Dr Casey Bergman (BSc, MAT, PhD) - research
Genome Annotation and Functional Genomics
As much of post-genomic biological research relies upon high quality genome annotations, we are actively engaged in the development and application of computational methods to improve the annotation of functional biological features in genome sequences. Our work focuses on improving annotation of conserved noncoding sequences (CNSs), cis-regulatory modules (CRMs), transcription factor binding sites (TFBSs), transposable elements (TEs) and noncoding RNA (ncRNA) genes. Current projects include improving the (i) annotation of TEs in the fly and yeast genomes, (ii) annotation of CRMs and TFBSs in the fly genome, and (iii) analysis of P-element insertion collections in flies.
Genome and Molecular Evolution
Whole genome sequence data offers an unparalled resource for the evolutionary analysis of biological sequences, and allows new analyses of regions and types of mutations that were not available in the pre-genomic era. We use diverse comparative sequence analysis methods to understand the patterns, rates and forces of genome evolution within and between species. Currently, our work focuses on (i) the evolution of CNSs and ncRNA genes in the fly genome, (ii) the evolution of TEs in fly and yeast genomes, and (iii) the effects of amino acid biosynthetic cost on evolution of protein coding sequences in yeast.
Text and Data Mining
The growing rate of publication in biological sciences has resulted in an explosion of information that can no longer be synthesised by individual scientists. To cope with this flood of information, we are increasingly interested applying text and data mining methods to the areas of genome annotation and functional genomics. Currently, we are pursuing methods for the automated extraction of CRMs and TFBSs from full-text articles and mapping to genomes sequences.
For more details, please see my research page at http://bergmanlab.smith.man.ac.uk/.