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John Novembre

Professor
jnovembre@uchicago.edu
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
Biosciences Graduate Program Association
Publications

  1. Modeling the spatiotemporal spread of beneficial alleles using ancient genomes. Elife. 2022 Dec 20; 11. View in: PubMed

  2. Addressing the challenges of polygenic scores in human genetic research. Am J Hum Genet. 2022 Dec 01; 109(12):2095-2100. View in: PubMed

  3. Population genetic models for the spatial spread of adaptive variants: A review in light of SARS-CoV-2 evolution. PLoS Genet. 2022 09; 18(9):e1010391. View in: PubMed

  4. The background and legacy of Lewontin's apportionment of human genetic diversity. Philos Trans R Soc Lond B Biol Sci. 2022 06 06; 377(1852):20200406. View in: PubMed

  5. Getting genetic ancestry right for science and society. Science. 2022 04 15; 376(6590):250-252. View in: PubMed

  6. Properties of 2-locus genealogies and linkage disequilibrium in temporally structured samples. Genetics. 2022 05 05; 221(1). View in: PubMed

  7. Ancient genomes from the Himalayas illuminate the genetic history of Tibetans and their Tibeto-Burman speaking neighbors. Nat Commun. 2022 03 08; 13(1):1203. View in: PubMed

  8. Haplotype-based inference of the distribution of fitness effects. Genetics. 2022 04 04; 220(4). View in: PubMed

  9. Indigenous Ancestry and Admixture in the Uruguayan Population. Front Genet. 2021; 12:733195. View in: PubMed

  10. Parental relatedness through time revealed by runs of homozygosity in ancient DNA. Nat Commun. 2021 09 14; 12(1):5425. View in: PubMed

  11. Fast and flexible estimation of effective migration surfaces. Elife. 2021 07 30; 10. View in: PubMed

  12. Public attitudes toward genetic risk scoring in medicine and beyond. Soc Sci Med. 2021 04; 274:113796. View in: PubMed

  13. A variant-centric perspective on geographic patterns of human allele frequency variation. Elife. 2020 12 22; 9. View in: PubMed

  14. 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

  15. Exploring Population Structure with Admixture Models and Principal Component Analysis. Methods Mol Biol. 2020; 2090:67-86. View in: PubMed

  16. Genetic Landscapes Reveal How Human Genetic Diversity Aligns with Geography. Mol Biol Evol. 2020 04 01; 37(4):943-951. View in: PubMed

  17. De Novo Mutation Rate Estimation in Wolves of Known Pedigree. Mol Biol Evol. 2019 Nov 01; 36(11):2536-2547. View in: PubMed

  18. Estimating recent migration and population-size surfaces. PLoS Genet. 2019 01; 15(1):e1007908. View in: PubMed

  19. A tribute to a true conservation innovator, Brad McRae, 1966-2017. Conserv Biol. 2019 Apr; 33(2):480-482. View in: PubMed

  20. The genetic prehistory of the Andean highlands 7000 years BP though European contact. Sci Adv. 2018 11; 4(11):eaau4921. View in: PubMed

  21. Circuit-theory applications to connectivity science and conservation. Conserv Biol. 2019 04; 33(2):239-249. View in: PubMed

  22. A tribute to a true conservation innovator, Brad McRae, 1966-2017. Conserv Biol. 2018 Oct 11. View in: PubMed

  23. Genomic history of the Sardinian population. Nat Genet. 2018 10; 50(10):1426-1434. View in: PubMed

  24. Inference and visualization of DNA damage patterns using a grade of membership model. Bioinformatics. 2019 04 15; 35(8):1292-1298. View in: PubMed

  25. 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

  26. Brad McRae (1966-2017). Mol Ecol. 2018 08; 27(15):3035-3036. View in: PubMed

  27. The first horse herders and the impact of early Bronze Age steppe expansions into Asia. Science. 2018 06 29; 360(6396). View in: PubMed

  28. 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

  29. Using pseudoalignment and base quality to accurately quantify microbial community composition. PLoS Comput Biol. 2018 04; 14(4):e1006096. View in: PubMed

  30. Tread Lightly Interpreting Polygenic Tests of Selection. Genetics. 2018 Apr; 208(4):1351-1355. View in: PubMed

  31. Estimating Time to the Common Ancestor for a Beneficial Allele. Mol Biol Evol. 2018 04 01; 35(4):1003-1017. View in: PubMed

  32. 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

  33. Correction: A longitudinal cline characterizes the genetic structure of human populations in the Tibetan plateau. PLoS One. 2017; 12(8):e0183407. View in: PubMed

  34. A longitudinal cline characterizes the genetic structure of human populations in the Tibetan plateau. PLoS One. 2017; 12(4):e0175885. View in: PubMed

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

  36. Population- and individual-specific regulatory variation in Sardinia. Nat Genet. 2017 May; 49(5):700-707. View in: PubMed

  37. 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

  38. Visualizing the geography of genetic variants. Bioinformatics. 2017 02 15; 33(4):594-595. View in: PubMed

  39. Recent advances in the study of fine-scale population structure in humans. Curr Opin Genet Dev. 2016 Dec; 41:98-105. View in: PubMed

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

  41. Conflation of Short Identity-by-Descent Segments Bias Their Inferred Length Distribution. G3 (Bethesda). 2016 05 03; 6(5):1287-96. View in: PubMed

  42. Visualizing spatial population structure with estimated effective migration surfaces. Nat Genet. 2016 Jan; 48(1):94-100. View in: PubMed

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

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

  45. 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

  46. Genome sequencing highlights the dynamic early history of dogs. PLoS Genet. 2014 Jan; 10(1):e1004016. View in: PubMed

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

  48. Characterizing bias in population genetic inferences from low-coverage sequencing data. Mol Biol Evol. 2014 Mar; 31(3):723-35. View in: PubMed

  49. 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

  50. Maximum likelihood estimation of frequencies of known haplotypes from pooled sequence data. Mol Biol Evol. 2013 May; 30(5):1145-58. View in: PubMed

  51. 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

  52. Perspectives on human population structure at the cusp of the sequencing era. Annu Rev Genomics Hum Genet. 2011; 12:245-74. View in: PubMed

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

  54. Inferring genetic ancestry: opportunities, challenges, and implications. Am J Hum Genet. 2010 May 14; 86(5):661-73. View in: PubMed

  55. Principal component analysis under population genetic models of range expansion and admixture. Mol Biol Evol. 2010 Jun; 27(6):1257-68. View in: PubMed

  56. Spatial patterns of variation due to natural selection in humans. Nat Rev Genet. 2009 Nov; 10(11):745-55. View in: PubMed

  57. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009 Sep; 19(9):1655-64. View in: PubMed

  58. Genes mirror geography within Europe. Nature. 2008 Nov 06; 456(7218):98-101. View in: PubMed

  59. Interpreting principal component analyses of spatial population genetic variation. Nat Genet. 2008 May; 40(5):646-9. View in: PubMed

  60. The geographic spread of the CCR5 Delta32 HIV-resistance allele. PLoS Biol. 2005 Nov; 3(11):e339. View in: PubMed

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