‹‹ Back to SVS Home

[Abt 2001]   Abt, M., Lim, Y., Sacks, J., , Xie, M., and Young, S. S., (2001), ‘A Sequential Approach for Identifying Lead Compounds in Large Chemical Databases’, Statistical Science, 16, 154-168.

[Affymetrix 2007]   Affymetrix (2007), ‘CNAT 4.0: Copy Number and Loss of Heterozygosity Estimation Algorithms for the GeneChip^® Human Mapping 10/50/100/250/500K Array Set’, Revision Version 1.2

[Biggs 1991]   Biggs, D., B. deVille, and E. Suen (1991). ‘A method of choosing multiway partitions for classification and decision trees’, Journal of Applied Statistics 18, 49.

[Bolstad 2003]   Bolstad, B.M., Irisarry, R.A., Astrand, M., Speed, T.P. (2003) ‘A Comparison of Normalization Methods for High Density Oligonucleotide Array Data based on Variance and Bias’. Bioinformatics Vol 19 no. 2, p.185–193

[Bolstad 2001]   Bolstad, Ben (2001), ‘Probe Level Quantile Normalization of High Density Oligonucleotide Array Data’, Division of Biostatistics, University of California, Berkley.

[Carlson 2004]   Carlson, C., Eberle, M., Rieder, M., Yi, Q., Kruglyak, L., Nickerson, D., (2004), ‘Selecting a Maximally Informative Set of Single-Nucleotide Polymorphisms for Association Analysis Using Linkage Disequilibrium’, Am. J. Hum. Genet. 74, 106–120.

[Chiano 1998]   Chiano M. N., Clayton D. G. (1998), ‘Fine genetic mapping using haplotype analysis and the missing data problem.’ Ann. Hum. Genet. 62, 55–60.

[Dempster 1977]   Dempster, A. P., Laird, N. M., Rubin D., (1977), ‘Maximum likelihood from incomplete data via the EM algorithm.’ J of the Royal Stat Soc B 39: 1-38.

[Devlin and Roeder 1999]   B. Devlin, Kathryn Roeder, ‘Genomic Control for Association Studies’, Biometrics, Vol. 55, No. 4 (Dec., 1999), pp. 997–1004

[Durstenfeld 1964]   Durstenfeld, Richard, (July 1964), ‘Algorithm 235: Random permutation’ Communications of the ACM Vol 7 no. 7, p.420.

[Emigh 1980]   Emigh, T. H., (1980), ‘Comparison of tests for Hardy-Weinberg Equilibrium’ Biometrics 36: 627–642.

[Excoffier 1995]   Excoffier L, Slatkin M (1995) ‘Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population.’ Molecular Biology and Evolution 12: 921–927.

[Fallin 2000]   Fallin D, Schork NJ (2000) ‘Power of omnibus likelihood ratio test for haplotype-based case-control studies.’ Am J Hum Genet 67(S2): 214 (abstract).

[Fardo 2009]   Fardo DW, Ionita-Laza I, Lange C, 2009 On Quality Control Measures in Genome-Wide Association Studies: A Test to Assess the Genotyping Quality of Individual Probands in Family-Based Association Studies and an Application to the HapMap Data. PLoS Genet 5(7): e1000572. doi:10.1371/journal.pgen.1000572

[Gabriel 2002]   Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, et al. (2002) ‘The structure of haplotype blocks in the human genome.’ Science 296: 2225–2229.

[The Genome Sequencing Consortium 2001]   The Genome Sequencing Consortium (2001 Feb 15). ‘Initial sequencing and analysis of the human genome’. Nature, 409(6822), 860–921.

[Green 1997]   Green, W.H. Econometric Analysis, 3rd Ed. Prentice Hall, NJ, (1997), pp 882–886.

[Hawkins 2002]   Hawkins, D. M., (2002). ‘Fitting multiple change-points to data’, Computational Statistics and Data Analysis, 37, 323–341.

[Hawkins 2001]   Hawkins. D. M., and Musser, B. J. (2001), ‘Feature selection with nondeterministic recursive partitioning’, Proceedings of the American Statistical Association [CD-ROM] Alexandria, VA: ASA.

[Hawkins 1999]   Hawkins, D. M. and Musser, B. J., (1999) ‘One tree or a forest? Alternative dendrographic models’, Computing Science and Statistics, 30, 534–542.

