THIS SCHEDULE IS PRELIMINARY, AND SUBJECT TO CHANGE
| Monday, March 31 8.30-9.20 |
1.1 Mendel's laws. 1.1 Hardy-Weinberg equilibrium. 1.1 Meiosis and Recombination |
Background on Genetics Background on likelihood Homework 1 (due 4/4/2014)) Chap 1.1 to 1.4 (posted 3/29/2014) |
| Wednesday, April 2 8.30-9:20 |
1.2.1 Allele and genotype frequencies; 1.2.2-3 Estimating frequencies 1.2.4 Population subdivision. |
Setup for Computing (3/30/2014) |
| Friday, April 4 8.30-9:20 |
Computing setup; getting started; Homework 1 discussion |
Some software info (3/30/2014) Homework 1 due |
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| Monday, April 7 8.30-9.20 |
1.2.5 Another estimation example 1.3.1 Testing HWE 1.3.2-5 Testing the ABO blood groups | Homework 2 (Posted 4/01/2014) |
| Wednesday, April 9 8.30-9:20 | 1.4 Gene counting and the EM algorithm | 4-minute Synthesis 1.1-1.2.4; Brenda. |
| Friday, April 11 8.30-9:20 |
Homework 2 discussion; More on computing/software. |
Homework 2 due Lab 1 (posted 4/08/2014) |
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| Monday, April 14 8.30-9.20 | 1.5 Haplotypes and Phasing. |
Chap 1.5 to 1.6 (posted 4/08/2014) Homework 3 (posted 4/08/2014) First half only: Q1 and Q4 Stephens' ppt on Clark |
| Wednesday, April 16 8.30-9:20 |
1.6 Linkage disequilibrium. |
Chap 2.1, 2.2 (posted 4/13/2014) 4-minute Synthesis 1.2.5-1.4; Jane. |
| Friday, April 18 8.30-9:20 | Lab 1 and Homework 3 discussion. | Homework 3 (Q1 and Q4 ONLY) and Lab 1 due. |
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| Monday, April 21 8.30-9.20 |
2.1 Defining pedigrees and relationships 2.2.1 Gene identity by descent |
Lab 2
and (optional)
Pedfiddler information. NOTE: All should be ok for lab-2 now. A note on Homework-3 Qu.1 (posted 04/19/2014) See also this paper. |
| Wednesday, April 23 8.30-9:20 |
2.2.2-4 Kinship and inbreeding 2.2.5 Inbreeding and genotype frequencies |
Synthesis of 1.5, 1.6: Ju An interesting pedigree! (posted 04/19/2014) |
| Friday, April 25 8:30-9:20 |
Discussion of Lab 2 More from homework 3. Hutterite pedigrees? |
Homework 3, Q2 and Q3 due. Likelihood vs q1 & q4. Likelihood vs q1 & q2. Also Lab 2 due. |
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| Monday, April 28 8.30-9.20 |
2.2.5 Inbreeding and genotype frequencies (ctd) 2.3 IBD in pairs of non-inbred relatives |
Chap 2.3, 2.4, 2.5 (posted 4/19/2014,updated 05/04/2014)) Homework 4 (Posted 04/24/2014). |
| Wednesday, April 30 8.30-9:20 | 2.4 Probabilities of data on relatives. |
Synthesis of 2.1, 2.2 --Jun Hwang Lab 3 (Posted 04/28/2014) |
| Friday, May 2 8.30-9:20 |
Finish up section 2.4; Discuss Hwk 4. Note on the COGA study | Homework 4 due. |
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| Monday, May 5 8.30-9.20 | 2.5 Joint data on more relatives | Chap 3.1,3.2 (posted 05/04/2014)) |
| Wednesday, May 7 8.30-9:20 | 3.1 Linkage, recombination and genetic maps. |
Synthesis of 2.3, 2.4 -- Xianbang Sun Preliminary project info |
| Friday, May 9 8.30-9:20 | Hutterite pedigrees. Lab 3 discussion. | Lab 3 due. |
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| Monday, May 12 8.30-9.20 | 3.2 Likelihood and linkage lod scores | Homework 5 (Posted 05/01/2014: Updated/finalized 05/07/2014). |
| Wednesday, May 14 8.30-9:20 | 3.3 Linkage designs, power and sample size. |
Synthesis 2.5, 3.1 -- Brayan Ortiz Chap 3.3, 3.4, 3.5 (posted 05/11/2014) |
| Friday, May 16 8.30-9:20 | Homework 5 discussion. | Homework 5 due. |
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| Monday, May 19 8.30-9.20 |
3.3 ctd, Power and Information 3.4 IBD at two loci |
Lab 4 (Posted May 15, 2014)
Homework 6a (Half homework: Posted 05/16/2014) |
| Wednesday, May 21 8.30-9:20 | 3.5 Linkage likelihoods for homozygosity mapping |
Synthesis 3.2, 3.3 -- Nan Jiang Chap 3.3, 3.4, 3.5 (updated 05/22/2014) |
| Friday, May 23 8.30-9:20 | Lab 4 and half-homework 6a discussion. |
Lab 4 due.
Half-Homework 6a due. |
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| Monday, May 26 8.30-9.20 | MEMORIAL DAY --no classes | Homework 7 (posted 05/23/2014) |
| Wednesday, May 28 8.30-9:20 |
4.1 Multilocus inheritance: the dependence model 4.2 Estimating genetic maps |
Synthesis 3.4, 3.5 -- Wendy Wang Chap 4.1, 4.2, 4.3 (posted 05/22/2014, updated 6/04/2014) |
| Friday, May 30 8.30-9:20 |
Finish 4.2: Testing locus order and interference Homework 7 discussion. |
Homework 7 due. Lab 5 (posted 05/27/2014, updated 05/29/2014) |
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| Monday, June 2 8.30-9.20 |
4.3 Baum algorithm and linkage lod scores 4.4 Backwards Baum and Probs of IBD |
Chap 4.4 to 4.6 (posted 05/22/2014)
Half-Homework 6b (posted 05/23/2014) |
| Wednesday, June 4 8.30-9:20 |
4.4 EM for genetic maps, and Monte Carlo versions of EM 4.5 Large pedigrees with many markers (skimmed) 4.6 MCMC for IBD probabilities and map-specific lod scores (outline) |
Online course evaluation available. Final list of papers for projects updated. Chap 4.4, 4.5, 4.6 (Updated 06/04/2014) |
| Friday, June 6 8.30-9:20 |
Lab 5 and Homework 6b discussion Relationship of Labs 4 and 5 to MCMC in Notes Ch 4.6 | Lab 5 and Half-Homework 6b due. |
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| EXAMS WEEK, June 9-13 | Projects due. | Projects due 11:59 p.m. June 10 (PDF file by email) |
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