About

I am a post-doctoral researcher in the field of computational biology at the University of Oregon in the Cresko Lab.

Research Interests

My primary research focuses on the evolution of the genome and I am currently at work identifying large structural variation in populations of threespine stickleback. I am using a synthesis of genetic mapping, genome assembly, and mate-pair sequencing to search for large scale structural variation in marine and freshwater sticklebacks.

To enable much of my experimental work, I have written Stacks, a parallelized software system that can assemble and genotype tens of thousands of restriction enzyme-based markers in thousands of individuals. Stacks can be used to develop ultra dense genetic maps, or it can be used to identify evolutionarily divergent segments of the genome using population genomic statistics such as π and F_ST.

In my previous work as a graduate student I developed the Synteny Database to detect conserved synteny (conserved gene neighborhoods between organisms). 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.

• Stacks can be found here.
• The Synteny Database and its associated tools can be found here.

Media

• I was recently interviewed on the Molecular Ecologist blog about the internal workings of Stacks: Part 1 and Part 2.

Publications

• J. Catchen, P. Hohenlohe, S. Bassham, A. Amores, and W. Cresko. Stacks: an analysis tool set for population genomics. Molecular Ecology. 2013. [reprint]
• J. Catchen, S. Bassham, T. Wilson, M. Currey, C. O’Brien, Q. Yeates, and W. Cresko. The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing. Molecular Ecology. 2013. [reprint]
• M. Schartl, R. Walter, Y. Shen, T. Garcia, J. Catchen, A. Amores, I. Braasch, D. Chalopin, J. Volff, K. Lesch, A. Bisazza, P. Minx, L. Hillier, R. Wilson, S. Fuerstenberg, J. Boore, S. Searle, J. Postlethwait, and W. Warren. The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits. Nature Genetics. 45:567-572, 2013. [reprint]
• J. Catchen, A. Amores, P. Hohenlohe, W. Cresko, and J. Postlethwait. Stacks: building and genotyping loci de novo from short-read sequences. G3: Genes, Genomes, Genetics, 1:171-182, 2011. [reprint]
• A. Amores, J. Catchen, A. Ferrara, Q. Fontenot and J. Postlethwait. Genome evolution and meiotic maps by massively parallel DNA sequencing: Spotted gar, an outgroup for the teleost genome duplication. Genetics, 188:799-808, 2011. [reprint]
• J. Davey, P. Hohenlohe, P. Etter, J. Boone, J. Catchen and M. Blaxter. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics, 12:499-510. 2011. [reprint]
• Y. Shen, J. Catchen, T. Garcia, A. Amores, I. Beldortha, J. Wagnera, Z. Zhang, J. Postlethwait, W. Warren, M. Schartl, R. Walter. Identification of transcriptome SNPs between Xiphophorus lines and species for assessing allele specific gene expression within F1 interspecies hybrids Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology. In Press. 2011. [reprint]
• T. Garcia, Y. Shen, J. Catchen, A. Amores, M. Schartl, J. Postlethwait, R. Walter. Effects of short read quality and quantity on a de novo vertebrate transcriptome assembly. Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology. In Press. 2011. [reprint]
• P. Hohenlohe, S. Amish, J. Catchen, F. Allendorf, G. Luikart. RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow trout and westslope cutthroat trout. Molecular Ecology Resources, 11: 117-122. 2011. [reprint]
• K. Emerson, C. Merz, J. Catchen, P. Hohenlohe, W. Cresko, W. Bradshaw, C. Holzapfel. Resolving postglacial phylogeography using high-throughput sequencing. Proceedings of the National Academy of Science, 107(37):16196-200, 2010. [reprint]
• B. Eames, A. Singer, G. Smith, Z. Wood, J. Catchen, Y.-L. Yan, X. He, J. Polizzi, A. Rodríguez-Marí, T. Linbo, D. Raible, J. Postlethwait. Uxs1 is required for proper morphogenesis and histogenesis of the craniofacial skeleton. Developmental Biology, 341(2):400-15, 2010. [reprint]
• 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. The Journal of Immunology, 183(9):5896-5908 2009. [reprint]
• 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, 19:1497-1505. 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, 314B(1):33-56, 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, J. Conery, and J. Postlethwait. Inferring Ancestral Gene Order. Methods in Molecular Biology. 452: 365-383, 2008. [reprint]
• J. Conery, J. Catchen, and M. Lynch. Rule-based workflow management for bioinformatics. VLDB Journal 14(3): 318-329, 2005. [reprint]

Presentations

• J. Catchen, A. Amores, P. Hohenlohe, K. Emerson, W. Cresko, J. Postlethwait. Generating markers from short-read, de novo RAD-Tags for genetic mapping and phylogenetics. Talk. EVO-WIBO, Port Townsend, WA, April 24, 2010.
• 
  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.
• 
  Catchen, Julian M., Conery, John S., and Postlethwait, John H. Inferring Ancestral Chromosomes. Poster. NSF IGERT Minisymposium Indiana University, Bloomington, IN. October 7, 2006.

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

Last Updated: Fri May 24 17:36:21 PST 2013