R. Bowden, H. Sakaoka, R. Ward, and P.
Donnelly. Global patterns of HSV-1 molecular diversity and inferences of human migrations. Infection, Genetics
and Evolution, 6:63–74, 2005.
Details
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[pdf]
Altshuler, David, Brooks, Lisa D, Chakravarti, Aravinda, Collins, Francis S, Daly, Mark J, and P.
Donnelly. A haplotype map of the human genome. Nature, 437(7063):1299–1320, Oct 2005.
Details
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[HTML]
Jeffreys, Alec J, Neumann, Rita, Panayi, Maria, S. Myers, and P.
Donnelly. Human recombination hot spots hidden in regions of strong marker association. Nat Genet, 37(6):601–606,
Jun 2005.
Details
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[HTML]
J. Marchini, L. Cardon, and P.
Donnelly. Genome-wide strategies for detecting multiple loci influencing complex diseases. Nature Genetics,
37:413–417, 2005.
Details
Download:
[pdf]
S. Myers, Bottolo, Leonardo, Freeman, Colin, G.
McVean, and P. Donnelly. A fine-scale map of recombination
rates and hotspots across the human genome. Science, 310(5746):321–324, Oct 2005.
Details
Download:
[HTML]
W. Winckler, S. Myers, D. Richter, R. Onofrio, G. McDonald, R. Bontrop, G. McVean, S. Gabriel, D. Reich, P.
Donnelly, and D. Altshuler. Comparison of Fine-Scale Recombination Rates in Humans and Chimpanzees. Science,
Feb 2005.
Details
Download:
[HTML]
R. Bowden, H. Sakaoka, P.
Donnelly, and R. Ward. High recombination rate in herpes simplex virus type 1 natural populations suggests significant
co-infection. Infection, Genetics and Evolution, 4:115–123, 2004.
Details
Download:
[HTML]
P. Fearnhead, R. M. Harding, J. A. Schneider, S.
Myers, and P. Donnelly. Application of coalescent
methods to reveal fine-scale rate variation and recombination hotspots. Genetics, 167:2067–2081, 2004.
Details
Download:
[HTML]
J. Marchini, L. Cardon, M. Phillips, and P.
Donnelly . The effects of human population structure on large genetic association studies. Nature Genetics,
36:512–517, 2004.
Details
Download:
[pdf]
G. McVean, S. Myers, S. Hunt,
P. Deloukas, D. Bentley, and P. Donnelly. The fine-scale
structure of recombination rate variation in the human genome. Science, 304(5670):581–584, 2004.
Details
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[pdf]
A. Helgason, G. Nicholson, K. Stefánsson,, and P. Donnelly.
A reassessment of genetic diversity in Icelanders: strong evidence from multiple loci for relative homogeneity caused by
genetic drift. Ann. Hum. Genet., 67:281–297, 2003.
Details
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[HTML]
M. Stephens and P. Donnelly. Ancestral inference in population
genetics models with selection (with discussion). Aust. N.Z. J. of Stats., 45:395–430, 2003.
Details
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[HTML]
M. Stephens and P. Donnelly. A Comparison of Bayesian
methods for haplotype reconstruction from population genotype data. Am. J. Hum. Genet., 73:1162–1169, 2003.
Details
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[pdf]
P. Fearnhead and P. Donnelly. Approximate likelihood
methods for estimating local recombination rates (with discussion). J. Roy. Stat. Soc. B., 64:657–680, 2002.
Details
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(unavailable)
G. Nicholson, A. V. Smith, F. Jonsson, O. Gustafsson, K. Steffanson, and P.
Donnelly. Assessing population differentiation and isolation from single-nucleotide polymorphism data. J. Roy.
Stat. Soc. B., 64:695–715, 2002.
Details
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(unavailable)
P. Donnelly, P. Joyce, and M. Nordborg. Likelihoods and
simulation methods for a class of non-neutral population genetics models. Genetics, 159:853–867, 2001.
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[pdf]
P. Donnelly and R. Foley, editors. Genes, Fossils
and Behaviour: an Integrated Approach to Human Evolution., NATO Science Series, IOS Press, Amsterdam, 2001.
