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Biostatistics 830: Main Page (view source)

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→‎Required Reading
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== Required Reading ==
 
== Required Reading ==
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Browning SR, Browning BL (2007) Rapid and accurate haplotype phasing and
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missing-data inference for whole-genome association studies by use of localized
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haplotype clustering. ''Am J Hum Genet.'' '''81''':1084-97. PMID: 17924348
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Coventry A, Bull-Otterson LM, Liu X, Clark AG, Maxwell TJ, Crosby J, Hixson
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JE, Rea TJ, Muzny DM, Lewis LR, Wheeler DA, Sabo A, Lusk C, Weiss KG, Akbar H,
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Cree A, Hawes AC, Newsham I, Varghese RT, Villasana D, Gross S, Joshi V,
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Santibanez J, Morgan M, Chang K, Iv WH, Templeton AR, Boerwinkle E, Gibbs R, Sing
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CF (2010) Deep resequencing reveals excess rare recent variants consistent with
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explosive population growth. ''Nat Commun.'' '''1''':131. PMID: 21119644
    
Delaneau O, Zagury JF, Marchini J (2013) Improved whole-chromosome phasing for
 
Delaneau O, Zagury JF, Marchini J (2013) Improved whole-chromosome phasing for
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disease and population genetic studies. Nat Methods. 10:5-6. PMID: 23269371
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disease and population genetic studies. ''Nat Methods.'' '''10''':5-6. PMID: 23269371
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Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR (2012) Fast and accurate
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genotype imputation in genome-wide association studies through pre-phasing. ''Nat
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Genet.'' '''44''':955-9. PMID: 22820512
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Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G (2012) De novo assembly and
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genotyping of variants using colored de Bruijn graphs. ''Nat Genet.'' '''44''':226-32.
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PMID: 22231483
    
Jun G, Flickinger M, Hetrick KN, Romm JM, Doheny KF, Abecasis GR, Boehnke M,
 
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
 
Kang HM (2012) Detecting and estimating contamination of human DNA samples in
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sequencing and array-based genotype data. Am J Hum Genet. 91:839-48. PMID:
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sequencing and array-based genotype data. ''Am J Hum Genet.'' '''91''':839-48. PMID:
 
23103226
 
23103226
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Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR (2012) Fast and accurate
+
Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling
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genotype imputation in genome-wide association studies through pre-phasing. Nat
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variants using mapping quality scores. ''Genome Res.'' '''18''':1851-8. PMID: 18714091
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Genet. 44:955-9. PMID: 22820512
     −
Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G (2012) De novo assembly and
+
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler
−
genotyping of variants using colored de Bruijn graphs. Nat Genet. 44:226-32.  
+
transform. ''Bioinformatics.'' '''25''':1754-60. PMID: 19451168
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PMID: 22231483
      
Li H, Durbin R (2011) Inference of human population history from individual
 
Li H, Durbin R (2011) Inference of human population history from individual
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whole-genome sequences. Nature. 475:493-6. PMID: 21753753
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whole-genome sequences. ''Nature.'' '''475''':493-6. PMID: 21753753
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Wen X, Stephens M (2010) Using linear predictors to impute allele frequencies from
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summary or pooled genotype data. Ann Appl Stat. 4:1158-1182. PMID: 21479081
  −
 
  −
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
      
Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR (2010) MaCH: using sequence and
 
Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR (2010) MaCH: using sequence and
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genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol.
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genotype data to estimate haplotypes and unobserved genotypes. ''Genet Epidemiol.''
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34:816-34. PMID: 21058334
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'''34''':816-34. PMID: 21058334
    
Lin DY, Zeng D (2010) Meta-analysis of genome-wide association studies: no
 
Lin DY, Zeng D (2010) Meta-analysis of genome-wide association studies: no
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efficiency gain in using individual participant data. Genet Epidemiol. 34:60-6.  
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efficiency gain in using individual participant data. ''Genet Epidemiol.'' '''34''':60-6.  
 
PMID: 19847795
 
PMID: 19847795
   −
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler
+
Wen X, Stephens M (2010) Using linear predictors to impute allele frequencies from
−
transform. Bioinformatics. 25:1754-60. PMID: 19451168
+
summary or pooled genotype data. ''Ann Appl Stat.'' '''4''':1158-1182. PMID: 21479081
−
 
  −
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
      
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly
 
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly
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using de Bruijn graphs. Genome Res. 18:821-9. PMID: 18349386
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using de Bruijn graphs. ''Genome Res.'' '''18''':821-9. PMID: 18349386
−
 
  −
Browning SR, Browning BL (2007) Rapid and accurate haplotype phasing and
  −
missing-data inference for whole-genome association studies by use of localized
  −
haplotype clustering. Am J Hum Genet. 81:1084-97. PMID: 17924348
      
== Course History ==
 
== Course History ==
    
This course is an ad-hoc course, first taught by Goncalo Abecasis in the Fall of 2013.
 
This course is an ad-hoc course, first taught by Goncalo Abecasis in the Fall of 2013.
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/8490"

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