@article{wang_weir_zeng_2006, title={A population-based latent variable approach for association mapping of quantitative trait loci}, volume={70}, ISSN={["0003-4800"]}, DOI={10.1111/j.1469-1809.2006.00264.x}, abstractNote={Summary}, journal={ANNALS OF HUMAN GENETICS}, author={Wang, T and Weir, B and Zeng, ZB}, year={2006}, month={Jul}, pages={506–523} }
 @article{anderson_weir_2006, title={It was one of my brothers}, volume={120}, ISSN={["1437-1596"]}, DOI={10.1007/s00414-005-0017-2}, abstractNote={When DNA evidence is used to implicate a suspect, it may be of interest to know whether it is likely that the suspect's near relatives also share the suspect's DNA profile. In this study we discuss methods for evaluating the probability that at least one of a set of the suspect's full or half-siblings shares the suspect's DNA profile. We present three such methods: exact calculation, estimation via Monte Carlo simulations, and estimation by means of sandwiching the probability between an upper and a lower bound. We show that, under many circumstances, this upper bound itself provides an extremely quick and accurate estimate of the probability that at least one of the relatives matches the suspect's profile.}, number={2}, journal={INTERNATIONAL JOURNAL OF LEGAL MEDICINE}, author={Anderson, AD and Weir, BS}, year={2006}, month={Mar}, pages={95–104} }
 @article{liu_weir_2005, title={Genotypic probabilities for pairs of inbred relatives}, volume={360}, number={1459}, journal={Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences}, author={Liu, W. L. and Weir, B. S.}, year={2005}, pages={1379–1385} }
 @article{weir_cardon_anderson_nelson_hill_2005, title={Measures of human population structure show heterogeneity among genomic regions}, volume={15}, ISSN={1088-9051}, url={http://dx.doi.org/10.1101/gr.4398405}, DOI={10.1101/gr.4398405}, abstractNote={Estimates of genetic population structure (FST) were constructed from all autosomes in two large SNP data sets. The Perlegen data set contains genotypes on ∼1 million SNPs segregating in all three samples of Americans of African, Asian, and European descent; and the Phase I HapMap data set contains genotypes on ∼0.6 million SNPs segregating in all four samples from specific Caucasian, Chinese, Japanese, and Yoruba populations. Substantial heterogeneity of FST values was found between segments within chromosomes, although there was similarity between the two data sets. There was also substantial heterogeneity among population-specific FST values, with the relative sizes of these values often changing along each chromosome. Population-structure estimates are often used as indicators of natural selection, but the analyses presented here show that individual-marker estimates are too variable to be useful. There is inherent variation in these statistics because of variation in genealogy even among neutral loci, and values at pairs of loci are correlated to an extent that reflects the linkage disequilibrium between them. Furthermore, it may be that the best indications of selection will come from population-specific FST values rather than the usually reported population-average values.}, number={11}, journal={Genome Research}, publisher={Cold Spring Harbor Laboratory}, author={Weir, B. S. and Cardon, L.R. and Anderson, A.D. and Nelson, D.M. and Hill, W.G.}, year={2005}, month={Nov}, pages={1468–1476} }
 @misc{gibson_weir_2005, title={The quantitative genetics of transcription}, volume={21}, ISSN={["0168-9525"]}, DOI={10.1016/j.tig.2005.08.010}, abstractNote={Quantitative geneticists have become interested in the heritability of transcription and detection of expression quantitative trait loci (eQTLs). Linkage mapping methods have identified major-effect eQTLs for some transcripts and have shown that regulatory polymorphisms in cis and in trans affect expression. It is also clear that these mapping strategies have little power to detect polygenic factors, and some new statistical approaches are emerging that paint a more complex picture of transcriptional heritability. Several studies imply pervasive non-additivity of transcription, transgressive segregation and epistasis, and future studies will soon document the extent of genotype-environment interaction and population structure at the transcriptional level. The implications of these findings for genotype-phenotype mapping and modeling the evolution of transcription are discussed.}, number={11}, journal={TRENDS IN GENETICS}, author={Gibson, G and Weir, B}, year={2005}, month={Nov}, pages={616–623} }
 @article{liu_weir_2004, title={Affected sib pair tests in inbred populations}, volume={68}, number={Nov-04}, journal={Annals of Human Genetics}, author={Liu, W. and Weir, B. S.}, year={2004}, pages={606–619} }
 @article{weir_bagdonavicius_blair_eckhoff_pearman_stringer_sutton_west_wynen_2004, title={Allele frequency data for profiler plus loci in Australia}, volume={49}, number={5}, journal={Journal of Forensic Sciences}, author={Weir, B. S. and Bagdonavicius, A. and Blair, B. and Eckhoff, C. and Pearman, C. and Stringer, P. and Sutton, J. and West, J. and Wynen, L.}, year={2004}, pages={1121–1123} }
 @article{weir_hill_cardon_2004, title={Allelic association patterns for a dense SNP map}, volume={27}, ISSN={["0741-0395"]}, DOI={10.1002/gepi.20038}, abstractNote={Abstract}, number={4}, journal={GENETIC EPIDEMIOLOGY}, author={Weir, BS and Hill, WG and Cardon, LR}, year={2004}, month={Dec}, pages={442–450} }
 @article{chu_weir_wolfinger_2004, title={Comparison of Li-Wong and loglinear mixed models for the statistical analysis of oligonucleotide arrays}, volume={20}, ISSN={["1460-2059"]}, DOI={10.1093/bioinformatics/btg435}, abstractNote={Abstract}, number={4}, journal={BIOINFORMATICS}, author={Chu, TM and Weir, BS and Wolfinger, RD}, year={2004}, month={Mar}, pages={500–506} }
 @article{nielsen_ehm_zaykin_weir_2004, title={Effect of Two- and Three-Locus Linkage Disequilibrium on the Power to Detect Marker/Phenotype Associations}, volume={168}, ISSN={0016-6731 1943-2631}, url={http://dx.doi.org/10.1534/genetics.103.022335}, DOI={10.1534/genetics.103.022335}, abstractNote={Abstract}, number={2}, journal={Genetics}, publisher={Genetics Society of America}, author={Nielsen, Dahlia M. and Ehm, Margaret G. and Zaykin, Dmitri V. and Weir, Bruce S.}, year={2004}, month={Oct}, pages={1029–1040} }
 @article{weir_2004, title={Matching and partial-matching DNA profiles}, volume={49}, number={5}, journal={Journal of Forensic Sciences}, author={Weir, B. S.}, year={2004}, pages={1009–1014} }
