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Revision as of 03:43, 5 January 2017
, 03:43, 5 January 2017→Scheduling
== Scheduling ==
== Scheduling ==
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 ==
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.
=== Class Worksheets ===
=== Class Worksheets ===
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)]]
September 22 - [[Media:Question_Sheet_-_Howie_et_al_(2012)_Nat_Genet.pdf|Howie et al (2012)]]
September 29 - [[Media:Question_Sheet_-_Menelaou_et_al_(2013)_Bioinformatics.pdf|Menelaou et al (2013)]]
'''October 6 - School of Public Health Symposium'''
October 7 - Delaneau et al (2013)
'''October 13/14 - University Fall Break'''
'''October 20/21 - American Society of Human Genetics Meeting'''
October 27 - [[Media:Question_Sheet_-_Li_and_Durbin_(2009)_Bioinformatics.pdf|Li and Durbin (2009)]]
November 3 - [[Media:Question_Sheet_-_Iqbal_et_al_(2012)_Nature_Genetics.pdf|Iqbal et al (2012)]]
November 17 - [[Media:Question_Sheet_-_Albers_et_al_(2010)_Genome_Research.pdf|Albers et al (2010)]]
November 24 - [[Media:Question_Sheet_-_Kircher_et_al_(2014)_Nature_Genetics.pdf|Kircher et al (2014)]]
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)]]
== Standards of Academic Conduct ==
== Standards of Academic Conduct ==
* 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
* Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J (2013) A general framework for estimating the relative pathogenicity of human genetic variants. ''Nat. Genet.'' '''46''' 310–315
* 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
* 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
* Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ''Bioinformatics.'' '''25''':1754-60. PMID: 19451168
* 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]]]
* Menelaou A, Marchini J (2013) Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold. ''Bioinformatics.'' '''29''':84-91. PMID: 23093610
* 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
* Schiffels S, Durbin R (2014) Inferring human population size and separation history from multiple genome sequences. ''Nat Genet.'' '''46''':919-25
* Schiffels S, Durbin R (2014) Inferring human population size and separation history from multiple genome sequences. ''Nat Genet.'' '''46''':919-25
* 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) ''Nat Genet. 2014'' '''46''':409-15
* 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
* 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
* 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
* 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
