Jim Balhoff
I'm a research programmer at the National Evolutionary Synthesis Center (NESCent). I'm work on software for evolutionary biology and bioinformatics. I am particularly interested in data representation in biology, especially the use of ontologies and the Semantic Web. I am currently working with the Phenoscape project to develop a knowledgebase of evolutionary phenotypes. I also work with the Hymenoptera Anatomy Ontology project, applying semantic technologies to taxonomic data.
I obtained my Ph.D. in Greg Wray's lab in the Duke Biology department. My research concerned the molecular evolution of DNA sequences involved in gene regulation.
Projects I develop or contribute to:
My user accounts on Sourceforge and GitHub link to source code for most of the projects I work on.
Some very old projects.
Dahdul, W.M., J.P. Balhoff, J. Engeman, T. Grande, E.J. Hilton, C. Kothari, H. Lapp, J.G. Lundberg, P.E. Midford, T.J. Vision, M. Westerfield, and P.M. Mabee. 2010. Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature. PLoS ONE 5(5): e10708. DOI
Balhoff, J.P., W.M. Dahdul, C.R. Kothari, H. Lapp, J.G. Lundberg, P.M. Mabee, P.E. Midford, M. Westerfield, and T.J. Vision. 2010. Phenex: ontological annotation of phenotypic diversity. PLoS ONE 5(5): e10500. DOI
Dahdul, W.M., J.G. Lundberg, P.E. Midford, J.P. Balhoff, H. Lapp, T.J. Vision, M.A. Haendel, M. Westerfield, and P.M. Mabee. 2010. The teleost anatomy ontology: anatomical representation for the genomics age. Systematic Biology DOI
Horvath, 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.