Genome analysis: Genome assembly, genome and chromosome annotation, gene finding, alternative splicing, EST analysis and comparative genomics. 

Sequence analysis: Multiple sequence alignment, sequence search and clustering, function prediction, motif discovery, functional site recognition in protein, RNA and DNA sequences. 

Phylogenetics: Phylogeny estimation, models of evolution, comparative biological methods, population genetics.

Structural Bioinformatics: Structure matching, prediction, analysis and comparison; methods and tools for docking; protein design 

Analysis of high-throughput biological data: Microarrays (nucleic acid, protein, array CGH, genome tiling, and other arrays), EST, SAGE, MPSS, proteomics, mass spectrometry.

Genetics and population analysis: Linkage analysis, association analysis, population simulation, haplotyping, marker discovery, genotype calling.

Systems biology: Systems approaches to molecular biology, multiscale modeling, pathways, gene networks.