#
*640:338:01 Discrete and Probabilistic Models in
Biology*

Spring 04

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Takehome Exam
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Takehome Exam Solutions
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##
General Information

See the Main course page for the catalog description.

**THE SPRING 2004 **semester
will focus on probabilistic and
dynamic programming methods in the analysis of
biological sequences and in genetics.

**SYLLABUS:** Click here for the syllabus by
topic and here for the lecture by lecture
schedule.
Here is a summary:

- Basic populations genetics
as an introduction to probabilistic models in biology.
- Continuous random variables. Independent, identically distributed
random sequences, geometric, exponential, and normal random variables,
and Poisson processes. Application to coverage analysis in DNA
sequencing strategies.
- Likelihood functions, MLE and hypothesis testing and application
to models for biological sequences.
- Dynamic Programming and sequence alignment.
- Markov chain basics and Hidden Markov models
- Application to BLAST and models of sequence evolution and
population genetics.

**TEXT:** There is no text to buy for this course.
Instead, course notes
and problem sets will be provided
on-line at this site. There is an optional text that is
available for this course on sale at the Rutgers book store.
It is:
W.J. Ewens and G.R. Grant, **Statistical Methods in
Bioinformatics**,
Springer-Verlag, 2001, ISBN 0-387-95229-2.
I recommend buying this text if you want to read further and
deeper into the topics we cover.

**TESTS, HOMEWORK, AND GRADES:** There will be
weekly, graded problem sets, two midterms and a final.
The final grade will be computed from an average
of final (200 points), midterms (100 points each),
hoemwork (100 points). The midterms are tentatively
scheduled for February 26 and April 6.

**PROBLEM SETS** Follow this
link to access problems sets.

** Class time and place:** Tuesday/Thursday 4:30-5:50 PM (6th period), in
SEC-218

** Instructor:**
Daniel Ocone -
518 Hill
Center - ocone@math. Office hours:
T,Th 5 or by appointment.