Next generation sequencing data analysis [ Software ]
Next generation sequencing has revolutionized biomedical sciences. However, the vast amounts of short reads it generates are difficult to analyze, demanding new and sophisticated bioinformatics methods. Our lab is developing algorithms and software tools to analyze next generation sequencing data to answer questions in biology and medicine.
Alternative splicing and RNA editing [ Software ]
Alternative splicing and RNA editing are important post-transcriptional regulatory mechanisms that contribute to creating functional diversity. Dysregulation in splicing and editing have been associated with diseases. We are developing methods to discover and catalogue alternative splicing and RNA editing variations from the vast amounts of gene sequence data generated with conventional and second generation sequencing.
Genome assembly and gene annotation [ Software ]
Next generation sequencing has tremendously accelerated the pace of producing new genomes, but the short reads lead to fragmented assemblies that are difficult to analyze. We are developing algorithms and tools to aid in genome assembly and assembly curation, as well as to compare and annotate genomes.
Host-pathogen interaction [ Software ]
Genome analyses of bacterial and viral pathogens have provided unique insights into their virulence, host adaptation and evolution, and as determinants and markers of disease. We are developing algorithms to identify genomic features such as virus encoded non-coding RNAs and selection signatures, as well as tools to compare and visualize microbial genomes.