Journal of Artificial Intelligence Research, May 1, 2008
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tre... more A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called supertrees, whilst respecting the relationships in the original trees. A rooted tree exhibits an ultrametric property; that is, for any three leaves of the tree it must be that one pair has a deeper most recent common ancestor than the other pairs, or that all three have the same most recent ...
Proceedings of the 5th ACM/IEEE-CS joint conference on Digital libraries - JCDL '05, 2005
We demonstrate the Edition Production Technology (EPT), an integrated development environment for... more We demonstrate the Edition Production Technology (EPT), an integrated development environment for building Image-based Electronic Editions (IBEE). EPT is developed in Java on top of Eclipse platform and benefits from the openness of Eclipse's plugin architecture and its portability (currently EPT runs on Windows XP, Linux, and Mac OS X). EPT provides software support for building image-based digital libraries of historic documents. Starting with high resolution images of manuscripts and transcriptions of them, EPT tools provide support for creating XML encoding of the electronic edition, searching the electronic edition, linking text and images, and publishing the electronic edition (using filters and XSLT).
The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psy... more The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some-including the infamous ergot alkaloids-have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses.
Image-based electronic editions enable researchers to view and study in an electronic environment... more Image-based electronic editions enable researchers to view and study in an electronic environment historical manuscript images intricately linked to edition, transcript, glossary and apparatus files. Building image-based electronic editions poses a two-fold challenge. For humanities scholars, it is important to be able to use image and text to successfully encode the desired features of the manuscripts. Computer Scientists must find mechanisms for representing markup in its association both with the images, text and other auxiliary files and for making the representation available for efficient querying. This paper addresses the architecture of one such solution, that uses efficient data structures to store image-based encodings in main memory and on disk.
We propose a statistical method to test whether two phylogenetic trees with given alignments are ... more We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing point estimations of trees. This statistical approach can be applied to gene tree analysis for example, detecting unusual events in genome evolution such as horizontal gene transfer and reshuffling. Our method uses difference of means to compare two distributions of trees, after embedding trees in a vector space. Bootstrapping alignment columns can then be applied to obtain p-values. To compute distances between means, we employ a "kernel trick" which speeds up distance calculations when trees are embedded in a high-dimensional feature space, e.g. splits or quartets feature space. In this pilot study, first we test our statistical method's ability to distinguish between sets of gene trees generated under coalescence models with species trees of varying dissimilarity. We follow our simulation results with applications to various data sets of gophers and lice, grasses and their endophytes, and different fungal genes from the same genome. A companion toolkit, Phylotree, is provided to facilitate computational experiments.
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Papers by Neil Moore