[Hawkins 1997]   Hawkins, D. M., Young, S. S., and Rusinko, A., (1997), ‘Analysis of a large structure-activity data set using recursive partitioning, Quantitative Structure Activity Relationships’, 16, 296–302.

[Hawkins 1995a]   Hawkins, D. M. and McKenzie, D. P., (1995). ‘A data-based comparison of some recursive partitioning procedures’, Proceedings, Statistical Computing Section, American Statistical Association, 245–252.

[Hawkins 1995b]   Hawkins, D. M. (1995). ‘FIRM: Formal Inference-based Recursive Modeling, release 2.’ Technical Report 546, University of Minnesota, School of Statistics.

[Hawkins 1982]   Hawkins, D. M. and G. V. Kass (1982). ‘Automatic interaction detection’. In D. M. Hawkins (Ed.), Topics in Applied Multivariate Analysis. Cambridge University Press.

[Hawkins 1973]   Hawkins, D. M. and Merriam, D. F. (1973) ‘Optimal zonation of digitized sequential data’. Jour. Math Geology, v. 5, no. 4, p. 389–395.

[Hawkins 1972]   Hawkins, D. M. (1972) ‘On the choice of segments in piecewise approximation’. Jour. Inst. Math. Applications, v. 9, no. 2, p. 250–256.

[Hill 1997]   Hill, D. A., L. M. Delaney, and S. Roncal (1997). ‘A Chi-Squared Automatic Interaction Detection (CHAID) analysis of factors determining critical outcomes’, The Journal of Trauma: Injury, Infection and Critical Care 42, 62–66.

[Hooton 1981]   Hooton, T. M., Haley, R.W., Culver, D. H., White, J. W., Morgan, W. M., and Carroll, R. J., (1981), ‘The joint associations of multiple risk factors with the occurrence of nosocomial infections’, American Journal of Medicine, 70, 960–970.

[Hosmer and Lemeshow 2000]   Hosmer, David W., and Lemeshow, Stanley, Applied Logistic Regression, second edition, John Wiley and Sons, 2000. See pp. 1 – 42 for a discussion of standard error and other related statistics for logistic regressions, with standard error specifically shown on p. 35.

[Horvath 2004]   Horvath, S., Xu, X., Lake, S.L., Silverman, E.K., Weiss, S.T. and Laird, N.M. (2004), ‘Family-based tests for associating haplotypes with general phenotype data: application to asthma genetics’, Genet Epidemiol, 26, 61–69.

[Huang 1993]   Huang, H. C., T. K. Lin, and P. W. Ngui (1993). ‘Analyzing a mental health survey by Chi-Squared Automatic Interaction Detection’, Annals of the Academy of Medicine 22, 332–337.

[Ionita-Laza 2007]   Ionita-Laza, Iuliana, Perry, George H., Raby, Benjamin A., Klanderman, Barbara, Lee, Charles, Laird, Nan M., Weiss, Scott T., and Lange, Christoph, (2007). ‘On the Analysis of Copy-Number Variations in Genome-Wide Association Studies: A Translation of the Family-Based Association Test’, Genetic Epidemiology 32, 1–11.

[Karolchik 2004]   Karolchik, D., Hinrichs, A.S., Furey, T.S., et al (2004 Jan 1). ‘The UCSC Table Browser data retrieval tool’. Nucleic Acids Res., 32(Database issue), D493–6.

[Kass 1980]   Kass, G. V., (1980), ‘An exploratory technique for investigating large quantities of categorical data’, Applied Statistics, 29, 119–127.

[Kass 1975]   Kass, G. V. (1975). ‘Significance testing in, and some extensions of Automatic Interaction Detection.’ Ph. D. thesis, University of the Witwatersrand, Johannesburg.

[Kent 2002a]   Kent, W.J. (2002 April). ‘BLAT - the BLAST -like alignment tool’. Genome Res. 12(4), 656–64.

[Kent 2002b]   Kent, W.J., Sugnet, C.W., Roskin, K.M., Pringle T.H., Zahler, A.M., Haussler, D. (2002, June). ‘The human genome browser at UCSC’, Genome Res., 12(6), 996–1006.

