Special Topics in Genetics and Genomics (140.668)


Articles for discussion, Second Term, 2006-2007

Articles in bold take priority. Read others as you are able and according to your interest.

Nov 6

McPeek MS, Speed TP (1995) Modeling interference in genetic recombination. Genetics 139:1031-1044 [pdf]

Zhao H, Speed TP, McPeek MS (1995) Statistical analysis of crossover interference using the chi-square model. Genetics 139:1045-1056 [pdf]

Broman KW, Rowe LB, Churchill GA, Paigen K (2002) Crossover interference in the mouse. Genetics 160:1123-1131 [pdf]

Nov 13

Lander ES, Green P (1987) Construction of multilocus genetic linkage maps in humans. Proceedings of the National Academy of Sciences USA 84:2363-2367 [pdf]

Rabiner LR (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77:257-286 [pdf]

Lincoln SE, Lander ES (1992) Systematic detection of errors in genetic linkage data. Genomics 14:604-610 [pdf]

Armstrong NJ, McPeek MS, Speed TP (2006) Incorporating interference into linkage analysis for experimental crosses. Biostatistics 7:374-386 [pdf]

Nov 20

Dempster AP, Laird NM, Rubin DB (1977) Maximum likelihood from incomplete data via the EM algorithm (with discussion). Journal of the Royal Statistical Society Series B 39:1-38 [pdf]

Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185-199 [pdf]

Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963-971 [pdf]

Nov 27

Haley CS, Knott SA (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69:315-324

Feenstra B, Skovgaard IM, Broman KW (2006) Mapping quantitative trait loci by an extension of the Haley-Knott regression method using estimating equations. Genetics 173:2269-2282 [pdf]

Sen S, Churchill GA (2001) A statistical framework for quantitative trait mapping. Genetics 159:371-387 [pdf]

Dec 4

Kruglyak L, Lander ES (1995) A nonparametric approach for mapping quantitative trait loci. Genetics 139:1421-1428 [pdf]

Xu S, Atchley WR (1996) Mapping quantitative trait loci for complex binary diseases using line crosses. Genetics 143:1417-1424 [pdf]

Broman KW (2003) Mapping quantitative trait loci in the case of a spike in the phenotype distribution. Genetics 163:1169-1175 [pdf]

Dec 11

Zeng Z-B (1993) Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. Proceedings of the National Academy of Sciences USA 90:10972-10976 [pdf]

Zeng Z-B (1994) Precision mapping of quantitative trait loci. Genetics 136:1457-1468 [pdf]

Dec 18

Kao C-H, Zeng Z-B (1997) General formulas for obtaining the MLEs and the asymptotic variance-covariance matrix in mapping quantitative trait loci when using the EM algorithm. Biometrics 53:653-665 [pdf]

Zeng Z-B, Kao C-H, Basten CJ (1999) Estimating the genetic architecture of quantitative traits. Genet Res 74:279-289 [pdf]

Broman KW, Speed TP (2002) A model selection approach for the identification of quantitative trait loci in experimental crosses (with discussion). J R Statist Soc B 64:641-656, 737-775 [pdf]

Yi N (2004) A unified Markov chain Monte Carlo framework for mapping multiple quantitative trait loci. Genetics 167:967-975 [pdf]

Yi N, Yandell BS, Churchill GA, Allison DB, Eisen EJ, Pomp D (2005) Bayesian model selection for genome-wide epistatic QTL analysis. Genetics 170:1333-1344 [pdf]


Course syllabus

Last modified: Wed Dec 13 09:51:25 EST 2006