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Broman KW, Sen Ś (2009) A Guide to QTL Mapping with R/qtl. Springer, New York (ISBN: 978-0-387-92124-2)
[Amazon | Springer | Online complements | R/qtl]

Journal articles

To appear

Kwak I-Y, Moore CR, Spalding EP, Broman KW. A simple regression-based method to map quantitative trait loci underlying function-valued phenotypes. Genetics, to appear
[PubMed | pdf (1.2M)]
Street VA, Kujawa SG, Manichaikul A, Broman KW, Kallman JC, Shilling DJ, Iwata AJ, Robinson LC, Robbins CA, Li J, Liberman MC, Tempel BL. Resistance to noise-induced hearing loss in 129S6 and MOLF mice: Identification of independent, overlapping, and interacting chromosomal regions. J Assoc Res Otolaryngol, to appear


Broman KW (2014) Fourteen years of R/qtl: Just barely sustainable. J Open Res Softw 2(1):e11
[Abstract | pdf (948k) | Source on GitHub]
Rowsey R, Gruhn J, Broman KW, Hunt PA, Hassold T (2014) Examining variation in recombination levels in the human female: A test of the production line hypothesis. Amer J Hum Genet 95:108-112
[PubMed | pdf (2.0M)]
Huang BE, Raghavan C, Mauleon R, Broman KW, Leung H (2014) Efficient imputation of missing markers in low-coverage genotyping-by-sequencing data from multi-parent crosses. Genetics 197:401-404
[PubMed | pdf (601k)]
Baier B, Hunt P, Broman KW, Hassold T (2014) Variation in genome-wide levels of meiotic recombination is established at the onset of prophase in mammalian males. PLoS Genetics 10:e1004125
[PubMed | pdf (1.5M)]


Gruhn JR, Rubio C, Broman KW, Hunt PA, Hassold T (2013) Cytological studies of human meiosis: sex-specific differences in recombination originate at, or prior to, establishment of double-strand breaks. PLoS ONE 8:e85075
[PubMed | pdf (1.6M)]
Moore CR, Johnson LS, Kwak I-Y, Livny M, Broman KW, Spalding EP (2013) High-throughput computer vision introduces the time axis to a quantitative trait map of a plant growth response. Genetics 195:1077-1086
[PubMed | (1.6M)]
Bautz DJ, Broman KW, Threadgill DW (2013) Identification of a novel polymorphism in X-linked sterol-4-alpha-carboxylate 3-dehydrogenase (Nsdhl) associated with reduced HDL cholesterol levels in I/LnJ mice. G3 3: 1819-1825
[PubMed | pdf (1.2M)]
Harris M, Burns CM, Becker EA, Braasch AT, Gostick E, Johnson RC, Broman KW, Price DA, Friedrich TC, O'Connor SL (2013) Acute-phase CD8 T cell responses that select for escape variants are needed to control live attenuated simian immunodeficiency virus. J Virol 87:9353-9364
[PubMed | pdf (1.5M)]
Maenner MJ, Baker MW, Broman KW, Tian J, Barnes JK, Atkins A, McPherson E, Hong J, Brilliant MH, Mailick MR (2013) FMR1 CGG expansions: Prevalence and sex ratios. Am J Med Genet B Neuropsychiatr Genet 162:466-473
[PubMed | pdf (399k)]


