Ragan Mark

Protein-protein interaction as a predictor of subcellular location (2009)

Shin Chang, Wong Simon, Davis Melissa, Ragan Mark

Abstract Background Many biological processes are mediated by dynamic interactions between and among proteins. In order to interact, two proteins must co-occur spatially and temporally. As...

A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution (2007)

Andersson Jan, Sjögren Åsa, Horner David, Murphy Colleen, Dyal Patricia, Svärd Staffan, ...

Abstract Background Comparative genomic studies of the mitochondrion-lacking protist group Diplomonadida (diplomonads) has been lacking, although Giardia lamblia has been intensively studied. We have...

The use of concept maps during knowledge elicitation in ontology development processes – the nutrigenomics use case (2006)

Castro Alexander, Rocca-Serra Philippe, Stevens Robert, Taylor Chris, Nashar Karim, Ragan Mark, ...

Abstract Background Incorporation of ontologies into annotations has enabled 'semantic integration' of complex data, making explicit the knowledge within a certain field. One of the major bottlenecks...

Detecting recombination in evolving nucleotide sequences (2006)

Chan Cheong, Beiko Robert, Ragan Mark

Abstract Background Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. These recombination events can be obscured by subsequent residue...

Bayesian and maximum likelihood phylogenetic analyses of protein sequence data under relative branch-length differences and model violation (2005)

Mar Jessica, Harlow Timothy, Ragan Mark

Abstract Background Bayesian phylogenetic inference holds promise as an alternative to maximum likelihood, particularly for large molecular-sequence data sets. We have investigated the performance of...

Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator (2005)

Garcia Castro Alexander, Thoraval Samuel, Garcia Leyla, Ragan Mark

Abstract Background Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are...

A hybrid clustering approach to recognition of protein families in 114 microbial genomes (2004)

Harlow Timothy, Gogarten J Peter, Ragan Mark

Abstract Background Grouping proteins into sequence-based clusters is a fundamental step in many bioinformatic analyses (e.g., homology-based prediction of structure or function). Standard clustering...