Details
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(unavailable)
P. Fearnhead and P. Donnelly. Estimating recombination
rates from population genetic data. Genetics, 159:1299–1318, 2001.
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[pdf]
J. Pritchard and P. Donnelly. Case-Control Studies of
Association in Structured or Admixed Populations.. Theor. Pop. Biol., 60:227–237, 2001.
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(unavailable)
M. Stephens, Smith, N.J., and P. Donnelly . A new statistical
method for haplotype reconstruction from population data. Am. J. Hum. Genet., 68:978–989, 2001.
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[pdf]
P. Donnelly and E. Rodrigues. Convergence to stationarity
in the Moran model. J. Appl. Probab., 37:705–717, 2000.
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(unavailable)
P. Donnelly, Evans, S. N., Fleischmann, K. Kurtz, T. G.,
and X. Zhou. Continuum-sites stepping-stone models, coalescing exchangeable partitions, and random trees. Ann. Probab.,
28:1063–1110, 2000.
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J. K.Pritchard, Stephens, M., Rosenberg N. A., and P. Donnelly.
Association mapping in structured populations. Am. J. Hum. Genet., 67:170–181, 2000.
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[pdf]
J. K. Pritchard, Stephens, M., and P. Donnelly. Inference
of population structure using multilocus genotype data. Genetics, 155:945–959, 2000.
Details
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[pdf]
S. Sigurdardottir, Helgason, A., Gulcher, J., Stefanson, K., and P.
Donnelly. The mutation rate in the human mtDNA control region. Am. J. Hum. Genet., 66:1599–1609, 2000.
Details
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[pdf]
M. Stephens and P. Donnelly. Inference in molecular population
genetics. J. R. Statist. Soc. B, 62:605–635, 2000.
Details
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(unavailable)
P. Donnelly. The coalescent and microsatellite variability.
In Goldstein, D. and C. Schlotterer, editors, Microsatellites: Evolution and Applications , pp. 116–128, Oxford
University Press, Oxford, 1999.
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(unavailable)
P. Donnelly and T. G. Kurtz. Particle representations
for measure-valued population models. Ann. Probab., 27:166–205, 1999.
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(unavailable)
P. Donnelly and R. D. Friedman. DNA database searches
and the legal consumption of scientific evidence. Michigan Law Review, pp. 931–984, 1999.
Details
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(unavailable)
C. Wiuf and P. Donnelly. Conditional genealogies and
the age of a neutral mutant. Theor. Pop. Biol., 56:183–201, 1999.
Details
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[pdf]
Griffiths
G. Coop and R. C. Griffiths. Ancestral inference on gene trees under selection.
Theor. Popul. Biol., 66:219–232, 2004.
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M. De Iorio and R. C. Griffiths. Importance sampling on coalescent histories.
I. Adv. Appl. Probab., 36:417–433, 2004.
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M. De Iorio and R. C. Griffiths. Importance sampling on coalescent histories.
II. Subdivided population models. Adv. Appl. Probab., 36:434–454, 2004.
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[HTML]
R. C. Griffiths and S. Tavaré. The genealogy of a neutral mutation.
In P. J. Green, N. L. Hjort, and S. Richardson, editors, Highly Structured Stochastic Systems, Oxford Statistical Science
Series, pp. 393–413, Oxford University Press, Oxford, 2003.
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R. C. Griffiths. The frequency spectrum of a mutation, and its age, in a
general diffusion model. Theor. Popul. Biol., 64:241–251, 2003.
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[HTML]
R. C. Griffiths. Discussion on the paper 'Inferences from DNA data:
population histories, evolutionary processes and forensic match probabilities' by I.A.
Wilson, M.E. Weale, and D.J. Balding. J. R. Statist. Soc. A., 166:192–193, 2003.
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[HTML]
S. R. Myers and R. C. Griffiths.
Bounds on the minimum number of recombination events in a sample history. Genetics, 163(1):375–394, 2003.
Details
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[pdf]
R. C. Griffiths. Ancestral inference from gene trees. In M. Veuille
and M. Slatkin, editors, Modern Developments in Theoretical Population Genetics: the Legacy of Gustave
Malécot, Oxford Biology Readers, pp. 94–117, Oxford University Press, New York, 2002.
