Download ECEN Information theory for genetics

ECEN 4012/5012
Fall 2005
Information Theory for Genetics
(Information Theory for Molecular Biology)
Instructor:
Office:
Class hours:
Office hours:
OLGICA MILENKOVIC
ECOT 253
M/W/F 10:00-10:50 a.m. ECEE 265 (Rescheduling is possible!)
To be scheduled in class
CLASS RULE #1: YOU HAVE TO HAVE FUN DURING THE LEARNING PROCESS!
CLASS RULE #2: YOU HAVE TO WORK HARD (WHILE HAVING FUN)!
CLASS RULE #3: YOU HAVE TO LOVE MATHEMATICS (AT LEAST SOMEWHAT)!
CLASS RULE #4: YOU ARE NOT SUPOSE TO BELIEVE IN INTELIGENT DESIGN!
Charles Darwin (1809-1882)
TEXTBOOK: None is required, several are recommended. You will receive plenty of
handouts and possibly class notes for this special topic. This is a new subject not
completely covered in any known text on bioinformatics, information theory and
genetics.
1. J. Pevsner, Bioinformatics and Functional Genomics, Wiley-Liss, 2003.
2. D. Gusfield, Algorithms on Strings, Trees, and Sequences: Computer
Science and Computational Biology
3. Watermann, Introduction to Computational Biology, 1995
4. R.S. Hawley, and C. Mori, The Human Genome, Harcourt Academic
Press, 1999.
5. J. Percus, Mathematics of Genome Analysis, Cambridge Studies in
Mathematical Biology, 2002.
6. A. M. Findley, S. P. McGlynn, and G. L. Findley, The Geometry of
Genetics, 1989.
7. C. Adams, The Knot Book, An Elementary Introduction to the
Mathematical Theory of Knots, American Mathematical Society, 2004.
Gregor Mendel (1822-1884)
Homework, Exam and Class Project Policy: There will be two (take-home)
midterm exams, bi-weekly homeworks and a final class project. The exams carry 25% of
the final grade each, the class project carries 30% , while homeworks account for 20% of
your grade. The homework and project assignments will be slightly different for
undergraduate and graduate students in the class.
Rosalynd Franklin (1920-1958)
Living beings are endowed with highly complex information storage and
processing systems that are regulated at many different levels, including the
macromolecular code stratum. Although some of the components of such systems are
well-analyzed from the biochemical point of view, very little is known about their
governing information-theoretic principles. It is therefore important to develop an
understanding of the mathematical, combinatorial, coding theoretic, signaling and
communication system aspects of biological units that lead to their observable selforganization and information processing traits. Furthermore, it is of interest to
investigate how known techniques from the area of information-content based data
analysis can be applied in the context of studying biological carriers of information.
The RNA Tie Club
The goal of this class is to provide a basic introduction to the problems
encountered in modern molecular biology that can be investigated from the perspective
of information theory. The topics to be covered include:
 A short introduction to the theory biological macromolecules: DNA, RNA
and proteins; you will receive a handout in the form of a disk by Roche
Genetics outlining the basic principles of genetics;
 Mendel’s laws of inheritance and some elementary probability;
 Sequence and multiple sequence alignment: micro-arrays and gene
expressions;
 Basic Local Alignment Search Tool (BLAST);
 Molecular phylogeny and evolution;
 DNA knots and knot invariants: an overview of related coding and
statistical physics problems;
 A description of non-extensive entropies and their application for
measuring the information content of DNA strands;
 An introduction to fractal and multi-fractal sequences and combinatorial
modeling of DNA strand properties; a description of the problem of DNA
compression;
 Coding theory and new distance measures for genetic sequence
comparison and analysis;
 Information-theoretic aspects of DNA proofreading;
 A treatment of gene regulatory networks and novel modeling techniques
for tumoro-genesis, with application to disease diagnostics and treatment;
 Fault tolerance analysis of genetic networks;
 The information-theoretic aspects of RNA/DNA folding, and the related
problem of protein folding, with applications to DNA computing/selfassembly;
 Several special topics to be chosen by the class!
