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- CSCI 1950L-S01: Algorithmic Foundations
of Computational Biology
Instructor: Sorin Istrail
Time and Place: Course Schedule
This course is devoted to computational and statistical methods as well as
software tools for DNA, RNA, and protein sequence analysis. The focus is on
understanding the algorithmic and mathematical foundations of the methods,
the design of the associated genomics tools, as well as on their applications.
A comprehensive set of programming assignments provides a hands-on journey
for the student into the complexities of real genomic data. These include:
basic components of a genome assembler, mapping sets of sequences to the genome,
as those generated by high-throughput sequencing like Illumina/Solexa and 454,
a BLAST-like search tool, HMM algorithms for gene prediction, suffix trees,
motif prediction for transcription factors promoters, and genome mapping of
genetic variation of SNPs, haplotypes, and copy number. The course has several
unifying themes such as alignment, comparative genomics, protein structure,
the newly unveiled role of RNA in the regulatory genome, and the intertwining
of statistics and algorithmics in the design of powerful genomic tools.
The course is open to computer and mathematical sciences students as well as
biological and medical students. Both advanced undergraduates and graduate students
are welcome. Biomed students compensate for programming assignments with comparable
work for a final project. Graduate credit is obtained by a final project devoted
to a research problem. Two grassroots projects are being built gradually by final
projects of students in this class. Genomathica is a library of biologist-friendly-code-tinkering
genomic tools written in Mathematica, and Cellarium is a programming
language framework for bioinformatics workflows. The instructor taught evolutionary
versions of this course in Departments of Biology, Computer Science, and Biochemistry
and Cell Biology (in the Medical School). For more information view the Course Catalog.
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