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Richard R. Hudson

TitleEmeritus/Emerita, Professor
InstitutionUniversity of Chicago
DepartmentEcology & Evolution
AddressChicago IL 60637
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    R01GM042447     (HUDSON, RICHARD R.)Jul 1, 1989 - Jun 30, 1993
    Role: Principal Investigator

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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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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    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; PMCID: PMC6408616.
      Citations: 5     Fields:    Translation:Humans
    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; PMCID: PMC5871013.
      Citations: 65     Fields:    Translation:Humans
    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; PMCID: PMC4664355.
      Citations: 156     Fields:    Translation:HumansCells
    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; PMCID: PMC5009997.
      Citations: 14     Fields:    Translation:Humans
    5. Hudson RR. A New Proof of the Expected Frequency Spectrum under the Standard Neutral Model. PLoS One. 2015; 10(7):e0118087. PMID: 26197064; PMCID: PMC4510065.
      Citations: 4     Fields:    
    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; PMCID: PMC4696508.
      Citations: 84     Fields:    Translation:AnimalsCells
    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; PMCID: PMC3556304.
      Citations:    Fields:    Translation:AnimalsCells
    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; PMCID: PMC3338262.
      Citations: 27     Fields:    Translation:HumansCells
    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; PMCID: PMC3111475.
      Citations: 68     Fields:    Translation:Animals
    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; PMCID: PMC3129251.
      Citations: 22     Fields:    Translation:Humans
    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; PMCID: PMC3102101.
      Citations: 33     Fields:    Translation:HumansCells
    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.
      Citations: 132     Fields:    Translation:HumansAnimalsCells
    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.
      Citations: 2     Fields:    
    14. Hudson RR. The variance of coalescent time estimates from DNA sequences. J Mol Evol. 2007 Jun; 64(6):702-5. PMID: 17487522.
      Citations: 14     Fields:    Translation:HumansCells
    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; PMCID: PMC1892965.
      Citations: 125     Fields:    Translation:Animals
    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; PMCID: PMC1635020.
      Citations: 35     Fields:    Translation:HumansAnimals
    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; PMCID: PMC1311907.
      Citations: 140     Fields:    Translation:Humans
    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.
      Citations: 114     Fields:    Translation:Humans
    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.
      Citations: 106     Fields:    Translation:HumansAnimals
    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.
      Citations: 96     Fields:    Translation:Humans
    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; PMCID: PMC1199293.
      Citations: 34     Fields:    Translation:Humans
    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; PMCID: PMC1448761.
      Citations: 79     Fields:    Translation:Humans
    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; PMCID: PMC1180398.
      Citations: 46     Fields:    Translation:HumansAnimalsCells
    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.
      Citations: 57     Fields:    Translation:Cells
    25. Hudson RR, Coyne JA, Hudson RR, Coyne JA. Mathematical consequences of the genealogical species concept. Evolution. 2002 Aug; 56(8):1557-65. PMID: 12353748.
      Citations: 108     Fields:    
    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; PMCID: PMC1462170.
      Citations: 50     Fields:    Translation:HumansCells
    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; PMCID: PMC447588.
      Citations: 42     Fields:    Translation:HumansAnimalsCells
    28. Hudson RR, Hudson RR. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics. 2002 Feb; 18(2):337-8. PMID: 11847089.
      Citations: 1110     Fields:    
    29. Hudson RR. Two-locus sampling distributions and their application. Genetics. 2001 Dec; 159(4):1805-17. PMID: 11779816; PMCID: PMC1461925.
      Citations: 236     Fields:    Translation:HumansCells
    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; PMCID: PMC1226068.
      Citations: 133     Fields:    Translation:Humans
    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.
      Citations: 25     Fields:    Translation:Animals
    32. Hudson RR, Haubold B. LIAN 3.0: detecting linkage disequilibrium in multilocus data. Linkage Analysis. Bioinformatics. 2000 Sep; 16(9):847-8. PMID: 11108709.
      Citations: 271     Fields:    Translation:Cells
    33. Hudson RR. A new statistic for detecting genetic differentiation. Genetics. 2000 Aug; 155(4):2011-4. PMID: 10924493; PMCID: PMC1461195.
      Citations: 203     Fields:    
    34. Przeworski M, Hudson RR, Di Rienzo A. Adjusting the focus on human variation. Trends Genet. 2000 Jul; 16(7):296-302. PMID: 10858659.
      Citations: 72     Fields:    Translation:Humans
    35. Antezana MA, Hudson RR, 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.
      Citations:    Fields:    
    36. Haubold B, Travisano M, Rainey PB, Hudson RR. Detecting linkage disequilibrium in bacterial populations. Genetics. 1998 Dec; 150(4):1341-8. PMID: 9832514; PMCID: PMC1460433.
