John Novembre

Research Summary
The Novembre 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.
Keywords
Population Genetics, Genomics, Human Genetics, Computational Biology, Molecular Evolution, Computational Statistics, Data Science
Publications
  1. Marcus JH, Posth C, Ringbauer H, Lai L, Skeates R, Sidore C, Beckett J, Furtwängler A, Olivieri A, Chiang CWK, Al-Asadi H, Dey K, Joseph TA, Liu CC, Der Sarkissian C, Radzeviciute R, Michel M, Gradoli MG, Marongiu P, Rubino S, Mazzarello V, Rovina D, La Fragola A, Serra RM, Bandiera P, Bianucci R, Pompianu E, Murgia C, Guirguis M, Orquin RP, Tuross N, van Dommelen P, Haak W, Reich D, Schlessinger D, Cucca F, Krause J, Novembre J. Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia. Nat Commun. 2020 02 24; 11(1):939. View in: PubMed

  2. Liu CC, Shringarpure S, Lange K, Novembre J. Exploring Population Structure with Admixture Models and Principal Component Analysis. Methods Mol Biol. 2020; 2090:67-86. View in: PubMed

  3. Peter BM, Petkova D, Novembre J. Genetic Landscapes Reveal How Human Genetic Diversity Aligns with Geography. Mol Biol Evol. 2020 Apr 01; 37(4):943-951. View in: PubMed

  4. Koch E, Schweizer RM, Schweizer TM, Stahler DR, Smith DW, Wayne RK, Novembre J. De novo mutation rate estimation in wolves of known pedigree. Mol Biol Evol. 2019 Jul 12. View in: PubMed

  5. Al-Asadi H, Petkova D, Stephens M, Novembre J. Estimating recent migration and population-size surfaces. PLoS Genet. 2019 01; 15(1):e1007908. View in: PubMed

  6. Lawler J, Beier P, Dickson B, Fargione J, Novembre J, Theobald D. A tribute to a true conservation innovator, Brad McRae, 1966-2017. Conserv Biol. 2019 Apr; 33(2):480-482. View in: PubMed

  7. Lindo J, Haas R, Hofman C, Apata M, Moraga M, Verdugo RA, Watson JT, Viviano Llave C, Witonsky D, Beall C, Warinner C, Novembre J, Aldenderfer M, Di Rienzo A. The genetic prehistory of the Andean highlands 7000 years BP though European contact. Sci Adv. 2018 11; 4(11):eaau4921. View in: PubMed

  8. Dickson BG, Albano CM, Anantharaman R, Beier P, Fargione J, Graves TA, Gray ME, Hall KR, Lawler JJ, Leonard PB, Littlefield CE, McClure ML, Novembre J, Schloss CA, Schumaker NH, Shah VB, Theobald DM. Circuit-theory applications to connectivity science and conservation. Conserv Biol. 2019 04; 33(2):239-249. View in: PubMed

  9. Lawler J, Beier P, Dickson B, Fargione J, Novembre J, Theobald D. A tribute to a true conservation innovator, Brad McRae, 1966-2017. Conserv Biol. 2018 Oct 11. View in: PubMed

  10. Chiang CWK, Marcus JH, Sidore C, Biddanda A, Al-Asadi H, Zoledziewska M, Pitzalis M, Busonero F, Maschio A, Pistis G, Steri M, Angius A, Lohmueller KE, Abecasis GR, Schlessinger D, Cucca F, Novembre J. Genomic history of the Sardinian population. Nat Genet. 2018 10; 50(10):1426-1434. View in: PubMed

  11. Al-Asadi H, Dey KK, Novembre J, Stephens M. Inference and visualization of DNA damage patterns using a grade of membership model. Bioinformatics. 2019 04 15; 35(8):1292-1298. View in: PubMed

  12. Jeong C, Witonsky DB, Basnyat B, Neupane M, Beall CM, Childs G, Craig SR, Novembre J, Di Rienzo A. Detecting past and ongoing natural selection among ethnically Tibetan women at high altitude in Nepal. PLoS Genet. 2018 09; 14(9):e1007650. View in: PubMed

  13. Novembre J, Beier P, Fargione J, Lawler J, Selkoe K. Brad McRae (1966-2017). Mol Ecol. 2018 08; 27(15):3035-3036. View in: PubMed