 @article{hill_weir_2004, title={Moment estimation of population diversity and genetic distance from data on recessive markers}, volume={13}, ISSN={["1365-294X"]}, DOI={10.1046/j.1365-294X.2004.02103.x}, abstractNote={Abstract}, number={4}, journal={MOLECULAR ECOLOGY}, author={Hill, WG and Weir, BS}, year={2004}, month={Apr}, pages={895–908} }
 @article{maiste_weir_2004, title={Optimal testing strategies for large, sparse multinomial models}, volume={46}, ISSN={["0167-9473"]}, DOI={10.1016/j.csda.2003.08.002}, abstractNote={Much has been written in the literature on testing for independence in contingency tables. A number of related topics have been studied, including the choice of test statistic, the appropriateness of asymptotic results versus exact tests, and the use of conditional or unconditional analyses. Much of the work to date has focused on relatively small contingency tables. The literature on testing for Hardy–Weinberg equilibrium (HWE) is substantive as well. Most of the focus to date has been on loci with relatively small numbers of alleles. The increased use of genetic markers with large numbers of alleles (e.g., forensic DNA profiling) is quickly dating this previous work. The size of the multinomial vectors under consideration grows quickly. Even relatively large samples will produce somewhat sparse multinomial data sets with small expected frequencies, calling asymptotic results into question. In the face of large, sparse multinomials, we provide a comprehensive comparison of test statistics and testing strategies (asymptotic versus exact, conditional versus unconditional) to test for independence (i.e., the presence of HWE) at one locus with many alleles. Attained significance level and power are evaluated. We find that Fisher's exact test is most appropriate for small samples, and the asymptotic chi-square goodness-of-fit statistic works well with large samples, relative to the number of multinomial categories. The log-likelihood ratio statistic performs poorly.}, number={3}, journal={COMPUTATIONAL STATISTICS & DATA ANALYSIS}, author={Maiste, PJ and Weir, BS}, year={2004}, month={Jun}, pages={605–620} }
 @article{czika_weir_2004, title={Properties of the multiallelic trend test}, volume={60}, ISSN={["0006-341X"]}, DOI={10.1111/j.0006-341X.2004.00166.x}, abstractNote={Summary.  Disease genes can be mapped on the basis of associations between genetic markers and disease status, with the case–control design having the advantage of not requiring individuals from different generations. When the marker loci have multiple alleles, there has been debate on whether the power of tests for association increases or decreases. We show here that the multiple‐allele version of Armitage's trend test has increased power over the two‐allele version under the requirement of equifrequent alleles, but not in general. The trend test has the advantage of remaining valid even when the sampled population is not in Hardy–Weinberg equilibrium. A departure from Hardy–Weinberg means that association tests depend on gametic and nongametic linkage disequilibrium between marker and disease loci, and we illustrate the magnitude of these effects with simulated data.}, number={1}, journal={BIOMETRICS}, author={Czika, W and Weir, BS}, year={2004}, month={Mar}, pages={69–74} }
 @article{laurie_weir_2003, title={Dependency effects in multi-locus match probabilities}, volume={63}, ISSN={["0040-5809"]}, DOI={10.1016/S0040-5809(03)00002-9}, abstractNote={For finite populations, differences in individual histories can cause between-locus allelic dependencies even for unlinked loci. The main motivation for this study is to quantify the effect of such dependencies on genotypic match probabilities. We compare the two-locus match probability, the probability that two individuals (four gametes) chosen at random will have the same genotype at both loci, with the probability computed as the product of the one-locus match probabilities. It is demonstrated that the product rule probability always underestimates the two-locus match probability. For highly mutable minisatellite loci, these probabilities can differ by an order of magnitude or more. A simplified three-locus problem is explored, providing evidence that the degree of under-estimation worsens for more loci.}, number={3}, journal={THEORETICAL POPULATION BIOLOGY}, author={Laurie, C and Weir, BS}, year={2003}, month={May}, pages={207–219} }
 @article{law_buckleton_triggs_weir_2003, title={Effects of population structure and admixture on exact tests for association between loci}, volume={164}, number={1}, journal={Genetics}, author={Law, B. and Buckleton, J. S. and Triggs, C. M. and Weir, B. S.}, year={2003}, pages={381–387} }
 @article{brenner_weir_2003, title={Issues and strategies in the DNA identification of World Trade Center victims}, volume={63}, ISSN={["0040-5809"]}, DOI={10.1016/S0040-5809(03)00008-X}, abstractNote={Identification of the nearly 3000 victims of the World Trade Center attack, represented by about 15,000 body parts, rests heavily on DNA. Reference DNA profiles are often from relatives rather than from the deceased themselves. With so large a set of victims, coincidental similarities between non-relatives abound. Therefore considerable care is necessary to succeed in correlating references with correct victims while avoiding spurious assignments. Typically multiple relatives are necessary to establish the identity of a victim. We describe a 3-stage paradigm—collapse, screen, test—to organize the work of sorting out the identities. Inter alia we present a simple and general formula for the likelihood ratio governing practically any potential relationship between two DNA profiles.}, number={3}, journal={THEORETICAL POPULATION BIOLOGY}, author={Brenner, CH and Weir, BS}, year={2003}, month={May}, pages={173–178} }
 @article{gibbs_belmont_hardenbol_willis_yu_yang_ch'ang_huang_liu_shen_et al._2003, title={The International HapMap Project}, volume={426}, ISSN={["1476-4687"]}, DOI={10.1038/nature02168}, abstractNote={The goal of the International HapMap Project is to determine the common patterns of DNA sequence variation in the human genome and to make this information freely available in the public domain. An international consortium is developing a map of these patterns across the genome by determining the genotypes of one million or more sequence variants, their frequencies and the degree of association between them, in DNA samples from populations with ancestry from parts of Africa, Asia and Europe. The HapMap will allow the discovery of sequence variants that affect common disease, will facilitate development of diagnostic tools, and will enhance our ability to choose targets for therapeutic intervention.}, number={6968}, journal={NATURE}, author={Gibbs, RA and Belmont, JW and Hardenbol, P and Willis, TD and Yu, FL and Yang, HM and Ch'ang, LY and Huang, W and Liu, B and Shen, Y and et al.}, year={2003}, month={Dec}, pages={789–796} }
