Pavel Pevzner, Phillip E. C. Compeau and Nikolay
Vyahhi
This course will
cover some of the common algorithms underlying the following fundamental topics
in bioinformatics: assembling genomes, comparing DNA and protein sequences,
predicting genes, finding regulatory motifs, analyzing gene expression,
constructing evolutionary trees, analyzing genome rearrangements, and
identifying proteins.
Workload: 8-10 hours/week
About the Course
The sequencing of
the human genome a decade ago began a computational revolution in biology,
which has arguably been an impetus for more new algorithms than any
other fundamental realm of science. The newly formed links
between computer science and biology affect the way we teach computational
ideas to biologists, as well as how applied algorithms are taught to computer
scientists.
Genome sequencing is
just one of hundreds of biological problems that have become inextricable from
the computational methods required to solve them. In this course, we will take
a look at some of the algorithmic ideas that are fundamental to
an understanding of modern biology. Computational concepts like
dynamic programming and network analysis will help us explore algorithms
applied to a wide range of biological topics, from finding genes to
reconstructing the tree of life. Throughout the process, we will
apply real bioinformatics
algorithms to real genetic
data.
In order to
streamline homework assignments and solidify the material covered in the course,
we will employ Rosalind, a fun new resource
for learning bioinformatics that was founded by the instructors. We
hope that Rosalind will show you how fun solving problems
in bioinformatics can be.
Course Syllabus
Note:
the syllabus may undergo revisions throughout the course.
Each homework will contain approximately 5 programming assignments and will utilize the Rosalind bioinformatics online education platform.
The course will consist of the following six primary topics:
Each homework will contain approximately 5 programming assignments and will utilize the Rosalind bioinformatics online education platform.
The course will consist of the following six primary topics:
·
Finding
the Replication Origin
·
Sequencing
Antibiotics
·
Genome
Assembly
·
Genome
Rearrangements
·
Sequence
Alignment
·
Short
Read Mapping
Post a Comment
Thanks for reading my blog.
Note: only a member of this blog may post a comment.