BIOINFORMATICS APPLICATIONS NOTE Genome analysis Combo: a whole genome comparative browser (2008)
Reinhard Engels, Tamara Yu, Chris Burge, Jill P. Mesirov, David Decaprio, James E. Galagan
Summary: Combo is a comparative genome browser that provides a dynamic view of whole genome alignments along with their associated annotations. Combo provides two different visualization...
Article The Complete Genome and Proteome of Mycoplasma mobile (2008)
Jacob D. Jaffe, Nicole Stange-thomann, Cherylyn Smith, David Decaprio, Sheila Fisher, Jonathan Butler, ...
Although often considered “minimal ” organisms, mycoplasmas show a wide range of diversity with respect to host environment, phenotypic traits, and pathogenicity. Here we report the complete...
Jade P. Vinson, Stacey Luoma, David Decaprio, Matthew D. Pearson, James E. Galagan
Computational gene prediction using generative models has reached a plateau, with several groups converging to a generalized hidden Markov model (GHMM) incorporating phylogenetic models of nucleotide...
Gene Prediction with Conditional Random Fields (2007)
Matthew K. Doherty, James Galagan, Assoc Director, David Decaprio, Arthur C. Smith, Matthew K. Doherty
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis (2006)
Kahmann, Regine, Bölker, Michael, Ma, Li-Jun, Brefort, Thomas, Saville, Barry J, ...
Ustilago maydis is a ubiquitous pathogen of maize and a well-established model organism for the study of plant-microbe interactions. This basidiomycete fungus does not use aggressive virulence...
Combo: a whole genome comparative browser (2006)
Engels, Reinhard, Yu, Tamara, Burge, Chris, Mesirov, Jill P., DeCaprio, David, Galagan, James E.
Summary: Combo is a comparative genome browser that provides a dynamic view of whole genome alignments along with their associated annotations. Combo provides two different visualization...
The Complete Genome and Proteome of Mycoplasma mobile (2004)
Jaffe, Jacob D., Stange-Thomann, Nicole, Smith, Cherylyn, DeCaprio, David, Fisher, Sheila, Butler, Jonathan, ...
Although often considered “minimal” organisms, mycoplasmas show a wide range of diversity with respect to host environment, phenotypic traits, and pathogenicity. Here we report the complete...
The Complete Genome and Proteome of Mycoplasma mobile
Jaffe, Jacob D., Stange-Thomann, Nicole, Smith, Cherylyn, DeCaprio, David, Fisher, Sheila, Butler, Jonathan, ...
Although often considered “minimal” organisms, mycoplasmas show a wide range of diversity with respect to host environment, phenotypic traits, and pathogenicity. Here we report the complete...
The Complete Genome and Proteome of Mycoplasma mobile
Jaffe, Jacob D., Stange-Thomann, Nicole, Smith, Cherylyn, DeCaprio, David, Fisher, Sheila, Butler, Jonathan, ...
Although often considered “minimal” organisms, mycoplasmas show a wide range of diversity with respect to host environment, phenotypic traits, and pathogenicity. Here we report the complete...
Conrad: Gene prediction using conditional random fields
DeCaprio, David, Vinson, Jade P., Pearson, Matthew D., Montgomery, Philip, Doherty, Matthew, Galagan, James E.
We present Conrad, the first comparative gene predictor based on semi-Markov conditional random fields (SMCRFs). Unlike the best standalone gene predictors, which are based on generalized hidden...
A High-Density Single Nucleotide Polymorphism Map for Neurospora crassa
Lambreghts, Randy, Shi, Mi, Belden, William J., DeCaprio, David, Park, Danny, Henn, Matthew R., ...
We report the discovery and validation of a set of single nucleotide polymorphisms (SNPs) between the reference Neurospora crassa strain Oak Ridge and the Mauriceville strain (FGSC 2555), of...