CSCI2820

Algorithmic Foundations in Computational Biology

Spring 2026

The aim of this course is to provide computer science and mathematical sciences foundations, as well as biological insights, for numerous seminal algorithms in the field of computational biology, i.e., algorithmic foundations for Computational Biology. Topics include: The BLAST Algorithm and Karlin-Altschul Statistics, Genome Assembly Algorithms and Haplotype Assembly Algorithms, Hidden Markov Models (HMM) Algorithms: The Learning Problem, Recombination and Ancestral Recombination Graphs Algorithms, Rigorous Clustering: Spectral Graph Theory Algorithms, Algorithms for Constructing Suffix Trees in Linear Time, Protein Folding Algorithms (An Introduction). Each chapter is devoted to a class of fundamental computational problems of genomics related to the analysis of DNA, RNA, protein sequences and protein structures and their molecular biology function.