Additional slides with animations to strengthen your understanding of
the central dogma of molecular biology, sickle cell anemia, etc..
biotechnology companies in the Bay Area.
Information about the Instructor
Name: Sami Khuri
Office: 418 MacQuarrie Hall
Tuesdays and Thursdays: 11:45 to 13:50.
This practical course, cross-listed with biology, continues to
cover the computational methods used for searching, classifying,
analyzing, and modeling protein sequences. The course also continues to
cover tools for analyzing DNA and RNA sequences. More advanced topics,
such as genetic algorithms and simulated annealing which can be used to
address folding problems, are covered.
Biology/CS123A or by permission of the instructor.
Guidelines Last update: February 6, 2010.
by Marketa Zvelebil and Jeremy Baum,
Garland Science, 2008, ISBN 0-815-34024-9.
- We shall continue covering most of the topics from chapters 7, 9,
and 10, and some selected topics from chapters 8 and 12.
- Before reaching the end of a chapter, I will announce which
topics of the following chapter will be covered cover.
- A copy of my powerpoint slides (6 per page) will be available
to the students enrolled in the class.
Use case studies in homework and in-class hands-on exercises to extract
To continue acquainting students with some of the most challenging
problems in life science and show how computer science can be used to
solve some of these problems.
Study various techniques for identifying genes, promoters,
transcription factor binding sites, etc..
Upon successful completion of this course, students should be able to
assess and evaluate novel computational methods for use in bioinformatics,
including machine learning techniques,
mainly Hidden Markov Models, neural networks, genetic algorithms,
and pattern recognition techniques.
- Problem Sets:
Five homework assignments.
The purpose of the assignments is to develop your understanding
of the material and your skills in problem-solving.
Only a subset of the assigned problems on any given problem set
will be graded. You will get the homework back
one week after submitting it.
No late homework will be accepted. However,
under exceptional circumstances, one problem set
per student might be accepted late.
It will need to be handed in prior to the following class meeting and
will be graded with 30% off. Such an extension should be requested
from the instructor.
Any homework not picked up during
class time will be left on the shelves near my
Assignments are due in the beginning
of the lecture on the following dates:
- HW One:
due on Thursday, February 9, 2012.
Article: A vision for the future of
genomic research article for Problem 2.
Gene regulation in hematopoiesis: new lessons from Thalassemia
for Problem 5.
De Novo assembly using Illumina reads
for Problem 6.
- HW Two:
due on Thursday, February 23, 2012.
How do RNA folding algorithms work? for Problem 1.
BayesFold: Rational 2 folds that combine thermodynamic,
covariation, and chemical data for aligned RNA sequences for Problem
- HW Three:
due on Thursday, March 15, 2012.
- HW Four:
due on Thursday, April 5, 2012.
What is a hidden Markov model? for Problem 5.
- HW Five:
due on Thursday, April 26, 2012.
Finding the genes in genomic DNA for Problem 3.
Microbial gene identification using interpolated Markov models for
Bovine Rhodopsin for Problem 5.
Cover sheet for all assignments
(Updated on December 21, 2011).
This is a group project. Each group consists of two students.
As mentioned in the project description, the
Team Formation is due by Tuesday, March 6, 2012.
The Progress Report is due by Tuesday, April 10, 2012
at the begining of the class. The final
due on Thursday, May 3, 2012 at the beginning of the lecture.
for the final project report
Exam One: Tuesday, March 6, 2012.
Exam Two: Tuesday, April 17, 2012.
Final Exam: Tuesday, May 22, 2012, from 7:15 to 9:30 am.
Exam One and Exam Two are each one hour and fifteen minutes
long. All exams are in-class,
closed-book and comprehensive. You will get back your exams
within one week at which time we'll go over them in class.
Exams will be collected and kept with me.
There will be no make-up exams.
Class attendance is strongly encouraged.
In class, we shall cover many
topics and examples that are neither in the class notes
nor in the textbook. If you miss a lecture,
it is your responsibility to find out what was covered in
class (this includes: handouts given
out during your absence, corrected typos and errors,
examples discussed in class - that
are neither in the book nor in the notes - clarifications
and changes made to assignments or the project, etc...).
The final grade will be computed as shown below:
Exam One: 20%
Exam Two: 20%
[97, 100] A+
[93, 97) A
[90, 93) A-
[87, 90) B+
[82, 87) B
[80, 82) B-
[77, 80) C+
[72, 77) C
[70, 72) C-
[67, 70) D+
[62, 67) D
[60, 62) D-
[0, 60) F
For those wishing to add this course, the deadline is February 14, 2011.
The last day to drop with a full refund is February 7, 2011.
According to University and Department guidelines, dropping after
February 7, 2011, requires a serious and compelling reason to drop a
Grades alone do not constitute reason to drop a course.
Students who stop attending without officially dropping will
be issued a U at the end of the semester which is counted as
an F in calculations of GPA. See University Catalog.
Your own commitment to learning, as evidenced by
your enrollment at San José State University, and the University's
Academic Integrity Policy requires you to be honest in all your
academic course work. Faculty members are required to report all
infractions to the Office of Student Conduct and Ethical Development.
The "Policy on Academic Integrity"
can be found
Disability Resource Center
If you need course adaptations or accommodations because of a
or if you need special arrangements in case the building must be
evacuated, please make an appointment with us as soon as possible, or
us during office hours. Presidential Directive 97-03 requires that
students with disabilities requesting accommodations must register with
DRC to establish a record of their disability. (Please let us know as
soon as possible in order to more effectively accommodate your needs.)
Summer 2011 Internships and Research Programs