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Jeff Wall, PhD, MS

Title(s)Professor, Epidemiology & Biostatistics
SchoolSchool of Medicine
Phone415-476-4063
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    Collapse Research 
    Collapse Research Activities and Funding
    Estimating fine scale changes in recombination rates across species
    NIH R01GM115433Aug 1, 2015 - Apr 30, 2019
    Role: Principal Investigator
    Development of a pedigreed baboon genome resource for biomedical research
    NIH R24OD017859Jul 1, 2014 - Jun 30, 2018
    Role: Principal Investigator
    Genomic Patterns of Polymorphism in Primates
    NIH R01HG005226May 28, 2010 - Apr 30, 2014
    Role: Principal Investigator
    Simulation algorithms for genome-wide data and application to admixed data
    NIH R01HG004049Aug 16, 2007 - Jun 30, 2011
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Hanna ZR, Dumbacher JP, Bowie RCK, Henderson JB, Wall JD. Whole-Genome Analysis of Introgression Between the Spotted Owl and Barred Owl (Strix occidentalis and Strix varia, Respectively; Aves: Strigidae) in Western North America. G3 (Bethesda). 2018 12 10; 8(12):3945-3952. PMID: 30355766.
      View in: PubMed
    2. Jagoda E, Lawson DJ, Wall JD, Lambert D, Muller C, Westaway M, Leavesley M, Capellini TD, Mirazón Lahr M, Gerbault P, Thomas MG, Migliano AB, Willerslev E, Metspalu M, Pagani L. Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans. Mol Biol Evol. 2017 Dec 06. PMID: 29220488.
      View in: PubMed
    3. Hanna ZR, Henderson JB, Wall JD, Emerling CA, Fuchs J, Runckel C, Mindell DP, Bowie RCK, DeRisi JL, Dumbacher JP. Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes. Genome Biol Evol. 2017 10 01; 9(10):2522-2545. PMID: 28992302.
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    4. Wall JD. Inferring Human Demographic Histories of Non-African Populations from Patterns of Allele Sharing. Am J Hum Genet. 2017 May 04; 100(5):766-772. PMID: 28475859.
      View in: PubMed
    5. Malaspinas AS, Westaway MC, Muller C, Sousa VC, Lao O, Alves I, Bergström A, Athanasiadis G, Cheng JY, Crawford JE, Heupink TH, Macholdt E, Peischl S, Rasmussen S, Schiffels S, Subramanian S, Wright JL, Albrechtsen A, Barbieri C, Dupanloup I, Eriksson A, Margaryan A, Moltke I, Pugach I, Korneliussen TS, Levkivskyi IP, Moreno-Mayar JV, Ni S, Racimo F, Sikora M, Xue Y, Aghakhanian FA, Brucato N, Brunak S, Campos PF, Clark W, Ellingvåg S, Fourmile G, Gerbault P, Injie D, Koki G, Leavesley M, Logan B, Lynch A, Matisoo-Smith EA, McAllister PJ, Mentzer AJ, Metspalu M, Migliano AB, Murgha L, Phipps ME, Pomat W, Reynolds D, Ricaut FX, Siba P, Thomas MG, Wales T, Wall CM, Oppenheimer SJ, Tyler-Smith C, Durbin R, Dortch J, Manica A, Schierup MH, Foley RA, Lahr MM, Bowern C, Wall JD, Mailund T, Stoneking M, Nielsen R, Sandhu MS, Excoffier L, Lambert DM, Willerslev E. A genomic history of Aboriginal Australia. Nature. 2016 Oct 13; 538(7624):207-214. PMID: 27654914.
