Broman KW, Sen Ś. A Guide to QTL Mapping with R/qtl. Springer, New York, to appear (expected August, 2009)

Cox A, Ackert-Bicknell C, Dumont BL, Ding Y, Bell, JT, Brockmann GA, Wergedal JE, Bult C, Paigen B, Flint J, Tsaih S-W, Churchill GA, Broman KW. A new standard genetic map for the laboratory mouse. Genetics, to appear

Manichaikul A, Broman KW. Binary trait mapping in experimental crosses with selective genotyping. Genetics, to appear

Sen Ś, Johannes F, Broman KW (2009) Selective genotyping and phenotyping strategies in a complex trait context. Genetics 181:1613-1626

Manichaikul A, Moon JY, Sen Ś, Yandell BS, Broman KW (2009) A model selection approach for the identification of quantitative trait loci in experimental crosses, allowing epistasis. Genetics 181:1077-1086

Shao H, Burrage LC, Sinasac DS, Hill AE, Ernest SR, O'Brien W, Courtland HW, Jepsen KJ, Kirby A, Kulbokas EJ, Daly MJ, Broman KW, Lander ES, Nadeau JH (2008) Genetic architecture of complex traits: Large phenotypic effects and pervasive epistasis. Proc Natl Acad Sci USA 105:19910-19914

Lupi I, Broman KW, Tzuo S-C, Gutenberg A, Martino E, Caturegli P (2008) Novel autoantigens in autoimmune hypophysitis. Clin Endocrinol 69:269-278

Paigen K, Szatkiewicz JP, Sawyer K, Leahy N, Parvanov ED, Ng SH, Graber JH, Broman KW, Petkov PM (2008) The recombinational anatomy of a mouse chromosome. PLoS Genet 4(7):e1000119

Bjornsson HT, Albert TJ, Ladd-Acosta CM, Green RD, Rongione MA, Middle CM, Irizarry RA, Broman KW, Feinberg AP (2008) SNP-specific array-based allele-specific expression analysis. Genome Res 18:771-779

Manichaikul A, Palmer AA, Sen Ś, Broman KW (2007) Significance thresholds for quantitative trait locus mapping under selective genotyping. Genetics 177:1963-1966

Teuscher F, Broman KW (2007) Haplotype probabilities for multiple-strain recombinant inbred lines. Genetics 175:1267-1274

Broman KW, Sen Ś, Owens SE, Manichaikul A, Southard-Smith EM, Churchill GA (2006) The X chromosome in quantitative trait locus mapping. Genetics 174:2151-2158

Manichaikul A, Dupuis J, Sen Ś, Broman KW (2006) Poor performance of bootstrap confidence intervals for the location of a quantitative trait locus. Genetics 174:481-489

Feenstra B, Skovgaard IM, Broman KW (2006) Mapping quantitative trait loci by an extension of the Haley-Knott regression method using estimating equations. Genetics 173:2269-228

Broman KW (2005) Mapping expression in randomized rodent genomes. Nat Genet 37:209-210

Broman KW (2005) The genomes of recombinant inbred lines. Genetics 169:1133-1146

The Complex Trait Consortium (2004) The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nat Genet 36:1133-1137

Broman KW, Feingold E (2004) SNPs made routine. Nat Methods 1:104-105

Broman KW, Wu H, Sen Ś, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889-890

Broman KW, Matsumoto N, Giglio S, Martin CL, Roseberry JA, Zuffardi O, Ledbetter DH, Weber JL (2003) Common long human inversion polymorphism on chromosome 8p. In: Goldstein DR (ed) Science and Statistics: A Festschrift for Terry Speed. IMS Lecture Notes-Monograph Series, Vol 40, pp 237-245

Broman KW, Speed TP (2002) A model selection approach for the identification of quantitative trait loci in experimental crosses (with discussion). J Roy Stat Soc B 64:641-656, 731-775

Broman KW, Rowe LB, Churchill GA, Paigen K (2002) Crossover interference in the mouse. Genetics 160:1123-1131

Broman KW, Weber JL (2000) Characterization of human crossover interference. Am J Hum Genet 66:1911-1926

Broman KW, Weber JL (1999) Long homozygous chromosomal segments in reference families from the Centre d'Étude du Polymorphisme Humain. Am J Hum Genet 65:1493-1500

Broman KW, Murray JC, Sheffield VC, White RL, Weber JL (1998) Comprehensive human genetic maps: Individual and sex-specific variation in recombination. Am J Hum Genet 63:861-869