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Richard R. Hudson

TitleEmeritus/Emerita, Professor
InstitutionUniversity of Chicago
DepartmentEcology & Evolution
AddressChicago IL 60637
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    Collapse Bibliographic 
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Nakagome S, Hudson RR, Di Rienzo A. Inferring the model and onset of natural selection under varying population size from the site frequency spectrum and haplotype structure. Proc Biol Sci. 2019 02 13; 286(1896):20182541. PMID: 30963935.
      View in: PubMed
    2. Simons YB, Bullaughey K, Hudson RR, Sella G. A population genetic interpretation of GWAS findings for human quantitative traits. PLoS Biol. 2018 03; 16(3):e2002985. PMID: 29547617.
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    3. Ling S, Hu Z, Yang Z, Yang F, Li Y, Lin P, Chen K, Dong L, Cao L, Tao Y, Hao L, Chen Q, Gong Q, Wu D, Li W, Zhao W, Tian X, Hao C, Hungate EA, Catenacci DV, Hudson RR, Li WH, Lu X, Wu CI. Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution. Proc Natl Acad Sci U S A. 2015 Nov 24; 112(47):E6496-505. PMID: 26561581.
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    4. Nakagome S, Alkorta-Aranburu G, Amato R, Howie B, Peter BM, Hudson RR, Di Rienzo A. Estimating the Ages of Selection Signals from Different Epochs in Human History. Mol Biol Evol. 2016 Mar; 33(3):657-69. PMID: 26545921.
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    5. Hudson RR. A New Proof of the Expected Frequency Spectrum under the Standard Neutral Model. PLoS One. 2015; 10(7):e0118087. PMID: 26197064.
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    6. Karasov TL, Kniskern JM, Gao L, DeYoung BJ, Ding J, Dubiella U, Lastra RO, Nallu S, Roux F, Innes RW, Barrett LG, Hudson RR, Bergelson J. The long-term maintenance of a resistance polymorphism through diffuse interactions. Nature. 2014 Aug 28; 512(7515):436-440. PMID: 25043057.
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    7. Watt WB, Hudson RR, Wang B, Wang E. A genetic polymorphism evolving in parallel in two cell compartments and in two clades. BMC Evol Biol. 2013 Jan 12; 13:9. PMID: 23311980.
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    8. Meyer WK, Arbeithuber B, Ober C, Ebner T, Tiemann-Boege I, Hudson RR, Przeworski M. Evaluating the evidence for transmission distortion in human pedigrees. Genetics. 2012 May; 191(1):215-32. PMID: 22377632.
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    9. He Z, Zhai W, Wen H, Tang T, Wang Y, Lu X, Greenberg AJ, Hudson RR, Wu CI, Shi S. Two evolutionary histories in the genome of rice: the roles of domestication genes. PLoS Genet. 2011 Jun; 7(6):e1002100. PMID: 21695282.
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    10. Luca F, Hudson RR, Witonsky DB, Di Rienzo A. A reduced representation approach to population genetic analyses and applications to human evolution. Genome Res. 2011 Jul; 21(7):1087-98. PMID: 21628451.
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    11. Jha AR, Nixon DF, Rosenberg MG, Martin JN, Deeks SG, Hudson RR, Garrison KE, Pillai SK. Human endogenous retrovirus K106 (HERV-K106) was infectious after the emergence of anatomically modern humans. PLoS One. 2011; 6(5):e20234. PMID: 21633511.
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    12. Tian D, Wang Q, Zhang P, Araki H, Yang S, Kreitman M, Nagylaki T, Hudson R, Bergelson J, Chen JQ. Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes. Nature. 2008 Sep 04; 455(7209):105-8. PMID: 18641631.
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    13. Hudson RR. Estimating the recombination parameter of a finite population model without selection. Genet Res. 2007 Dec; 89(5-6):427-32. PMID: 18976531.
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    14. Hudson RR. The variance of coalescent time estimates from DNA sequences. J Mol Evol. 2007 Jun; 64(6):702-5. PMID: 17487522.