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R. C. Griffiths. Discussion on the paper 'Assessing population differentiation
and isolation from single--nucleotide polymorphism data' by G. Nicholson, A.V. Smith, F. Jónsson,
Ó. Gústafsson, K. Stefánsson, and P. Donnelly. J. R. Statist. Soc. B., 64:742–743,
2002.
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A. C. Stone, R. C. Griffiths, S. L. Zegura, and M. F. Hammer. High levels
of Y-chromosome nucleotide diversity in the genus \it \MakeUppercasePan. PNAS, 99:43–49, 2002.
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[pdf]
M. Bahlo and R. C. Griffiths. Coalescence time for two genes from a subdivided
population. J. Math. Biol., 43:397–410, 2001.
Details
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[HTML]
R. C. Griffiths. Ancestral inference from gene trees. In P.
Donnelly and R. A. Foley, editors, Genes, Fossils, and Behaviour: an Integrated Approach to Human Evolution, NATO
Science Series A, Life Sciences, pp. 137–172, IOS Press, Amsterdam, 2001.
Details
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[HTML]
M. Bahlo and R. C. Griffiths. Inference from gene trees in a subdivided
population. Theor. Popul. Biol., 57:79–95, 2000.
Details
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[HTML]
A. D. Barbour, S. N. Ethier, and R. C. Griffiths. A transition function
expansion for a diffusion model with selection. Ann. Appl. Probab., 10:123–162, 2000.
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[HTML]
R. C. Griffiths. Discussion on the paper 'Inference in molecular population
genetics' by M. Stephens and P. Donnelly. J. R. Statist. Soc. B., 62:638–639, 2000.
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[HTML]
R. C. Griffiths. Time to the ancestor along sequences with recombination.
Theor. Popul. Biol., 55:137–144, 1999.
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[HTML]
R. C. Griffiths and S. Tavaré. The ages of mutations in gene trees.
Ann. Appl. Probab., 9:567–590, 1999.
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[HTML]
R. C. Griffiths. Ancestral inference from gene trees in a subdivided population.
Bulletin of the International Statistical Institute. 52nd Session, ISI99, Helsinki. Book 1, pp. 353–356,
1999.
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(unavailable)
T. M. Karafet, S. L. Zegura, O. Posukh, L. Osipova, A. Bergen, J. Long, D. Goldman, W. Klitz, S. Harihara, P. de Knijff, V.
Wiebe, R. C. Griffiths, A. R. Templeton, and M. F. Hammer. Ancestral Asian
source(s)of New World Y-chromosome founder haplotypes. Am. J. Hum. Genet., 64:817–831, 1999.
Details
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[pdf]
R. C. Griffiths and S. Tavaré. The age of a mutation in a general
coalescent tree. Stochastic Models, 14:273–295, 1998.
Details
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(unavailable)
M. F. Hammer, T. Karafet, A. Rasanayagam, E. T. Wood, T. K. Altheide, T. Jenkins, R.
C. Griffiths, A. R. Templeton, and S. L. Zegura. Out of Africa and back again: Nested cladistic analysis of human
Y chromosome variation. Mol. Biol. Evol., 15:427–441, 1998.
Details
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[pdf]
McVean
Hanchard, Neil A, Rockett, Kirk A, C. Spencer, Coop, Graham, Pinder, Margaret,
Jallow, Muminatou, Kimber, Martin, G. McVean, Mott, Richard, and Kwiatkowski,
Dominic P. Screening for recently selected alleles by analysis of human haplotype similarity. Am J Hum Genet,
78(1):153–159, Jan 2006.
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D. J. Wilson and G. McVean. Estimating diversifying selection andfunctional
constraint in the presence of recombination. Genetics, 172:1411–1425, 2006.
Details
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[HTML]
Jolley, K A, Wilson, D J, Kriz, P, G. McVean, and Maiden, M C J. The influence
of mutation, recombination, population history, and selection on patterns of genetic diversity in Neisseria meningitidis.
Mol Biol Evol, 22(3):562–569, Mar 2005.