      Citations: 43     Fields:    Translation:Cells
    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; PMCID: PMC22505.
      Citations: 62     Fields:    Translation:HumansAnimals
    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; PMCID: PMC24259.
      Citations: 32     Fields:    Translation:AnimalsCells
    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.
      Citations: 6     Fields:    
    40. Hudson RR, Ayala FJ, Sáez AG. 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; PMCID: PMC33684.
      Citations: 31     Fields:    Translation:Animals
    41. Hudson RR, Kaplan NL. Deleterious background selection with recombination. Genetics. 1995 Dec; 141(4):1605-17. PMID: 8601498; PMCID: PMC1206891.
      Citations: 193     Fields:    Translation:Animals
    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.
      Citations: 22     Fields:    Translation:AnimalsCells
    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; PMCID: PMC1206652.
      Citations: 254     Fields:    Translation:Animals
    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; PMCID: PMC44288.
      Citations: 44     Fields:    Translation:Animals
    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; PMCID: PMC1205914.
      Citations: 152     Fields:    Translation:AnimalsCells
    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; PMCID: PMC47152.
      Citations: 3     Fields:    Translation:Animals
    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; PMCID: PMC1205159.
      Citations: 595     Fields:    
    48. Nguyen TT, Hudson RR, Lenski RE, Souza V, Piñero D. 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; PMCID: PMC49924.
      Citations: 44     Fields:    Translation:AnimalsCells
    49. Hudson RR. Gene trees, species trees and the segregation of ancestral alleles. Genetics. 1992 Jun; 131(2):509-13. PMID: 1644284; PMCID: PMC1205022.
      Citations: 25     Fields:    
    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.
      Citations: 325     Fields:    Translation:AnimalsCells
    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; PMCID: PMC1204643.
      Citations: 527     Fields:    Translation:HumansAnimalsCells
    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; PMCID: PMC1204384.
      Citations: 111     Fields:    Translation:AnimalsCells
    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.
      Citations: 12     Fields:    Translation:Animals
    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.
      Citations: 5     Fields:    Translation:HumansAnimalsCells
    55. Kaplan NL, Hudson RR, Langley CH. The "hitchhiking effect" revisited. Genetics. 1989 Dec; 123(4):887-99. PMID: 2612899; PMCID: PMC1203897.
      Citations: 514     Fields:    Translation:Cells
    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.
      Citations: 9     Fields:    Translation:HumansAnimals
    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.
      Citations: 4     Fields:    
    58. Kaplan NL, Darden T, Hudson RR. The coalescent process in models with selection. Genetics. 1988 Nov; 120(3):819-29. PMID: 3066685; PMCID: PMC1203559.
      Citations: 112     Fields:    
    59. Hudson RR, Kaplan NL. The coalescent process in models with selection and recombination. Genetics. 1988 Nov; 120(3):831-40. PMID: 3147214; PMCID: PMC1203560.
      Citations: 172     Fields:    Translation:Animals
    60. Hudson RR. Estimating the recombination parameter of a finite population model without selection. Genet Res. 1987 Dec; 50(3):245-50. PMID: 3443297.
      Citations: 171     Fields:    Translation:HumansAnimals
    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; PMCID: PMC1203113.
      Citations: 721     Fields:    Translation:AnimalsCells
    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; PMCID: PMC1202911.
      Citations: 18     Fields:    Translation:Animals
    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.
      Citations: 27     Fields:    Translation:Cells
    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; PMCID: PMC1202594.
      Citations: 643     Fields:    Translation:Cells
    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; PMCID: PMC1216291.
      Citations: 58     Fields:    
    66. Hudson RR, Golding GB. Variance of sequence divergence. Mol Biol Evol. 1984 Nov; 1(6):439-41. PMID: 6599975.
      Citations:    Fields:    Translation:Cells
    67. Hudson RR. Properties of a neutral allele model with intragenic recombination. Theor Popul Biol. 1983 Apr; 23(2):183-201. PMID: 6612631.
      Citations: 285     Fields:    
    68. Hudson RR. TESTING THE CONSTANT-RATE NEUTRAL ALLELE MODEL WITH PROTEIN SEQUENCE DATA. Evolution. 1983 Jan; 37(1):203-217. PMID: 28568026.
      Citations: 93     Fields:    
    69. Hudson RR. Estimating genetic variability with restriction endonucleases. Genetics. 1982 Apr; 100(4):711-9. PMID: 6288514; PMCID: PMC1201843.
      Citations: 26     Fields:    Translation:Cells
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