 @article{weir_2003, title={Uses of DNA and genetic markers for forensics and population studies}, volume={63}, ISSN={["1096-0325"]}, DOI={10.1016/S0040-5809(03)00009-1}, abstractNote={3β-Hydroxysteroid dehydrogenases (3βHSD) are supposed to be involved in cardenolide biosynthesis in plants. Erysimum crepidifolium Rchb., a member of the Brassicaceae accumulating cardenolides, is a close relative to Arabidopsis thaliana. Full length cDNAs encoding for three individual 3βHSDs (EcHSD1, EcHSD2, EcHSD3) were isolated from E. crepidifolium leaves. EcHSD1 and EcHSD2 encode proteins assembled from 257 amino acids whereas EcHSD3 encodes a protein assembled from 260 amino acids. All three proteins qualify as members of the short-chain dehydrogenases/reductases family of proteins (SDRs). EcHSD1 and EcHSD2 shared a high amino acid sequence identity of about 86% and 91% with putative 3βHSDs of A. thaliana (AT2G47140 and AT2G47130). EcHSD3 showed high homology to the A. thaliana SDRs AT2G47150 (74%) and AT2G47120 (81%). All three EcHSD genes were expressed in Escherichia coli and the recombinant enzymes were characterized biochemically. All three recombinant EcHSDs catalyzed the dehydrogenation of pregnenolone and the 3-reduction of 5α/β-pregnane-3,20-dione when NAD and NADH were used as cosubstrates, respectively. After exposure to different stress conditions, no increased transcription was seen for EcHSD1 whereas EcHSD2 was expressed four times higher under osmotic stress than under control conditions. EcHSD3 expression was 10 times and 6 times higher after osmotic stress and MeJA treatment, respectively, than in controls.}, number={3}, journal={THEORETICAL POPULATION BIOLOGY}, author={Weir, BS}, year={2003}, month={May}, pages={171–172} }
 @article{chu_weir_wolfinger_2002, title={A systematic statistical linear modeling approach to oligonucleotide array experiments}, volume={176}, ISSN={["0025-5564"]}, DOI={10.1016/S0025-5564(01)00107-9}, abstractNote={We outline and describe steps for a statistically rigorous approach to analyzing probe-level Affymetrix GeneChip data. The approach employs classical linear mixed models and operates on a gene-by-gene basis. Forgoing any attempts at gene presence or absence calls, the method simultaneously considers the data across all chips in an experiment. Primary output includes precise estimates of fold change (some as low as 1.1), their statistical significance, and measures of array and probe variability. The method can accommodate complex experiments involving many kinds of treatments and can test for their effects at the probe level. Furthermore, mismatch probe data can be incorporated in different ways or ignored altogether. Data from an ionizing radiation experiment on human cell lines illustrate the key concepts.}, number={1}, journal={MATHEMATICAL BIOSCIENCES}, author={Chu, TM and Weir, B and Wolfinger, R}, year={2002}, month={Mar}, pages={35–51} }
 @article{spruill_lu_hardy_weir_2002, title={Assessing sources of variability in microarray gene expression data}, volume={33}, number={4}, journal={Biotechniques}, author={Spruill, S. E. and Lu, J. and Hardy, S. and Weir, B.}, year={2002}, pages={916-} }
 @misc{weir_hill_2002, title={Estimating F-statistics}, volume={36}, ISSN={["1545-2948"]}, DOI={10.1146/annurev.genet.36.050802.093940}, abstractNote={ ▪ Abstract  A moment estimator of θ, the coancestry coefficient for alleles within a population, was described by Weir & Cockerham in 1984 ( 100 ) and is still widely cited. The estimate is used by population geneticists to characterize population structure, by ecologists to estimate migration rates, by animal breeders to describe genetic variation, and by forensic scientists to quantify the strength of matching DNA profiles. This review extends the work of Weir & Cockerham by allowing different levels of coancestry for different populations, and by allowing non-zero coancestries between pairs of populations. All estimates are relative to the average value of θ between pairs of populations. Moment estimates for within- and between-population θ values are likely to have large sampling variances, although these may be reduced by combining information over loci. Variances also decrease with the numbers of alleles at a locus, and with the numbers of populations sampled. This review also extends the work of Weir & Cockerham by employing maximum likelihood methods under the assumption that allele frequencies follow the normal distribution over populations. For the case of equal θ values within populations and zero θ values between populations, the maximum likelihood estimate is the same as that given by Robertson & Hill in 1984 ( 70 ). The review concludes by relating functions of θ values to times of population divergence under a pure drift model. }, journal={ANNUAL REVIEW OF GENETICS}, author={Weir, BS and Hill, WG}, year={2002}, pages={721–750} }
 @article{de luca_rose_bonafe_garasto_greco_weir_franceschi_de benedictis_2002, title={Sex-specific longevity associations defined by tyrosine hydroxylase-insulin-insulin growth factor 2 haplotypes on the 11p15.5 chromosomal region (vol 36, pg 1663, 2001)}, volume={37}, number={4}, journal={Experimental Gerontology}, author={De Luca, M. and Rose, G. and Bonafe, M. and Garasto, S. and Greco, V. and Weir, B. S. and Franceschi, C. and De Benedictis, G.}, year={2002}, pages={607–608} }
 @article{zaykin_zhivotovsky_westfall_weir_2002, title={Truncated product method for combining P-values}, volume={22}, ISSN={["0741-0395"]}, DOI={10.1002/gepi.0042}, abstractNote={Abstract}, number={2}, journal={GENETIC EPIDEMIOLOGY}, author={Zaykin, DV and Zhivotovsky, LA and Westfall, PH and Weir, BS}, year={2002}, month={Feb}, pages={170–185} }
 @article{liu_weir_2001, title={Affected sib pair tests in inbred populations.}, volume={69}, number={4}, journal={American Journal of Human Genetics}, author={Liu, W. and Weir, B. S.}, year={2001}, pages={2012} }
