BTRY_6890_2013

BTRY 6890
Topics in Population Genetics and Genomics
Spring 2013

 

Instructor: Alon Keinan (ak735[at]cornell.edu)
Biological Statistics and Computational Biology (BSCB), 221 Weill Hall

To subscribe: Send a mail to statgenj-l-request@list.cornell.edu with the word 'join' in the body of the message

Where: Weill Hall 221
When: Wednesdays from 1:30 to 2:20 pm

Description:
BTRY 6890 is graduate seminar on population genetics and comparative genomics. It takes the form of a Journal Club, where each week students, post-doc and faculty meet to discuss a short scientific publication. During these meetings, one participant of the group gives a brief overview of a pre-defined paper and then the group discusses the methods and the results.

A list of papers to pick for discussion will be presented during the first meeting.
These papers are carefully chosen to be representative of recent research in population genetics and statistical genetics.

Having several weeks around the same topic will permit to: 1) acquire a broad understanding of the topics of interest, 2) in-depth study of current scientific issues and challenges related to these topics, 3) develop a critical approach to scientific results.

This is a 1 credit course (S/U). The requirements for taking it for credit are:
1. Lead the discussion for one of the weeks of the class.
2. Attendance and participation in discussions.
 

Schedule of presentations:
 

Date Presenter Paper Link
01/23/2013 Alon Keinan (ak735) Introduction  
Kaixiong Ye (ky279) Sex-biased genetic effects on gene regulation in humans. (Dimas AS et al. 2012) Click Here
01/30/2013 Haley Hunter-Zinck (hsh37) Identifying Personal Genomes by Surname Inference. (Melissa Gymrek et al. 2013) Click Here
02/06/2013 Kaixiong Ye (ky279) Seventy-five genetic loci influencing the human red blood cell. (Pim van der et al. 2012) Click Here
02/13/2013 Katherine Wilkins (kew226) Recombination drives vertebrate genome contraction. (Nam K et al. 2012) Click Here
02/20/2013 Elodie Gazave (eeg47) Population demographic history can cause the appearance of recombination hotspots. (Johnston HR, 2012) Click Here
02/27/2013 Ilan Gronau (ig67) Inference of population splits and mixtures from genome-wide allele frequency data. (Pickrell JK et al. 2012) Click Here
03/06/2013 Nick Fletcher (nkf32) Inference of population structure using dense haplotype data. (Lawson DJ et al. 2012) Click Here
03/13/2013 Sri Raj (smr46) Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant. (Kamberov YG et al. 2013)
Identifying Recent Adaptations in Large-Scale Genomic Data. (Grossman SR et al. 2013)
Click Here
Click Here
03/20/2013 Spring Break … Spring Break … Spring Break
03/27/2013 Diana Chang (dc584) Common Risk Alleles for Inflammatory Diseases Are Targets of Recent Positive Selection. (Raj T et al. 2013) Click Here
04/03/2013 Nick Mason (nam232) Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture. (Pool JE et al. 2012) Click Here
04/10/2013 Li Ma (lm529) Properties and Modeling of GWAS when Complex Disease Risk Is Due to Non-Complementing,
Deleterious Mutations in Genes of Large Effect. (Thornton KR et al. 2013)
Click Here
04/17/2013 Feng Gao (fg237) A model-based approach for analysis of spatial structure in genetic data. (Yang WY et al. 2012) Click Here
04/24/2013 CANCELLED
05/01/2013 Chau Nguyen (cmn68) Estimating the human mutation rate using autozygosity in a founder population. (Campbell CD et al. 2012) Click Here

 

 

Paper List:

 

1. Reich D, Patterson N, Campbell D, Tandon A, Mazieres S,et al. Reconstructing Native American population history. Nature. 2012 Aug 16;488(7411):370-4. doi: 10.1038/nature11258. Click Here

2. Pim van der Harst P, Zhang W, Mateo Leach I, Rendon A, et al. Seventy-five genetic loci influencing the human red blood cell. Nature. 2012 Dec 20;492(7429):369-75. doi: 10.1038/nature11677. Click Here

3. Melissa Gymrek, Amy L. McGuire, David Golan, Eran Halperin, Yaniv Erlich. Identifying Personal Genomes by Surname Inference. Science. 2013 Jan 18;339 (6117):321-324. doi:10.1126/science.1229566. Click Here

4. Wong LP, Ong RT, Poh WT, Liu X, Chen P, et al. Deep whole-genome sequencing of 100 southeast asian malays. Am J Hum Genet. 2013 Jan 10;92(1):52-66. doi: 10.1016/j.ajhg.2012.12.005. Click Here

5. Charlesworth B. Background Selection 20 Years on: The Wilhelmine E. Key 2012 Invitational Lecture. J Hered. 2013 Jan 8. Click Here

