Advanced Topics in Bioinformatics (236633)

Winter 2006-7

General Information

Staff

Course Outline

Assignments

Bibliography


News

 

Homework 2 postponed till 1/1/2007

On 23/11 there will be two hours tutorial instead of lecture

On 30/11 there will be three hours lecture

 

General Course Information

This course is offered at the Computer Sciences Department at the Technion -Israel Institute of Technology

 

Day

Time

Place

Teacher

Thursday

13:30-15:30

Taub 8

Prof. Dan Geiger

Day

Time

Place

Teacher

Thursday

15:30-16:30

Taub 8

Anna Tzemach

 

 


Staff

Thursday 15:30-16:30

Teacher

Office

Tel.

e-mail

Reception Hours

Prof. Dan Geiger

Taub 616

4339

dang@cs

Sunday 14:00-15:00

 

 

 

Anna Tzemach

Taub 645

2979

anna_bi@cs

Thursday13:30-14:30

 

Course Outline

Week

Lecture

Readings

Tutorial

1 Introduction to Genetics ppt "An Introduction to Genetic Analysis" (7th edition), Chapter #2. Basic Concepts in Genetics
(ppt)
2 Principles of Population Genetics ppt "An Introduction to Genetic Analysis" (7th edition), Chapter #5. Linkage and Recombination
(ppt)

3

Models for linkage ppt "An Introduction to Genetic Analysis" (7th edition), Chapter #6. Maximum Likelihood Estimation
(ppt)

4

Genehunter ppt "Mathematical and Statistical Methods for Genetic Analysis", Chapter #1. Hardy-Weinberg Equilibrium & Linkage Equilibrium
(ppt)

5

Superlink ppt 1) "Construction of multilocus genetic linkage maps in humans", Lander E., and Green P. Proceedings of National Academy of Science (USA), 84, 2363-2367  (1986).
2) "Biological Sequence Analysis", Chapter #3.
Detecting Input Errors
(ppt)

6

Non-parametric linkage ppt 1) "Rapid Multipoint Linkage Analysis of Recessive Traits in Nuclear Families, including Homozygosity Mapping", Kruglyak L., Daly M., and Lander E. Am. J. Hum. Genet., 56: 519-527 (1995).
2) "Parametric and nonparametric linkage analysis: a unified multipoint approach", Kruglyak L., Daly M., Reeve-Daly M., and Lander E. Am. J. Hum. Genet. 58: 1347-1363 (1996).
3) http://stat-www.berkeley.edu/users/terry/Classes/s260.1998/
Non-Parametric Linkage Analysis
(ppt)

7

Hardness results ppt 1) "The VITESSE algorithm for rapid exact multilocus linkage analysis via genotype set-recoding and fuzzy inheritance", O'Connell JR, Weeks DE, Nature Genetics 11:402-408, December 1995.
2) "Exact Genetic Linkage Computations for General Pedigrees", Fishelson M. and Geiger D. Bioinformatics,  Volume 18 Suppl. 1: S189-S198 (July 2002).
Bucket-Elimination Algorithm
(ppt)

8

Approximate Inference ppt Chapters #25 & #26 in "Handbook of Human Genetic Linkage" Elston-Stewart Algorithm
(ppt)

9

Learning Bayesian networks ppt   Vitesse + Allele Recoding Algorithm
(ppt)

10

    Inference (ppt)

11


HaploBlock  pdf
Merlin—rapid analysis of dense genetic maps using sparse gene flow trees

Computing the Probability of Marker Data Given an Inheritance Vector
(ppt)

12

Students lectures

An Introduction to Binary Decision Diagrams" Henrik Reif Andersen

" Multi-Terminal Binary Decision Diagrams:An Efficient Data Structure for Matrix Representation" M. Fujita, P.C. Mcgeer, J.C.-Y. Yang

"Genetic Linkage Analysis Algorithms and Their Implementation" A. Ingolfsdottir1 and D. Gudbjartsson

 
Merlin algorithm (ppt)

13

Students lectures

"Linkage analysis using sex-specific recombination fractions with GENEHUNTER-MODSCORE" J. Dietter M. Mattheisen, R. Fuš rst, F. Ruš schendorf, F. Wienker, K. Strauch

"Using Genomic Inbreeding Coefficient Estimates for Homozygosity Mapping of Rare Recessive Traits: Application to Taybi-Linder Syndrome" AL Leutenegger, A. Labalme, E. GeŽnin, A. Toutain, E. Steichen, F. Clerget-Darpoux, P. Edery

 

Variation methods for Bayes nets pdf
14 MALD lecture ppt    

Assignments

There will be 5 Assignments. Assignments are obligatory.
Assignments can be submitted in couples.
Assignment grades will constitute 50% of the final grade if exam grade is more than 55.

#

Homework

Due date

Readings

Solution

1 Hw1 7/12/06 "An Introduction to Genetic Analysis" (7th edition), Chapter #2.tic Analysis" (7th edition), for more background  
2 Hw2 1/1/07

"Mathematical and Statistical Methods for Genetic Analysis", Chapter #1.

 
3 Hw3 15/1/07    
4 Hw4 28/2/07    
         


 


Bibliography