Broman KW, Kim S, Sen Ś, Ané C, Payseur BA (2012) Mapping quantitative trait loci onto a phylogenetic tree. Genetics 192:267-279
[PubMed | pdf (1.9M) | source on github]
Rice CA, Riehl J, Broman K, Soukup JW, Gengler WR (2012) Comparing the degree of exothermic polymerization in commonly used acrylic and provisional composite resins for intraoral appliances. J Vet Dent 29: 78-83
[PubMed | pdf (1.8M)]
Galvan A, Colombo F, Noci S, Pazzaglia S, Mancuso M, Manenti G, Broman KW, Saran A, Dragani TA (2012) The Lsktm1 locus modulates lung and skin tumorigenesis in the mouse. G3 2:1041-1046
[PubMed | pdf (913k)]
Greene JM, Chin EN, Budde ML, Lhost JJ, Hines PJ, Burwitz BJ, Broman KW, Nelson JE, Friedrich TC, O'Connor DH (2012) Ex vivo SIV-specific CD8 T cell responses in heterozygous animals are primarily directed against peptides presented by a single MHC haplotype. PLoS ONE 7:e43690
[PubMed | pdf (767k)]
Neto EC, Keller MP, Broman AF, Attie AD, Jansen RC, Broman KW, Yandell BS (2012) Quantile-based permutation thresholds for quantitative trait loci hotspots. Genetics 191:1355-1365
[PubMed | pdf (1.1M)]
King EG, Merkes CM, McNeil CL, Hoofer SR, Sen S, Broman KW, Long AD, Macdonald SJ (2012) Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource. Genome Res 22:1558-1566
[PubMed | pdf (1.8M) | Supplementary material]
Wang CY, Stapleton DS, Schueler KL, Rabaglia ME, Oler AT, Keller MP, Kendziorski CM, Broman KW, Yandell BS, Schadt EE, Attie ED (2012) Tsc2, a positional candidate gene underlying a quantitative trait locus for hepatic steatosis. J Lipid Res 53:1493-1501
[PubMed | pdf (1.0M) | Supplementary material]
Arends D, van der Velde KJ, Prins P, Broman KW, Möller S, Jansen RC, Swertz MA (2012) xQTL workbench: a web based environment for xQTL analysis. Bioinformatics 28:1042-1044
[PubMed | pdf (424) |]
Amlin-Van Schaick JC, Kim S, Broman KW, Reilly KM (2012) Scram1 is a modifier of spinal cord resistance for astrocytoma on mouse chromosome 5. Mamm Genome 23:277-285
[PubMed | pdf (755k)]
Broman KW (2012) Genotype probabilities at intermediate generations in the construction of recombinant inbred lines. Genetics 190:403-412
[PubMed | pdf (1.1M) | source on github]
Broman KW (2012) Haplotype probabilities in advanced intercross populations. G3 2:199-202
[PubMed | pdf (649k) | source on github]
Collaborative Cross Consortium [97 authors] (2012) The genome architecture of the Collaborative Cross mouse genetic reference population. Genetics 190:389-401
[PubMed | pdf (4.9M)]
Amlin-Van Schaick JC, Kim S, DiFabio C, Lee M-H, Broman KW, Reilly KM (2012) Arlm1 is a male-specific modifier of astrocytoma resistance on mouse chr 12. Neuro Oncol 14:160-174
[PubMed | pdf (1.3M)]
Davis RC, Van Nas A, Castellani LW, Zhao Y, Zhou Z, Wen P, Yu S, Qi H, Rosales M, Schadt EE, Broman KW, Peterfy M, Lusis AJ (2012) Systems genetics of susceptibility to obesity-induced diabetes in mice. Physiol Genomics 44:1-13
[PubMed | pdf (2.1M) | Supplementary material]


