Selected Publications

For a full listing of publications see Pubmed or Google Scholar.

Italics indicate current/former lab members. * indicates authors contributed equally.

Preprints

Karp - Accurate and fast taxonomic classification using pseudoalignment
Mark Reppell, John Novembre [ bioRxiv ]

Population history of the Sardinian people inferred from whole-genome sequencing
Charleston W.K. Chiang, Joseph H. Marcus, Carlo Sidore, Hussein Al-Asadi, Magdalena Zoledziewska, Maristella Pitzalis, Fabio Busonero, Andrea Maschio, Giorgio Pistis, Maristella Steri, Andrea Angius, Kirk E. Lohmueller, Goncalo R Abecasis, David Schlessinger, Francesco Cucca, John Novembre [ bioRxiv ]

Estimating Time to the Common Ancestor for a Beneficial Allele.
Smith J, Coop G, Stephens M, Novembre J. [ bioRxiv ]

2017

Overexpression of the Cytokine BAFF and Autoimmunity Risk
Steri M, Orrù V, Idda ML, Pitzalis M, Pala M, Zara I, Sidore C, Faà V, Floris M, Deiana M, Asunis I, Porcu E, Mulas A, Piras MG, Lobina M, Lai S, Marongiu M, Serra V, Marongiu M, Sole G, Busonero F, Maschio A, Cusano R, Cuccuru G, Deidda F, Poddie F, Farina G, Dei M, Virdis F, Olla S, Satta MA, Pani M, Delitala A, Cocco E, Frau J, Coghe G, Lorefice L, Fenu G, Ferrigno P, Ban M, Barizzone N, Leone M, Guerini FR, Piga M, Firinu D, Kockum I, Lima Bomfim I, Olsson T, Alfredsson L, Suarez A, Carreira PE, Castillo-Palma MJ, Marcus JH, Congia M, Angius A, Melis M, Gonzalez A, Alarcón Riquelme ME, da Silva BM, Marchini M, Danieli MG, Del Giacco S, Mathieu A, Pani A, Montgomery SB, Rosati G, Hillert J, Sawcer S, D’Alfonso S, Todd JA, Novembre J, Abecasis GR, Whalen MB, Marrosu MG, Meloni A, Sanna S, Gorospe M, Schlessinger D, Fiorillo E, Zoledziewska M, Cucca F. [ New England Journal of Medicine 376(17):1615-1626 ]

A longitudinal cline characterizes the genetic structure of human populations in the Tibetan plateau
Jeong C et al [ PLoS One 12(4):e0175885 ]

A Temporal Perspective on the Interplay of Demography and Selection on Deleterious Variation in Humans
Koch E, Novembre J [ G3 7(3):1027-1037 ]

Visualizing the Geography of Genetic Variants.
Marcus JH, Novembre J. [ Bioinformatics 33(4):594-595 ]

2016

Pritchard, Stephens, and Donnelly on Population Structure.
Novembre J. [ Genetics 204:391-393 ]

Recent advances in the study of fine-scale population structure in humans.
Novembre J, Peter B. [ Current Opinion in Genetics and Development 41:98-105 ]

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, Vilà 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. [ PLoS Genetics 12:e1005851 ]

Conflations of short IBD blocks can bias inferred length of IBD.
Chiang CWK, Ralph P, Novembre J. [ G3 6:1287-96 ]

Technical Report- Assessment of the genetic analysis of Rasmussen et al. (2015).
Novembre J, Witonsky D, Di Rienzo A. [ Report provided to the U.S. Army Corps of Engineers, St. Louis District ]

Visualizing spatial population structure with estimated effective migration surfaces.
Petkova D, Novembre J, Stephens M. [ Nature Genetics 48:94-100 ]

2015

Height-reducing variants and selection for short stature on the island of Sardinia.
Zoledziewska M, Sidore C, Chiang CWK, Sanna S, Mulas A, Steri M, Busonero F, Marcus JH, Marongiu M, Maschio A, Ortega Del Vecchyo D, Floris M, Meloni A, Delitala A, Concas MP, Murgia F, Biino G, Vaccargiu S, Nagaraja R, Lohmueller KE, UK10K consortium, Timpson NJ, Soranzo N, Tachmazidou I Dedoussis G, Zeggini E, The Understanding Society Scientific Group, Uzzau S, Jones C, Lyons R, Angius A, Abecasis GR, Novembre J, Schlessinger D, Cucca F*. [ Nature Genetics 47:1352-6 ]

Human Evolution - ancient DNA steps into the language debate.
Novembre J. [ Nature News and Views 11:164-165 ]

Power analysis of artificial selection experiments using efficient whole genome simulation of quantitative traits
Kessner D, Novembre J. [ Genetics 199:991-1005 ]

Fast and accurate site frequency spectrum estimation from low coverage sequence data
Han E, Sinsheimer JS, Novembre J [ Bioinformatics 31:720-7 ]

2014

Spatial localization of recent ancestors for admixed individuals
Yang WY, Platt A, Chiang CW, Eskin E, Novembre J, Pasaniuc B [ G3 4:2505-18 ]

Demographic events and evolutionary forces shaping European genetic diversity
Veeramah KR, Novembre J. [ Cold Spring Harb Perspect Biol 6(9):a008516 ]

Variations on a Common STRUCTURE - New Algorithms for a Valuable Model
Novembre, J [ Genetics 197:809-811 ]

Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European
Olalde I, Allentoft ME, Sánchez-Quinto F, Santpere G, Chiang CW, Degiorgio M, Prado-Martinez J, Rodríguez JA, Rasmussen S, Quilez J, Ramírez O, Marigorta UM, Fernández-Callejo M, Prada ME, Encinas JM, Nielsen R, Netea MG, Novembre J, Sturm RA, Sabeti P, Marquès-Bonet T, Navarro A, Willerslev E, Lalueza-Fox C. [ Nature 507(7491):225-8 ]

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, Vilà C, Squire K, Geffen E, Kusak J, Boyko AR, Parker HG, Lee C, Tadigotla V, Siepel A, Bustamante CD, Harkins TT, Nelson SF, Ostrander EA, Marques-Bonet T, Wayne RK, Novembre J. [ PLoS Genetics 10:e1004016 ]

Analysis of rare variant population structure in Europeans explains differential stratification of gene-based tests
Zawistowski M, Reppell M, Wegmann D, St Jean PL, Ehm MG, Nelson MR, Novembre J, Zöllner S. [ Eur J Hum Genet 22:1137–1144 ]

2013

forqs - forward-in-time simulation of recombination, quantitative traits and selection.
Kessner D, Novembre J. [ Bioinformatics 30(4):576-7 ]

Characterizing bias in population genetic inferences from low coverage sequencing data
Han E, Sinsheimer JS, Novembre J. [ Molecular Biology and Evolution ]

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. [ Molecular Ecology 22(16):4163-76 ]

Maximum Likelihood Estimation of Frequencies of Known Haplotypes from Pooled Sequence Data.
Kessner D, Turner TL, Novembre J. [ Molecular Biology and Evolution 30:1145-58 ]

2012

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, Zöllner S, Whittaker JC, Chissoe SL, Novembre J, Mooser V. [ Science 337:100-4 ]

2011

Genetic variation in the Sorbs of eastern Germany in the context of broader European genetic diversity.
Veeramah KR, Tönjes A, Kovacs P, Gross A, Wegmann D, Geary P, Gasperikova D, Klimes I, Scholz M, Novembre J, Stumvoll M. [ European Journal of Human Genetics 19(9):995-1001 ]

Perspectives on human population structure at the cusp of the sequencing era.
Novembre J, Ramachandran S. [ Annual Review of Genomics and Human Genetics 12:245-74 ]

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 [ Nature Genetics 43:847-53 ]

A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids.
vonHoldt BM, Pollinger JP, Earl DA, Knowles JC, Boyko AR, Parker H, Geffen E, Pilot M, Jedrzejewski W, Jedrzejewska B, Sidorovich V, Greco C, Randi E, Musiani M, Kays R, Bustamante CD, Ostrander EA, Novembre J, Wayne RK. [ Genome Research 21:1294-305 ]

2010

Principal component analysis under population genetic models of range expansion and admixture.
François O, Currat M, Ray N, Han E, Excoffier L, Novembre J. [ Molecular Biology and Evolution 27:1257-68 ]

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 [ Nature 464:898-902 ]

2009

Likelihood-based inference in isolation-by-distance models using the spatial distribution of low-frequency alleles.
Novembre J, Slatkin M [ Evolution 63:2914-25 ]

Spatial patterns of variation due to natural selection in humans.
Novembre J, Di Rienzo A [ Nature Reviews Genetics 10:745-55 ]

Fast model-based estimation of ancestry in unrelated individuals.
Alexander DH, Novembre J, Lange K [ Genome Research 19:1655-64 ]

The role of geography in human adaptation.
Coop G, Pickrell JK, Novembre J, Kudaravalli S, Li J, Absher D, Myers RM, Cavalli-Sforza LL, Feldman MW, Pritchard JK [ PLoS Genetics 5:e1000500 ]

Signals of recent positive selection in a worldwide sample of human populations.
Pickrell JK, Coop G, Novembre J, Kudaravalli S, Li JZ, Absher D, Srinivasan BS, Barsh GS, Myers RM, Feldman MW, Pritchard JK [ Genome Research 19:826-37 ]

Global distribution of genomic diversity underscores rich complex history of continental human populations.
Auton A, Bryc K, Boyko AR, Lohmueller KE, Novembre J, Reynolds A, Indap A, Wright MH, Degenhardt JD, Gutenkunst RN, King KS, Nelson MR, Bustamante CD [ Genome Research 19:795-803 ]

2008

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 [ Nature 456:98-101 ]

The Population Reference Sample, POPRES - a resource for population, disease, and pharmacological genetics research.
Nelson MR, Bryc K, King KS, Indap A, Boyko AR, Novembre J, Briley LP, Maruyama Y, Waterworth DM, Waeber G, Vollenweider P, Oksenberg JR, Hauser SL, Stirnadel HA, Kooner JS, Chambers JC, Jones B, Mooser V, Bustamante CD, Roses AD, Burns DK, Ehm MG, Lai EH [ American Journal of Human Genetics 83:347-58 ]

Interpreting principal component analyses of spatial population genetic variation.
Novembre J, Stephens M [ Nature Genetics 40:646-9 ]

2007 - 2000

Ascertainment bias in spatially structured populations - A case study in the eastern fence lizard
Rosenblum EB, Novembre J [ The Journal of Heredity 98:331-6 ]

The geographic spread of the CCR5 Delta32 HIV-resistance allele.
Novembre J, Galvani AP, Slatkin [ PLoS Biology 3:e339 ]

Finding haplotype block boundaries by using the minimum-description-length principle.
Anderson EC, Novembre J [ American Journal of Human Genetics 73:336-54 ]

Accounting for background nucleotide composition when measuring codon usage bias.
Novembre J [ Molecular Biology and Evolution 19:1390-4 ]

SIMCOAL- a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography.
Excoffier L, Novembre J, Schneider S [ The Journal of heredity 91:506-9 ]