BTRY 6820/4820 Statistical Genomics:
Coalescent Theory and Human Population Genomics
Spring 2016


Course Syllabus

A copy of the course syllabus can be found here


Staff Information

Lectures: Tuesday/Thursday 10:10 - 11:25 AM, Comstock B108
Session: Thursday 12:20 - 1:10 PM, Comstock B108

Instructor: Alon Keinan
Office Hours: Tuesdays 4-5pm, 102C Weill Hall
ak735 at cornell dot edu

TA: Andrea Slavney, ajs592
Office Hours: Tuesdays 1-2pm, 102 Weill Hall Conference Room


Course Information

Course Summary: 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 will connect the theory to current research in the field of human population genomics, including studies on modern human adaptation, genetic history, admixture with archaic hominids, the recent explosive growth of human populations, human population structure, and tools employed by direct-to-consumer services such as offered by 23andMe and the Genographic Project.

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 component 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: The course is intended for graduate and advanced undergraduate students in fields/majors such as computational biology, biometry, statistics, applied math, genetics and development, ecology and evolutionary biology, and computer science. While there are no strict prerequisites for this course, statistical, mathematical, and computational skills are highly encouraged. Homework will include programming (preferably in C/C++, Python, or Java, 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 TAs.

Main Textbook: Coalescent Theory: An Introduction / John Wakeley. Roberts & Co. Publishers, 2009 (ISBN: 978-0-9747077-5-4)
Class materials will be made available on Blackboard