Analytical methods for immunogenetic population data.

[1]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[2]  E. Thorsby,et al.  Immunogenetics as a tool in anthropological studies , 2011, Immunology.

[3]  M. Stephens,et al.  Inferring weak population structure with the assistance of sample group information , 2009, Molecular ecology resources.

[4]  M Setterholm,et al.  A bioinformatics approach to ascertaining the rarity of HLA alleles. , 2008, Tissue antigens.

[5]  Yongtao Guan,et al.  Practical Issues in Imputation-Based Association Mapping , 2008, PLoS genetics.

[6]  Steven J Mack,et al.  Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies. , 2008, Human immunology.

[7]  Kui Zhang,et al.  Haplotype inference for present-absent genotype data using previously identified haplotypes and haplotype patterns , 2007, Bioinform..

[8]  N. Ebrahimi,et al.  A new method of testing for Hardy-Weinberg equilibrium and ordering populations , 2007, Journal of Genetics.

[9]  A. Cambon-Thomsen,et al.  Preliminary analysis of a KIR haplotype estimation algorithm: a simulation study. , 2007, Tissue antigens.

[10]  G Thomson,et al.  PyPop update--a software pipeline for large-scale multilocus population genomics. , 2007, Tissue antigens.

[11]  Sylvie C. Fail,et al.  The IMGT/HLA and IPD databases , 2006, Human mutation.

[12]  Jinko Graham,et al.  LDheatmap: An R Function for Graphical Display of Pairwise Linkage Disequilibria Between Single Nucleotide Polymorphisms , 2006 .

[13]  P. Smouse,et al.  genalex 6: genetic analysis in Excel. Population genetic software for teaching and research , 2006 .

[14]  A. Dobra,et al.  Monte Carlo Algorithms for Hardy–Weinberg Proportions , 2006, Biometrics.

[15]  Santiago Rodríguez,et al.  MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers , 2006, BMC Bioinformatics.

[16]  P. Hedrick.  A STANDARDIZED GENETIC DIFFERENTIATION MEASURE , 2005, Evolution; international journal of organic evolution.

[17]  A. Cambon-Thomsen,et al.  Strategies in analysis of the genetic component of multifactorial diseases; biostatistical aspects. , 2005, Transplant immunology.

[18]  Mark Daly,et al.  Haploview: analysis and visualization of LD and haplotype maps , 2005, Bioinform..

[19]  W. G. Hill,et al.  Linkage disequilibrium in finite populations , 1968, Theoretical and Applied Genetics.

[20]  Patrick J. F. Groenen,et al.  Modern multidimensional scaling: Theory and applications, 2nd ed. , 2005 .

[21]  T. Niu.  Algorithms for inferring haplotypes , 2004, Genetic epidemiology.

[22]  S. Tishkoff,et al.  Implications of biogeography of human populations for 'race' and medicine , 2004, Nature Genetics.

[23]  A. Chakravarti.  Information content of the Centre d'Etude du Polymorphisme Humain (CEPH) family structures for linkage studies , 1991, Human Genetics.

[24]  H. Hattemer,et al.  Genetic distance between populations , 1982, Theoretical and Applied Genetics.

[25]  A. Yuan,et al.  Exact test of Hardy-Weinberg equilibrium by Markov chain Monte Carlo. , 2003, Mathematical medicine and biology : a journal of the IMA.

[26]  Peter Donnelly,et al.  A comparison of bayesian methods for haplotype reconstruction from population genotype data. , 2003, American journal of human genetics.

[27]  M. Feldman,et al.  The application of molecular genetic approaches to the study of human evolution , 2003, Nature Genetics.

[28]  M. Feldman,et al.  Genetic Structure of Human Populations , 2002, Science.

[29]  Zhaohui S. Qin,et al.  Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms. , 2002, American journal of human genetics.

[30]  Katherine M Kirk,et al.  The impact of genotyping error on haplotype reconstruction and frequency estimation , 2002, European Journal of Human Genetics.

[31]  George Karypis,et al.  CLUTO - A Clustering Toolkit , 2002 .

[32]  Jill A Hollenbach,et al.  Haplotype frequency estimation in patient populations: The effect of departures from Hardy‐Weinberg proportions and collapsing over a locus in the HLA region , 2002, Genetic epidemiology.

[33]  Zhaohui S. Qin,et al.  Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. , 2002, American journal of human genetics.

[34]  P. Donnelly,et al.  A new statistical method for haplotype reconstruction from population data. , 2001, American journal of human genetics.

[35]  N. Schork,et al.  Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data. , 2000, American journal of human genetics.

[36]  K K Kidd,et al.  The accuracy of statistical methods for estimation of haplotype frequencies: an example from the CD4 locus. , 2000, American journal of human genetics.

[37]  P. Donnelly,et al.  Inference of population structure using multilocus genotype data. , 2000, Genetics.

[38]  Gonçalo R. Abecasis,et al.  GOLD-Graphical Overview of Linkage Disequilibrium , 2000, Bioinform..

[39]  D. Groggel.  Practical Nonparametric Statistics , 1972, Technometrics.

[40]  G. Thomson,et al.  The Variance for the Disequilibrium Coefficient in the Individual Hardy–Weinberg Test , 1999, Biometrics.

[41]  M. King,et al.  Hardy-Weinberg testing for HLA class II (DRB1, DQA1, DQB1, and DPB1) loci in 26 human ethnic groups. , 1999, Tissue antigens.

[42]  G Thomson,et al.  Evolution of HLA class II molecules: Allelic and amino acid site variability across populations. , 1999, Genetics.

[43]  T. Bergström,et al.  Recent origin of HLA-DRB1 alleles and implications for human evolution , 1998, Nature Genetics.