 @article{hardy_weir_kaplan_martin_2001, title={Analysis of single nucleotide polymorphisms in candidate genes using the pedigree disequilibrium test}, volume={21}, ISSN={["0741-0395"]}, DOI={10.1002/gepi.2001.21.s1.s441}, abstractNote={The pedigree disequilibrium test (PDT) has been proposed recently as a test for association in general pedigrees [Martin et al., Am J Hum Genet 67:146–54, 2000]. The Genetic Analysis Workshop (GAW) 12 simulated data, with many extended pedigrees, is an example the type of data to which the PDT is ideally suited. In replicate 42 from the general population the PDT correctly identifies candidate genes 1, 2, and 6 as containing single nucleotide polymorphisms (SNPs) that arc significantly associated with the disease. We also applied the truncated product method (TPM) [Zaykin et al., Genet Epidemiol, in press] to combine p‐values in overlapping windows across the genes. Our results show that the TPM is helpful in identifying significant SNPs as well as removing spurious false positives. Our results indicate that, using the PDT, functional disease‐associated SNPs can be successfully identified with a dense map of moderately polymorphic SNPs. © 2001 Wiley‐Liss, Inc.}, journal={GENETIC EPIDEMIOLOGY}, author={Hardy, SW and Weir, BS and Kaplan, NL and Martin, ER}, year={2001}, pages={S441–S446} }
 @article{nielsen_weir_2001, title={Association Studies under General Disease Models}, volume={60}, ISSN={0040-5809}, url={http://dx.doi.org/10.1006/tpbi.2001.1539}, DOI={10.1006/tpbi.2001.1539}, abstractNote={There is great expectation that the levels of association found between genetic markers and disease status will play a role in the location of disease genes. This expectation follows from regarding association as being proportional to linkage disequilibrium and therefore inversely related to recombination value. For disease genes with more than two alleles, the association measure is instead a weighted average of linkage disequilibria, with the weights depending on allele frequencies and genotype susceptibilities at the disease loci. There is no longer a simple relationship, even in expectation, with recombination. We adopt a general framework to examine association mapping methods which helps to clarify the nature of case-control and transmission/disequilibrium-type tests and reveals the relationship between measures of association and coefficients of linkage disequilibrium. In particular, we can show the consequences of additive and nonadditive effects at the trait locus on the behavior of these tests. These concepts have a natural extension to marker haplotypes. The association of two-locus marker haplotypes with disease phenotype depends on a weighted average of three-locus disequilibria (two markers with each disease locus). It is likely that these two-marker analyses will provide additional information in association mapping studies.}, number={3}, journal={Theoretical Population Biology}, publisher={Elsevier BV}, author={Nielsen, Dahlia M. and Weir, B.S.}, year={2001}, month={Nov}, pages={253–263} }
 @article{rahman_afroze_weir_2001, title={DNA typing results from two urban subpopulations of Pakistan}, volume={46}, number={1}, journal={Journal of Forensic Sciences}, author={Rahman, Z. and Afroze, T. and Weir, B. S.}, year={2001}, pages={111–115} }
 @article{zaykin_ehm_weir_2001, title={Determining success of haplotyping algorithms using densely mapped genomic regions.}, volume={69}, number={4}, journal={American Journal of Human Genetics}, author={Zaykin, D. V. and Ehm, M. G. and Weir, B. S.}, year={2001}, pages={116} }
 @article{huang_weir_2001, title={Estimating the total number of alleles using a sample coverage method}, volume={159}, number={3}, journal={Genetics}, author={Huang, S. P. and Weir, B. S.}, year={2001}, pages={1365–1373} }
 @article{weir_2001, title={Introduction: Transmission/disequilibrium test/association group}, volume={21}, ISSN={["0741-0395"]}, DOI={10.1002/gepi.2001.21.s1.s421}, abstractNote={A range of study designs, using unrelated or family controls, were used to investigate the pattern of association with disease of single nucleotide polymorphisms (SNPs) within candidate gene 1 (simulated data). Strong evidence of disease association at the functional locus was detected using all study designs, and in the "general" but not the "isolated" population the functional polymorphism displayed considerably higher association than surrounding SNPs. There was much variation in the strength of association of SNPs with disease, up to 70% of which was explained by SNP allele frequency and distance from the functional polymorphism. Some common polymorphisms very close to the functional locus however showed no association with disease. Analysis of short haplotypes of SNPs reduced but did not totally remove this feature.}, journal={GENETIC EPIDEMIOLOGY}, author={Weir, BS}, year={2001}, pages={S421–S422} }
 @article{de luca_rose_bonafe_garasto_greco_weir_franceschi_de benedictis_2001, title={Sex-specific longevity associations defined by Tyrosine Hydroxylase-Insulin-Insulin Growth Factor 2 haplotypes on the 11p15.5 chromosomal region}, volume={36}, ISSN={["0531-5565"]}, DOI={10.1016/S0531-5565(01)00146-2}, abstractNote={By studies in centenarians, it was recently found that an STR marker of the Tyrosine Hydroxylase (TH, 11p15.5) gene is associated with human longevity. The aim of the present study was to continue the exploration of the 11p15.5 chromosomal region in human longevity by analyzing two additional RFLP markers, which lie in the Insulin (INS) and Insulin Growth Factor 2 (IGF2) genes. Both the genes, which are localized downstream TH, are indeed good candidates in longevity, as ascertained on the basis of laboratory studies in experimental models. Neither INS nor IGF2 markers did reveal association with longevity. Nevertheless, linkage disequilibrium analyses showed sex-specific longevity associations defined by both TH–INS and TH–IGF2 haplotypes. On the whole, the results reinforce the involvement of the chromosomal region spanning from TH to IGF2 loci in controlling the longevity phenotype in humans.}, number={10}, journal={EXPERIMENTAL GERONTOLOGY}, author={De Luca, M and Rose, G and Bonafe, A and Garasto, S and Greco, V and Weir, BS and Franceschi, C and De Benedictis, G}, year={2001}, month={Nov}, pages={1663–1671} }
 @article{meng_zaykin_ehm_weir_2001, title={Testing the association of quantitative traits and haplotypes considering treatment effects.}, volume={69}, number={4}, journal={American Journal of Human Genetics}, author={Meng, Z. and Zaykin, D. V. and Ehm, M. G. and Weir, B. S.}, year={2001}, pages={1286} }