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    15. Shapiro JA, Huang W, Zhang C, Hubisz MJ, Lu J, Turissini DA, Fang S, Wang HY, Hudson RR, Nielsen R, Chen Z, Wu CI. Adaptive genic evolution in the Drosophila genomes. Proc Natl Acad Sci U S A. 2007 Feb 13; 104(7):2271-6. PMID: 17284599.
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    16. Evans PD, Mekel-Bobrov N, Vallender EJ, Hudson RR, Lahn BT. Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage. Proc Natl Acad Sci U S A. 2006 Nov 28; 103(48):18178-83. PMID: 17090677.
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    17. Voight BF, Adams AM, Frisse LA, Qian Y, Hudson RR, Di Rienzo A. Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes. Proc Natl Acad Sci U S A. 2005 Dec 20; 102(51):18508-13. PMID: 16352722.
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    18. Evans PD, Gilbert SL, Mekel-Bobrov N, Vallender EJ, Anderson JR, Vaez-Azizi LM, Tishkoff SA, Hudson RR, Lahn BT. Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans. Science. 2005 Sep 09; 309(5741):1717-20. PMID: 16151009.
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    19. Mekel-Bobrov N, Gilbert SL, Evans PD, Vallender EJ, Anderson JR, Hudson RR, Tishkoff SA, Lahn BT. Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens. Science. 2005 Sep 09; 309(5741):1720-2. PMID: 16151010.
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    20. Di Rienzo A, Hudson RR. An evolutionary framework for common diseases: the ancestral-susceptibility model. Trends Genet. 2005 Nov; 21(11):596-601. PMID: 16153740.
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    21. Vander Molen J, Frisse LM, Fullerton SM, Qian Y, Del Bosque-Plata L, Hudson RR, Di Rienzo A. Population genetics of CAPN10 and GPR35: implications for the evolution of type 2 diabetes variants. Am J Hum Genet. 2005 Apr; 76(4):548-60. PMID: 15696418.
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    22. Adams AM, Hudson RR. Maximum-likelihood estimation of demographic parameters using the frequency spectrum of unlinked single-nucleotide polymorphisms. Genetics. 2004 Nov; 168(3):1699-712. PMID: 15579718.
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    23. Wall JD, Frisse LA, Hudson RR, Di Rienzo A. Comparative linkage-disequilibrium analysis of the beta-globin hotspot in primates. Am J Hum Genet. 2003 Dec; 73(6):1330-40. PMID: 14628290.
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    24. Hudson RR, Turelli M. Stochasticity overrules the "three-times rule": genetic drift, genetic draft, and coalescence times for nuclear loci versus mitochondrial DNA. Evolution. 2003 Jan; 57(1):182-90. PMID: 12643581.
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    25. Hudson RR, Coyne JA. Mathematical consequences of the genealogical species concept. Evolution. 2002 Aug; 56(8):1557-65. PMID: 12353748.
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    26. Pluzhnikov A, Di Rienzo A, Hudson RR. Inferences about human demography based on multilocus analyses of noncoding sequences. Genetics. 2002 Jul; 161(3):1209-18. PMID: 12136023.
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    27. Fullerton SM, Bartoszewicz A, Ybazeta G, Horikawa Y, Bell GI, Kidd KK, Cox NJ, Hudson RR, Di Rienzo A. Geographic and haplotype structure of candidate type 2 diabetes susceptibility variants at the calpain-10 locus. Am J Hum Genet. 2002 May; 70(5):1096-106. PMID: 11891618.
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    28. Hudson RR. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics. 2002 Feb; 18(2):337-8. PMID: 11847089.
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    29. Hudson RR. Two-locus sampling distributions and their application. Genetics. 2001 Dec; 159(4):1805-17. PMID: 11779816.
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    30. Frisse L, Hudson RR, Bartoszewicz A, Wall JD, Donfack J, Di Rienzo A. Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. Am J Hum Genet. 2001 Oct; 69(4):831-43. PMID: 11533915.