Weinfurter JT, Brunner K, Capuano SV III, Li C, Broman KW, Kawaoka Y, Friedrich T (2011) Cross-reactive T cells are involved in rapid clearance of 2009 pandemic H1N1 influenza virus in nonhuman primates. PLoS Pathog 7:e1002381
[PubMed | pdf (879k)]
Aylor DL, Valdar W, Foulds-Mathes W, Buus RJ, Verdugo RA, Baric RS, Ferris MT, Frelinger JA, Heise M, Frieman MB, Gralinski LE, Bell TA, Didion JD, Hua K, Nehrenberg DL, Powell CL, Steigerwalt J, Xie Y, Kelada SNP, Collins F, Yang IV, Schwartz DA, Branstetter LA, Chesler EJ, Miller DR, Spence J, Liu EY, McMillan L, Sarkar A, Wang J, Wang W, Zhang Q, Broman KW, Korstanje R, Durrant C, Mott R, Iraqi FA, Pomp D, Threadgill D, Pardo-Manuel de Villena F, Churchill GA (2011) Genetic analysis of complex traits in the emerging Collaborative Cross. Genome Res 21: 1213-1222
[PubMed | pdf (1.0M) | Supplementary material]
Greene JM, Wiseman RW, Lank SM, Bimber BN, Karl JA, Burwitz BJ, Lhost JJ, Hawkins OE, Kunstman KJ, Broman KW, Wolinsky SM, Hildebrand WH, O'Connor DH (2011) Differential MHC class I expression in distinct leukocyte subsets. BMC Immunol 12:39
[PubMed | pdf (747k)]
Bradley KM, Breyer JP, Melville DB, Broman KW, Knapik EW, Smith JR (2011) An SNP-based linkage map for zebrafish reveals sex determination loci. G3 1:3-9
[PubMed | pdf (1.0M)]
Moreland AJ, Guethlein LA, Reeves RK, Broman KW, Johnson RP, Parham P, O'Connor DH, Bimber BN (2011) Characterization of killer immunoglobulin-like receptor genetics and comprehensive genotyping by pyrosequencing in rhesus macaques. BMC Genomics 12:295
[PubMed | pdf (1.1M)]
Svetec N, Werzner A, Wilches R, Pavlidis P, Álvarez-Castro JM, Broman KW, Metzler D, Stephan W (2011) Identification of X-linked quantitative trait loci affecting cold tolerance in Drosophila melanogaster and fine-mapping by selective sweep analysis. Mol Ecol 20:530-544
[PubMed | pdf (450k)]


Murdoch B, Owen N, Shirley S, Crumb S, Broman KW, Hassold T (2010) Multiple loci contribute to genome-wide recombination levels in male mice. Mamm Genome 21:550-555
[PubMed | pdf (341k)]
Billings T, Sargent EE, Szatkiewicz JP, Leahy N, Kwak, I-Y, Bektassova N, Walker M, Hassold T, Graber JH, Broman KW, Petkov PM (2010) Patterns of recombination activity on mouse chromosome 11 revealed by high resolution mapping. PLoS One 5:e15340
[PubMed | pdf (483k)]
Arends D, Prins P, Jansen RC, Broman KW (2010) R/qtl: High-throughput multiple QTL mapping. Bioinformatics 26:2990-2992
[PubMed | pdf (181k)]
Bader HL, Ruhe AL, Wang LW, Wong AK, Walsh KF, Packer RA, Mitelman J, Robertson KR, O'Brien DP, Broman KW, Shelton GD, Apte SS, Neff MW (2010) An ADAMTSL2 founder mutation causes Musladin-Lueke Syndrome, a heritable disorder of beagle dogs, featuring stiff skin and joint contractures. PLoS One 5:e12817
[PubMed | pdf (564k)]
Jurisic G, Sundberg JP, Bleich A, Leiter EH, Broman KW, Buechler G, Alley L, Vestweber D, Detmar M (2010) Quantitative lymphatic vessel trait analysis suggests Vcam1 as candidate modifier gene of inflammatory bowel disease. Genes Immun 11:219-231
[PubMed | pdf (1013k) | Supplementary material (pdf, 1.6M)]
Burrage LC, Baskin-Hill AE, Sinasac DS, Singer JB, Croniger CM, Kirby A, Kulbokas EJ, Daly MJ, Lander ES, Broman KW, Nadeau JH (2010) Genetic resistance to diet-induced obesity in chromosome substitution strains of mice. Mamm Genome 21:115-129
[PubMed | pdf (673k)]
Greene JM, Lhost JJ, Burwitz BJ, Budde ML, Macnair CE, Weiker MK, Gostick E, Friedrich TC, Broman KW, Price DA, O'Connor SL, O'Connor DH (2010) Extralymphoid CD8+ T cells resident in tissue from Simian Immunodeficiency Virus SIVmac239Δnef-vaccinated macaques suppress SIVmac239 replication ex vivo. J Virol 84:3362-3372
[PubMed | pdf (3.4M)]
Wong AK, Ruhe AL, Dumont BL, Robertson KR, Guerrero G, Shull SM, Ziegle JS, Millon LV, Broman KW, Payseur BA, Neff MW (2010) A comprehensive linkage map of the dog genome. Genetics 184:595-605
[PubMed | pdf (32M) | Supporting Information]