      View in: PubMed
    6. Pagani L, Lawson DJ, Jagoda E, Mörseburg A, Eriksson A, Mitt M, Clemente F, Hudjashov G, DeGiorgio M, Saag L, Wall JD, Cardona A, Mägi R, Wilson Sayres MA, Kaewert S, Inchley C, Scheib CL, Järve M, Karmin M, Jacobs GS, Antao T, Iliescu FM, Kushniarevich A, Ayub Q, Tyler-Smith C, Xue Y, Yunusbayev B, Tambets K, Mallick CB, Saag L, Pocheshkhova E, Andriadze G, Muller C, Westaway MC, Lambert DM, Zoraqi G, Turdikulova S, Dalimova D, Sabitov Z, Sultana GNN, Lachance J, Tishkoff S, Momynaliev K, Isakova J, Damba LD, Gubina M, Nymadawa P, Evseeva I, Atramentova L, Utevska O, Ricaut FX, Brucato N, Sudoyo H, Letellier T, Cox MP, Barashkov NA, Skaro V, Mulahasanovic L, Primorac D, Sahakyan H, Mormina M, Eichstaedt CA, Lichman DV, Abdullah S, Chaubey G, Wee JTS, Mihailov E, Karunas A, Litvinov S, Khusainova R, Ekomasova N, Akhmetova V, Khidiyatova I, Marjanovic D, Yepiskoposyan L, Behar DM, Balanovska E, Metspalu A, Derenko M, Malyarchuk B, Voevoda M, Fedorova SA, Osipova LP, Lahr MM, Gerbault P, Leavesley M, Migliano AB, Petraglia M, Balanovsky O, Khusnutdinova EK, Metspalu E, Thomas MG, Manica A, Nielsen R, Villems R, Willerslev E, Kivisild T, Metspalu M. Genomic analyses inform on migration events during the peopling of Eurasia. Nature. 2016 Oct 13; 538(7624):238-242. PMID: 27654910.
      View in: PubMed
    7. Wall JD, Yoshihara Caldeira Brandt D. Archaic admixture in human history. Curr Opin Genet Dev. 2016 Dec; 41:93-97. PMID: 27662059.
      View in: PubMed
    8. Wall JD, Stevison LS. Detecting Recombination Hotspots from Patterns of Linkage Disequilibrium. G3 (Bethesda). 2016 08 09; 6(8):2265-71. PMID: 27226166; PMCID: PMC4978882.
      View in: PubMed, PubMed Central
    9. Wall JD, Schlebusch SA, Alberts SC, Cox LA, Snyder-Mackler N, Nevonen KA, Carbone L, Tung J. Genomewide ancestry and divergence patterns from low-coverage sequencing data reveal a complex history of admixture in wild baboons. Mol Ecol. 2016 07; 25(14):3469-83. PMID: 27145036.
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    10. Mostovoy Y, Levy-Sakin M, Lam J, Lam ET, Hastie AR, Marks P, Lee J, Chu C, Lin C, Džakula Ž, Cao H, Schlebusch SA, Giorda K, Schnall-Levin M, Wall JD, Kwok PY. A hybrid approach for de novo human genome sequence assembly and phasing. Nat Methods. 2016 07; 13(7):587-90. PMID: 27159086; PMCID: PMC4927370 [Available on 11/09/16].
      View in: PubMed, PubMed Central
    11. Hsieh P, Woerner AE, Wall JD, Lachance J, Tishkoff SA, Gutenkunst RN, Hammer MF. Corrigendum: Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies. Genome Res. 2016 05; 26(5):717.1. PMID: 27197244; PMCID: PMC4864460.
      View in: PubMed, PubMed Central
    12. Snyder-Mackler N, Majoros WH, Yuan ML, Shaver AO, Gordon JB, Kopp GH, Schlebusch SA, Wall JD, Alberts SC, Mukherjee S, Zhou X, Tung J. Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples. Genetics. 2016 06; 203(2):699-714. PMID: 27098910.
      View in: PubMed
    13. Eckalbar WL, Schlebusch SA, Mason MK, Gill Z, Parker AV, Booker BM, Nishizaki S, Muswamba-Nday C, Terhune E, Nevonen KA, Makki N, Friedrich T, VanderMeer JE, Pollard KS, Carbone L, Wall JD, Illing N, Ahituv N. Transcriptomic and epigenomic characterization of the developing bat wing. Nat Genet. 2016 05; 48(5):528-36. PMID: 27019111.
      View in: PubMed
    14. Hsieh P, Woerner AE, Wall JD, Lachance J, Tishkoff SA, Gutenkunst RN, Hammer MF. Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies. Genome Res. 2016 Mar; 26(3):291-300. PMID: 26888264; PMCID: PMC4772012.
      View in: PubMed, PubMed Central
    15. Hsieh P, Veeramah KR, Lachance J, Tishkoff SA, Wall JD, Hammer MF, Gutenkunst RN. Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection. Genome Res. 2016 Mar; 26(3):279-90. PMID: 26888263.
      View in: PubMed
    16. Stevison LS, Woerner AE, Kidd JM, Kelley JL, Veeramah KR, McManus KF, Bustamante CD, Hammer MF, Wall JD. The Time Scale of Recombination Rate Evolution in Great Apes. Mol Biol Evol. 2016 Apr; 33(4):928-45. PMID: 26671457.
