Human Population Genomics

Section 1:  Population genetic theory 
1.Coalescent models (all the basics)  (John Wakeley: wakeley@fas.harvard.edu) 
2.Linkage disequilibrium (Monty Slatkin: slatkin@berkeley.edu) a.r^2, D'b.LD and population historyc.Recombination and LD
3.Analysis of population structure (Per Sjödin, Lucie Gattepaille, Pontus Skoglund, Carina Schlebusch, and Mattias Jakobsson): mattias.jakobsson@ebc.uu.se) d.How do we quantify population structure?e.PCAf.Estimating Treesg.Likelihood based genealogical approachesh.FSTi.Estimation of parameters based on SFSj.STRUCTURE analysesk.Admixture HMMsl.D statistics? 4.Inferring selection from population genetic DNA sequence data (David Enard) m.Frequency spectrum-based approaches.Haplotype-based approacheso.Multi-population-based approaches

Section 2:  Association studies and medical genetics
5.Methods for association studies (John Witte and Rebecca Graff) a.Case-control studiesb.Family based studiesc.Quantitative traitsd.Controlling for stratification.Multiple testing, etc. 
6.IBD Mapping for complex traits (Elizabeth Thompson: eathomp@u.washington.edu) 

7.What have we learned from GWAS? (Ben Voight: bvoight@broadinstitute.org) p. Effect sizesq.Missing heritability 

Section 3:  Human evolutionary population genetics
8.Human origins and ancient human demographic history (Jeff Wall: WallJ@humgen.ucsf.edu) 
9.Evidence and examples of selective sweeps across the human genome (Leslie S. Emery and Josh Akey: akeyj@uw.edu) 

Kirk E. Lohmueller is an Associate Professor in the Department of Ecology and Evolutionary Biology as well as Human Genetics at UCLA. He received his PhD from Cornell University in 2010 and then was a Miller Fellow at UC Berkeley till 2013 when he joined the faculty at UCLA. Dr. Lohmueller is a population geneticist who studies a wide range of organisms, including humans, mice, dogs, wolves, foxes, birds, sea otters, and plants. A major focus of his research is understanding how deleterious mutations impact genomes and complex traits. He has received several awards including a Sloan Research Fellowship, Searle Scholar Award, and the Hellman Faculty Fellowship. His research has been supported by the National Institutes of Health, National Science Foundation, and National Institute of Justice.

Rasmus Nielsen is a Professor of computational biology in the Department of Integrative Biology and the Department of Statistics at the UC Berkeley, a position he has held since 2008. He obtained his PhD from UC Berkeley in 1998, did a two-year postdoc at Harvard University 1998-2000, was an Assistant Professor at Cornell University 2000-2004 and has also been a Professor at University of Copenhagen since 2004. His work focuses on statistical and computational methods in genetics, including methods for elucidating human history using genomic data. He has received multiple fellowships and awards for his work including a Fulbright fellowship, a Sloan Research Fellowship, the AAAS Newcomb Clevealand Price, and the Villum Kann Rasmussen Annual Award. He has published more than 300 peer reviewed publications which have been cited by other researchers more than 75,000 times.

"This book is likely to be most useful to PhD students in the early stages of their graduate degree ... . By reading this edited volume, researchers will feel empowered and be able to interpret complex human genomic datasets. ... Human Population Genomics: Introduction to Essential Concepts and Applications would be a valuable addition to the bookshelf of any research group that studies this topic." (Joseph Lachance, The Quarterly Review of Biology, Vol. 97 (3), September, 2022)