Shavit JA, Manichaikul A, Lemmerhirt HL, Broman KW, Ginsburg D (2009) Modifiers of von Willebrand factor identified by natural variation in inbred strains of mice. Blood 114:5368-5374
[PubMed | pdf (308k)]
Cheng EY, Hunt PA, Naluai-Cecchini TA, Fligner CL, Fujimoto VY, Pasternack TL, Schwartz JM, Steinauer JE, Woodruff TJ, Cherry SM, Hansen TA, Vallente RU, Broman KW, Hassold TJ (2009) Meiotic recombination in human oocytes. PLoS Genet 5:e1000661
[PubMed | pdf (759k)]
Fledel-Alon A, Wilson DJ, Broman K, Wen X, Ober C, Coop G, Przeworski M (2009) Broad-scale recombination patterns underlying proper disjunctions in humans. PLoS Genet 5:e1000658
[PubMed | pdf (353k)]
Cox A, Ackert-Bicknell CL, Dumont BL, Ding Y, Bell JT, Brockmann GA, Wergedal JE, Bult C, Paigen B, Flint J, Tsaih S-W, Churchill GA, Broman KW (2009) A new standard genetic map for the laboratory mouse. Genetics 182:1335-1344
[PubMed | pdf (3.4M)]
Dumont BL, Broman KW, Payseur BA (2009) Variation in genomic recombination rates among heterogeneous stock mice. Genetics 182:1345-1349
[PubMed | pdf (468k)]
Manichaikul A, Broman KW (2009) Binary trait mapping in experimental crosses with selective genotyping. Genetics 182:863-874
[PubMed | pdf (576k)]
Venkatesan M, Broman KW, Sellers M, Rasgon JL (2009) An initial linkage map of the West Nile Virus vector Culex tarsalis. Insect Mol Biol 18:453-463
[PubMed | pdf (265k)]
Sen Ś, Johannes F, Broman KW (2009) Selective genotyping and phenotyping strategies in a complex trait context. Genetics 181:1613-1626
[PubMed | pdf (469k)]
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
[PubMed | pdf (889k) | Erratum: Genetics 184:607, 2010 (pdf 89k)]


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
[PubMed | pdf (401k) | Supplementary material (pdf, 792k)]
Hill M, Broman KW, Stupka E, Smith WC, Jiang D, Sidow A (2008) The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution. Genome Res 18:1369-1379
[PubMed | pdf (814k) | Supplementary material]
Lupi I, Broman KW, Tzuo S-C, Gutenberg A, Martino E, Caturegli P (2008) Novel autoantigens in autoimmune hypophysitis. Clin Endocrinol 69:269-278
[PubMed | pdf (495k)]
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
[PubMed | pdf (491k) | Supplementary material]
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
[PubMed | pdf (1.4M) | Supplementary material | Data]
Peirce JL, Broman KW, Lu L, Chesler EJ, Zhou G, Airey DC, Birmingham AE, Williams RW (2008) Genome Reshuffling for Advanced Intercross Permutation (GRAIP): Simulation and permutation for advanced intercross population analysis. PLoS ONE 3(4):e1977
[PubMed | pdf (468k)]
Roy-Gagnon M-H, Mathias RA, Fallin MD, Jee SH, Broman KW, Wilson AF (2008) An extension of the regression of offspring on mid-parent to test for association and estimate locus-specific heritability: The revised ROMP method. Ann Hum Genet 72:115-125
[PubMed | pdf (519k)]
Sinha D, Klise A, Sergeev Y, Hose S, Bhutto IA, Hackler L, Malpic-Ilanos T, Samtani S, Grebe R, Goldberg MF, Hejtmancik JF, Nath A, Zack DJ, Fariss RN, McLeod DS, Sundin O, Broman KW, Lutty GA, Zigler JS Jr (2008) βA3/A1-crystallin in astroglial cells regulates retinal vascular remodeling during development. Mol Cell Neurosci 37:85-95
[PubMed | pdf (2.3M)]


