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| == Scheduling == | | == Scheduling == |
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− | For Fall 2013, classes are scheduled for Mondays and Tuesdays, 3:00 - 4:30 pm room M4318 SPH II. | + | For Fall 2014, classes are scheduled for Mondays and Tuesdays, 3:00 - 4:30 pm room M4318 SPH II. |
| + | Tentatively, we will aim for Wednesday 2:00 - 3:30 for office hours and any classes that must be rescheduled. |
| + | |
| + | == Grading == |
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| The final grade will take into account your performance in problem sets and worksheets as well as your participation in class. | | The final grade will take into account your performance in problem sets and worksheets as well as your participation in class. |
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| === Class Worksheets === | | === Class Worksheets === |
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− | September 9 - [[Media:Question_Sheet_-_Li_et_al_(2010)_Gen_Epid.pdf|Li et al (2010)]] | + | September 8 - [[Media:Question_Sheet_-_Li_et_al_(2010)_Gen_Epid.pdf|Li et al (2010)]] |
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| + | September 22 - [[Media:Question_Sheet_-_Howie_et_al_(2012)_Nat_Genet.pdf|Howie et al (2012)]] |
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| + | September 29 - [[Media:Question_Sheet_-_Menelaou_et_al_(2013)_Bioinformatics.pdf|Menelaou et al (2013)]] |
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| + | '''October 6 - School of Public Health Symposium''' |
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| + | October 7 - Delaneau et al (2013) |
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| + | '''October 13/14 - University Fall Break''' |
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| + | '''October 20/21 - American Society of Human Genetics Meeting''' |
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| + | October 27 - [[Media:Question_Sheet_-_Li_and_Durbin_(2009)_Bioinformatics.pdf|Li and Durbin (2009)]] |
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| + | November 3 - [[Media:Question_Sheet_-_Iqbal_et_al_(2012)_Nature_Genetics.pdf|Iqbal et al (2012)]] |
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| + | November 17 - [[Media:Question_Sheet_-_Albers_et_al_(2010)_Genome_Research.pdf|Albers et al (2010)]] |
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| + | November 24 - [[Media:Question_Sheet_-_Kircher_et_al_(2014)_Nature_Genetics.pdf|Kircher et al (2014)]] |
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| + | December 1 - [[Media:Question_Sheet_-_Liu_et_al_(2013)_Nature_Genetics.pdf|Liu et al (2014)]] |
| + | |
| + | December 8 - [[Media:Question_Sheet_-_Kang_et_al_(2010)_Nature_Genetics.pdf|Kang et al (2010)]] |
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| == Standards of Academic Conduct == | | == Standards of Academic Conduct == |
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| * Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nat Genet.'' '''44''':226-32. PMID: 22231483 | | * Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nat Genet.'' '''44''':226-32. PMID: 22231483 |
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| + | * Kang HM, Sul JH, Service SK, Zaitlen NA, Kong SY, Freimer NB, Sabatti C, Eskin E (2010) Variance component model to account for sample structure in genome-wide association studies. ''Nat. Genet.'' '''42''':348-354 |
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| + | * Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J (2014) A general framework for estimating the relative pathogenicity of human genetic variants. ''Nat. Genet.'' '''46''' 310–315 |
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| + | * Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ''Bioinformatics.'' '''25''':1754-60. PMID: 19451168 |
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| * Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR (2010) MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. ''Genet Epidemiol.'' '''34''':816-34. PMID: 21058334 [[Biostatistics 830 - Code Snippets|[Code Snippets]]] | | * Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR (2010) MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. ''Genet Epidemiol.'' '''34''':816-34. PMID: 21058334 [[Biostatistics 830 - Code Snippets|[Code Snippets]]] |
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| + | * Menelaou A, Marchini J (2013) Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold. ''Bioinformatics.'' '''29''':84-91. PMID: 23093610 |
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| * Lin DY, Zeng D (2010) Meta-analysis of genome-wide association studies: no efficiency gain in using individual participant data. ''Genet Epidemiol.'' '''34''':60-6. PMID: 19847795 | | * Lin DY, Zeng D (2010) Meta-analysis of genome-wide association studies: no efficiency gain in using individual participant data. ''Genet Epidemiol.'' '''34''':60-6. PMID: 19847795 |
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− | * Wen X, Stephens M (2010) Using linear predictors to impute allele frequencies from summary or pooled genotype data. ''Ann Appl Stat.'' '''4''':1158-1182. PMID: 21479081 | + | * Liu DJ, Peloso GM, Zhan X, Holmen OL, Zawistowski M, Feng S, Nikpay M, Auer PL, Goel A, Zhang H, Peters U, Farrall M, Orho-Melander M, Kooperberg C, McPherson R, Watkins H, Willer CJ, Hveem K, Melander O, Kathiresan S, Abecasis GR (2014) Meta-analysis of gene-level tests for rare variant association. ''Nat Genet.'' '''46''':200-4 |
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| + | * Schiffels S, Durbin R (2014) Inferring human population size and separation history from multiple genome sequences. ''Nat Genet.'' '''46''':919-25 |
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| + | * Yang J, Zaitlen NA, Goddard ME, Visscher PM, Price AL (2014) Advantages and pitfalls in the application of mixed-model association methods. ''Nat. Genet.'' '''46''':100-106 |
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| + | * Wang C, Zhan X, Bragg-Gresham J, Kang HM, Stambolian D, Chew EY, Branham KE, Heckenlively J; FUSION Study, Fulton R, Wilson RK, Mardis ER, Lin X, Swaroop A, Zöllner S, Abecasis GR (2014) Ancestry estimation and control of population stratification for sequence-based association studies. ''Nat Genet. 2014'' '''46''':409-15 |
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| + | * Wen X, Stephens M (2010) Using linear predictors to impute allele frequencies from summary or pooled genotype data. ''Ann Appl Stat.'' '''4''':1158-1182. PMID: 21479081 |
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| == Course History == | | == Course History == |