@article{wu_ma_painter_zeng_2002, title={Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species}, volume={61}, ISSN={["1096-0325"]}, DOI={10.1006/tpbi.2002.1577}, abstractNote={With the advent of new molecular marker technologies, it is now feasible to initiate genome projects for outcrossing plant species, which have not received much attention in genetic research, despite their great agricultural and environmental value. Because outcrossing species typically have heterogeneous genomes, data structure for molecular markers representing an entire genome is complex: some markers may have more alleles than others, some markers are codominant whereas others are dominant, and some markers are heterozygous in one parent but fixed in the other parent whereas the opposite can be true for other markers. A major difficulty in analyzing these different types of marker at the same time arises from uncertainty about parental linkage phases over markers. In this paper, we present a general maximum-likelihood-based algorithm for simultaneously estimating linkage and linkage phases for a mixed set of different marker types containing fully informative markers (segregating 1:1:1:1) and partially informative markers (or missing markers, segregating 1:2:1, 3:1, and 1:1) in a full-sib family derived from two outbred parent plants. The characterization of linkage phases is based on the posterior probability distribution of the assignment of alternative alleles at given markers to two homologous chromosomes of each parent, conditional on the observed phenotypes of the markers. Two- and multi-point analyses are performed to estimate the recombination fraction and determine the most likely linkage phase between different types of markers. A numerical example is presented to demonstrate the statistical properties of the model for characterizing the linkage phase between markers.}, number={3}, journal={THEORETICAL POPULATION BIOLOGY}, author={Wu, RL and Ma, CX and Painter, I and Zeng, ZB}, year={2002}, month={May}, pages={349–363} }
 @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{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{thorne_kishino_painter_1998, title={Estimating the rate of evolution of the rate of molecular evolution}, volume={15}, ISSN={["0737-4038"]}, DOI={10.1093/oxfordjournals.molbev.a025892}, abstractNote={A simple model for the evolution of the rate of molecular evolution is presented. With a Bayesian approach, this model can serve as the basis for estimating dates of important evolutionary events even in the absence of the assumption of constant rates among evolutionary lineages. The method can be used in conjunction with any of the widely used models for nucleotide substitution or amino acid replacement. It is illustrated by analyzing a data set of rbcL protein sequences.}, number={12}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Thorne, JL and Kishino, H and Painter, IS}, year={1998}, month={Dec}, pages={1647–1657} }
 @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{painter_1997, title={Sibship reconstruction without parental information}, volume={2}, number={2}, journal={Journal of Agricultural, Biological, and Environmental Statistics}, author={Painter, I.}, year={1997}, pages={212–229} }