 @article{weir_2000, title={Challenges facing statistical genetics}, volume={95}, number={449}, journal={Journal of the American Statistical Association}, author={Weir, B. S.}, year={2000}, pages={319–322} }
 @article{graham_curran_weir_2000, title={Conditional genotypic probabilities for microsatellite loci}, volume={155}, number={4}, journal={Genetics}, author={Graham, J. and Curran, J. and Weir, B. S.}, year={2000}, pages={1973–1980} }
 @misc{evett_foreman_weir_2000, title={Letter to the editor of Biometrics}, volume={56}, number={4}, journal={Biometrics}, author={Evett, I. W. and Foreman, L. A. and Weir, B. S.}, year={2000}, pages={1274–1275} }
 @misc{weir_2000, title={What is the structure of human populations?}, volume={32}, number={2000}, journal={Evolutionary Biology}, author={Weir, B. S.}, year={2000}, pages={195–202} }
 @article{nielsen_weir_1999, title={A classical setting for associations between markers and loci 
affecting quantitative traits}, volume={74}, ISSN={0016-6723 1469-5073}, url={http://dx.doi.org/10.1017/s0016672399004231}, DOI={10.1017/S0016672399004231}, abstractNote={We examine the relationships between a genetic marker and a locus affecting a quantitative trait 
by decomposing the genetic effects of the marker locus into additive and dominance effects under a 
classical genetic model. We discuss the structure of the associations between the marker and the 
trait locus, paying attention to non-random union of gametes, multiple alleles at the marker and 
trait loci, and non-additivity of allelic effects at the trait locus. We consider that this greater-than-usual level of generality leads to additional insights, in a way reminiscent of Cockerham's 
decomposition of genetic variance into five terms: three terms in addition to the usual additive and 
dominance terms. Using our framework, we examine several common tests of association between 
a marker and a trait.}, number={3}, journal={Genetical Research}, publisher={Cambridge University Press (CUP)}, author={Nielsen, Dahlia M. and Weir, B. S.}, year={1999}, month={Dec}, pages={271–277} }
 @misc{shoemaker_painter_weir_1999, title={Bayesian statistics in genetics - a guide for the uninitiated}, volume={15}, ISSN={["0168-9525"]}, DOI={10.1016/S0168-9525(99)01751-5}, abstractNote={Statistical analyses are used in many fields of genetic research. Most geneticists are taught classical statistics, which includes hypothesis testing, estimation and the construction of confidence intervals; this framework has proved more than satisfactory in many ways. What does a Bayesian framework have to offer geneticists? Its utility lies in offering a more direct approach to some questions and the incorporation of prior information. It can also provide a more straightforward interpretation of results. The utility of a Bayesian perspective, especially for complex problems, is becoming increasingly clear to the statistics community; geneticists are also finding this framework useful and are increasingly utilizing the power of this approach.}, number={9}, journal={TRENDS IN GENETICS}, author={Shoemaker, JS and Painter, IS and Weir, BS}, year={1999}, month={Sep}, pages={354–358} }
 @article{curran_triggs_buckleton_weir_1999, title={Interpreting DNA mixtures in structured populations}, volume={44}, number={5}, journal={Journal of Forensic Sciences}, author={Curran, J. M. and Triggs, C. M. and Buckleton, J. and Weir, B. S.}, year={1999}, pages={987–995} }
 @article{shoemaker_painter_weir_1998, title={A Bayesian characterization of Hardy-Weinberg disequilibrium}, volume={149}, number={4}, journal={Genetics}, author={Shoemaker, J. and Painter, I. and Weir, B. S.}, year={1998}, pages={2079–2088} }
 @article{monks_kaplan_weir_1998, title={A comparative study of sibship tests of linkage and/or association}, volume={63}, ISSN={["0002-9297"]}, DOI={10.1086/302104}, abstractNote={Population-based tests of association have used data from either case-control studies or studies based on trios (affected child and parents). Case-control studies are more prone to false-positive results caused by inappropriate controls, which can occur if, for example, there is population admixture or stratification. An advantage of family-based tests is that cases and controls are well matched, but parental data may not always be available, especially for late-onset diseases. Three recent family-based tests of association and linkage utilize unaffected siblings as surrogates for untyped parents. In this paper, we propose an extension of one of these tests. We describe and compare the four tests in the context of a complex disease for both biallelic and multiallelic markers, as well as for sibships of different sizes. We also examine the consequences of having some parental data in the sample.}, number={5}, journal={AMERICAN JOURNAL OF HUMAN GENETICS}, author={Monks, SA and Kaplan, NL and Weir, BS}, year={1998}, month={Nov}, pages={1507–1516} }
 @book{weir_buckleton_1998, title={Characterizing population structure for assigning weight to DNA matching profiles}, publisher={Rockville, MD: National Institute of Justice}, author={Weir, B. S. and Buckleton, J. S.}, year={1998} }
 @article{nielsen_ehm_weir_1998, title={Detecting Marker-Disease Association by Testing for Hardy-Weinberg Disequilibrium at a Marker Locus}, volume={63}, ISSN={0002-9297}, url={http://dx.doi.org/10.1086/302114}, DOI={10.1086/302114}, abstractNote={We review and extend a recent suggestion that fine-scale localization of a disease-susceptibility locus for a complex disease be done on the basis of deviations from Hardy-Weinberg equilibrium among affected individuals. This deviation is driven by linkage disequilibrium between disease and marker loci in the whole population and requires a heterogeneous genetic basis for the disease. A finding of marker-locus Hardy-Weinberg disequilibrium therefore implies disease heterogeneity and marker-disease linkage disequilibrium. Although a lack of departure of Hardy-Weinberg disequilibrium at marker loci implies that disease susceptibilityweighted linkage disequilibria are zero, given disease heterogeneity, it does not follow that the usual measures of linkage disequilibrium are zero. For disease-susceptibility loci with more than two alleles, therefore, care is needed in the drawing of inferences from marker Hardy-Weinberg disequilibria.}, number={5}, journal={The American Journal of Human Genetics}, publisher={Elsevier BV}, author={Nielsen, Dahlia M. and Ehm, M.G. and Weir, B.S.}, year={1998}, month={Nov}, pages={1531–1540} }
