About
I am a post-doctoral researcher in the field of computational biology at the University of Oregon. I am a member of the Institute of Neuroscience, where I perfrom my day-to-day work in the Postlethwait Lab.
Researh 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, in order to define regions of conserved synteny.
- The Synteny Database and its associated tools can be found here.
Publications
- C. Sullivan, J. Charette, J. Catchen, C. Lage, G. Giasson, J. Postlethwait, P. Millard, and C. Kim. The gene history of zebrafish tlr4a and tlr4b is predictive of divergent functions. Submitted, 2009.
- J. Catchen. Automated Methods to Infer Ancient Homology and Synteny. Diss. University of Oregon, 2009. [reprint]
- 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]
Education
- Ph.D. in Computer Science from the University of Oregon, 2009
- M.S. in Computer Science from the University of Oregon, 2006
- B.S. in Computer Science from Pennsylvania State University, 2000