Rajagopal SK, Ma Q, Obler D, Shen J, Manichaikul A, Tomita-Mitchell A, Boardman K, Briggs C, Garg V, Srivastava D, Goldmuntz E, Broman KW, Benson DW, Smoot LB, Pu, WT (2007) Spectrum of heart disease associated with murine and human GATA4 mutation. J Mol Cell Cardiol 43:677-685
[PubMed | pdf (1.2M)]
Manichaikul A, Palmer AA, Sen Ś, Broman KW (2007) Significance thresholds for quantitative trait locus mapping under selective genotyping. Genetics 177:1963-1966
[PubMed | pdf (93k)]
Petkov PM, Broman KW, Szatkiewicz JP, Paigen K (2007) Crossover interference underlies sex differences in recombination rates. Trends Genet 23:539-542
[PubMed | pdf (266k) | Supplementary material (pdf 225k)]
Peirce JL, Broman KW, Lu L, Williams RW (2007) A simple method for combining genetic mapping data from multiple crosses and experimental designs. PLoS ONE 2(10):e1036
[PubMed | pdf (215k)]
Teuscher F, Broman KW (2007) Haplotype probabilities for multiple-strain recombinant inbred lines. Genetics 175:1267-1274
[PubMed | pdf (722k)]
Sen Ś, Satagopan JM, Broman KW, Churchill GA (2007) R/qtlDesign: Inbred line cross experimental design. Mamm Genome 18:87-93
[PubMed | pdf (138k)]
Lemmerhirt HL, Broman KW, Shavit JA, Ginsburg D (2007) Genetic regulation of plasma von Willebrand factor levels: Quantitative trait loci analysis in a mouse model. J Thromb Haemost 5:329-335
[PubMed | pdf (1.1M)]
Nichols KM, Broman KW, Sundin K, Young JM, Wheeler PA, Thorgaard GH (2007) Quantitative trait loci by maternal cytoplasmic environment interaction for development rate in Oncorhynchus mykiss. Genetics 175:335-347
[PubMed | pdf (1035k)]


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
[PubMed | pdf (169k)]
Shrestha S, Smith MW, Broman KW, Farzadegan H, Vlahov D, Strathdee SA (2006) Multi-person-use of syringes among injection drug users in a needle exchange program: A gene based molecular epidemiological analysis. J Acquir Immune Defic Syndr 43:335-343
[PubMed | pdf (174k)]
Kess D, Lindqvist AK, Peters T, Wang H, Zamek J, Nischt R, Broman KW, Blakytny R, Krieg T, Holmdahl R, Scharffetter-Kochanek K (2006) Identification of susceptibility loci for skin disease in a murine psoriasis model. J Immunol 177:4612-4619
[PubMed | pdf (211k)]
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
[PubMed | pdf (1033k)]
Sundin OH, Broman KW, Chang HH, Vito ECL, Stark WJ, Gottsch JD (2006) A common locus for late-onset Fuchs corneal dystrophy maps to 18q21.2-q21.32. Invest Ophthalmol Vis Sci 47:3919-3926
[PubMed | pdf (631k)]
Feenstra B, Skovgaard IM, Broman KW (2006) Mapping quantitative trait loci by an extension of the Haley-Knott regression method using estimating equations. Genetics 173:2269-2282
[PubMed | pdf (290k)]
Chadwick LH, Pertz L, Broman KW, Bartolomei MS, Willard HF (2006) Genetic control of X chromosome inactivation in mice: Definition of the Xce candidate interval. Genetics 173:2111-2119
[PubMed | pdf (193k)]
Grant GG, Robinson SW, Edwards RE, Clothier B, Davies R, Judah DJ, Broman KW, Smith AG (2006) Multiple polymorphic genes determine 'normal' hepatic and splenic iron status in mice. Hepatology 44:174-185
[PubMed | pdf (902k)]
Orgogozo V, Broman KW, Stern DL (2006) High-resolution QTL mapping reveals sign epistasis controlling ovariole number between two Drosophila species. Genetics 173:197-205
[PubMed | pdf (425k)]
Shrestha S, Strathdee SA, Broman KW, Smith MW (2006) Unknown biological mixtures evaluation using STR analytical quantification. Electrophoresis 27:409-415
[PubMed | pdf (125k)]
Reilly KM, Broman KW, Bronson RT, Tsang S, Loisel DA, Christy ES, Sun Z, Diehl J, Munroe DJ, Tuskan RG (2006) An imprinted locus epistatically influences Nstr1 and Nstr2 to control resistance to nerve sheath tumors in a neurofibromatosis type 1 mouse model. Cancer Res 66:62-68
[PubMed | pdf (1.9M)]
Sundin OH, Jun AS, Broman KW, Liu SH, Sheehan SE, Vito ECL, Stark WJ, Gottsch JD (2006) Linkage of late-onset Fuchs corneal dystrophy to a novel locus at 13pTel-13q12.13. Invest Ophthalmol Vis Sci 47:140-145
[PubMed | pdf (316k)]


