Chih-Hao Hsu

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We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the(More)
Gene conversion events are often overlooked in analyses of genome evolution. In a conversion event, an interval of DNA sequence (not necessarily containing a gene) overwrites a highly similar sequence. The event creates relationships among genomic intervals that can confound attempts to identify orthologs and to transfer functional annotation between(More)
Many software tools for comparative analysis of genomic sequence data have been released in recent decades. Despite this, it remains challenging to determine evolutionary relationships in gene clusters due to their complex histories involving duplications, deletions, inversions, and conversions. One concept describing these relationships is orthology.(More)
In a wireless environment, the bandwidth of the channels and the energy of the portable devices are limited. Data broadcast has become an excellent method for efficient data dissemination. In this paper, the problem for generating a broadcast program of a set of data items with the associated access frequencies on multiple channels is explored. In our(More)
In a wireless environment, the bandwidth of the channels and the energy of the portable devices are limited. Data broadcast has become an excellent method for efficient data dissemination. In this paper, the problem for generating a broadcast program of a set of data items with the associated access frequencies on multiple channels is explored. In our(More)
Genomic intervals that contain a cluster of similar genes are of extreme biological interest, but difficult to sequence and analyze. One goal for interspecies comparisons of such intervals is to reconstruct a parsimonious series of duplications, deletions, and speciation events (a putative evolutionary history) that could have created the contemporary(More)
SUMMARY OmicCircos is an R software package used to generate high-quality circular plots for visualizing genomic variations, including mutation patterns, copy number variations (CNVs), expression patterns, and methylation patterns. Such variations can be displayed as scatterplot, line, or text-label figures. Relationships among genomic features in different(More)
In a wireless environment, the bandwidth of the channels and the energy of the portable devices are limited. Data broadcast has become an excellent method for efficient data dissemination. In this paper, the problem for generating a broadcast program of a set of data items with the associated access frequencies on multiple channels is explored. In our(More)