      View in: PubMed
    17. McManus KF, Kelley JL, Song S, Veeramah KR, Woerner AE, Stevison LS, Ryder OA, Ape Genome Project G, Kidd JM, Wall JD, Bustamante CD, Hammer MF. Inference of gorilla demographic and selective history from whole-genome sequence data. Mol Biol Evol. 2015 Mar; 32(3):600-12. PMID: 25534031; PMCID: PMC4327160.
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    18. Seguin-Orlando A, Korneliussen TS, Sikora M, Malaspinas AS, Manica A, Moltke I, Albrechtsen A, Ko A, Margaryan A, Moiseyev V, Goebel T, Westaway M, Lambert D, Khartanovich V, Wall JD, Nigst PR, Foley RA, Lahr MM, Nielsen R, Orlando L, Willerslev E. Paleogenomics. Genomic structure in Europeans dating back at least 36,200 years. Science. 2014 Nov 28; 346(6213):1113-8. PMID: 25378462.
      View in: PubMed
    19. Wall JD, Tang LF, Zerbe B, Kvale MN, Kwok PY, Schaefer C, Risch N. Estimating genotype error rates from high-coverage next-generation sequence data. Genome Res. 2014 Nov; 24(11):1734-9. PMID: 25304867; PMCID: PMC4216915.
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    20. Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, Chiatante G, Cree A, Damert A, de Jong PJ, Dumas L, Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, Hernandez-Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvák Z, Jablonski NG, Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA, O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, ten Hallers B, Terhune E, Thomas GW, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF, Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC, Rogers J, Wilson RK, Gibbs RA. Gibbon genome and the fast karyotype evolution of small apes. Nature. 2014 Sep 11; 513(7517):195-201. PMID: 25209798.
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    21. Kidd JM, Sharpton TJ, Bobo D, Norman PJ, Martin AR, Carpenter ML, Sikora M, Gignoux CR, Nemat-Gorgani N, Adams A, Guadalupe M, Guo X, Feng Q, Li Y, Liu X, Parham P, Hoal EG, Feldman MW, Pollard KS, Wall JD, Bustamante CD, Henn BM. Exome capture from saliva produces high quality genomic and metagenomic data. BMC Genomics. 2014 Apr 04; 15:262. PMID: 24708091.
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    22. Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prüfer K, Pybus M, Johnstone L, Lachmann M, Alkan C, Twigg D, Petit N, Baker C, Hormozdiari F, Fernandez-Callejo M, Dabad M, Wilson ML, Stevison L, Camprubí C, Carvalho T, Ruiz-Herrera A, Vives L, Mele M, Abello T, Kondova I, Bontrop RE, Pusey A, Lankester F, Kiyang JA, Bergl RA, Lonsdorf E, Myers S, Ventura M, Gagneux P, Comas D, Siegismund H, Blanc J, Agueda-Calpena L, Gut M, Fulton L, Tishkoff SA, Mullikin JC, Wilson RK, Gut IG, Gonder MK, Ryder OA, Hahn BH, Navarro A, Akey JM, Bertranpetit J, Reich D, Mailund T, Schierup MH, Hvilsom C, Andrés AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T. Great ape genetic diversity and population history. Nature. 2013 Jul 25; 499(7459):471-5. PMID: 23823723.
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    23. Leffler EM, Gao Z, Pfeifer S, Ségurel L, Auton A, Venn O, Bowden R, Bontrop R, Wall JD, Sella G, Donnelly P, McVean G, Przeworski M. Multiple instances of ancient balancing selection shared between humans and chimpanzees. Science. 2013 Mar 29; 339(6127):1578-82. PMID: 23413192.
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    24. Wall JD, Yang MA, Jay F, Kim SK, Durand EY, Stevison LS, Gignoux C, Woerner A, Hammer MF, Slatkin M. Higher levels of neanderthal ancestry in East Asians than in Europeans. Genetics. 2013 May; 194(1):199-209. PMID: 23410836; PMCID: PMC3632468.
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    25. Oksenberg N, Stevison L, Wall JD, Ahituv N. Function and regulation of AUTS2, a gene implicated in autism and human evolution. PLoS Genet. 2013; 9(1):e1003221. PMID: 23349641.