  14. de Barros Damgaard P, Martiniano R, Kamm J, Moreno-Mayar JV, Kroonen G, Peyrot M, Barjamovic G, Rasmussen S, Zacho C, Baimukhanov N, Zaibert V, Merz V, Biddanda A, Merz I, Loman V, Evdokimov V, Usmanova E, Hemphill B, Seguin-Orlando A, Yediay FE, Ullah I, Sjögren KG, Iversen KH, Choin J, de la Fuente C, Ilardo M, Schroeder H, Moiseyev V, Gromov A, Polyakov A, Omura S, Senyurt SY, Ahmad H, McKenzie C, Margaryan A, Hameed A, Samad A, Gul N, Khokhar MH, Goriunova OI, Bazaliiskii VI, Novembre J, Weber AW, Orlando L, Allentoft ME, Nielsen R, Kristiansen K, Sikora M, Outram AK, Durbin R, Willerslev E. The first horse herders and the impact of early Bronze Age steppe expansions into Asia. Science. 2018 06 29; 360(6396). View in: PubMed

  15. Schweizer RM, Durvasula A, Smith J, Vohr SH, Stahler DR, Galaverni M, Thalmann O, Smith DW, Randi E, Ostrander EA, Green RE, Lohmueller KE, Novembre J, Wayne RK. Natural Selection and Origin of a Melanistic Allele in North American Gray Wolves. Mol Biol Evol. 2018 05 01; 35(5):1190-1209. View in: PubMed

  16. Reppell M, Novembre J. Using pseudoalignment and base quality to accurately quantify microbial community composition. PLoS Comput Biol. 2018 04; 14(4):e1006096. View in: PubMed

  17. Novembre J, Barton NH. Tread Lightly Interpreting Polygenic Tests of Selection. Genetics. 2018 Apr; 208(4):1351-1355. View in: PubMed

  18. Smith J, Coop G, Stephens M, Novembre J. Estimating Time to the Common Ancestor for a Beneficial Allele. Mol Biol Evol. 2018 04 01; 35(4):1003-1017. View in: PubMed

  19. Serres-Armero A, Povolotskaya IS, Quilez J, Ramirez O, Santpere G, Kuderna LFK, Hernandez-Rodriguez J, Fernandez-Callejo M, Gomez-Sanchez D, Freedman AH, Fan Z, Novembre J, Navarro A, Boyko A, Wayne R, Vilà C, Lorente-Galdos B, Marques-Bonet T. Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing. BMC Genomics. 2017 Dec 19; 18(1):977. View in: PubMed

  20. Jeong C, Peter BM, Basnyat B, Neupane M, Beall CM, Childs G, Craig SR, Novembre J, Di Rienzo A. Correction: A longitudinal cline characterizes the genetic structure of human populations in the Tibetan plateau. PLoS One. 2017; 12(8):e0183407. View in: PubMed

  21. Jeong C, Peter BM, Basnyat B, Neupane M, Beall CM, Childs G, Craig SR, Novembre J, Di Rienzo A. A longitudinal cline characterizes the genetic structure of human populations in the Tibetan plateau. PLoS One. 2017; 12(4):e0175885. View in: PubMed

  22. 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. Overexpression of the Cytokine BAFF and Autoimmunity Risk. N Engl J Med. 2017 04 27; 376(17):1615-1626. View in: PubMed

  23. Pala M, Zappala Z, Marongiu M, Li X, Davis JR, Cusano R, Crobu F, Kukurba KR, Gloudemans MJ, Reinier F, Berutti R, Piras MG, Mulas A, Zoledziewska M, Marongiu M, Sorokin EP, Hess GT, Smith KS, Busonero F, Maschio A, Steri M, Sidore C, Sanna S, Fiorillo E, Bassik MC, Sawcer SJ, Battle A, Novembre J, Jones C, Angius A, Abecasis GR, Schlessinger D, Cucca F, Montgomery SB. Population- and individual-specific regulatory variation in Sardinia. Nat Genet. 2017 May; 49(5):700-707. View in: PubMed

  24. Koch E, Novembre J. A Temporal Perspective on the Interplay of Demography and Selection on Deleterious Variation in Humans. G3 (Bethesda). 2017 03 10; 7(3):1027-1037. View in: PubMed

  25. Marcus JH, Novembre J. Visualizing the geography of genetic variants. Bioinformatics. 2017 02 15; 33(4):594-595. View in: PubMed

