Our research group uses computational tools to study genetic diversity in natural populations. Our goal is to develop widely used statistical methods for intelligently extracting information from large-scale genomic data with the aim to improve understanding of: (1) basic genomic biology, (2) the biology of heritable disease traits, (3) the genetic basis of evolutionary processes, and (4) the history and evolution of various species, especially humans.
From a disciplinary perspective, most of the ideas we use are from theoretical population genetics, statistical genetics, and computational statistics. Much of our work is invigorated by addressing data from emerging genotyping and sequencing technologies applied to large or particularly interesting population samples.
Our core projects address the following broad problems:
Methods for studying and visualizing population structure
Methods for leveraging haplotype data for methods for inference in population genetics
The impact of recent demographic processes, particularly rapid recent growth
Much of our work focuses on human genetic data, motivated in equal parts by an inherent curiosity, by the biomedical importance, and by the relevance for a broader understanding of evolution in all organisms. Our projects address:
Patterns of population structure in human populations especially within world regions and finer spatial-scales
The impact of recent demographic processes, particularly rapid recent growth, on human genetics
The interaction of selection and demographic history in human evolutionary history
Inference of relative recombination rates from local ancestry patterns in admixed populations
Correcting for population structure in human genome-wide association studies
Personalized genomics: Inference of detailed individual ancestry from genetic data
Human ancient DNA studies
With the help of great collaborators, we have worked on several additional questions in evolutionary genetics and molecular evolution:
Canid evolution: With Bob Wayne (UCLA), we work on problems regarding wolf population structure, early dog domestication, wolf-dog introgression, and canid mutation rates.
Dobzhansky-Muller incompabilitites (DMIs) in mice: With Bret Payseur (Wisconsin), we work on the local ancestry signatures made by DMIs.
Avian migration: With Kristen Ruegg (UCSC) and Tom Smith (UCLA), we have worked on methods for studying seasonal bird migrations.
Evolve-and-resequence studies: With Tom Turner (UCSB), we have developed methods and simulations for understanding evolve-and-resequence studies in Drosophila.
Codon usage bias: With Dennis Wall and Josh Herbeck (when we were all back at UC-Berkeley), we produced a method for measuring for codon usage bias while accounting for background nucleotide composition.
Beyond our research goals, we have the following training and outreach aims:
Train graduate students and postdoctoral fellows in the interdisciplinary skills necessary to make independent, insightful contributions to contemporary research problems in human genetics and evolutionary biology.
Develop teaching materials and courses to help: (1) prepare a new generation of biologists that will need strong skills in quantitative reasoning and computation to address the vast amounts of data now readily available; (2) prepare future citizens who are well-informed and capable of sound decision-making in a world in which science and particularly genetics will play an increasingly important role for society.
Promote international collaborative experiences for students to help foster individual growth and to strengthen scientific institutions and training programs through exchange.
John Novembre, PhD
Department of Human Genetics
Department of Ecology & Evolution
University of Chicago
BA, The Colorado College (2000)
PhD, University of California-Berkeley (2006)
Our paper, led by PhD student Joel Smith, on inferring coalsecent times for selected alleles came out in Molecular Biology and Evolution.1/17
Dan Rice helped put together a fun 2-day lab retreat/workshop on presentation skills (the "Talkathon").11/17
The lab enjoyed a visit from Constanza de la Fuente, a PhD student with Eske Willerslev at the GeoGenetics Institute in Copenhagen. Constanza brought a wealth of information about ancient DNA and population genetic analysis of Siberian populations.11/17
We welcomed a new scientific programmer, Chi-Chun Liu! Chi-Chun just finished his masters in Statistics working with Dan Nicolae on admixture models and local ancestry inference.10/17
Members of the lab attended and presented at the ASHG meeting in Orlando, Florida.10/17
Dan Rice and Hussein attended the Probabilistic Modeling in Genomics (ProbGen) meeting in Aarhus, where Dan gave a talk on his work on multiple merger coalescents and Hussein presented a poster on his work on migration maps.9/17
We said goodbye to Ben Peter, who is now a group leader at the Max Planck Institute in Leipzig, Germany!8/17
The lab attended the fourth Midwest PopGen Meeting at Michigan State University. Visiting Rich Lenski's lab to see the home of his famous artificial evolution experiment was a great highlight.6/17
We bid farewell to Mark Reppell, who is now a senior scientist at AbbVie Pharmaceuticals!5/17
PhD student Arjun Biddanda successfully defended his PhD proposal.