Details
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[pdf]
Goriely, Anne, G. McVean, van Pelt, Ans M M, O'Rourke, Anthony W, Wall, Steven
A, de Rooij, Dirk G, and Wilkie, Andrew O M. Gain-of-function amino acid substitutions drive positive selection of FGFR2
mutations in human spermatogonia. Proc Natl Acad Sci U S A, 102(17):6051–6056, Apr 2005.
Details
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[pdf]
Shrivastava, Jaya, Qian, Bao Zhen, G. Mcvean, and Webster, Joanne P. An
insight into the genetic variation of Schistosoma japonicum in mainland China using DNA microsatellite markers. Mol
Ecol, 14(3):839–849, Mar 2005.
Details
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[pdf]
G. McVean, C. Spencer, and
R. Chaix. Perspectives on Human Genetic Variation from the HapMap Project. PLoS Genet, 1(4):e54, Oct 2005.
Details
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[pdf]
G. McVean and N. Cardin. Approximating the coalescent with recombination.
Philos Trans R Soc Lond B Biol Sci, 360(1459):1387–1393, Jul 2005.
Details
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[HTML]
S. Myers, Bottolo, Leonardo, Freeman, Colin, G.
McVean, and P. Donnelly. A fine-scale map of recombination
rates and hotspots across the human genome. Science, 310(5746):321–324, Oct 2005.
Details
Download:
[HTML]
W. Winckler, S. Myers, D. Richter, R. Onofrio, G. McDonald, R. Bontrop, G. McVean, S. Gabriel, D. Reich, P.
Donnelly, and D. Altshuler. Comparison of Fine-Scale Recombination Rates in Humans and Chimpanzees. Science,
Feb 2005.
Details
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[HTML]
R. M. Harding and G. McVean.
A structured ancestral population for the evolution of modern humans.. Current Opinion in Genetics & Development,
14(6):667–674, 2004.
Details
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[HTML]
G. McVean, S. Myers, S. Hunt,
P. Deloukas, D. Bentley, and P. Donnelly. The fine-scale
structure of recombination rate variation in the human genome. Science, 304(5670):581–584, 2004.
Details
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[pdf]
A. Goriely, G. A. T. McVean, M. Rojmyer, B. Ingermarsson, and A. Wilkie. Evidence
for selective advantage of pathogenic FGFR2mutations in the male germ line. Science, 301:643–646, 2003.
Details
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[pdf]
M. P. H. Stumpf and G. A. T. McVean. Estimating recombination rates from
population genetic data. Nature Revs Genet., 4:959–968, 2003.
Details
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[pdf]
G. McVean, P. Awadalla, and P. Fearnhead. A coalescent-based method for
detecting and estimating recombinaton form gene sequences. Genetics, 160:1231–1241, 2002.
Details
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[pdf]
G. A. T. McVean. A genealogical interpretation of linkage disequilibrium.
Genetics, 162:987–991, 2002.
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[HTML]
D. E. Reich, S. F. Schaffner, M. J. Daly, G. McVean, J. C. Mullikin, J. M.
Higgins, D. J. Richter, E. S. Lander, and D. Altshuler. Human genome sequence variation and the influence of gene history,
mutation and recombination. Nature Genetics, 32:135–142, 2002.
Details
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[HTML]
D. Charlesworth, B. Charlesworth, and G. McVean. Genome sequences and evolutionary
biology, a two-way interaction. Trends Ecol. Evol., 16:235–242, 2001.
Details
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(unavailable)
G. A. T. McVean and J. Vieira. Inferring parameters of mutation, selection
and demography from patterns of synonymous site evolution in Drosophila. Genetics, pp. 245–257, 2001.
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G. A. T. McVean. What do patterns of variability reveal about mitochondrial
recombination?. Heredity, 87:613–620, 2001.
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[HTML]
Marchini
J. Marchini, D. Cutler, N. Patterson, M. Stephens, E. Eskin, E. Halperin,
S. Lin, Z. S. Qin, H. M. Munro, G. Abecasis, and P. Donnelly for the International HapMap Consortium. A comparison of phasing
algorithms for trios and unrelated individuals. Am J Hum Genet, 78, 2006.
