Our research group develops and applies computational tools to study genetic diversity in natural populations. Our goal is to analyze and interpret large-scale genomic data to improve the 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. We enjoy analyzing data from emerging genotyping/sequencing technologies especially from 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
Variation in the intensity of mutation and negative selection across the genomic landscape
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. Some past examples include:
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 review on population genetics models of the spread of advantageous alleles is out in PLoS Genetics!9/22
Ahmed Selim and Hao Shen have joined the lab!8/22
Heather Skeen finished her PhD and has started a teaching/research fellowship at the University of Conneticut!2/21
We are excited to be recruiting for postdocs and/or staff computational scientists. Please contact John with a CV and cover letter if interested.1/21
Our 'GeoVar' paper came out in eLife over the holidays!12/20
Postdoc Dan Rice moves to the NCBI to take a position as a Data Scientist Outreach Coordinator. In this position, Dan will pursue his passion for outreach and education by designing and leading hackathons to bring together researchers and focus them on interesting problems.12/20
Arjun Biddanda finished his PhD and joins Palamara Lab (Oxford)9/20
Joe Marcus completed his Phd and moves to join Grail Biosciences7/20
Xinyi Li and Chi-Chun Liu join the lab2/20
John enjoyed giving talks in the Iowa City Darwin Day celebration and as a plenary speaker at the Advances in Genome Biology and Technology Meeting.