[44]  A. Hughes,et al.  Natural selection at major histocompatibility complex loci of vertebrates. , 1998, Annual review of genetics.

[45]  T. Bergström,et al.  Analysis of intron sequences at the class II HLA-DRB1 locus: implications for the age of allelic diversity. , 2004, Hereditas.

[46]  T. Bergström,et al.  HLA class II alleles in Amerindian populations: implications for the evolution of HLA polymorphism and the colonization of the Americas. , 2004, Hereditas.

[47]  P. Groenen,et al.  Modern Multidimensional Scaling: Theory and Applications , 1999 .

[48]  D. Watkins,et al.  Heirs of the jaguar and the anaconda: HLA, conquest and disease in the indigenous populations of the Americas. , 1997, Tissue antigens.

[49]  M Slatkin,et al.  A correction to the exact test based on the Ewens sampling distribution. , 1996, Genetical research.

[50]  Laurent Excoffier,et al.  Testing for linkage disequilibrium in genotypic data using the Expectation-Maximization algorithm , 1996, Heredity.

[51]  D. F. Roberts,et al.  The History and Geography of Human Genes , 1996 .

[52]  M. Carrington,et al.  Discordant patterns of linkage disequilibrium of the peptide-transporter loci within the HLA class II region. , 1995, American journal of human genetics.

[53]  K. Kidd,et al.  HAPLO: a program using the EM algorithm to estimate the frequencies of multi-site haplotypes. , 1995, The Journal of heredity.

[54]  R. Cann.  The history and geography of human genes , 1995, The Journal of Asian Studies.

[55]  J. Long,et al.  An E-M algorithm and testing strategy for multiple-locus haplotypes. , 1995, American journal of human genetics.

[56]  M Slatkin,et al.  A measure of population subdivision based on microsatellite allele frequencies. , 1995, Genetics.

[57]  M Slatkin,et al.  An exact test for neutrality based on the Ewens sampling distribution. , 1994, Genetical research.

[58]  Cécile Fizames,et al.  The 1993–94 Généthon human genetic linkage map , 1994, Nature Genetics.

[59]  M. Lynch,et al.  Analysis of population genetic structure with RAPD markers , 1994, Molecular ecology.

[60]  J. Weber,et al.  Mutation of human short tandem repeats. , 1993, Human molecular genetics.

[61]  E. Thompson,et al.  Performing the exact test of Hardy-Weinberg proportion for multiple alleles. , 1992, Biometrics.

[62]  M. Slatkin.  Inbreeding coefficients and coalescence times. , 1991, Genetical research.

[63]  B S Weir,et al.  A disequilibrium coefficient approach to Hardy-Weinberg testing. , 1989, Biometrics.

[64]  M. Nei,et al.  Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection , 1988, Nature.

[65]  E J Louis,et al.  An exact test for Hardy-Weinberg and multiple alleles. , 1987, Biometrics.

[66]  P. Hedrick,et al.  Gametic disequilibrium measures: proceed with caution. , 1987, Genetics.

[67]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[68]  J. Felsenstein.  CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.

[69]  D. Penny,et al.  TESTING METHODS OF EVOLUTIONARY TREE CONSTRUCTION , 1985, Cladistics : the international journal of the Willi Hennig Society.

[70]  B. Weir,et al.  ESTIMATING F‐STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE , 1984, Evolution; international journal of organic evolution.

[71]  N. Morton,et al.  Estimation of haplotype frequencies. , 2008, Tissue antigens.

[72]  B S Weir,et al.  Estimation of the coancestry coefficient: basis for a short-term genetic distance. , 1983, Genetics.

[73]  T. H. Emigh,et al.  A comparison of tests for Hardy-Weinberg equilibrium. , 1980, Biometrics.

[74]  N. Yasuda.  Estimation of haplotype frequency and linkage disequilibrium parameter in the HLA system. , 1978, Tissue antigens.

[75]  M. Nei,et al.  Estimation of average heterozygosity and genetic distance from a small number of individuals. , 1978, Genetics.

[76]  G. A. Watterson.  The homozygosity test of neutrality. , 1978, Genetics.

[77]  M. Nei,et al.  F‐statistics and analysis of gene diversity in subdivided populations , 1977, Annals of human genetics.

[78]  D. Rubin,et al.  Maximum likelihood from incomplete data via the EM - algorithm plus discussions on the paper , 1977 .

[79]  S. Wright.  Evolution and the Genetics of Populations, Volume 3: Experimental Results and Evolutionary Deductions , 1977 .

[80]  J Ott,et al.  Counting methods (EM algorithm) in human pedigree analysis: Linkage and segregation analysis , 1977, Annals of human genetics.

[81]  S. Jain,et al.  GENETIC STRUCTURE OF POPULATIONS. , 1975, Evolution; international journal of organic evolution.

[82]  W. Ewens.  The sampling theory of selectively neutral alleles. , 1972, Theoretical population biology.

[83]  L. Cavalli-Sforza,et al.  PHYLOGENETIC ANALYSIS: MODELS AND ESTIMATION PROCEDURES , 1967, Evolution; international journal of organic evolution.

[84]  R. Lewontin.  The Interaction of Selection and Linkage. I. General Considerations; Heterotic Models. , 1964, Genetics.

[85]  Robert R. Sokal,et al.  A statistical method for evaluating systematic relationships , 1958 .

[86]  N. Metropolis,et al.  Equation of State Calculations by Fast Computing Machines , 1953, Resonance.

[87]  S WRIGHT,et al.  Genetical structure of populations. , 1950, Nature.

[88]  H. Levene.  On a Matching Problem Arising in Genetics , 1949 .

[89]  Karl Pearson F.R.S..  LIII. On lines and planes of closest fit to systems of points in space , 1901 .