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 biologist 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)
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.5/17
PhD student Arjun Biddanda successfully defended his PhD proposal.5/17-7/17
PhD student Evan Koch is participating in the NSF GROW program by spending a few months in Uppsala, Sweden where he is working in the lab of Hans Ellegren.5/17
John gave a keynote at the Great Lakes Bioinformatics Meeting here in Chicago.5/17
John served as an external examiner for the PhD of Jose Victor Moreno Mayar, a student of Eske Willerslev and Anna Sapfo Malaspinas in the GeoGenetics Institute in Copenhagen.5/17
The SardiNIA/Progenia project had a paper led by Mauro Pala and Stephen Montgomery's team published in Nature Genetics and the long awaited BAFF paper led by Maristella Steri and Francesco Cucca's team was published in the New England Journal of Medicine!5/17
The search for a population geneticist in the Ecology and Evolution department is complete and we're excited that Matthias Steinrucken will be coming this September to join our faculty!4/17
A long interview article published by Quanta magazine featured John.4/17
The lab enjoyed a visit from Erik Lundgreen, a PhD student with Peter Ralph, working on non-stationary isolation-by-distance problems.3/17
We welcomed a new postdoctoral fellow Daniel Rice, who is part of the prestigious Chicago Fellows program!