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    31. Wall JD, Hudson RR. Coalescent simulations and statistical tests of neutrality. Mol Biol Evol. 2001 Jun; 18(6):1134-5; author reply 1136-8. PMID: 11371601.
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    32. Haubold B, Hudson RR. LIAN 3.0: detecting linkage disequilibrium in multilocus data. Linkage Analysis. Bioinformatics. 2000 Sep; 16(9):847-8. PMID: 11108709.
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    33. Hudson RR. A new statistic for detecting genetic differentiation. Genetics. 2000 Aug; 155(4):2011-4. PMID: 10924493.
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    34. Przeworski M, Hudson RR, Di Rienzo A. Adjusting the focus on human variation. Trends Genet. 2000 Jul; 16(7):296-302. PMID: 10858659.
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    35. Antezana MA, Hudson RR. Type I error and the power of the s-test: old lessons from a new, analytically justified statistical test for phylogenies. Syst Biol. 1999 Jun; 48(2):300-16. PMID: 12066709.
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    36. Haubold B, Travisano M, Rainey PB, Hudson RR. Detecting linkage disequilibrium in bacterial populations. Genetics. 1998 Dec; 150(4):1341-8. PMID: 9832514.
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    37. Rich SM, Licht MC, Hudson RR, Ayala FJ. Malaria's Eve: evidence of a recent population bottleneck throughout the world populations of Plasmodium falciparum. Proc Natl Acad Sci U S A. 1998 Apr 14; 95(8):4425-30. PMID: 9539753.
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    38. Rich SM, Hudson RR, Ayala FJ. Plasmodium falciparum antigenic diversity: evidence of clonal population structure. Proc Natl Acad Sci U S A. 1997 Nov 25; 94(24):13040-5. PMID: 9371796.
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    39. Antezana MA, Hudson RR. Before crossing over: the advantages of eukaryotic sex in genomes lacking chiasmatic recombination. Genet Res. 1997 Aug; 70(1):7-25. PMID: 9369095.
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    40. Hudson RR, Sáez AG, Ayala FJ. DNA variation at the Sod locus of Drosophila melanogaster: an unfolding story of natural selection. Proc Natl Acad Sci U S A. 1997 Jul 22; 94(15):7725-9. PMID: 9223255.
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    41. Hudson RR, Kaplan NL. Deleterious background selection with recombination. Genetics. 1995 Dec; 141(4):1605-17. PMID: 8601498.
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    42. Hudson RR, Kaplan NL. The coalescent process and background selection. Philos Trans R Soc Lond B Biol Sci. 1995 Jul 29; 349(1327):19-23. PMID: 8748015.
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    43. Braverman JM, Hudson RR, Kaplan NL, Langley CH, Stephan W. The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics. 1995 Jun; 140(2):783-96. PMID: 7498754.
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    44. Hudson RR. How can the low levels of DNA sequence variation in regions of the drosophila genome with low recombination rates be explained? Proc Natl Acad Sci U S A. 1994 Jul 19; 91(15):6815-8. PMID: 8041702.
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    45. Hudson RR, Bailey K, Skarecky D, Kwiatowski J, Ayala FJ. Evidence for positive selection in the superoxide dismutase (Sod) region of Drosophila melanogaster. Genetics. 1994 Apr; 136(4):1329-40. PMID: 8013910.
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    46. Hudson RR. Levels of DNA polymorphism and divergence yield important insights into evolutionary processes. Proc Natl Acad Sci U S A. 1993 Aug 15; 90(16):7425-6. PMID: 8356036.
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    47. Hudson RR, Slatkin M, Maddison WP. Estimation of levels of gene flow from DNA sequence data. Genetics. 1992 Oct; 132(2):583-9. PMID: 1427045.
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    48. Souza V, Nguyen TT, Hudson RR, Piñero D, Lenski RE. Hierarchical analysis of linkage disequilibrium in Rhizobium populations: evidence for sex? Proc Natl Acad Sci U S A. 1992 Sep 01; 89(17):8389-93. PMID: 1518873.