 @book{weir_1998, title={Estimation of population structure parameters, final report}, publisher={Rockville, MD: National Institute of Justice}, author={Weir, B. S.}, year={1998} }
 @book{evett_weir_1998, title={Interpreting DNA evidence: Statistical genetics for forensic scientists}, ISBN={0878931554}, publisher={Sunderland, MA: Sinauer Associates}, author={Evett, I. W. and Weir, B. S.}, year={1998} }
 @article{kaplan_martin_morris_weir_1998, title={Marker selection for the transmission/disequilibrium test, in recently admixed populations}, volume={62}, ISSN={["0002-9297"]}, DOI={10.1086/301760}, abstractNote={Recent admixture between genetically differentiated populations can result in high levels of association between alleles at loci that are <=10 cM apart. The transmission/disequilibrium test (TDT) proposed by Spielman et al. (1993) can be a powerful test of linkage between disease and marker loci in the presence of association and therefore could be a useful test of linkage in admixed populations. The degree of association between alleles at two loci depends on the differences in allele frequencies, at the two loci, in the founding populations; therefore, the choice of marker is important. For a multiallelic marker, one strategy that may improve the power of the TDT is to group marker alleles within a locus, on the basis of information about the founding populations and the admixed population, thereby collapsing the marker into one with fewer alleles. We have examined the consequences of collapsing a microsatellite into a two-allele marker, when two founding populations are assumed for the admixed population, and have found that if there is random mating in the admixed population, then typically there is a collapsing for which the power of the TDT is greater than that for the original microsatellite marker. A method is presented for finding the optimal collapsing that has minimal dependence on the disease and that uses estimates either of marker allele frequencies in the two founding populations or of marker allele frequencies in the current, admixed population and in one of the founding populations. Furthermore, this optimal collapsing is not always the collapsing with the largest difference in allele frequencies in the founding populations. To demonstrate this strategy, we considered a recent data set, published previously, that provides frequency estimates for 30 microsatellites in 13 populations.}, number={3}, journal={AMERICAN JOURNAL OF HUMAN GENETICS}, author={Kaplan, NL and Martin, ER and Morris, RW and Weir, BS}, year={1998}, month={Mar}, pages={703–712} }
 @article{buckleton_evett_weir_1998, title={Setting bounds for the likelihood ratio when multiple hypotheses are postulated}, volume={38}, number={1}, journal={Science and Justice}, author={Buckleton, J. S. and Evett, I. W. and Weir, B. S.}, year={1998}, pages={23–26} }
 @inbook{weir_1998, title={Statistical methods employed in evaluation of single-locus probe results in criminal identity cases}, volume={98}, booktitle={Forensic DNA profiling protocols  (Methods in molecular biology (Clifton, N.J.) ; 98)}, publisher={Totowa, N.J.: Humana Press}, author={Weir, B. S.}, editor={P. J. Lincoln and Thomson, J.Editors}, year={1998}, pages={83–96} }
 @article{weir_painter_1997, title={Bayesian analysis of DNA profiling data in forensic identification applications: discussion}, volume={160 (part3)}, number={1997}, journal={Journal of the Royal Statistical Society. Series A, General}, author={Weir, B. S. and Painter, I. S.}, year={1997}, pages={465–466} }
 @article{mcintyre_weir_1997, title={Hardy-Weinberg testing for continuous data}, volume={147}, number={4}, journal={Genetics}, author={McIntyre, L. M. and Weir, B. S.}, year={1997}, pages={1965–1975} }
 @article{weir_triggs_starling_stowell_walsh_buckleton_1997, title={Interpreting DNA mixtures}, volume={42}, number={2}, journal={Journal of Forensic Sciences}, author={Weir, B. S. and Triggs, C. M. and Starling, L. and Stowell, L. I. and Walsh, K. A. J. and Buckleton, J.}, year={1997}, pages={213–222} }
 @article{kaplan_martin_weir_1997, title={Power studies for the transmission/disequilibrium tests with multiple alleles}, volume={60}, number={1997}, journal={American Journal of Human Genetics}, author={Kaplan, N. L. and Martin, E. R. and Weir, B. S.}, year={1997}, pages={691–702} }
 @article{doerge_zeng_weir_1997, title={Statistical issues in the search for genes?}, volume={12}, number={1997}, journal={Statistical Science}, author={Doerge, R. W. and Zeng, Z. B. and Weir, B. S.}, year={1997}, pages={195–219} }
 @article{martin_kaplan_weir_1997, title={Tests for linkage and association in nuclear families}, volume={61}, ISSN={["0002-9297"]}, DOI={10.1086/514860}, abstractNote={The transmission/disequilibrium test (TDT) originally was introduced to test for linkage between a genetic marker and a disease-susceptibility locus, in the presence of association. Recently, the TDT has been used to test for association in the presence of linkage. The motivation for this is that linkage analysis typically identifies large candidate regions, and further refinement is necessary before a search for the disease gene is begun, on the molecular level. Evidence of association and linkage may indicate which markers in the region are closest to a disease locus. As a test of linkage, transmissions from heterozygous parents to all of their affected children can be included in the TDT; however, the TDT is a valid chi2 test of association only if transmissions to unrelated affected children are used in the analysis. If the sample contains independent nuclear families with multiple affected children, then one procedure that has been used to test for association is to select randomly a single affected child from each sibship and to apply the TDT to those data. As an alternative, we propose two statistics that use data from all of the affected children. The statistics give valid chi2 tests of the null hypothesis of no association or no linkage and generally are more powerful than the TDT with a single, randomly chosen, affected child from each family.}, number={2}, journal={AMERICAN JOURNAL OF HUMAN GENETICS}, author={Martin, ER and Kaplan, NL and Weir, BS}, year={1997}, month={Aug}, pages={439–448} }