Sundin OH, Leppert GS, Silva ED, Yang J-M, Dharmaraj S, Maumenee IH, Santos LC, Parsa CF, Traboulsi EI, Broman KW, DiBernardo C, Sunness JS, Toy J, Weinberg EM (2005) Extreme hyperopia is the result of null mutations in MFRP, which encodes a Frizzled-related protein. Proc Natl Acad Sci USA 102:9553-9558
[PubMed | pdf (859k)]
Gottsch JD, Sundin OH, Liu SH, Jun AS, Broman KW, Stark WJ, Vito EC, Narang AK, Thompson JM, Magovern M (2005) Inheritance of a novel COL8A2 mutation defines a distinct early-onset subtype of Fuchs corneal dystrophy. Invest Ophthalmol Vis Sci 46:1934-1939
[PubMed | pdf (302k)]
Owens SE, Broman KW, Wiltshire T, Elmore JB, Bradley KM, Smith JR, Southard-Smith EM (2005) Genome-wide linkage identifies novel modifier loci of aganglionosis in the Sox10Dom model of Hirschsprung disease. Hum Mol Genet 14:1549-1558
[PubMed | pdf (304k)]
Broman KW (2005) The genomes of recombinant inbred lines. Genetics 169:1133-1146
[PubMed | pdf (525k) | Related software | Erratum: Genetics 173:2419, 2006 (pdf 30k)]
Guler ML, Ligons DL, Wang Y, Bianco M, Broman KW, Rose NR (2005) Two autoimmune diabetes loci influencing T cell apoptosis control susceptibility to experimental autoimmune myocarditis. J Immunol 174:2167-2173
[PubMed | pdf (165k)]
Congdon N, Broman KW, Lai H, Munoz B, Bowie H, Gilbert D, Wojciechowski R, West SK (2005) Cortical, but not posterior subcapsular, cataract shows significant familial aggregation in an older population after adjustment for possible shared environmental factors. Ophthalmology 112:73-77
[PubMed | pdf (118k)]
Chen WM, Broman KW, Liang KY (2005) Power and robustness of linkage tests for quantitative traits in general pedigrees. Genet Epidemiol 28:11-23
[PubMed | pdf (160k)]