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    26. Wall JD, Kim SK, Luca F, Carbone L, Mootnick AR, de Jong PJ, Di Rienzo A. Incomplete lineage sorting is common in extant gibbon genera. PLoS One. 2013; 8(1):e53682. PMID: 23341974; PMCID: PMC3544895.
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    27. Wall JD. Great ape genomics. ILAR J. 2013; 54(2):82-90. PMID: 24174434; PMCID: PMC3814392.
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    28. Kim SK, Gignoux CR, Wall JD, Lum-Jones A, Wang H, Haiman CA, Chen GK, Henderson BE, Kolonel LN, Le Marchand L, Stram DO, Saxena R, Cheng I. Population genetic structure and origins of Native Hawaiians in the multiethnic cohort study. PLoS One. 2012; 7(11):e47881. PMID: 23144833.
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    29. Wall JD, Slatkin M. Paleopopulation genetics. Annu Rev Genet. 2012; 46:635-49. PMID: 22994357.
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    30. Hammer MF, Woerner AE, Mendez FL, Watkins JC, Wall JD. Genetic evidence for archaic admixture in Africa. Proc Natl Acad Sci U S A. 2011 Sep 13; 108(37):15123-8. PMID: 21896735; PMCID: PMC3174671.
      View in: PubMed, PubMed Central
    31. Kim SK, Carbone L, Becquet C, Mootnick AR, Li DJ, de Jong PJ, Wall JD. Patterns of genetic variation within and between Gibbon species. Mol Biol Evol. 2011 Aug; 28(8):2211-8. PMID: 21368318; PMCID: PMC3144381.
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    32. Wall JD, Jiang R, Gignoux C, Chen GK, Eng C, Huntsman S, Marjoram P. Genetic variation in Native Americans, inferred from Latino SNP and resequencing data. Mol Biol Evol. 2011 Aug; 28(8):2231-7. PMID: 21368315; PMCID: PMC3144384.
      View in: PubMed, PubMed Central
    33. Hammer MF, Woerner AE, Mendez FL, Watkins JC, Cox MP, Wall JD. The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes. Nat Genet. 2010 Oct; 42(10):830-1. PMID: 20802480.
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    34. Capra JA, Carbone L, Riesenfeld SJ, Wall JD. Genomics through the lens of next-generation sequencing. Genome Biol. 2010; 11(6):306. PMID: 20587080; PMCID: PMC2911104.
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    35. Cox MP, Morales DA, Woerner AE, Sozanski J, Wall JD, Hammer MF. Autosomal resequence data reveal Late Stone Age signals of population expansion in sub-Saharan African foraging and farming populations. PLoS One. 2009 Jul 29; 4(7):e6366. PMID: 19641603; PMCID: PMC2712685.
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    36. Carbone L, Harris RA, Vessere GM, Mootnick AR, Humphray S, Rogers J, Kim SK, Wall JD, Martin D, Jurka J, Milosavljevic A, de Jong PJ. Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution. PLoS Genet. 2009 Jun; 5(6):e1000538. PMID: 19557196; PMCID: PMC2695003.
      View in: PubMed, PubMed Central
    37. Wall JD, Lohmueller KE, Plagnol V. Detecting ancient admixture and estimating demographic parameters in multiple human populations. Mol Biol Evol. 2009 Aug; 26(8):1823-7. PMID: 19420049; PMCID: PMC2734152.
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    38. Schroeder KB, Jakobsson M, Crawford MH, Schurr TG, Boca SM, Conrad DF, Tito RY, Osipova LP, Tarskaia LA, Zhadanov SI, Wall JD, Pritchard JK, Malhi RS, Smith DG, Rosenberg NA. Haplotypic background of a private allele at high frequency in the Americas. Mol Biol Evol. 2009 May; 26(5):995-1016. PMID: 19221006; PMCID: PMC2734135.
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    39. Cox MP, Woerner AE, Wall JD, Hammer MF. Intergenic DNA sequences from the human X chromosome reveal high rates of global gene flow. BMC Genet. 2008 Nov 27; 9:76. PMID: 19038041; PMCID: PMC2620354.
      View in: PubMed, PubMed Central
    40. Chen GK, Marjoram P, Wall JD. Fast and flexible simulation of DNA sequence data. Genome Res. 2009 Jan; 19(1):136-42. PMID: 19029539; PMCID: PMC2612967.
      View in: PubMed, PubMed Central
    41. Hammer MF, Mendez FL, Cox MP, Woerner AE, Wall JD. Sex-biased evolutionary forces shape genomic patterns of human diversity. PLoS Genet. 2008 Sep 26; 4(9):e1000202. PMID: 18818765; PMCID: PMC2538571.
