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
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
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Teacher |
Office |
Tel. |
e-mail |
Reception |
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Prof. Dan Geiger |
Taub 616 |
4339 |
Sunday 14:00-15:00 |
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Anna Tzemach |
Taub 645 |
2979 |
Thursday13:30-14:30 |
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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) |
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10 |
Inference (ppt) | ||
|
11 |
HaploBlock pdf |
Merlinrapid 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. Gudbjartsso n |
Merlin algorithm (ppt) |
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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
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Variation methods for Bayes nets pdf |
| 14 | MALD lecture ppt |
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.
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# |
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. |
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| 3 | Hw3 | 15/1/07 | ||
| 4 | Hw4 | 28/2/07 | ||