-talk and cluster phasing being prominent. We introduce an explicit statistical model of t...
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Article
Open AccessA high-resolution map of human evolutionary constraint using 29 mammals
The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the ...
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Article
Open AccessPhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment
The Monte Carlo simulation of sequence evolution is routinely used to assess the performance of phylogenetic inference methods and sequence alignment algorithms. Progress in the field of molecular evolution fu...
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Article
Open AccessGenomic DNA k-mer spectra: models and modalities
The empirical frequencies of DNA k-mers in whole genome sequences provide an interesting perspective on genomic complexity, and the availability of large segments of genomic sequence from many organisms means tha...
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Article
Open AccessRelating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins
Gene duplications have been hypothesized to be a major factor in enabling the evolution of tissue differentiation. Analyses of the expression profiles of duplicate genes in mammalian tissues have indicated tha...
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Article
Open AccessRelationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins
The combination of complete genome sequence information with expression data enables us to characterize the relationship between a protein's evolutionary origin or functional category and its expression patter...