      View in: PubMed, PubMed Central
    42. Wall JD, Cox MP, Mendez FL, Woerner A, Severson T, Hammer MF. A novel DNA sequence database for analyzing human demographic history. Genome Res. 2008 Aug; 18(8):1354-61. PMID: 18493019; PMCID: PMC2493425.
      View in: PubMed, PubMed Central
    43. Padhukasahasram B, Marjoram P, Wall JD, Bustamante CD, Nordborg M. Exploring population genetic models with recombination using efficient forward-time simulations. Genetics. 2008 Apr; 178(4):2417-27. PMID: 18430959; PMCID: PMC2323826.
      View in: PubMed, PubMed Central
    44. Wall JD, Kim SK. Inconsistencies in Neanderthal genomic DNA sequences. PLoS Genet. 2007 Oct; 3(10):1862-6. PMID: 17937503; PMCID: PMC2014787.
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    45. Conrad DF, Jakobsson M, Coop G, Wen X, Wall JD, Rosenberg NA, Pritchard JK. A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nat Genet. 2006 Nov; 38(11):1251-60. PMID: 17057719.
      View in: PubMed
    46. Wall JD, Hammer MF. Archaic admixture in the human genome. Curr Opin Genet Dev. 2006 Dec; 16(6):606-10. PMID: 17027252.
      View in: PubMed
    47. Padhukasahasram B, Wall JD, Marjoram P, Nordborg M. Estimating recombination rates from single-nucleotide polymorphisms using summary statistics. Genetics. 2006 Nov; 174(3):1517-28. PMID: 16980396; PMCID: PMC1667054.
      View in: PubMed, PubMed Central
    48. Plagnol V, Wall JD. Possible ancestral structure in human populations. PLoS Genet. 2006 Jul; 2(7):e105. PMID: 16895447; PMCID: PMC1523253.
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    49. Plagnol V, Padhukasahasram B, Wall JD, Marjoram P, Nordborg M. Relative influences of crossing over and gene conversion on the pattern of linkage disequilibrium in Arabidopsis thaliana. Genetics. 2006 Apr; 172(4):2441-8. PMID: 16299388; PMCID: PMC1456404.
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    50. Przeworski M, Coop G, Wall JD. The signature of positive selection on standing genetic variation. Evolution. 2005 Nov; 59(11):2312-23. PMID: 16396172.
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    51. Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, Zheng H, Bakker E, Calabrese P, Gladstone J, Goyal R, Jakobsson M, Kim S, Morozov Y, Padhukasahasram B, Plagnol V, Rosenberg NA, Shah C, Wall JD, Wang J, Zhao K, Kalbfleisch T, Schulz V, Kreitman M, Bergelson J. The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol. 2005 Jul; 3(7):e196. PMID: 15907155; PMCID: PMC1135296.
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    52. Wall JD. Estimating recombination rates using three-site likelihoods. Genetics. 2004 Jul; 167(3):1461-73. PMID: 15280255; PMCID: PMC1470930.
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    53. Wall JD. Close look at gene conversion hot spots. Nat Genet. 2004 Feb; 36(2):114-5. PMID: 14752518.
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    54. 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.
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    55. Andolfatto P, Wall JD. Linkage disequilibrium patterns across a recombination gradient in African Drosophila melanogaster. Genetics. 2003 Nov; 165(3):1289-305. PMID: 14668383; PMCID: PMC1462864.
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    56. Wall JD, Pritchard JK. Assessing the performance of the haplotype block model of linkage disequilibrium. Am J Hum Genet. 2003 Sep; 73(3):502-15. PMID: 12916017; PMCID: PMC1180676.
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    57. Wall JD, Pritchard JK. Haplotype blocks and linkage disequilibrium in the human genome. Nat Rev Genet. 2003 Aug; 4(8):587-97. PMID: 12897771.
      View in: PubMed
    58. Wall JD. Estimating ancestral population sizes and divergence times. Genetics. 2003 Jan; 163(1):395-404. PMID: 12586724; PMCID: PMC1462435.
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    59. Wall JD, Andolfatto P, Przeworski M. Testing models of selection and demography in Drosophila simulans. Genetics. 2002 Sep; 162(1):203-16. PMID: 12242234; PMCID: PMC1462246.
      View in: PubMed, PubMed Central
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