BTRY_4820_6820_2013

BTRY 6820/4820 Statistical Genomics:
Coalescent Theory and Human Population Genomics
Spring 2013

 

Staff Information

Lectures: Tuesday/Thursday 10:10 - 11:25 AM, Warren 145
Session: Thursday 12:20 - 1:10 PM, Warren 145

Instructor: Alon Keinan
OH: Thursday 3-4pm, 102C Weill Hall
ak735 at cornell dot edu

TA: Diana Chang
OH: Tuesday 4-5pm, 102 Weill Hall
dc584 at cornell dot edu

 

Course Information

Course Summary: Provides an introduction to quantitative molecular population genetics through a coalescent theory derived framework. We will discuss inference within and outside the coalescent framework, with a focus on methods for non-model organisms and human population genomics. We will also cover statistical tests for natural selection utilizing the coalescent theory and other frameworks. Throughout the course, we aim to connect the theory to current research in the field of human population genomics, including studies on modern human adaptation, genetic history, admixture with Neandertals and other extinct hominid species, human population structure, and tools employed by direct-to-consumer genetic testing companies such as 23andMe.

Specific topics include: The Moran and Wright-Fisher models, Standard coalescent, Properties of coalescent genealogies, Evidence of Neandertal-Human gene flow, Infinite-sites model, Allele-frequency based tests of "neutrality", Site frequency spectrum for varying demographic history, Structured coalescent, Models of geographic structure, Principle compenent analysis and population structure, Selective sweeps and balancing selection, Natural selection tests via comparison of polymorphism and divergence, Long range haplotype tests of natural selection, Natural selection evidence in human populations, Diploid and two sexes coalescent, Ancestral recombination graph, Linkage disequilibrium in human populations, Coalescent simulations, Statistical inference and the coalescent

Primary Audience / Prerequisites: Graduate and advanced undergraduate students in computational biology, biometry, applied math, genetics and development, ecology and evolutionary biology, statistics and computer science. While there are no strict prerequisites for this course, statistical and computational skills are highly encouraged. Most homework assignments will involve programming (preferably in Java, C/C++, or Python, but R, Matlab, Perl and others can also be considered). A background in genetics will also be helpful. If in any doubt about your background, please do not hesitate to contact the instructor or the TA.

Main Textbook: Coalescent Theory: An Introduction (John Wakeley 2009)
Available on Reserve at Mann Library. Students can also purchase the textbook from the Cornell Store.

Class materials will be made available on Blackboard