Publications

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

Selected publications shown.  For a complete listing see Pubmed or Google Scholar. In most cases the articles are open access and/or pdfs have been deposited to Pubmed Central and so I provide PMID links. If not follow this link (and e-mail me if a particular one is of interest and not present)

Karp: Accurate and fast taxonomic classification using pseudoalignment
Mark Reppell, John Novembre
bioRxiv doi: https://doi.org/10.1101/097949

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 doi: https://doi.org/10.1101/092148

Estimating Time to the Common Ancestor for a Beneficial Allele.
Smith J, Coop G, Stephens M, Novembre J.
bioRxiv doi: http://dx.doi.org/10.1101/071241

Visualizing the Geography of Genetic Variants.
Marcus JH, Novembre J. (2016)
Bioinformatics (in press). PMID:27742697

Pritchard, Stephens, and Donnelly on Population Structure.
Novembre J. (2016)
Genetics 204:391-393.  PMID:27729489

Recent advances in the study of fine-scale population structure in humans.
Novembre J, Peter B. (2016).
Current Opinion in Genetics and Development 41:98-105. PMID:27662060

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. (2016)
PLoS Genetics 12:e1005851.PMID:26943675

Conflations of short IBD blocks can bias inferred length of IBD.
Chiang CWK, Ralph P, Novembre J. (2016)
G3 doi: 10.1534/g3.116.027581. PMID:26935417

Technical Report: Assessment of the genetic analysis of Rasmussen et al. (2015).
Novembre J, Witonsky D, Di Rienzo A. (2016)
Report provided to the U.S. Army Corps of Engineers, St. Louis District and available from: http://cdm16021.contentdm.oclc.org/cdm/ref/collection/p16021coll11/id/950.

Visualizing spatial population structure with estimated effective migration surfaces.
Petkova D, Novembre J, Stephens M. (2016)
Nature Genetics 48:94-100. PMID:26642242

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*. (2015)
Nature Genetics 47:1352-6. [with Sidore et al, featured in News & Views] PMID:26366551

Human Evolution: ancient DNA steps into the language debate.
Novembre J. (2015).
Nature (New and Views) 11:164-165. PMID:26062506

Power analysis of artificial selection experiments using efficient whole genome simulation of quantitative traits
Kessner D, Novembre J. (2015)
Genetics 199:991-1005. doi: 10.1534/genetics.115.175075. Epub 2015 Feb 10. PMID: 25672748

Fast and accurate site frequency spectrum estimation from low coverage sequence data
Han E, Sinsheimer JS, Novembre J. (2015)
Bioinformatics 31:720-7. doi: 10.1093/bioinformatics/btu725. Epub 2014 Oct 30. PMID: 25359894

Spatial localization of recent ancestors for admixed individuals
Yang WY, Platt A, Chiang CW, Eskin E, Novembre J, Pasaniuc B. (2014)
G3 (Bethesda) 4:2505-18. doi: 10.1534/g3.114.014274. PMID: 25371484

Demographic events and evolutionary forces shaping European genetic diversity.
Veeramah KR, Novembre J. (2014)
Cold Spring Harb Perspect Biol 6(9):a008516. doi:10.1101/cshperspect.a008516. PMID:25059709

Variations on a Common STRUCTURE: New Algorithms for a Valuable Model
Novembre, J. (2014)
Genetics 197:809-811. PMID: 25024035

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. (2014)
Nature PMID: 24463515

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. (2014)
PLoS Genet 10:e1004016 PMID: 24453982

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. (2014)
Eur J Hum Genet  [Epub ahead of print]. PMID: 24398795

forqs: forward-in-time simulation of recombination, quantitative traits and selection.
Kessner D, Novembre J. (2013)
Bioinformatics 2013 Dec 28. [Epub ahead of print] PMID:24336146

Characterizing bias in population genetic inferences from low coverage sequencing data
Han E, Sinsheimer JS, Novembre J.  (2013)
Molecular Biology and Evolution. PMID:24288159 (Epub ahead of print)

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)
Molecular Ecology 22(16):4163-76. PMID:23906339 (Full Text) (News and Views)

Maximum Likelihood Estimation of Frequencies of Known Haplotypes from Pooled Sequence Data.
Kessner D, Turner TL, Novembre J.  (2013)
Molecular Biology and Evolution 30:1145-58 PMID: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, Zöllner S, Whittaker JC, Chissoe SL, Novembre J*, Mooser V*.  (2012)
Science 337:100-4 PMID:22604722

A model-based approach for analysis of spatial structure in genetic data. 
Yang WY, Novembre J, Eskin E, Halperin E. (2012)
Nature Genetics 44(6):725-31 PMID:22610118 (Full Text)

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. (2011)
European Journal of Human Genetics : EJHG 19(9):995-1001 PMID:21559053 (Full Text)

Perspectives on human population structure at the cusp of the sequencing era.
Novembre J, Ramachandran S. (2011)
Annual Review of Genomics and Human Genetics 12:245-74 PMID: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)
Nature Genetics 43:847-53 PMID:21775992

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. (2011)
Genome Research 21:1294-305 PMID:21566151 (Full Text)

Principal component analysis under population genetic models of range expansion and admixture.
François O, Currat M, Ray N, Han E, Excoffier L, Novembre J (2010)
Molecular Biology and Evolution 27:1257-68 PMID:20097660

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 (Apr 2010)
Nature 464:898-902 PMID:20237475 (Full Text)

Likelihood-based inference in isolation-by-distance models using the spatial distribution of low-frequency alleles.
Novembre J, Slatkin M (2009)
Evolution: International Journal of Organic Evolution 63:2914-25 PMID:19624728

Spatial patterns of variation due to natural selection in humans.
Novembre J, Di Rienzo A (2009)
Nature Reviews Genetics 10:745-55 PMID:19823195

Fast model-based estimation of ancestry in unrelated individuals.
Alexander DH, Novembre J, Lange K (2009)
Genome Research 19:1655-64 PMID:19648217 (Full Text)

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 (Jun 2009)
PLoS Genetics 5:e1000500 PMID:19503611 (Full Text)

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 (2009)
Genome Research 19:826-37 PMID:19307593 (Full Text)

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 (2009)
Genome Research 19:795-803 PMID:19218534 (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)
Nature 456:98-101 PMID:18758442 (Full Text)

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 (2008)
American Journal of Human Genetics 83:347-58 PMID:18760391 (Full Text)

Interpreting principal component analyses of spatial population genetic variation.
Novembre J, Stephens M (2008)
Nature Genetics 40:646-9 PMID:18425127

Ascertainment bias in spatially structured populations: A case study in the eastern fence lizard
Rosenblum EB, Novembre J (2007)
The Journal of Heredity 98:331-6 PMID:17611259

The geographic spread of the CCR5 Delta32 HIV-resistance allele.
Novembre J, Galvani AP, Slatkin (2005)
PLoS Biology 3:e339 PMID:16216086 (Full Text)

Finding haplotype block boundaries by using the minimum-description-length principle.
Anderson EC, Novembre J (2003)
American Journal of Human Genetics 73:336-54 PMID:12858289 (Full Text)

Accounting for background nucleotide composition when measuring codon usage bias.
Novembre J (2002)
Molecular biology and evolution 19:1390-4 PMID:12140252

SIMCOAL: a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography.
Excoffier L, Novembre J, Schneider S (2000)
The Journal of heredity 91:506-9 PMID:11218093

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