 @article{shaw_weir_shaw_1997, title={The occurrence and significance of epistatic variance for quantitative characters and its measurement in haploids}, volume={51}, ISSN={["1558-5646"]}, DOI={10.1111/j.1558-5646.1997.tb02421.x}, abstractNote={Epistatic genetic variance for quantitative traits may play an important role in evolution, but detecting epistasis in diploid organisms is difficult and requires complex breeding programs and very large sample sizes. We develop a model for detecting epistasis in organisms with a free‐living haploid stage in their life cycles. We show that epistasis is indicated by greater variance among families of haploid progeny derived from individual diploids than among clonally replicated haploid sibs from the same sporophyte. Simulations show that the power to detect epistasis is linearly related to the number of sporophytes and the number of haploids per sporophyte in the dataset. We illustrate the model with data from growth variation among gametophytes of the moss, Ceratodon purpureus. The experiment failed to detect epistatic variance for biomass production, although there was evidence of additive variance.}, number={2}, journal={EVOLUTION}, author={Shaw, AJ and Weir, BS and Shaw, FH}, year={1997}, month={Apr}, pages={348–353} }
 @misc{kaplan_martin_weir_1997, title={Transmission/disequilibrium tests for multiallelic loci: reply}, volume={61}, number={3}, journal={American Journal of Human Genetics}, author={Kaplan, N. L. and Martin, E. R. and Weir, B. S.}, year={1997}, pages={778} }
 @article{weir_gaut_1993, title={VARIANCES FOR DISTANCES BETWEEN PLANT SEQUENCES}, volume={31}, ISSN={["0028-825X"]}, DOI={10.1080/0028825X.1993.10419509}, abstractNote={Abstract Phylogenetic trees may be constructed from pairwise distances among the taxonomic units. When the data consist of DNA sequences, appropriate distances can be defined to reflect the mutation model and to have expected values proportional to the time of divergence of the sequences. With the growing amount of sequence data, it is also necessary to incorporate within-species sequence variation into measures of distance between sequences. This additional feature requires attention to be paid to drift and recombination as well as mutation, and greatly increases the difficulty of estimating variances of estimated distances. Numerical resampling seems appropriate. These concepts are illustrated with some sequence data from the Adhl gene from maize and pearl millet.}, number={3}, journal={NEW ZEALAND JOURNAL OF BOTANY}, author={WEIR, BS and GAUT, BS}, year={1993}, pages={317–322} }
 @article{weir_basten_1990, title={SAMPLING STRATEGIES FOR DISTANCES BETWEEN DNA-SEQUENCES}, volume={46}, ISSN={["0006-341X"]}, DOI={10.2307/2532079}, abstractNote={An international effort is now underway to obtain the DNA sequence for the entire human genome (Watson and Jordan, 1989, Genomics 5, 654-656; Barnhart, 1989, Genomics 5, 657-660). This Human Genome Initiative will generate sequence data from several species other than humans, and will result in several copies per species of at least some regions of the genome. Although the project has generated much interest, it is but one aspect of the widespread effort to generate DNA sequence data. Published sequences are collected in common databases, and release 63 of GenBank in March 1990 contained 40,127,752 bases from 33,337 reported sequences (News from GenBank 3; Mountain View, California: Intelligenetics, Inc., 1990). Large though this database is, it is only about 1% of the number of bases in the human genome. Interpretations of data of such magnitude are going to require the collaborative efforts of biometricians and molecular biologists, and an aim of this paper is to show that there is also a role for readers of this journal in the design of surveys of DNA sequences. Discussion here will center on the use of sequence data in evolutionary studies, where some region of DNA is sequenced in several different species. The object is to infer the evolutionary history of that particular region, or of the species themselves. Statistical issues in the very important studies on sequences to locate and characterize regions responsible for human diseases will not be addressed here. We will discuss appropriate ways of measuring distances between DNA sequences and of predicting the sampling properties of the distances. There are procedures for inferring evolutionary histories for a set of elements that depend on a matrix of distances between each pair of elements, and the precision of resulting trees must be influenced by the precision of the distances. We will show that account needs to be taken of two sampling processes--the sampling of sequences by the investigator ("statistical sampling"), and the sampling of genetic material involved in the formation of offspring from a parental population ("genetic sampling").}, number={3}, journal={BIOMETRICS}, author={WEIR, BS and BASTEN, CJ}, year={1990}, month={Sep}, pages={551–572} }
 @article{weir_reynolds_dodds_1990, title={THE VARIANCE OF SAMPLE HETEROZYGOSITY}, volume={37}, ISSN={["0040-5809"]}, DOI={10.1016/0040-5809(90)90038-W}, abstractNote={The variance of sample heterozygosity, averaged over several loci, is studied in a variety of situations. The variance depends on the sampling implicit in the mating system as well as on that explicit in the loci scored and individuals sampled. There are also effects of allelic distributions over loci and of linkage or linkage disequilibrium between pairs of loci. Results are obtained for populations in drift and mutation balance, for infinite populations undergoing mixed self and random mating, and for finite monoecious populations with or without selfing. For unlinked loci in drift/mutation balance, variances appear to be lessened more by increasing the number of loci scored than by increasing the number of individuals sampled. For infinite populations under the mixed self and random mating system, however, the reverse is true. Methods for estimating the variance of sample heterozygosity are discussed, with attention being paid to unbalanced data where not all loci are scored in all individuals.}, number={1}, journal={THEORETICAL POPULATION BIOLOGY}, author={WEIR, BS and REYNOLDS, J and DODDS, KG}, year={1990}, month={Feb}, pages={235–253} }