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    49. Hudson RR. Gene trees, species trees and the segregation of ancestral alleles. Genetics. 1992 Jun; 131(2):509-13. PMID: 1644284.
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    50. Hudson RR, Boos DD, Kaplan NL. A statistical test for detecting geographic subdivision. Mol Biol Evol. 1992 Jan; 9(1):138-51. PMID: 1552836.
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    51. Slatkin M, Hudson RR. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics. 1991 Oct; 129(2):555-62. PMID: 1743491.
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    52. Kreitman M, Hudson RR. Inferring the evolutionary histories of the Adh and Adh-dup loci in Drosophila melanogaster from patterns of polymorphism and divergence. Genetics. 1991 Mar; 127(3):565-82. PMID: 1673107.
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    53. Kaplan N, Hudson RR, Iizuka M. The coalescent process in models with selection, recombination and geographic subdivision. Genet Res. 1991 Feb; 57(1):83-91. PMID: 1904048.
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    54. Kwiatowski J, Hudson RR, Ayala FJ. The rate of Cu,Zn superoxide dismutase evolution. Free Radic Res Commun. 1991; 12-13 Pt 1:363-70. PMID: 2071040.
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    55. Kaplan NL, Hudson RR, Langley CH. The "hitchhiking effect" revisited. Genetics. 1989 Dec; 123(4):887-99. PMID: 2612899.
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    56. Hudson RR. How often are polymorphic restriction sites due to a single mutation? Theor Popul Biol. 1989 Aug; 36(1):23-33. PMID: 2572069.
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    57. Darden T, Kaplan NL, Hudson RR. A numerical method for calculating moments of coalescent times in finite populations with selection. J Math Biol. 1989; 27(3):355-68. PMID: 2746143.
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    58. Kaplan NL, Darden T, Hudson RR. The coalescent process in models with selection. Genetics. 1988 Nov; 120(3):819-29. PMID: 3066685.
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    59. Hudson RR, Kaplan NL. The coalescent process in models with selection and recombination. Genetics. 1988 Nov; 120(3):831-40. PMID: 3147214.
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    60. Hudson RR. Estimating the recombination parameter of a finite population model without selection. Genet Res. 1987 Dec; 50(3):245-50. PMID: 3443297.
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    61. Hudson RR, Kreitman M, Aguadé M. A test of neutral molecular evolution based on nucleotide data. Genetics. 1987 May; 116(1):153-9. PMID: 3110004.
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    62. Hudson RR, Kaplan NL. On the divergence of alleles in nested subsamples from finite populations. Genetics. 1986 Aug; 113(4):1057-76. PMID: 3744026.
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    63. Kaplan N, Hudson RR. The use of sample genealogies for studying a selectively neutral m-loci model with recombination. Theor Popul Biol. 1985 Dec; 28(3):382-96. PMID: 4071443.
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    64. Hudson RR, Kaplan NL. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics. 1985 Sep; 111(1):147-64. PMID: 4029609.
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    65. Hudson RR. The sampling distribution of linkage disequilibrium under an infinite allele model without selection. Genetics. 1985 Mar; 109(3):611-31. PMID: 3979817.
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    66. Hudson RR, Golding GB. Variance of sequence divergence. Mol Biol Evol. 1984 Nov; 1(6):439-41. PMID: 6599975.
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    67. Hudson RR. Properties of a neutral allele model with intragenic recombination. Theor Popul Biol. 1983 Apr; 23(2):183-201. PMID: 6612631.
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    68. Hudson RR. TESTING THE CONSTANT-RATE NEUTRAL ALLELE MODEL WITH PROTEIN SEQUENCE DATA. Evolution. 1983 Jan; 37(1):203-217. PMID: 28568026.
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    69. Hudson RR. Estimating genetic variability with restriction endonucleases. Genetics. 1982 Apr; 100(4):711-9. PMID: 6288514.
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