John Novembre, Ph.D.


Office address: CLSC 421
Telephone number: 773 834 8217

Research Description

My research group uses computational approaches to answer questions regarding the evolutionary processes that have shaped human genetic diversity and disease.  The questions that drive our research are: What explains the frequency spectrum of human genetic diversity and its variation across functional categories of sites?  How is human genetic diversity distributed across global and local scales?  What can the spatial distribution of variation reveal about past human migrations/dispersal and selective processes?  How can we best make individual-based predictions of genetic risk and ancestry?  How can we use evolutionary insights to improve the genetic mapping of disease traits?

To address these questions, we develop and test computational methods for population genetic analysis and apply these methods to large-scale data.  In our work, we rely on an interdisciplinary skill set that draws from computation, statistics, genetics, human history, and anthropology.  Examples of our results include analyses of high-throughput genotyping array and sequencing data to reveal the spatial structure of variation in Europe; analyses of large-scale sequencing data to describe the abundance and distribution of rare variants in humans; and development of methods for generation recombination maps from admixed individuals.

The group also has an aim to translate advances in human population genetics to non-model organisms.  In this arena, we have helped advance studies of dog domestication and wolf population history, developed methods to empower studies of bird migration by way of combining genetic and isotopic methods for spatial assignment, and developed methods to extract more subtle information from pooled sequences and metagenomic data.


Selected Publications

Visualizing the Geography of Genetic Variants.
Marcus JH, Novembre J
(2016 Oct) Bioinformatics. 2016 Oct 14. pii: btw643. 27742697

Recent advances in the study of fine-scale population structure in humans.
Novembre J, Peter BM
(2016 Sep) Curr Opin Genet Dev. 2016 Sep 20;41:98-105. doi: 10.1016/j.gde.2016.08.007. 27662060

Conflation of Short Identity-by-Descent Segments Bias Their Inferred Length Distribution.
Chiang CW, Ralph P, Novembre J
(2016 May) G3 (Bethesda). 2016 May 3;6(5):1287-96. doi: 10.1534/g3.116.027581. 26935417 (Full Text)

Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs.
Freedman AH, Schweizer RM, Ortega-Del Vecchyo D, Han E, Davis BW, Gronau I, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Ramirez O, Hormozdiari F, Alkan C, Vila C, Squire K, Geffen E, Kusak J, Boyko AR, Parker HG, Lee C, Tadigotla V, Siepel A, Bustamante CD, Harkins TT, Nelson SF, Marques-Bonet T, Ostrander EA, Wayne RK, Novembre J
(2016 Mar) PLoS Genet. 2016 Mar 4;12(3):e1005851. doi: 10.1371/journal.pgen.1005851. eCollection 2016 Mar. 26943675 (Full Text)

Visualizing spatial population structure with estimated effective migration surfaces.
Petkova D, Novembre J, Stephens M
(2016 Jan) Nat Genet. 2016 Jan;48(1):94-100. doi: 10.1038/ng.3464. Epub 2015 Dec 7. 26642242 (Full Text)

Height-reducing variants and selection for short stature in Sardinia.
Zoledziewska M, Sidore C, Chiang CW, Sanna S, Mulas A, Steri M, Busonero F, Marcus JH, Marongiu M, Maschio A, Del Vecchyo DO, Floris M, Meloni A, Delitala A, Concas MP, Murgia F, Biino G, Vaccargiu S, Nagaraja R, Lohmueller KE, Timpson NJ, Soranzo N, Tachmazidou I, Dedoussis G, Zeggini E, Uzzau S, Jones C, Lyons R, Angius A, Abecasis GR, Novembre J, Schlessinger D, Cucca F
(2015 Nov) Nat Genet. 2015 Nov;47(11):1352-6. doi: 10.1038/ng.3403. Epub 2015 Sep 14. 26366551 (Full Text)

Characterizing bias in population genetic inferences from low-coverage sequencing data.
Han E, Sinsheimer JS, Novembre J
(2014 Mar) Mol Biol Evol. 2014 Mar;31(3):723-35. doi: 10.1093/molbev/mst229. Epub 2013 Nov 27. 24288159 (Full Text)

forqs: forward-in-time simulation of recombination, quantitative traits and selection.
Kessner D, Novembre J
(2014 Feb) Bioinformatics. 2014 Feb 15;30(4):576-7. doi: 10.1093/bioinformatics/btt712. Epub 2013 Dec 10. 24336146 (Full Text)

Genome sequencing highlights the dynamic early history of dogs.
Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, Han E, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Beale H, Ramirez O, Hormozdiari F, Alkan C, Vila C, Squire K, Geffen E, Kusak J, Boyko AR, Parker HG, Lee C, Tadigotla V, Wilton A, Siepel A, Bustamante CD, Harkins TT, Nelson SF, Ostrander EA, Marques-Bonet T, Wayne RK, Novembre J
(2014 Jan) PLoS Genet. 2014 Jan;10(1):e1004016. doi: 10.1371/journal.pgen.1004016. Epub 2014 Jan 16. 24453982 (Full Text)