 @misc{weir_ohta_tachida_1985, title={GENE CONVERSION MODELS}, volume={116}, ISSN={["1095-8541"]}, DOI={10.1016/S0022-5193(85)80127-2}, abstractNote={The variances and covariances of digenic descent measures are studied for a two-locus model incorporating mutation, gene conversion, recombination, drift, and finite sampling. Gene conversion can occur between allelic pairs of genes or between non-allelic pairs on the same or different gametes within individuals. Most interest therefore centers on pairs of genes, and five digenic identity measures are required. The behavior over time of these measures is studied, with an emphasis on the effects of gene conversion. Because of the stochastic nature of the forces of drift, recombination, mutation, and conversion, the actual identity status of gene pairs can vary from expectation among replicate populations. To study this variation we compute the expected variances and covariances of the measures, and show that this requires the introduction of trigenic and quadrigenic measures. Allowing for conversion between genes on different gametes requires a large number of these higher-order measures.}, number={1}, journal={JOURNAL OF THEORETICAL BIOLOGY}, author={WEIR, BS and OHTA, T and TACHIDA, H}, year={1985}, pages={1–8} }
 @article{weir_cockerham_1984, title={ESTIMATING F-STATISTICS FOR THE ANALYSIS OF POPULATION-STRUCTURE}, volume={38}, ISSN={["0014-3820"]}, DOI={10.2307/2408641}, number={6}, journal={EVOLUTION}, author={WEIR, BS and COCKERHAM, CC}, year={1984}, pages={1358–1370} }
 @article{reynolds_weir_cockerham_1983, title={Estimation of the co-ancestry coefficient - basis for a short-term genetic-distance}, volume={105}, number={3}, journal={Genetics}, author={Reynolds, J. and Weir, B. S. and Cockerham, C. C.}, year={1983}, pages={767–779} }
 @article{weir_avery_hill_1980, title={EFFECT OF MATING STRUCTURE ON VARIATION IN INBREEDING}, volume={18}, ISSN={["0040-5809"]}, DOI={10.1016/0040-5809(80)90061-1}, abstractNote={An analysis is made of the variation among individuals in finite populations of the proportion of their genes which are identical by descent. There are two causes of this variability: variation in pedigree among individuals, and linkage which causes whole blocks of genes to be identical or nonidentical by descent. The variation between and within populations is analyzed in detail for several mating systems: monoecious populations with and without random selfing, and dioecious populations with and without a hierarchical mating structure. Transition matrices for two-locus descent measures are given for each system. Total variability is obtained by integrating these measures over the distribution of map distances over whole chromosomes. Approximate methods are also developed for unlinked loci. Unless populations have a very small effective size (Ne) there is little variation in inbreeding between populations. For unlinked loci, the coefficient of variation in nonidentity within populations approaches about 1√3Ne for random selfing, 1√6Ne for monogamous matings and 1√12Ne for monoecy with selfing excluded or dioecy with random pairing. If there is no association between map distance and initial heterozygosity or effect on quantitative traits, the coefficient of variation in mean heterozygosity over the genome is related to that in nonidentity, and the additional variation in a quantitative trait due to dominant genes equals the product of the square of the initial inbreeding depression and the squared coefficient of variation of nonidentity.}, number={3}, journal={THEORETICAL POPULATION BIOLOGY}, author={WEIR, BS and AVERY, PJ and HILL, WG}, year={1980}, pages={396–429} }
 @article{weir_hill_1980, title={Effect of mating structure on variation in linkage disequilibrium}, volume={95}, number={2}, journal={Genetics}, author={Weir, B. S. and Hill, W. G.}, year={1980}, pages={477} }
 @article{weir_1979, title={INFERENCES ABOUT LINKAGE DISEQUILIBRIUM}, volume={35}, ISSN={["0006-341X"]}, DOI={10.2307/2529947}, abstractNote={Existing theory for inferences about linkage disequilibrium is restricted to a measure defined on gametic frequencies. Unless gametic frequencies are directly observable, they are inferred from genotypic frequencies under the assumption of random union of gametes. Primary emphasis in this paper is given to genotypic data, and disequilibrium coefficients are defined for all subsets of two or more of the four genes, two at each of two loci, carried by an individual. Linkage disequilibrium coefficients are defined for genes within and between gametes, and methods of estimating and testing these coefficients are given for gametic data. For genotypic data, when coupling and repulsion double heterozygotes cannot be distinguished. Burrows' composite measure of linkage disequilibrium is discussed. In particular, the estimate for this measure and hypothesis tests based on it are compared to the usual maximum likelihood estimate of gametic linkage disequilibrium, and corresponding likelihood ratio or contingency chi-square tests. General use of the composite measure, whether or not random union of gametes is an appropriate assumption, is recommended. Attention is given to small samples, where the non-normality of gene frequencies will have greatest effect on methods of inference based on normal theory. Even tools such as Fisher's z-transformation for the correlation of gene frequencies are found to perform quite satisfactorily.}, number={1}, journal={BIOMETRICS}, author={WEIR, BS}, year={1979}, pages={235–254} }
 @article{weir_cockerham_1978, title={Testing hypotheses about linkage disequilibrium with multiple alleles}, volume={88}, number={3}, journal={Genetics}, author={Weir, B. S. and Cockerham, C. C.}, year={1978}, pages={633} }
 @article{weir_brown_marshall_1976, title={Testing for selective neutrality of electrophoretically detectable protein polymorphisms}, volume={84}, number={3}, journal={Genetics}, author={Weir, B. S. and Brown, A. H. D. and Marshall, D. R.}, year={1976}, pages={639} }
 @article{weir_cockerham_1974, title={BEHAVIOR OF PAIRS OF LOCI IN FINITE MONOECIOUS POPULATIONS}, volume={6}, ISSN={["1096-0325"]}, DOI={10.1016/0040-5809(74)90015-X}, abstractNote={Transition equations are established for descent measures for pairs of loci in finite randomly mating monoecious populations. The two special cases of equal chance gamete formation and two gametes per parent are considered in detail. The descent measures allow genotypic frequencies to be found but are used mainly to evaluate three quadrigenic moments, including the variance of the linkage disequilibrium. Numerical properties of these moments are compared to previously reported values.}, number={3}, journal={THEORETICAL POPULATION BIOLOGY}, author={WEIR, BS and COCKERHAM, CC}, year={1974}, pages={323–354} }