Publications

A selection of recent publications is included here. My full list of indexed publications is on Google Scholar.

Pseudogenes and intrinsic error in genomic data

• Publication
• GitHub repository of plots and results

Modern genomic annotation pipelines like PGAP and EGAP provide features annotated as pseudogenes. What these annotations realistically represent depends in part on the technologies used to generate the source sequence data and the strategies used to assemble the genomic data being annotated. A pseudogene annotation can represent either a true, recent mutation that causes loss or modulation of function in a clearly identifiable feature, or a sequencing or assembly error that has been incorporated into the assembled genomic data.

Functional classification of protein coding sequences

• Publication
• GitHub repository of plots and results

Accurate classification of protein coding sequences is difficult. A functional classifier based on the previously existing taxonomic classifier IDTAXA was developed with an emphasis on specificity. Benchmarking classification strategies with misclassification and overclassification rates provides a clear picture of the strengths and weaknesses of different methods.