@article{sanchez_basten_ferrenberg_asmussen_arnold_2006, title={Exact sample sizes needed to detect dependence in 2 x 3 tables}, volume={69}, ISSN={["1096-0325"]}, DOI={10.1016/j.tpb.2005.11.001}, abstractNote={Many medical and biological studies entail classifying a number of observations according to two factors, where one has two and the other three possible categories. This is the case of, for example, genetic association studies of complex traits with single-nucleotide polymorphisms (SNPs), where the a priori statistical planning, analysis, and interpretation of results are of critical importance. Here, we present methodology to determine the minimum sample size required to detect dependence in 2 x 3 tables based on Fisher's exact test, assuming that neither of the two margins is fixed and only the grand total N is known in advance. We provide the numerical tools necessary to determine these sample sizes for desired power, significance level, and effect size, where only the computational time can be a limitation for extreme parameter values. These programs can be accessed at . This solution of the sample size problem for an exact test will permit experimentalists to plan efficient sampling designs, determine the extent of statistical support for their hypotheses, and gain insight into the repeatability of their results. We apply this solution to the sample size problem to three empirical studies, and discuss the results with specified power and nominal significance levels.}, number={2}, journal={THEORETICAL POPULATION BIOLOGY}, author={Sanchez, MS and Basten, CJ and Ferrenberg, AM and Asmussen, MA and Arnold, J}, year={2006}, month={Mar}, pages={111–120} }
 @article{hall_basten_willis_2006, title={Pleiotropic quantitative trait loci contribute to population divergence in traits associated with life-history variation in Mimulus guttatus}, volume={172}, ISSN={["0016-6731"]}, DOI={10.1534/genetics.105.051227}, abstractNote={Abstract}, number={3}, journal={GENETICS}, author={Hall, MC and Basten, CJ and Willis, JH}, year={2006}, month={Mar}, pages={1829–1844} }
 @article{halverson_basten_2005, title={A  PCR multiplex and database for forensic DNA identification of dogs}, volume={50}, number={2}, journal={Journal of Forensic Sciences}, author={Halverson, J. L. and Basten, C.}, year={2005}, pages={352–363} }
 @article{halverson_basten_2005, title={Forensic DNA identification of animal-derived trace evidence: Tools for linking victims and suspects}, volume={46}, number={4}, journal={Croatian Medical Journal}, author={Halverson, J. L. and Basten, C.}, year={2005}, pages={598–605} }
 @article{kirst_basten_myburg_zeng_sederoff_2005, title={Genetic architecture of transcript-level variation in differentiating xylem of a eucalyptus hybrid}, volume={169}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.104.039198}, abstractNote={Abstract}, number={4}, journal={GENETICS}, author={Kirst, M and Basten, CJ and Myburg, AA and Zeng, ZB and Sederoff, RR}, year={2005}, month={Apr}, pages={2295–2303} }
 @article{stuurman_hoballah_broger_moore_basten_kuhlemeier_2004, title={Dissection of floral pollination syndromes in petunia}, volume={168}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.104.031138}, abstractNote={Abstract}, number={3}, journal={GENETICS}, author={Stuurman, J and Hoballah, ME and Broger, L and Moore, J and Basten, C and Kuhlemeier, C}, year={2004}, month={Nov}, pages={1585–1599} }
 @article{rauh_basten_buckler_2002, title={Quantitative trait loci analysis of growth response to varying nitrogen sources in Arabidopsis thaliana}, volume={104}, ISSN={["0040-5752"]}, DOI={10.1007/s00122-001-0815-y}, abstractNote={Nitrogen absorption and assimilation is variable among plants as a result of two factors: the source of nitrogen available and the genetic variation among species within the resulting nitrogen pathways. Several genes involved in nitrogen cycling have been identified, yet little is known about the genes that control quantitative responses to different nitrogen sources. With quantitative trait loci (QTL) mapping in Arabidopsis thaliana recombinant inbred lines (Columbia x Landsberg erecta) we have identified chromosomal regions controlling aerial mass, root mass, and root length when plants are grown in nitrate, ammonium, ammonium nitrate, or low nitrogen treatments. A total of 16 QTL ( P < 0.01) were identified among the nitrogen treatments. Most of the QTL were specific to a single treatment. The percentage additive genetic effects of significant QTL were as high as 17%. Five significant QTL corresponded to the locations of candidate genes associated with nitrogen assimilation, while a few QTL corresponded with candidate genes in the developmental pathways. Most QTL were not shared across treatments, suggesting that there is no optimal genotype for all nitrogen sources.