Jim Balhoff
I'm a research programmer at the National Evolutionary Synthesis Center (NESCent). I'm interested in software for evolutionary biology and bioinformatics. I am currently working with the Phenoscape project to develop software for annotating evolutionary phenotypes using ontologies. So far this has been primarily through contributions to Phenote.
I obtained my Ph.D. in Greg Wray's lab in the Duke Biology Dept.. My research concerned the molecular evolution of DNA sequences involved in gene regulation.
On this page you can find my software and publications.
Here a few programs I've written or contributed to, mostly related to biological research.
Phenote is both a complete piece of software and a software toolkit designed to facilitate the annotation of biological phenotypes using ontologies. It provides an interface and infrastructure to record genotype-phenotype pairs, together with the provenance for the annotation. I have added several components for working with evolutionary data.
GARLI performs heuristic phylogenetic searches under the General Time Reversible (GTR) model of nucleotide substitution and its submodels, with or without gamma distributed rate heterogeneity and a proportion of invariant sites. I developed a graphical interface for Mac OS X which provides easy configuration of GARLI's options and allows you to view the progress of your tree search.
screenshotThis is a Mac OS X Service that allows you to select DNA sequence text in (almost) any application and replace it with the sequence of the complementary strand. Just drop ReverseComplement.service in ~/Library/Services (you may have to create this folder) and log out and back in. Now when you highlight some text, you should be able to select "Reverse & Complement" from the Services menu of the application (under the application name menu). Some applications don't support the Services menu, though. Click here to find out how to edit the base associations.
screenshotAn interface for Matt Hahn's "Heterogeneity Test". See his page for more details on how it works.
screenshotThis is the first program I ever wrote, while learning Cocoa. Use it to quickly determine reagent amounts for your PCR reactions (if you set them up the same way I do).
screenshotHorvath, J.E., D.W. Weisrock, S.L. Embry, I. Fiorentino, J.P. Balhoff, P. Kappeler, G.A. Wray, H.F. Willard, and A.D. Yoder. 2008. Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar’s lemurs. Genome Research 18:489-499. DOI
Lapp, H., S. Bala, J.P. Balhoff, A. Bouck, N. Goto, M. Holder, R. Holland, A. Holloway, T. Katayama, P.O. Lewis, A.J. Mackey, B.I. Osborne, W.H. Piel, S.L. Kosakovsky Pond, A.F.Y. Poon, W.-G. Qiu, J.E. Stajich, A. Stoltzfus, T. Thierer, A.J. Vilella, R.A. Vos, C.M. Zmasek, D.J. Zwickl and T.J. Vision. 2007. The 2006 NESCent phyloinformatics hackathon: a field report. Evolutionary Bioinformatics 3:357–366. link
Balhoff, J.P. and G.A. Wray. 2005. Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites. PNAS 102:8591-8596. DOI
Wray, G.A., M.W. Hahn, E. Abouheif, J.P. Balhoff, M. Pizer, M.V. Rockman, and L.A. Romano. 2003. The evolution of transcriptional regulation in eukaryotes. Molecular Biology and Evolution 20:1377-1419. DOI
Balhoff, J.P. and J.M. Stephens. 1998. Highly specific and quantitative activation of STATs in 3T3-L1 adipocytes. Biochemical and Biophysical Research Communications 247:894-900. DOI
The software on this page is free to download and use, and thus comes with no warranty of any kind.
