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    PerfectGenes2012slid
    (2012-05) Gilbert, Don
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    PerfectGenes2012post
    (2012-05) Gilbert, Don
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    PerfectGenes2010
    (2010-06) Gilbert, Don
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    Gene-omes built from mRNA-seq not genome DNA
    (2013-06) Gilbert, Don
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    Evigene_GalxGmod2016
    (2016-07) Gilbert, Don
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    Unlocated Arthropod genes, and ways to find them
    (2008-04) Gilbert, Don
    The Daphnia pulex genome is rich in tandem duplicate genes, some 20% of its 30,000+ genes. However some gene predictors have missed or incorrectly located almost half of these. Estimates from genome-wide tile expression suggest an additional 5,000 genes have been missed. Gene prediction for new genomes such as this first crustacean is still an uncertain task. Even in clades with a well-characterized model such as Drosophila, gene finding remains an uncertain task. Prediction tools are increasingly sophisticated and accurate. Today's methods draw on the range of available gene evidence and improved modeling of gene structures. Yet they are sensitive to available gene data and expected structures. They find well-known genes, but fail at accurate detection of novel and diverged genes. Measures from gene duplication and genome-wide tile expression can more accurately locate those genes missed by other methods. Computational methods are being developed to turn these signals to accurate gene models. Application of these methods to arthropod genomes, including Daphnia and Drosophila, uncovers some 10% to 25% additional species specific and diverged genes. This work includes development of new automated genome analysis pipelines on NSF TeraGrid shared cyberinfrastructure, as part of the Generic Model Organism Database project.
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    Aphid and Water flea have a High Rate of Gene Duplications Compared to Other Arthropods 2009
    (2009-06) Gilbert, Don
    Comparison of gene orthology and paralogy groups among thirteen arthropod genomes (insects.eugenes.org/arthropods/) finds the pea aphid Acyrthosiphon pisum and the water flea Daphnia pulex, both cyclical asexuals, have four times the gene duplications of other arthropods. These duplicates are not from whole genome duplication, and artifacts do not account for this. Gene models for these 13 arthropod genomes are summarized in Fig 2 in categories of orthologs or species unique, duplicate paralogs or singleton genes. This indicates the large difference in gene counts from 16,000 in dipterans to over 30,000 in Aphid and Daphnia. The main effects for high versus low gene count appear to be paralogs. Aphid has 2,475 genes in 625 groups compared to 621 average insect genes, a rate of 3.8 to 1. Daphnia has 2,621 duplicated genes in 589 groups, compared to 610 average insect genes, a rate of 4.4 to 1. These two species are also abundant in genes in many groups that lack homology (Fig. 2B).