Foox, Jonathan main content.

Jonathan Foox

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PhD Student, Richard Gilder Graduate School


2012–2016 PhD, Richard Gilder Graduate School, American Museum of Natural History

2007–2012 BA/MS, The George Washington University

Research Interests

I study the evolutionary genomics of Myxozoa, a bizarre assemblage of microscopic, oligocellular, obligate endoparasites of poikilothermic vertebrates such as fish and frogs as well as vermiform invertebrates such as oligochaetes. Despite their parasitic life strategy and extreme morphological degeneracy, myxozoans have been confirmed by recent studies to be highly reduced cnidarians, putatively sister to Medusozoa (e.g., jellyfish, hydras, box jellies). Using newly generated transcriptomic data from several myxozoan species, I am exploring in a comparative framework the genetic transition to parasitism of this lineage, the functional genetics of cnidarian features such as polar capsules (homologous to cnidae) and metazoan features such as cellular communication, and the phylogenetic position of Myxozoa within Cnidaria.

My research also focuses on computational biological pipelining. Using Python, R, and SQL databasing, I have written several bioinformatic workflows for the handling and interpretation of genomic data, including a software package for phylogenetic analysis and functional annotation of gene family content across a set of user-specified genomes.



Foox J, Ringuette M, Desser SS, Siddall ME. In silico hybridization enables transcriptomic illumination of the nature and evolution of Myxozoa. BMC Genomics, 16:840

Rosenfeld JA, Reeves D, Brugler MR, Narechania A, Simon S, Kolokotronis S, Durret R, Foox J, …, Mason C. Genome assembly, annotation, and geospatial phylogenomics of the bedbug (Cimex lecularius). Nature Communications, in press

Rosenfeld JA, Foox J, DeSalle R. Insect genome content phylogeny and functional annotation of core insect genomes. Molecular Phylogenetics and Evolution, in press

Foox J, Brugler MR, Siddall ME, Rodriguez E. Multiplexed Pyrosequencing of Nine Sea Anemone (Cnidaria: Anthozoa: Hexacorallia: Actiniaria) Mitochondrial Genomes. Mitochondrial DNA, 2015:1-7

Foox J, Siddall ME. The Road to Cnidaria: History of Phylogeny of the Myxozoa. Journal of Parasitology, 101:269-274

Teaching Experience

  • 2014 Teaching assistant, Richard Gilder Gradute School, American Museum of Natural History. Course: Next Generation Sequencing.
  • 2013 Teaching assistant, Department of Ecology, Evolution, and Environmental Biology, Columbia University. Course: Environmental Biology.
  • 2012 Teaching assistant, Department of Biological Sciences, The George Washington University. Courses: Introductory Bio: Cells & Molecules, Invertebrate Zoology. Created, taught, and graded lab sessions, assignments, and exams.