33
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchBiostatistics 866: Main Page (view source)
Revision as of 07:21, 18 April 2017
, 07:21, 18 April 2017→Student Presentations
== Scheduling ==
== Scheduling ==
For Winter 2017, classes are scheduled for Tuesdays and Thursday, 8:30 - 10 am.
For Winter 2017, classes are scheduled for Tuesdays and Thursdays, 8:30 - 10 am in SPH II, room 1152.
== Grading ==
== 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 ==
=== Hidden Markov Models ===
Week of January 8 - [[Media:Question_Sheet_-_Li_et_al_(2010)_Gen_Epid.pdf|Li et al (2010)]]
Week of January 15 - [[Media:Question_Sheet_-_Howie_et_al_(2012)_Nat_Genet.pdf|Howie et al (2012)]] (and, [[Media:866_-_Slides_for_Hyun.pdf|Discussion slides for January 19]])
Week of January 22 - [[Media:Question_Sheet_-_Delaneau_et_al_(2013)_Nature_Methods.pdf|Delaneau et al (2013)]]
Week of January 29 - [[Media:Question_Sheet_-_Boehnke_and_Cox_(1997)_AJHG.pdf|Boehnke and Cox (1997)]]
=== Short Read Sequencing ===
February 12 - [[Media:Question_Sheet_-_Li_et_al_(2008)_Genome_Research.pdf|Li et al (2008)]]
February 19 - [[Media:Question_Sheet_-_Li_and_Durbin_(2009)_Bioinformatics.pdf|Li and Durbin (2009)]]
March 5 - [[Media:Question_Sheet_-_Zerbino_and_Birney_(2008)_Bioinformatics.pdf|Zerbino and Birney (2008)]]
March 12 - [[Media:Question_Sheet_-_Iqbal_et_al_(2012)_Nature_Genetics.pdf|Iqbal et al (2012)]]
=== Association Analysis ===
March 19 - [[Media:Question_Sheet_-_2017_-_Kang_et_al_(2010)_Nature_Genetics_.pdf|Kang et al (2010)]]
March 26 - [[Media:Question_Sheet_-_2017_-_Wu_et_al_(2011)_American_Journal_of_Human_Genetics.pdf|Wu et al (2011)]]
April 2 - [[Media:Question_Sheet_-_2017_-_Liu_et_al_(2013)_Nature_Genetics.pdf|Liu et al (2014)]]
=== Adventures in Statistical Genetics ===
April 9 - [[Media:2017.04_-_Adventures_in_Human_Genetics.pdf|Goncalo's Adventure in Human Genetics]]
== Student Presentations ==
*[[Media:Zajac_Journey_Lecture.pdf | Greg]]
*[https://www.dropbox.com/sh/9buuwbojq3tmp1f/AAADGOK-0yyKTfLiwG984QCHa?dl=0 Dropbox]
== Standards of Academic Conduct ==
== Standards of Academic Conduct ==
== Planned Reading ==
== Planned Reading ==
* Abecasis GR, Cherny SS, Cookson WO, Cardon LR (2002) Merlin--rapid analysis of dense genetic maps using sparse gene flow trees. ''Nat Genetics'' '''30''':97-101
* Boehnke M and Cox N (1997) Accurate Inference of Relationships in Sib-Pair Linkage Studies. ''Am J Hum Genet'' '''61''':423-429
* Coventry A, Bull-Otterson LM, Liu X, Clark AG, Maxwell TJ, Crosby J, Hixson JE, Rea TJ, Muzny DM, Lewis LR, Wheeler DA, Sabo A, Lusk C, Weiss KG, Akbar H, Cree A, Hawes AC, Newsham I, Varghese RT, Villasana D, Gross S, Joshi V, Santibanez J, Morgan M, Chang K, Iv WH, Templeton AR, Boerwinkle E, Gibbs R, Sing CF (2010) Deep resequencing reveals excess rare recent variants consistent with explosive population growth. ''Nat Commun.'' '''1''':131. PMID: 21119644
* Coventry A, Bull-Otterson LM, Liu X, Clark AG, Maxwell TJ, Crosby J, Hixson JE, Rea TJ, Muzny DM, Lewis LR, Wheeler DA, Sabo A, Lusk C, Weiss KG, Akbar H, Cree A, Hawes AC, Newsham I, Varghese RT, Villasana D, Gross S, Joshi V, Santibanez J, Morgan M, Chang K, Iv WH, Templeton AR, Boerwinkle E, Gibbs R, Sing CF (2010) Deep resequencing reveals excess rare recent variants consistent with explosive population growth. ''Nat Commun.'' '''1''':131. PMID: 21119644
* 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
* Yair Field, Evan A Boyle, Natalie Telis, Ziyue Gao, Kyle J Gaulton, David Golan, Loic Yengo, Ghislain Rocheleau, Philippe Froguel, Mark I McCarthy, Jonathan K Pritchard (2016) Detection of human adaptation during the past 2000 years. ''Science'' '''354''':760-764
* Field Y, Boyle EA, Telis N, Gao Z, Gaulton KJ, Golan D, Yengo L, Rocheleau G, Froguel P, McCarthy MI, Pritchard JK (2016) Detection of human adaptation during the past 2000 years. ''Science'' '''354''':760-764
* Jun G, Flickinger M, Hetrick KN, Romm JM, Doheny KF, Abecasis GR, Boehnke M, Kang HM (2012) Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data. ''Am J Hum Genet.'' '''91''':839-48. PMID: 23103226
* Jun G, Flickinger M, Hetrick KN, Romm JM, Doheny KF, Abecasis GR, Boehnke M, Kang HM (2012) Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data. ''Am J Hum Genet.'' '''91''':839-48. PMID: 23103226
* 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
* 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
* Kruglyak L, Daly MJ, Reeve-Daly MP, Lander ES (1996) Parametric and non-parametric linkage analysis: a unified multipoint approach. ''Am J Hum Genet'' '''58''':1347-63
* Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. ''Genome Res.'' '''18''':1851-8. PMID: 18714091
* Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ''Bioinformatics.'' '''25''':1754-60. PMID: 19451168
* Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ''Bioinformatics.'' '''25''':1754-60. PMID: 19451168
