Course CPS 260, also cross-listed
as BGT 204 in the Bioinformatics
and Genome Technology PhD program administered by Center
for Bioinformatics and Computational Biology, is intended to
provide a systematic introduction to the algorithmic techniques
behind the most commonly used tools in computational biology. While
the course will survey a wide range of methods and tools in the
field, the primary emphasis will be on understanding and analyzing
the algorithms behind these tools.
Topics to be covered include basic techniques in design
and analysis of algorithms, dynamic programming, string matching,
probabilistic techniques, hidden Markov models, geometric algorithms,
and data mining. These topics will be exposed in the context of
applications of sequence alignment, genome sequence assembly, gene
finding, gene expression and regulation, protein structure prediction,
protein dynamics.
Assignments:
25% weight
Four assignments will be given during the semester, which each student
has to complete individually. Collaboration is not permitted, but
if one does not understand the material on whcih the assignments are
based, contact the TA or the professor.
Research
Project: 50% weight
In groups of two three students
Intention is to produce a work of publishable or near-publishable
quality
Will consist of two parts:
(i)
proposal and survey and initial
work (due after fall break)
(ii)
research work (the first week
of December, a final paper and presentation).
Scribe:
25% weight
Each student has to scribe at least one lecture. Scribed notes should
be completed individually, but you can certainly ask your peers
to clarify any point that your notes leave unclear.