Seminar Bioinformatik

This seminar will focus on population genetics. We will use some of the following papers: (BSc students:- Hitch-hikingSmith, John Maynard, and John Haigh. “The Hitch-Hiking Effect of a
Favourable Gene.” Genetics Research 23, no. 01 (1974): 23–35.
doi:10.1017/S0016672300014634.- Background selection - 1000 Genomes Project http://www.1000genomes.org)

Introduction

Kingman, J. F. C. "On the Genealogy of Large Populations." Journal of Applied Probability 19 (January 1, 1982): 27-43. doi:10.2307/3213548.

Demography

Patterson, Nick, Alkes L Price, and David Reich. “Population Structure and Eigenanalysis.” PLoS Genet 2, no. 12 (December 22, 2006): e190. doi:10.1371/journal.pgen.0020190.

Falush, Daniel, Matthew Stephens, and Jonathan K. Pritchard. “Inference of Population Structure Using Multilocus Genotype Data: Linked Loci and Correlated Allele Frequencies.” Genetics 164, no. 4 (August 1, 2003): 1567–87.

Gutenkunst, Ryan N., Ryan D. Hernandez, Scott H. Williamson, and Carlos D. Bustamante. “Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data.” PLoS Genet 5, no. 10 (October 23, 2009): e1000695. doi:10.1371/journal.pgen.1000695.

Li, Heng, and Richard Durbin. “Inference of Human Population History from Individual Whole-Genome Sequences.” Nature 475, no. 7357 (July 28, 2011): 493–496. doi:10.1038/nature10231.

Sankararaman et al, The genomic landscape of Neanderthal ancestry in present-day humans, Nature 2014 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12961.html

Recombination inference

McVean, Gilean A. T., Simon R. Myers, Sarah Hunt, Panos Deloukas, David R. Bentley, and Peter Donnelly. “The Fine-Scale Structure of Recombination Rate Variation in the Human Genome.” Science 304, no. 5670 (April 23, 2004): 581–84. doi:10.1126/science.1092500.

Song, Yun S., Yufeng Wu, and Dan Gusfield. “Efficient Computation of Close Lower and Upper Bounds on the Minimum Number of Recombinations in Biological Sequence Evolution.” Bioinformatics 21, no. suppl 1 (June 1, 2005): i413–i422. doi:10.1093/bioinformatics/bti1033.

Selective sweeps and GWAS

Messer, Philipp W., and Dmitri A. Petrov. “Population Genomics of Rapid Adaptation by Soft Selective Sweeps.” Trends in Ecology & Evolution. Accessed September 26, 2013. doi:10.1016/j.tree.2013.08.003.

Sabeti, Pardis C., Patrick Varilly, Ben Fry, Jason Lohmueller, Elizabeth Hostetter, Chris Cotsapas, Xiaohui Xie, et al. “Genome-Wide Detection and Characterization of Positive Selection in Human Populations.” Nature 449, no. 7164 (October 18, 2007): 913–918. doi:10.1038/nature06250.

Lippert, Christoph, Jennifer Listgarten, Ying Liu, Carl M. Kadie, Robert I. Davidson, and David Heckerman. “FaST Linear Mixed Models for Genome-Wide Association Studies.” Nature Methods 8, no. 10 (October 2011): 833–35. doi:10.1038/nmeth.1681.

Schedule