Instructor | Dan DeBlasio | Time | TR 15:00-16:30 |

dfdeblasio _at_ utep.edu | Location | Online (Zoom, contact instructor for password) | |

Office | CCSB 3.1008 online until further notice: teamsChat.deblasiolab.org |
Office Hours: | M 2-3pm, R 1-2pm or by appointment (calendly.deblasiolab.org). |

Syllabus | updated: January 18 2021 |

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 studentsâ€™ 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.

We will use "Algorithms in Bioinformatics" by Wing-Kin Sung[1] as our primary text, but this will be supplemented with other literature soruces that will be provided.

[1] CRC Press, ISBN 9781420070330(Hardcover)/9780367659318(Paperback)

Date | Slides | Homework | Other |
---|---|---|---|

19 January 2021 (W1T) | Introduction Slides Algorithm Refresher |
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21 January 2021 (W1R) | Linear Programming | Welcome Survey |

- Algorithms1 (updated January 22 2021)
- ILP (updated January 21 2021)
- Syllabus (updated January 19 2021)