Novel statistical methods for integrating genetic and stable isotope data to infer individual-level migratory connectivity.
Rundel CW, Wunder MB, Alvarado AH, Ruegg KC, Harrigan R, Schuh A, Kelly JF, Siegel RB, Desante DF, Smith TB, Novembre J
(2013 Aug) Mol Ecol. 2013 Aug;22(16):4163-76. doi: 10.1111/mec.12393. Epub 2013 Jul 30. 23906339

Maximum likelihood estimation of frequencies of known haplotypes from pooled sequence data.
Kessner D, Turner TL, Novembre J
(2013 May) Mol Biol Evol. 2013 May;30(5):1145-58. doi: 10.1093/molbev/mst016. Epub 2013 Jan 30. 23364324 (Full Text)

An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people.
Nelson MR, Wegmann D, Ehm MG, Kessner D, St Jean P, Verzilli C, Shen J, Tang Z, Bacanu SA, Fraser D, Warren L, Aponte J, Zawistowski M, Liu X, Zhang H, Zhang Y, Li J, Li Y, Li L, Woollard P, Topp S, Hall MD, Nangle K, Wang J, Abecasis G, Cardon LR, Zollner S, Whittaker JC, Chissoe SL, Novembre J, Mooser V
(2012 Jul) Science. 2012 Jul 6;337(6090):100-4. doi: 10.1126/science.1217876. Epub 2012 May 17. 22604722 (Full Text)

Perspectives on human population structure at the cusp of the sequencing era.
Novembre J, Ramachandran S
(2011) Annu Rev Genomics Hum Genet. 2011;12:245-74. doi: 10.1146/annurev-genom-090810-183123. 21801023

Recombination rates in admixed individuals identified by ancestry-based inference.
Wegmann D, Kessner DE, Veeramah KR, Mathias RA, Nicolae DL, Yanek LR, Sun YV, Torgerson DG, Rafaels N, Mosley T, Becker LC, Ruczinski I, Beaty TH, Kardia SL, Meyers DA, Barnes KC, Becker DM, Freimer NB, Novembre J
(2011 Jul) Nat Genet. 2011 Jul 20;43(9):847-53. doi: 10.1038/ng.894. 21775992

Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication.
Vonholdt BM, Pollinger JP, Lohmueller KE, Han E, Parker HG, Quignon P, Degenhardt JD, Boyko AR, Earl DA, Auton A, Reynolds A, Bryc K, Brisbin A, Knowles JC, Mosher DS, Spady TC, Elkahloun A, Geffen E, Pilot M, Jedrzejewski W, Greco C, Randi E, Bannasch D, Wilton A, Shearman J, Musiani M, Cargill M, Jones PG, Qian Z, Huang W, Ding ZL, Zhang YP, Bustamante CD, Ostrander EA, Novembre J, Wayne RK
(2010 Apr) Nature. 2010 Apr 8;464(7290):898-902. doi: 10.1038/nature08837. Epub 2010 Mar 17. 20237475 (Full Text)

Likelihood-based inference in isolation-by-distance models using the spatial distribution of low-frequency alleles.
Novembre J, Slatkin M
(2009 Nov) Evolution. 2009 Nov;63(11):2914-25. doi: 10.1111/j.1558-5646.2009.00775.x. Epub 2009 Jul 16. 19624728 (Full Text)

Spatial patterns of variation due to natural selection in humans.
Novembre J, Di Rienzo A
(2009 Nov) Nat Rev Genet. 2009 Nov;10(11):745-55. doi: 10.1038/nrg2632. Epub 2009 Oct 13. 19823195 (Full Text)

Fast model-based estimation of ancestry in unrelated individuals.
Alexander DH, Novembre J, Lange K
(2009 Sep) Genome Res. 2009 Sep;19(9):1655-64. doi: 10.1101/gr.094052.109. Epub 2009 Jul 31. 19648217 (Full Text)

Genes mirror geography within Europe.
Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, Auton A, Indap A, King KS, Bergmann S, Nelson MR, Stephens M, Bustamante CD
(2008 Nov) Nature. 2008 Nov 6;456(7218):98-101. doi: 10.1038/nature07331. Epub 2008 Aug 31. 18758442 (Full Text)

Interpreting principal component analyses of spatial population genetic variation.
Novembre J, Stephens M
(2008 May) Nat Genet. 2008 May;40(5):646-9. doi: 10.1038/ng.139. Epub 2008 Apr 20. 18425127 (Full Text)

The geographic spread of the CCR5 Delta32 HIV-resistance allele.
Novembre J, Galvani AP, Slatkin M
(2005 Nov) PLoS Biol. 2005 Nov;3(11):e339. Epub 2005 Oct 18. 16216086 (Full Text)

Accounting for background nucleotide composition when measuring codon usage bias.
Novembre JA
(2002 Aug) Mol Biol Evol. 2002 Aug;19(8):1390-4. 12140252