  26. Novembre J, Peter BM. Recent advances in the study of fine-scale population structure in humans. Curr Opin Genet Dev. 2016 Dec; 41:98-105. View in: PubMed

  27. 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. Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs. PLoS Genet. 2016 Mar; 12(3):e1005851. View in: PubMed

  28. Chiang CW, Ralph P, Novembre J. Conflation of Short Identity-by-Descent Segments Bias Their Inferred Length Distribution. G3 (Bethesda). 2016 05 03; 6(5):1287-96. View in: PubMed

  29. Petkova D, Novembre J, Stephens M. Visualizing spatial population structure with estimated effective migration surfaces. Nat Genet. 2016 Jan; 48(1):94-100. View in: PubMed

  30. 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. Height-reducing variants and selection for short stature in Sardinia. Nat Genet. 2015 Nov; 47(11):1352-1356. View in: PubMed

  31. Kessner D, Novembre J. Power analysis of artificial selection experiments using efficient whole genome simulation of quantitative traits. Genetics. 2015 Apr; 199(4):991-1005. View in: PubMed

  32. 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. Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European. Nature. 2014 Mar 13; 507(7491):225-8. View in: PubMed

  33. 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, Wilton A, Siepel A, Bustamante CD, Harkins TT, Nelson SF, Ostrander EA, Marques-Bonet T, Wayne RK, Novembre J. Genome sequencing highlights the dynamic early history of dogs. PLoS Genet. 2014 Jan; 10(1):e1004016. View in: PubMed

  34. Kessner D, Novembre J. forqs: forward-in-time simulation of recombination, quantitative traits and selection. Bioinformatics. 2014 Feb 15; 30(4):576-7. View in: PubMed

  35. Han E, Sinsheimer JS, Novembre J. Characterizing bias in population genetic inferences from low-coverage sequencing data. Mol Biol Evol. 2014 Mar; 31(3):723-35. View in: PubMed

  36. Rundel CW, Wunder MB, Alvarado AH, Ruegg KC, Harrigan R, Schuh A, Kelly JF, Siegel RB, DeSante DF, Smith TB, Novembre J. Novel statistical methods for integrating genetic and stable isotope data to infer individual-level migratory connectivity. Mol Ecol. 2013 Aug; 22(16):4163-4176. View in: PubMed

  37. Kessner D, Turner TL, Novembre J. Maximum likelihood estimation of frequencies of known haplotypes from pooled sequence data. Mol Biol Evol. 2013 May; 30(5):1145-58. View in: PubMed

  38. 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. An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science. 2012 Jul 06; 337(6090):100-4. View in: PubMed

  39. Novembre J, Ramachandran S. Perspectives on human population structure at the cusp of the sequencing era. Annu Rev Genomics Hum Genet. 2011; 12:245-74. View in: PubMed

  40. 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. Recombination rates in admixed individuals identified by ancestry-based inference. Nat Genet. 2011 Jul 20; 43(9):847-53. View in: PubMed

  41. Royal CD, Novembre J, Fullerton SM, Goldstein DB, Long JC, Bamshad MJ, Clark AG. Inferring genetic ancestry: opportunities, challenges, and implications. Am J Hum Genet. 2010 May 14; 86(5):661-73. View in: PubMed

  42. François O, Currat M, Ray N, Han E, Excoffier L, Novembre J. Principal component analysis under population genetic models of range expansion and admixture. Mol Biol Evol. 2010 Jun; 27(6):1257-68. View in: PubMed

  43. Novembre J, Di Rienzo A. Spatial patterns of variation due to natural selection in humans. Nat Rev Genet. 2009 Nov; 10(11):745-55. View in: PubMed

  44. Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009 Sep; 19(9):1655-64. View in: PubMed

  45. Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, Auton A, Indap A, King KS, Bergmann S, Nelson MR, Stephens M, Bustamante CD. Genes mirror geography within Europe. Nature. 2008 Nov 06; 456(7218):98-101. View in: PubMed

  46. Novembre J, Stephens M. Interpreting principal component analyses of spatial population genetic variation. Nat Genet. 2008 May; 40(5):646-9. View in: PubMed

  47. Novembre J, Galvani AP, Slatkin M. The geographic spread of the CCR5 Delta32 HIV-resistance allele. PLoS Biol. 2005 Nov; 3(11):e339. View in: PubMed

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