Details
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[HTML]
J. Marchini, L. Cardon, and P.
Donnelly. Genome-wide strategies for detecting multiple loci influencing complex diseases. Nature Genetics,
37:413–417, 2005.
Details
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[pdf]
J. Marchini, L. Cardon, M. Phillips, and P.
Donnelly . The effects of human population structure on large genetic association studies. Nature Genetics,
36:512–517, 2004.
Details
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[pdf]
J. Marchini and L. R. Cardon. Discussion of Nicholson et al. (2002) Assessing
population differentiation and isolation from single-nucleotide polymorphism data. J. Roy. Stat. Soc. B., pp. 740–1,
2002.
Details
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(unavailable)
Myers
Jeffreys, Alec J, Neumann, Rita, Panayi, Maria, S. Myers, and P.
Donnelly. Human recombination hot spots hidden in regions of strong marker association. Nat Genet, 37(6):601–606,
Jun 2005.
Details
Download:
[HTML]
S. Myers, Bottolo, Leonardo, Freeman, Colin, G.
McVean, and P. Donnelly. A fine-scale map of recombination
rates and hotspots across the human genome. Science, 310(5746):321–324, Oct 2005.
Details
Download:
[HTML]
W. Winckler, S. Myers, D. Richter, R. Onofrio, G. McDonald, R. Bontrop, G. McVean, S. Gabriel, D. Reich, P.
Donnelly, and D. Altshuler. Comparison of Fine-Scale Recombination Rates in Humans and Chimpanzees. Science,
Feb 2005.
Details
Download:
[HTML]
P. Fearnhead, R. M. Harding, J. A. Schneider, S.
Myers, and P. Donnelly. Application of coalescent
methods to reveal fine-scale rate variation and recombination hotspots. Genetics, 167:2067–2081, 2004.
Details
Download:
[HTML]
G. McVean, S. Myers, S. Hunt,
P. Deloukas, D. Bentley, and P. Donnelly. The fine-scale
structure of recombination rate variation in the human genome. Science, 304(5670):581–584, 2004.
Details
Download:
[pdf]
S. R. Myers and R. C. Griffiths.
Bounds on the minimum number of recombination events in a sample history. Genetics, 163(1):375–394, 2003.
Details
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[pdf]
Nicholls
David Welch, Geoff K. Nicholls, Allen Rodrigo, and Wiremu Solomon. Integrating
Genealogy and Epidemiology: The Ancestral Infection and Selection Graph as a Model for Reconstructing Host Virus Histories.
Theoretical Population Biology, 68:65–75, 2005.
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Harding
Bisharat, Naiel, Cohen, Daniel I, R. Harding, D.
Falush, Crook, Derrick W, Peto, Tim, and Maiden, Martin C. Hybrid Vibrio vulnificus. Emerg Infect Dis, 11(1):30–35,
Jan 2005.
Details
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[pdf]
N. Bisharat, D. W. Crook, J. Leigh, R. M. Harding, P. N. Ward, T. J. Coffey,
M. C. Maiden, T. Peto, and N. Jones. Hyperinvasive neonatal group B streptococcus has arisen from a bovine ancestor.
J Clin Microbiol., 42(5):2161–7, 2004.
Details
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[pdf]
P. Fearnhead, R. M. Harding, J. A. Schneider, S.
Myers, and P. Donnelly. Application of coalescent
methods to reveal fine-scale rate variation and recombination hotspots. Genetics, 167:2067–2081, 2004.
Details
Download:
[HTML]
R. M. Harding and G. McVean.
A structured ancestral population for the evolution of modern humans.. Current Opinion in Genetics & Development,
14(6):667–674, 2004.
Details
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[HTML]
Bowden
R. Bowden and D. McGeoch. Herpes Simplex Viruses, Marcel Dekker
Inc, New York, 2006.
Details
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(unavailable)
R. Bowden, H. Sakaoka, R. Ward, and P.
Donnelly. Global patterns of HSV-1 molecular diversity and inferences of human migrations. Infection, Genetics
and Evolution, 6:63–74, 2005.
