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Some of our scientists' publications on informatics and partial-genome interpretations:

Alverson, A., S. K. Wyman, J. L. Boore and J. D. Palmer, 201x Annotation of plant mitochondrial genomes with Mitofy. Submitted.

Murtagh, V. J., D. O’meally, N. Sankovic, M. L. Delbridge, Y. Kuroki, J. L. Boore, A. Toyoda, K. S. Jordan, A. J. Pask, M. B. Renfree, A. Fujiyama, J. A. M. Graves and P. D. Waters, 2012 Evolutionary history of novel genes of the tammar wallaby Y chromosome: Implications for sex chromosome evolution. Genome Research, published online in advance of print (doi/10.1101/gr.120790.111).

O’Quin, K. E., D. Smith, Z. Naseer, J. Schulte, S. D. Engel, Y-H. E. Loh, J. T. Steelman, J. L. Boore and K. L. Carleton, 2011 Divergence in cis-regulatory sequences surrounding the opsin gene arrays of African cichlid fishes. BMC Evolutionary Biology 11: 120.

Baker, R. H., J. Morgan, X. Wang, J. L. Boore and G. S. Wilkinson, 2009 Genomic analysis of a sexually-selected character: EST sequencing and microarray analysis of eye-antennal imaginal discs in the stalk-eyed fly Teleopsis dalmanni (Diopsidae). BMC Genomics 10: 361.

Boore, J. L., 2008 Detecting evolutionary transfer of genes using PhIGs. Journal of Phycology 44: 19-22.

Simison, W. B., and J. L. Boore, 2008 Molluscan evolutionary genomics, in Phylogeny and Evolution of the Mollusca (W. Ponder and D. Lindberg, eds.) University of California Press, Berkeley, CA, pp. 447-461.

Anderson, S. J., C. L. Stone, M. Lucia Posada-Buitrago, J. L. Boore, B. A. Neelam, R. M. Stephens, D. G. Luster, R. D. Frederick and K. F. Pedley, 2008 Development of simple sequence repeat markers for the soybean rust fungus, Phakopsora pachyrhizi. Molecular Ecology Resources 8: 1310-1312.

Mueller, R. L., T. R. Gregory, S. M. Gregory, A. Hsieh and J. L. Boore, 2008 Genome size, cell size, and the evolution of enucleated erythrocytes in attenuate salamanders. Journal of Zoology 111: 218-230.

Field, D., G. Garrity, T. Gray, N. Morrison, J. Selengut, P. Sterk, T. Tatusova, N. Thomson, M. Allen, S. V. Angiuoli, M. Ashburner, N. Axelrod, S. Baldauf, S. Ballard, J. L. Boore, G. Cochrane, J. Cole, P. Dawyndt, P. de Vos, C. de Pamphilis, R. Edwards, N. Faruque, R. Feldman, J. Gilbert, P. Gilna, F. O. Glöckner, P. Goldstein, R. Guralnick, D. Haft, D. Hancock, H. Hermjakob, C. Hertz-Fowler, P. Hugenholtz, I. Joint, L. Kagan, M. Kane, J. Kennedy, G. Kowalchuk, R. Kottmann, E. Kolker, S. Kravitz, N. Kyripides, J. Leebens-Mack, S. Lewis, K. Li, A. Liste, P. Lord, N. Maltsev, V. Markowitz, J. Martiny, B. Methe, R. Moxon, K. Nelson, J. Parkhill, L. Proctor, S. Sansone, A. Spiers, R. Stevens, P. Swift, C. Taylor, Y. Tateno, A. Tett, S. Turner, D. Ussery, B. Vaughan, N. Ward, T. Whetzel, G. Wilson and A. Wipat, 2008 The minimum information about a genome sequence (MIGS) specification. Nature Biotechnology 26: 541-547.

Hoegg, S., J. V. Kuehl, J. L. Boore and A. Meyer, 2007 Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni. BMC Genomics 8: 317.

Boore, J. L., 2006 Requirements and standards for organelle genome databases. OMICS 10: 119-126.

Dehal, P., and J. L. Boore, 2006 A phylogenomic gene cluster resource: The Phylogenetically Inferred Groups (PhIGs) database. BMC Bioinformatics 7: 201.

Dehal, P., and J. L. Boore, 2005 Two rounds of genome duplication in the ancestral vertebrate genome. PLoS Biology 3: e314.

Wyman, S., R. K. Jansen and J. L. Boore, 2004 Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252-3255.

Bensasson, D., J. L. Boore and K. M. Nielsen, 2004 Genes without frontiers? Journal of Heredity 92: 483-489.

Wyman, S. K., and J. L. Boore, 2003 Annotating animal mitochondrial tRNAs: An experimental evaluation of four methods. In Proceedings of the European Conference on Computational Biology (ECCB), pp. 44-46.

Santini, S., J. L. Boore and A. Meyer, 2003 Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters. Genome Research 13: 1111-1122.


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