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.



Tuesday & Thursday 10:55-12:10
LSRC A158

Office Hours:
Pankaj Agarwal: Tue, Thu: 1:00-2:00
Leelavati Narlikar: Mon, Wed: 10:30-11:30



Pankaj K. Agarwal
LSRC D214A
(919) 660-6540
pankaj@cs.duke.edu
Leelavati Narlikar
North N-104
(919) 681-0228
lee@cs.duke.edu
 


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.



Intro to Computational Genetics (CPS 160.1)
BioGeometric Modeling (CPS 296.1)
Genome Informatics and Sequence Analysis (BGT 203)
Functional Genomics (BGT 208)
Design and Analysis of Algorithms (CPS 230)


BGT Programs
BioGeometry
NCBI
LATEX information:
README
scribing.template.tex
scribing.cls
The Not So Short Introduction To LATEX
M. Goossens, F. Mittelbach and A. Samarin. The LATEX Companion, Addison Wesley, 1994