Spring 2021 Course

I will be teaching a special topics in data science course this spring. The information can be found below or at http://specialtopics.deblasiolab.org/s21/. The course numbers are CS 4364 for undergrads and CS 5364 for graduates (the CRNs can be found on the CS department course schedule).

Special Topics in Data Science:
Algorithms for Computational Biology

This course will cover the algorithms that make modern computational biology and bioinformatics possible. The plan is to cover both foundational algorithms such as sequence alignment, as well as their modern applications in solving problems such a genome assembly. The focus of this course is on how computer scientists apply their knowledge to frame a computational problem inspired by a specific real-world problem and to solve such computational problems. In addition to standard algorithm development, the course will cover the influence of convex optimization (mainly integer linear programming) and machine learning on computational biology. The course assumes no previous knowledge in biology or genetics. The course will build on and enhance students’ basic understanding of the principle of algorithm design and analysis by applying such principles in the context of bioinformatics.

The topics discussed are likely to include:

  • Pairwise Sequence Alignment
  • Multiple Sequence Alignment
  • Genome Assembly
  • Metagenomic & Alignment-free Genomic Analaysis
  • Phylogenetic Reconstruction
  • Integer Linear Programming Applications
  • Machine Learning Applications

CS 2302 is a pre-requisite, please contact the instructor with any questions.

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