JCVI: About / Bios / Jonathan Badger
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Jonathan Badger, Ph.D.
Assistant Professor

Research Interests and Accomplishments

Dr. Jonathan Badger is a Staff Scientist in the Microbial and Environmental Genomics department of JCVI and has been so since 2003. His research focuses on the evolution and phylogeny of microbes with a focus on marine microorganisms. He has created bioinformatics tools, lead genome projects, and performed comparative genomic studies.

He is the creator of the APIS (Automatic Phylogenetic Inference System) which creates and interprets phylogenetic trees for a set of ORFs (generally the predicted peptides from a genomic or metagenomic project). He is also developing other tools such as CAGE (Comparative Algal Genomic Environment) as well as being the JCVI PI for the Teredinibacter turnerae, Streptomyces turgidiscabies, and Streptomyces ipomoeae genome projects and co-PI (with Andy Allen) on two phytoplankton EST projects. He is also involved in the analysis of the Global Ocean Survey data and in the analysis of various environmental 16S/18S ribosomal RNA projects.

Prior to joining JCVI/TIGR, Dr. Badger worked in the bioinformatics department of Montreal, Quebec based Caprion Pharmaceuticals (from 2001-2003) where he worked on methods for analyzing tandem mass spectra of peptides. He was a postdoc of Ming Li and Paul Kearney at the University of Waterloo in 1999-2000 where he worked on methods of phylogenetic inference, and received his doctorate from Gary Olsen's lab at the University of Illinois where he worked on genomic analysis (including creating the early prokaryotic gene finder CRITICA).

Select Publications

Zeigler Allen L, Allen EE, et al.
Influence of Nutrients and Currents on the Genomic Composition of Microbes Across an Upwelling Mosaic.

The ISME Journal. 2012 Jul 01; 6: 1403-14.[more]

Badger, J. H., Hoover, T. R., et al.
Comparative Genomic Evidence for a Close Relationship Between the Dimorphic Prosthecate Bacteria Hyphomonas neptunium and Caulobacter crescentus

J Bacteriol. 2006 Oct 01; 188(19): 6841-50.[more]

El-Sayed, N. M., Myler, P. J., et al.
Comparative Genomics of Trypanosomatid Parasitic Protozoa

Science. 2005 Jul 15; 309(5733): 404-9.[more]

Badger, J. H., Eisen, J. A., et al.
Genomic Analysis of Hyphomonas neptunium Contradicts 16S RRNA Gene-based Phylogenetic Analysis: Implications for the Taxonomy of the Orders 'Rhodobacterales' and Caulobacterales

Int J Syst Evol Microbiol. 2005 May 01; 55(0): 1021-6.[more]

Vogl, C., Badger, J., et al.
Probabilistic Analysis Indicates Discordant Gene Trees In Chloroplast Evolution

J Mol Evol. 2003 Mar 01; 56(3): 330-40.[more]

Badger, J., Kearney P.
Picking Fruit from the Tree of Life: Comments on Taxonomic Sampling and Quartet Methods.

16th ACM Symposium on Applied Computing. 2001 Mar 01; 16: 61-67.[more]

Badger, J. H., Olsen, G. J.
CRITICA: Coding Region Identification Tool Invoking Comparative Analysis

Mol Biol Evol. 1999 Apr 01; 16(4): 512-24.[more]

Haney, P. J., Badger, J. H., et al.
Thermal Adaptation Analyzed by Comparison of Protein Sequences from Mesophilic and Extremely Thermophilic Methanococcus Species

Proc Natl Acad Sci U S A. 1999 Mar 30; 96(7): 3578-83.[more]