BNFO 615 Usman Roshan

Projects and papers An opportunity to do hands on work Proposal presentations due by end of September Papers: present at least one paper related to the project Python programming (R is also fine)

Projects Genome alignment Metagenomics Variant detection Sequence alignment classification Whole genome phylogeny reconstruction

Genome alignment Contemporary sequence alignment problem Hard due to complex genome evolution Data – Simulated: evolver, alignathon – Real Programs – LASTZ New alignment methods for distant genomes

Metagenomics Contemporary alignment problem Simulated data Real data Comparison of short read mappers for metagenomics New metagenomics methods

Variant detection Key in cancer genomics and understand disease Variant detection in unmapped reads – First we map them – Then look for variants

Sequence alignment classifier Popular problem in bioinformatics Plethora of sequence alignment programs available Can we create a machine learning classifier that would give us the best alignment? K-means style deep learning method

Whole genome phylogeny Phylogenies from whole genome sequences data Hard to study on real data Simulated data via evolver