Details
Download:
[pdf]
R. Bowden, H. Sakaoka, P.
Donnelly, and R. Ward. High recombination rate in herpes simplex virus type 1 natural populations suggests significant
co-infection. Infection, Genetics and Evolution, 4:115–123, 2004.
Details
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[HTML]
DN Kakoola, J Sheldon, N Byabazaire, RJ Bowden, E Katongole-Mbidde, TF Schulz
TF, and AJ Davison. Recombination in human herpesvirus-8 strains from Uganda and evolution of the K15 gene. Journal
of General Virology, 82:2393–2404, 2001.
Details
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Falush
Kraft, Christian, Stack, Allison, Josenhans, Christine, Niehus, Eike, Dietrich, Guido, Correa, Pelayo, Fox, James G, D.
Falush, and Suerbaum, Sebastian. Genomic Changes during Chronic Helicobacter pylori Infection. J Bacteriol,
188(1):249–254, Jan 2006.
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[pdf]
Dingle, Kate E, Colles, Frances M, D. Falush, and Maiden, Martin C J. Sequence
typing and comparison of population biology of Campylobacter coli and Campylobacter jejuni. J Clin Microbiol, 43(1):340–347,
Jan 2005.
Details
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[pdf]
Bisharat, Naiel, Cohen, Daniel I, R. Harding, D.
Falush, Crook, Derrick W, Peto, Tim, and Maiden, Martin C. Hybrid Vibrio vulnificus. Emerg Infect Dis, 11(1):30–35,
Jan 2005.
Details
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[pdf]
A. V. Harter, K. A. Gardner, D. Falush, D. L. Lentz, R. A. Bye, and L. H.
Rieseberg. Origin of extant domesticated sunflowers in Eastern North America. Nature, 430:201–205, 2004.
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D. R. Langbehn, R. R. Brinkmann, D. Falush, J. S. Paulsen, and M. R. Hayden.
A new model for the prediction of the age of onset and penetrance for Huntington's disease based on CAG length. Clinical
Genetics, 65:267–277, 2004.
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X. Wirth, Wang, B. Linz, R. P. Novick, K. J. Lum, M. J. Blaser, G. Morelli, D.
Falush, and M. Achtman. Distinguishing human ethic groups by means of sequences from Helicobacter pylori: lessons from
Ladkh. PNAS, 101:4646–4651, 2004.
Details
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[pdf]
Spencer
Hanchard, Neil A, Rockett, Kirk A, C. Spencer, Coop, Graham, Pinder, Margaret,
Jallow, Muminatou, Kimber, Martin, G. McVean, Mott, Richard, and Kwiatkowski,
Dominic P. Screening for recently selected alleles by analysis of human haplotype similarity. Am J Hum Genet,
78(1):153–159, Jan 2006.
Details
Download:
[HTML]
G. McVean, C. Spencer, and
R. Chaix. Perspectives on Human Genetic Variation from the HapMap Project. PLoS Genet, 1(4):e54, Oct 2005.
Details
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[pdf]
C. Spencer and G. Coop. SelSim: A program to simulate population genetic
data withselection and recombination. Bioinformatics, 20(18):3673–5, 2004.
Details
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[HTML]
Chaix
G. McVean, C. Spencer, and
R. Chaix. Perspectives on Human Genetic Variation from the HapMap Project. PLoS Genet, 1(4):e54, Oct 2005.
Details
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[pdf]
Nicholson
A. Helgason, G. Nicholson, K. Stefánsson,, and P. Donnelly.
A reassessment of genetic diversity in Icelanders: strong evidence from multiple loci for relative homogeneity caused by
genetic drift. Ann. Hum. Genet., 67:281–297, 2003.
Details
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[HTML]
G. Nicholson, A. V. Smith, F. Jonsson, O. Gustafsson, K. Steffanson, and P.
Donnelly. Assessing population differentiation and isolation from single-nucleotide polymorphism data. J. Roy.
Stat. Soc. B., 64:695–715, 2002.
Details
Download:
(unavailable)
Cardin
G. McVean and N. Cardin. Approximating the coalescent with recombination.
Philos Trans R Soc Lond B Biol Sci, 360(1459):1387–1393, Jul 2005.
Details
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[HTML]