COS598G: Algorithms in Computational Biology
Spring 2017

Professor: Ben Raphael

Time: Monday/Wednesday 11:00am-12:20pm [COS 302]


This course seminar will explore algorithmic challenges that emerge in the analysis and interpretation of genome sequencing data, with a particular focus on applications in cancer genomics and immunogenomics. Areas of focus include:

  • The mutational process of cancer evolution. The underlying algorithmic problem is to construct trees that represent the relationships between cells from mutational data. We will explore tree reconstruction algorithms using phylogenetic techniques (perfect phylogeny and Dollo parsimony) and population genetic techniques (branching processes and the coalescent).
  • The identification of combinations of cancer causing mutations. Such combinations typically result from biological interactions between genes, which are represented via graphs, or networks. We will examine algorithms to analyze data on graphs including random walks (e.g. PageRank), diffusion processes, community detection, and spectral methods for graph partitioning.
  • Course Organization



    Outline of Topics



    Proposal:Due TBD (Specific Aims and Significance) and TBD (All).

    Paper Reviews