[Knapp 1999]   Knapp, M. (1999), ‘A Note on Power Approximations for the Transmission/Disequilibrium Test.’ Am J Hum Genet 64:1177–1185.

[Lange 2002a]   Lange C, DeMeo D, Laird NM (2002) ‘Power and design considerations for a general class of family-based association tests: Quantitative traits.’ Am J Hum Genet 71:1330–1341.

[Lange 2002b]   Lange C, Laird NM (2002) ‘On a general class of conditional tests for family-based association studies in genetics: the asymptotic distribution, the conditional power and optimality considerations.’ Genetic Epidemiology 23:165–180.

[Lange 2002c]   Lange C, Laird NM (2002) ‘Analytical sample size and power calculations for a general class of family-based association tests: dichotomous traits.’ Am J Hum Genet 71:575–584.

[Lencz 2007]   Lencz T, Lambert C, DeRosse P, Burdick KE, Morgan V, Kane JM, Kucherlapati R, Malhotra AK. (in press) ‘Runs of Homozygosity Reveal Highly Penetrant Recessive Loci in Schizophrenia.’ Submitted PNAS, 2007.

[Mehta and Patel 1983]   Mehta C, Patel N (1983) J. Am. Stat. Assoc. 78:427–434

[Mehta and Patel 1986]   Mehta C, Patel N (1986) ‘FEXACT: a FORTRAN subroutine for Fisher’s exact test on unordered rc contingency tables’ ACM Transactions on Mathematical Software (TOMS) Volume 12 Issue 2 pp. 154–161.

[Musser 1999]   Musser, B. J. (1999) ‘Extensions to Recursive Partitioning’ Ph.D. Thesis, University of Minnesota School of Statistics.

[Nielson 1998]   Nielsen D, Ehm M, Weir BS (1998) ‘Detecting marker-disease association by testing for Hardy-Weinberg disequilibrium at a marker locus.’ Am J Hum Genet 63: 1531–1540.

[Patterson 2006]   Patterson N, Price AL, Reich D (2006) Population Structure and Eigenanalysis PLoS Genet 2(12): e190. doi:10.1371/journal.pgen.0020190.

[Price 2006]   Price, Alkes L., Patterson, Nick J. Plenge, Robert M. Weinblatt, Michael E. Shadick, Nancy A. Reich, David. (2006). ‘Principal Components Analysis Corrects for Statification in Genome-Wide Asssociation Studies’. Nature Genetics 38, 904–909.

[Rhead 2009]   Rhead, B., Karolchik, D., et al (2009 Nov 11). ‘The UCSC Genome Browser database: update 2010’. Nucleic Acids Res. Epub, 38(Database issue), D613–9.

[Storey 2002]   Storey, John D. (2002) ‘A direct approach to false discovery rates’, J. R. Statist. Soc. B 64, Part 3, pp. 479–498.

[Weir 1996]   Weir BS (1996) ‘Genetic Data Analysis II.’ Sinauer Associates.

[Xie 1993]   Xie X, Ott J (1993) ‘Testing linkage disequilibrium between a disease gene and marker loci.’ Am J Hum Genet 53, 1107 (abstract).

[Zaykin 2002]   Zaykin DV, Westfall PH, Young SS, Karnoub MA, Wagner MJ, Ehm MG. (2002) ‘Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals.’ Human Heredity, 53:79–91.

[Zaykin 2001]   Zaykin DV, Ehm, MG, Weir BS (2001) ‘Evaluating new haplotyping methods for predicting clinical response using dense maps of single nucleotide polymorphisms (SNPs).’ Work in progress. Presented at Bioinformatics Seminar Series, Research Triangle Institute, NC.

[Zaykin 2000]   Zaykin DV, Nielsen DM (2000) ‘Hardy-Weinberg disequilibrium (HWD) fine mapping for case-control samples.’ Am J Hum Genet 67: 1238(S).

[Zaykin (unknown)]   Zaykin DV, Ehm MG, Weir BS. ‘The composite haplotype method for association mapping of complex traits in out-bred populations.’ Accepted for publication in Genetic Epidemiology.

[Zhao 2000]   Zhao JH, Curtis D, Sham PC (2000) ‘Model-free analysis and permutation tests for allelic associations.’ Human Heredity 2000: 50 133—139.