Peer Reviewed Publications



Grant J.R., Katz LA. Building a Phylogenomic Pipeline for the Eukaryotic Tree of Life – Addressing Deep Phylogenies with Genome-Scale Data. PLOS Currents Tree of Life. 2014 Apr 2. Edition 1. doi: 10.1371/currents.tol.c24b6054aebf36.02748ac042ccc8f2e9.

Grant, J.R., Lahr, D.J.G, Rey, F.E., Gordon, J.I., Knight, R., Molestina, R.E., and L. A. Katz. Gene discovery in the transcriptomes of three diverse microbial eukaryotes: Corallomyxa tenera, Chilodonella uncinata, and Subulatomonas tetraspora. Submitted.

Katz, LA, LW Parfrey, J. R.Grant, JG Burleigh. 2012. Turning the crown upside down: gene tree parsimony roots the eukaryotic tree of life. Syst Biol.

Lahr, D. J. G., Grant, J. R., Nguyen, T., Lin, J.H. and L. A. Katz. 2011. Comprehensive Phylogenetic Reconstruction of Amoebozoa Based on Concatenated Analyses of SSUrDNA and Actin Gene. PLOS One. 6(7).

Katz, L. A., Grant, J. R., Parfrey, L. W., Gant, A., O'Kelley, C. J., Anderson, O. R., Molestina, R. E. & Nerad, T. 2011. Subulatomonas tetraspora nov. gen. nov. sp. is a member of a previously unrecognized major clade of eukaryotes. Protist.

Lahr, D. J. G., E. Barbero, J. R. Grant, and L.A. Katz. 2011. Evolution of the actin gene family in testate lobose amoebae (Arcellinida) is characterized by 2 distinct clades of paralogs and recent independent expansions. Mol. Biol. Evol. 28(1):223-36

Parfrey, L. W., J. R. Grant, Y. I. Tekle, E. Lasek-Nesselquist, H. G. Morrison, M. L. Sogin, D. J. Patterson, and L. A. Katz. 2010. Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life.  Syst. Biol.

Tekle, Y. I., Grant J.R., Kovner, A., L.A. Katz. 2010. Identification of new molecular markers for assembling the eukaryotic tree of life. Mol Phylogenet Evol.

Cole J., Andersen O.R., Tekle Y. I., J.R. Grant, Katz L. A., and T. Nerad. 2010. A description of a new ‘Amoebozoa’ isolated from the American Lobster, Homarus americanus. J. Euk. Micro.

Grant J.R., Tekle, Y.I., O.R. Anderson, Patterson D.J., and L.A. Katz. 2009. Multigene evidence for the placement of a heterotrophic amoeboid lineage Leukarachnion sp. among photosynthetic stramenopiles. Protist. 160: 376—385.

Tekle, Y.I., J.R. Grant, L. O.R. Anderson, J.C. Cole, T. Nerad, and L.A. Katz. 2008. Phylogenetic placement of diverse amoebae inferred from multigene analyses and assessment of clade stability within ‘Amoebozoa’ upon removal of varying rate classes of SSU-rDNA. Mol. Phylo. Evol. 47: 339-352.

Yoon, H-S, J.R. Grant, Y.I. Tekle, M. Wu, B.C. Chao, J.C. Cole, J.M. Logsdon, D.J. Patterson, D. Bhattacharya, and L.A. Katz. 2008. Broadly sampled multigene tree of eukaryotes. BMC Evol Biol. 8: 14.

ABOUT ME

I am a molecular biologist and an enthusiastic python coder

My CV

PRODUCTS

My products include Python scripts that address quality control of next gen sequence assemblies, and a pipeline that integrates custom scripts and third party software to streamline phylogenetic analyses.

I have developed products to run on a HPC and on the Amazon AWS cloud.

Peer Reviewed Publications

Let's work together to see what I can produce for you.

SKILLS
  • Data analysis and interpretation
  • Next gen sequence assembly and analysis
  • Python scripting
  • Manipulating large datasets
  • Genome annotation
  • Phylogenetics/phylogenomics
  • Training and teaching