6. Pool JE, Corbett-Detig RB, Sugino RP, Stevens KA, et al. Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture. PLoS Genet. 2012 Dec;8(12):e1003080. doi: 10.1371/journal.pgen.1003080. Click Here

7. Dimas AS, Nica AC, Montgomery SB, Stranger BE, Raj T, et al. Sex-biased genetic effects on gene regulation in humans. Genome Res. 2012 Dec;22(12):2368-75. doi: 10.1101/gr.134981.111. Click Here

8. Jakobsson M, Edge MD, Rosenberg NA. The Relationship Between FST and the Frequency of the Most Frequent Allele. Genetics. 2012 Nov 19. Click Here

9. Gautier M, Vitalis R. Inferring Population Histories Using Genome-Wide Allele Frequency Data. Mol Biol Evol. 2012 Dec 14. Click Here

10. Pickrell JK, Pritchard JK. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 2012 Nov;8(11):e1002967. doi:10.1371/journal.pgen.1002967. Click Here

11. Yang MA, Malaspinas AS, Durand EY, Slatkin M. Ancient structure in Africa unlikely to explain neanderthal and non-african genetic similarity. Mol Biol Evol. 2012 Oct;29(10):2987-95. Click Here

12. Lawson DJ, Hellenthal G, Myers S, Falush D. Inference of population structure using dense haplotype data. PLoS Genet. 2012 Jan;8(1):e1002453. doi:10.1371/journal.pgen.1002453. Click Here

13. Henn BM, Botigué LR, Gravel S, Wang W, et al. Genomic ancestry of North Africans supports back-to-Africa migrations. PLoS Genet. 2012 Jan;8(1):e1002397. doi: 10.1371/journal.pgen.1002397. Click Here

14. Schadt EE, Woo S, Hao K. Bayesian method to predict individual SNP genotypes from gene expression data. Nat Genet. 2012 May;44(5):603-8. doi: 10.1038/ng.2248. Click Here

15. Chen LS, Hsu L, Gamazon ER, Cox NJ, Nicolae DL. An exponential combination procedure for set-based association tests in sequencing studies. Am J Hum Genet. 2012 Dec 7;91(6):977-86. doi: 10.1016/j.ajhg.2012.09.017. Click Here

16. Rohlfs RV, Fullerton SM, Weir BS. Familial identification: population structure and relationship distinguishability. PLoS Genet. 2012 Feb;8(2):e1002469. doi: 10.1371/journal.pgen.1002469. Click Here

17. Yang WY, Novembre J, Eskin E, Halperin E. A model-based approach for analysis of spatial structure in genetic data. Nat Genet. 2012 May 20;44(6):725-31. doi: 10.1038/ng.2285. Click Here

18. Palamara PF, Lencz T, Darvasi A, Pe'er I. Length distributions of identity by descent reveal fine-scale demographic history. Am J Hum Genet. 2012 Nov 2;91(5):809-22. doi: 10.1016/j.ajhg.2012.08.030. Click Here

19. Ladouceur M, Dastani Z, Aulchenko YS, Greenwood CM, Richards JB. The empirical power of rare variant association methods: results from sanger sequencing in 1,998 individuals. PLoS Genet. 2012 Feb;8(2):e1002496. doi: 10.1371/journal.pgen.1002496. Click Here

20. Campbell CD, Chong JX, Malig M, Ko A, et al. Estimating the human mutation rate using autozygosity in a founder population. Nat Genet. 2012 Nov;44(11):1277-81. doi: 10.1038/ng.2418. Click Here

21. Ehret GB, Lamparter D, Hoggart CJ; Genetic Investigation of Anthropometric Traits Consortium, Whittaker JC, Beckmann JS, Kutalik Z. A multi-SNP locus-association method reveals a substantial fraction of the missing heritability. Am J Hm Genet. 2012 Nov 2;91(5):863-71. doi: 10.1016/j.ajhg.2012.09.013. Click Here

22. Johnston HR, Cutler DJ. Population demographic history can cause the appearance of recombination hotspots. Am J Hum Genet. 2012 May 4;90(5):774-83. doi: 10.1016/j.ajhg.2012.03.011. Click Here

23. 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 Nov 1;491(7422):56-65. doi: 10.1038/nature11632. Click Here

24. Nam K, Ellegren H. Recombination drives vertebrate genome contraction. PLoS Genet. 2012;8(5):e1002680. doi: 10.1371/journal.pgen.1002680. Click Here

25. Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K, Kosakovsky Pond SL. Detecting individual sites subject to episodic diversifying selection. PLoS Genet. 2012;8(7):e1002764. doi: 10.1371/journal.pgen.1002764. Click Here

26. Multiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees. (Ellen M. Leffler et al. 2013, Science) Click Here