COMPUTATIONAL MOLECULAR BIOLOGY
COMP 4300/5108
Winter 2011

1. CONTACTS:
   
   • Instructor: Evangelos Kranakis
   • Office hrs
2. CONTENTS OF LECTURES:
   

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   Week/Dates	Lecture	Assignment/Test/Project	Other Resources Bio2010
   Week 01 Jan 03	How Old is Life? History of CMB I: Life & all that		Wilf Cohen Watson-Crick RNA Advances Revolution
   Week 02 Jan 10	Restriction Mapping II: Life & all that	Project (Grad students only)	Alzheimer's Masses Giant
   Week 03 Jan 17	Regulatory Motifs Genome Rearrangements	Assignment 1	Papa and Gates Christie and Irving Bourque and Pevzner Optimal Sorting By Reversals (Survey) Lysenko et al
   Week 04 Jan 24	No Class
   Week 05 Jan 31	RNA Structures	Assignment 1 Corrected
   Week 06 Feb 07	Gene Similarity Sequence Similarity	Project Abstract (Grad Students only)	Vazirani Anson & Myers Frieze & Szpankowski
   Week 07 Feb 14	Alignments Sequencing I	Undergrad Project Assignment 2	Blue Roses Paper for problem 4, in assignment 2
   Spring Break Feb 21-25		Assignment 1 (Due: Thu, Feb 24, 12 noon) What/How to Submit
   Week 08 Feb 28	Sequencing II Sequencing III		Algs and Issues
   Week 09 Mar 07	Evolution: Clustering Phylogenies I
   Week 10 Mar 14	Phylogenies II Randomized Motif Finding		Tracing Ancestors Tracing Lice
   Week 11 Mar 21	Cloning Data Training: MMs & HMMs	Assignment 2: Submit only problems: 1, 2, 3, 6, 9, 10
   Week 12 Mar 28	Test (Open Book, Notes)	Material Covered in Class
   Week 13 Apr 04	Student Lectures	Assignment 2 & (Grad/Ugrad) Projects (Due) What/How to Submit: April 08, midnight
   	Undergraduate Student Research Awards USRA (NSERC)

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3. COURSE OUTLINE: Fundamental mathematical and algorithmic concepts underlying molecular computational biology; physical and genetic mapping, sequence analysis (including alignment and probabilistic models), genomic rearrangements, phylogenetic inference, computational proteomics and systemic modeling of the whole cell.
   Precludes additional credit for Algorithms in Bioinformatics (CSI 4126).
   Prerequisites: COMP 3804, CSI 3105 or equivalent.
   Course can be taken by both senior undergraduate and graduate students; there will be differences between undergraduate and graduate course requirements (for more information please come to class).
4. TEXTBOOKS:
   • Primary: Neil C. Jones, Pavel Pevzner, An Introduction to Bioinformatics Algorithms, MIT Press, 2004. ISBN 0-262-10106-8
   • Secondary: R. Durbin, S. Eddy, A. Krogh, G. Mitchison, Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Cambridge University Press, 1998. ISBN-10: 0521629713,
5. USEFUL REFERENCES:
   • Here you can find useful references.
6. STUDENTS' REQUIREMENTS:
   1. All assignments are compulsory and must be handed in on the due date/time. Late assignments will not be accepted. The assignments-mark will be averaged over the remaining assignments if there is a serious reason (like, health problem) in which case a written certificate from the appropriate authority is required. Missing assignments are worth 0 %.
   2. Email completed assignments/projects to me as follows:
      1. In case of single file: Label assignment with LastName-FirstName-ID
      2. In case of multiple files a) place them in a folder, b) label folder LastName-FirstName-ID, c) zip the folder, d) mail the zip archive.
   3. Plagiarism will not be tolerated. You must always write up the solutions to assignment problems on your own and acknowledge your sources in case you used library material. On the first occasion, plagiarizing an assignment will result in assigning a 0 to all the students involved and continuation of this practice may have severe repercussions for the student(s) involved.
   4. No Books/Notes/Computing Devices of any kind allowed during the tests!
   5. Make-up tests are not possible. In case of absence from a test and in order to average your mark over the remaining exams a written certificate from the appropriate authority is required, else you will receive 0 %. You may be asked to take an oral test as a substitute.
   6. Remarking of individual questions in a test is not possible; the whole test will be remarked, in which case your grade for this test may either increase or decrease.
7. GRADING SCHEME
   
   1. In-class exam (Duration 120 min). This will contribute 50% to the final grade.
   2. Two assignments will contribute
      • for grad students 30%
      • for undergrad students 30%
      to the final grade.
   3. (Only) Grad students must complete a research project, make an in-class presentation (date/time/duration TBA) and submit (by email) to instructor
      1. a one-page abstract of the final project,
      2. the presentation in electronic form, presentation),
      3. the final project in electronic form (due last day of class).
      The project should follow (guidelines for project/paper abstract preparation). This will contribute 20% of the final grade.
   4. (Only) Undergrad students must complete a programming assignment and submit (by email) to instructor. This will contribute 20% of the final grade.
8. CONDITIONS FOR THE PROJECT/PAPER
   
   1. The topic of the project/paper may be suggested by the student (subject to approval of instructor), must be relevant to the material covered in the course, (see propsed project)
   2. The written presentation of the project/paper must have the quality of a journal publication. (See guidelines for project/paper preparation).
   3. In addition, students must make an oral presentation of their selected project/paper in-class. Here you can find helpful hints on making a presentation