Julian Catchen
catchen@cs.uoregon.edu

University of Oregon
Institute of Neuroscience
1254 University of Oregon
Eugene, OR 97403-1254 USA

Advisors:
John Conery Department of Computer and Information Science
John Postlethwait Institute of Neuroscience

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Research Interests

Several times in the history of life whole-genome duplication events played a significant role in shaping organismal evolution. In addition to the two rounds of genome duplication that occurred near the time of the vertebrate radiation, an additional round of genome duplication occurred at the base of the radiation of teleost fish (the crown group of ray-fin fish, like zebrafish, and pufferfish, distinct from basally diverging ray-fin fish, like sturgeon and gar). This third whole-genome event generated duplicate chromosome segments in teleosts corresponding to single chromosome segments in humans and other mammals. For example, teleosts possess two copies of the human HOXA cluster (hoxaa and hoxab) surrounded by duplicate copies of many additional genes on the homeologous chromosomes.

This conservation of genomic structure provides information about organismal origin and change over time. My research interests include investigating this conservation through a high-volume, automated analysis of genomic data, applying fundamental Computer Science principles such as data mining, search, tree construction, and parallelism to the study of these evolutionary forces. My primary research project involves the identification and characterization of co-ortholog genes and their corresponding chromosome segments in zebrafish.

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Publications

J. Catchen, J. Conery, and J. Postlethwait. Automated identification of conserved synteny after whole genome duplication. Genome Research, In Press. 2009. [reprint]

R. Jovelin, Y. Yan, X. He, J. Catchen, A. Amores, H. Yokoi, C. Canestro, J. Postlethwait. Evolution of developmental regulation in the vertebrate FgfD subfamily. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, In Press. 2009. [reprint]

C. Canestro, J. Catchen, A. Rodriguez-Mari, H. Yokoi, and J. Postlethwait. Consequences of lineage-specific gene loss gene loss on functional evolution of surviving ohnologs in vertebrate genomes: ALDH1A and retinoic acid signaling. PLoS Genetics, 5(5):e1000496, 2009. [reprint]

H. Yokoi, Y. Yan, M. Miller, R. BreMiller, J. Catchen, E. Johnson, and J. Postlethwait. Expression profiling of zebrafish sox9 mutants reveals that Sox9 is required for retinal differentiation. Developmental Biology. 329(1):1-15, 2009. [reprint]

J. Bridgham, J. Brown, A. Rodriguez-Mari, J. Catchen, J. Thornton. Evolution of a new function by degenerative mutation in cephalochordate steroid receptors. PLoS Genetics 4(9):e1000191, 2008. [reprint]

J. Catchen, X. Li, J. Postlethwait, and J. Conery. Automated Methods to Identify Conserved Synteny. Poster. NSF IGERT Minisymposium. University of Oregon, Eugene, OR. April 5, 2008.

J. Catchen, J. Conery, and J. Postlethwait. Inferring Ancestral Gene Order. Methods in Molecular Biology. 452: 365-383, 2008. [reprint]

Catchen, Julian M., Conery, John S., and Postlethwait, John H. Inferring Ancestral Chromosomes. Poster. NSF IGERT Minisymposium Indiana University, Bloomington, IN. October 7, 2006.

J. Conery, J. Catchen, and M. Lynch. Rule-based workflow management for bioinformatics. VLDB Journal 14(3): 318-329, 2005. [reprint]