}, number={5}, journal={THEORETICAL AND APPLIED GENETICS}, author={Rauh, BL and Basten, C and Buckler, ES}, year={2002}, month={Apr}, pages={743–750} }
 @article{jenkins_haverty_basten_nelson_page_forschler_2000, title={Correlation of mitochondrial haplotypes with cuticular hydrocarbon phenotypes of sympatric Reticulitermes species from the southeastern United States}, volume={26}, ISSN={["0098-0331"]}, DOI={10.1023/A:1005548111591}, number={6}, journal={JOURNAL OF CHEMICAL ECOLOGY}, author={Jenkins, TM and Haverty, MI and Basten, CJ and Nelson, LJ and Page, M and Forschler, BT}, year={2000}, month={Jun}, pages={1525–1542} }
 @article{buckleton_curran_basten_2000, title={Evaluating the statistical significance of single band profiles in VNTR analyses}, volume={40}, number={1}, journal={Science and Justice}, author={Buckleton, J. and Curran, J. M. and Basten, C. J.}, year={2000}, pages={27–31} }
 @article{zeng_kao_basten_1999, title={Estimating the genetic architecture of quantitative traits}, volume={74}, ISSN={["0016-6723"]}, DOI={10.1017/S0016672399004255}, abstractNote={Understanding and estimating the structure and parameters associated with the genetic architecture 
of quantitative traits is a major research focus in quantitative genetics. With the availability of a 
well-saturated genetic map of molecular markers, it is possible to identify a major part of the 
structure of the genetic architecture of quantitative traits and to estimate the associated 
parameters. Multiple interval mapping, which was recently proposed for simultaneously mapping 
multiple quantitative trait loci (QTL), is well suited to the identification and estimation of the 
genetic architecture parameters, including the number, genomic positions, effects and interactions 
of significant QTL and their contribution to the genetic variance. With multiple traits and multiple 
environments involved in a QTL mapping experiment, pleiotropic effects and QTL by environment 
interactions can also be estimated. We review the method and discuss issues associated with 
multiple interval mapping, such as likelihood analysis, model selection, stopping rules and 
parameter estimation. The potential power and advantages of the method for mapping multiple 
QTL and estimating the genetic architecture are discussed. We also point out potential problems 
and difficulties in resolving the details of the genetic architecture as well as other areas that require 
further investigation. One application of the analysis is to improve genome-wide marker-assisted 
selection, particularly when the information about epistasis is used for selection with mating.}, number={3}, journal={GENETICAL RESEARCH}, author={Zeng, ZB and Kao, CH and Basten, CJ}, year={1999}, month={Dec}, pages={279–289} }
 @article{tomsey_basten_budowle_giles_ermlick_gotwald_1999, title={Use of combined frequencies for RFLP and PCR based loci in determining match probability}, volume={44}, number={2}, journal={Journal of Forensic Sciences}, author={Tomsey, C. S. and Basten, C. J. and Budowle, B. and Giles, B. A. and Ermlick, S. and Gotwald, S.}, year={1999}, pages={385–388} }
 @article{basten_asmussen_1997, title={The exact test for cytonuclear disequilibria}, volume={146}, number={3}, journal={Genetics}, author={Basten, C. J. and Asmussen, M. A.}, year={1997}, pages={1165–1171} }
 @article{basten_weir_1990, title={EFFECT OF GENE CONVERSION ON VARIANCES OF DIGENETIC IDENTITY MEASURES}, volume={38}, ISSN={["1096-0325"]}, DOI={10.1016/0040-5809(90)90007-I}, 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={2}, journal={THEORETICAL POPULATION BIOLOGY}, author={BASTEN, CJ and WEIR, BS}, year={1990}, month={Oct}, pages={125–148} }