(1) If you qualify for accommodations because of a disability, please submit to me a letter from
Disability Services in a timely manner so that your needs may be addressed. Disability Services
determines accommodations based on documented disabilities. Contact: 303-492-8671, Willard
322, and
http://www.Colorado.EDU/disabilityservices
(2) Campus policy regarding religious observances requires that faculty make every effort to
reasonably and fairly deal with all students who, because of religious obligations, have conflicts
with scheduled exams, assignments or required attendance. In this class, {{insert your
procedures here}} See full details at http://www.colorado.edu/policies/fac_relig.html
(3) Students and faculty each have responsibility for maintaining an appropriate learning
environment. Students who fail to adhere to such behavioral standards may be subject to
discipline. Faculty have the professional responsibility to treat all students with understanding,
dignity and respect, to guide classroom discussion and to set reasonable limits on the manner in
which they and their students express opinions. Professional courtesy and sensitivity are
especially important with respect to individuals and topics dealing with differences of race,
culture, religion, politics, sexual orientation, gender variance, and nationalities. Class rosters are
provided to the instructor with the student's legal name. I will gladly honor your request to
address you by an alternate name or gender pronoun. Please advise me of this preference early in
the semester so that I may make appropriate changes to my records. See polices at
http://www.colorado.edu/policies/classbehavior.html and at
http://www.colorado.edu/studentaffairs/judicialaffairs/code.html#student_code
(4) All students of the University of Colorado at Boulder are responsible for knowing and
adhering to the academic integrity policy of this institution. Violations of this policy may include:
cheating, plagiarism, aid of academic dishonesty, fabrication, lying, bribery, and threatening
behavior. All incidents of academic misconduct shall be reported to the Honor Code Council at
[email protected]; 303-725-2273.
Students who are found to be in violation of the academic integrity policy will be subject to both
academic sanctions from the faculty member and non-academic sanctions (including but not
limited to university probation, suspension, or expulsion). Other information on the Honor Code
can be found at
http://www.colorado.edu/policies/honor.html and at
http://www.colorado.edu/academics/honorcode/
(5) The University of Colorado at Boulder policy on Discrimination and Harassment - see
http://www.colorado.edu/policies/discrimination.html the University of Colorado policy on Sexual Harassment and the University of Colorado policy on
Amorous Relationships applies to all students, staff and faculty. Any student, staff or faculty
member who believes s/he has been the subject of discrimination or harassment based upon race,
color, national origin, sex, age, disability, religion, sexual orientation, or veteran status should
contact the Office of Discrimination and Harassment (ODH) at 303-492-2127 or the Office of
Judicial Affairs at 303-492-5550. Information about the ODH and the campus resources available
to assist individuals regarding discrimination or harassment can be obtained at
http://www.colorado.edu/odh
List of handouts
1)
2)
3)
4)
5)
6)
7)
8)
9)
10)
11)
12)
13)
14)
15)
16)
17)
18)
19)
20)
21)
22)
23)
Class Syllabus
The Cell (lecture notes)
The Guide: The famous DNA experiments
http://www.dnaftb.org/dnaftb/
The Guide: The packing of DNA in eukaryotes
http://library.thinkquest.org/27819/ch6_2.shtml
Chromatin Structure: Section D
http://www.web-books.com/MoBio/Free/Ch3D.htm
Ehrenfeucht et.al.: Computation in Living Cells
Glossary (from the book by Howley and Mori)
Signal Processing in the Genetic Channel
The Genetic Code (Geometry of Genetics)
Mutations: Damage and Repair of DNA (Chapter 7), Maroni
World’s Toughest Bacterium has a Taste for Waste
Male Chromosome to Stick Around
DNA Replication, Repair, and Recombination (Garland
Science, Chapter 6)
http://www.bios.co.uk/textbooks/081533480X/pdf/ch06.pdf
Control of Gene Expression
http://staff.jccc.net/pdecell/expression/control.html
The Cell Cycle: A Universal Cellular Division Program
http://www.bioteach.ubc.ca/CellBiology/TheCellCycle/
Cancer: Basic Facts (NIH Web Page)
Genes and Cancer, Chapter 17 (from the book by Howley and
Mori)
Gene Regulatory Network – Circuit Representation of the
Cytokine Complex
How do we Sequence DNA?
http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/sequen
cing.html
Nano-technology for DNA sequencing
Whole Genome DNA Sequencing (Gene Myers)
Towards Simplifying and Accurately Formulating Fragment
Assembly (Gene Myers)
Saad Mneimneh’s web-page
http://engr.smu.edu/~saad/courses/cse8354/
Lecture 3,4,15
Slides 15