- Name: Gota Morota
- Office: 368 Litton Reaves Hall
- Email: morota@vt.edu
- Web: http://morotalab.org/
- Office Hours: By appointment

- Name: Haipeng Yu
- Office: 3695 Litton Reaves Hall
- Email: haipengyu@vt.edu
- Web: https://haipengu.github.io/
- Office Hours: By appointment

- Mon/Wed/Fri 12:20-1:10pm
- Wallace Hall 244

- understand the statistical theory behind commonly used quantitative methods in genomics
- apply statistical methods to high-dimensional genomic data and analyze them using statistical computing tools
- critically review current literature in statistical and quantitative genetics

- [PDF]

- 1/22 (W): Course overview and Introduction [HTML1][HTML2]
- 1/24 (F): Ordinary least-squares and the curse of dimensionality
- 1/27 (M): Ordinary least-squares and the curse of dimensionality
- 1/29 (W): Ordinary least-squares and the curse of dimensionality [R]
- 1/31 (F): Review of allele and genotypic frequencies [R]
- 2/3 (M): Variance of allelic counts [HW1]
- 2/5 (W): Linkage disequilibrium [R]
- 2/7 (F): Life Science Seminar by Dr. Scott Lowman [WWW1][WWW2]
- 2/10 (M): Covariance between allelic counts
- 2/12 (W): Correlation between allelic counts & Marker genotype imputation [R]
- 2/14 (F): Multi-locus additive genetic variance in the presence of linkage disequilibrium
- 2/17 (M): Whole-genome regression - ridge regression 1 [R][HW2]
- 2/19 (W): Whole-genome regression - ridge regression 2 [R]
- 2/21 (F): Whole-genome regression - ridge regression 3 [R]
- 2/24 (M): LASSO & Additive genomic relationship matrix [R]
- 2/26 (W): Additive genomic relationship matrix & Guest lecture by Dr. Luiz Peternelli - An overview of the sugarcane breeding program and its challenges [R]
- 2/28 (F): Genomic best linear unbiased prediction [R]
- 3/2 (M): Single-marker linear mixed model GWAS - 1
- 3/4 (W): Single-marker linear mixed model GWAS - 2
- 3/6 (F): Single-marker linear mixed model GWAS - 3 and Generalized least squares [R][R]
- 3/9 (M): Spring break
- 3/11 (W): Spring break
- 3/13 (F): Spring break
- 3/16 (M): Extended spring break
- 3/18 (W): Extended spring break
- 3/20 (F): Extended spring break
- 3/23 (M): HW1 review and Single-marker linear mixed model GWAS - 4 (moved to an online format due to COVID-19 pandemic) [HW3]
- 3/25 (W): Mixed model equations for single-marker linear mixed model GWAS & Ridge regression BLUP [R][R]
- 3/27 (F): Genomic BLUP MME & Weighted least squares single-marker GWAS [R][R]
- 3/30 (M): Decoding mixed model equations [R]
- 4/1 (W): Decoding mixed model equations & Single-marker MLM GWAS using GAPIT [R]
- 4/3 (F): Cross-validation for genomic prediction - 1 [R]
- 4/6 (M): Compressed mixed linear model GWAS & Cross-validation for genomic prediction - 2 [R][HW4]
- 4/8 (W): A list of papers for Zoom presentations [TXT]
- 4/10 (F): Multiple testing correction in GWAS [HTML]
- 4/13 (M): Variance components
- 4/15 (W): Variance components
- 4/17 (F): Variance components [HTML]
- 4/20 (M): HW5 [HW5]
- 4/22 (W): Bayesian ridge regression & Bayesian LASSO [HTML]
- 4/24 (F): Bayesian alphabet [HTML]
- 4/27 (M): Estimating genomic heritability from Bayesian marker-based regression models [HTML]
- 4/29 (W): Student presentations
- 5/1 (F): Student presentations
- 5/4 (M): Final exam [HTML]