Boyadjiev SA, Dodson JL, Radford CL, Ashrafi GH, Beaty TH, Mathews RI, Broman KW, Gearhart JP (2004) Clinical and molecular characterization of the bladder exstrophy-epispadias complex: Analysis of 232 families. BJU International 94:1337-1343
Note: The publisher requires that I make the following statement: "This is an electronic version of an article published in BJU International: complete citation information for the final version of the paper, as published in the print edition of BJU International, is available on the Blackwell Synergy online delivery service, accessible via the journals website at or"
[PubMed | pdf (168k)]
The Complex Trait Consortium [113 authors] (2004) The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nat Genet 36:1133-1137
[PubMed | pdf (177k)]
Chen S, Wang W, Broman KW, Katki HA, Parmigiani G (2004) BayesMendel: An R environment for Mendelian risk prediction. Stat Appl Genet Mol Biol 3(1): article 21
[PubMed | pdf (191k)]
Neff MW, Robertson KR, Wong AK, Safra N, Broman KW, Slatkin M, Mealey KL, Pedersen NC (2004) Breed distribution and history of canine mdr1-1Δ, a pharmacogenetic mutation that marks the emergence of breeds from the collie lineage. Proc Natl Acad Sci USA 101:11725-11730
[PubMed | pdf (312k) | Supporting info]
Tankersley CG, Broman KW (2004) Interactions in hypoxic and hypercapnic breathing are genetically linked to mouse chromosomes 1 and 5. J Appl Physiol 97:77-84
[PubMed | pdf (206k)]
Congdon N, Broman KW, Lai H, Munoz B, Bowie H, Gilbert D, Wojciechowski R, Alston C, West SK (2004) Nuclear cataract shows significant familial aggregation in an older population after adjustment for possible shared environmental factors. Invest Ophthalmol Vis Sci 45:2182-2186
[PubMed | pdf (90k)]
Tankersley CG, Campen M, Bierman A, Flanders SE, Broman KW, Rabold R (2004) Particle effects on heart-rate regulation in senescent mice. Inhal Toxicol 16:381-390
[PubMed | pdf (472k)]
Sivagnanasundaram S, Broman KW, Liu M, Petronis A (2004) Quasi-linkage: A confounding factor in linkage analysis of complex diseases? Hum Genet 114:588-593
[PubMed | pdf (149k) | Data]
Chen WM, Broman KW, Liang KY (2004) Quantitative trait linkage analysis by generalized estimating equations: Unification of variance components and Haseman-Elston regression. Genet Epidemiol 26:265-272
[PubMed | pdf (131k)]
Kieffer TL, Finucane MM, Nettles RE, Quinn TC, Broman KW, Ray SC, Persaud D, Siliciano RF (2004) Genotypic analysis of HIV-1 drug resistance at the limit of detection: Virus production without evolution in treated adults with undetectable HIV loads. J Infect Dis 189:1452-1456
[PubMed | pdf (1270k)]


Lidman O, Swanberg M, Horvath L, Broman KW, Olsson T, Piehl F (2003) Discrete gene loci regulate neurodegeneration, lymphocyte infiltration and major histocompatibility complex class II expression in the CNS. J Neurosci 23:9817-9823
[PubMed | pdf (477k)]
Glaser RL, Broman KW, Shulman RL, Eskenazi B, Wyrobek AJ, Jabs EW (2003) The paternal age effect in Apert syndrome is due in part to the increased frequency of mutations in sperm. Am J Hum Genet 73:939-947
[PubMed | pdf (321k)]
Denny P, Hopes E, Gingles N, Broman KW, McPheat W, Morten J, Alexander J, Andrew PW, Brown SDM (2003) A major locus conferring susceptibility to infection by Streptococcus pneumoniae in mice. Mamm Genome 14:448-453
[PubMed | pdf (154k)]
Lamichhane G, Zignol M, Blades NJ, Geiman DE, Dougherty A, Broman KW, Bishai WR (2003) A post-genomic method for predicting essential genes at subsaturation levels of mutagenesis: application to Mycobacterium tuberculosis. Proc Natl Acad Sci USA 100:7213-7218
[PubMed | pdf (260k) | software | related technical report (pdf 360k)]
Broman KW, Wu H, Sen Ś, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889-890
[PubMed | pdf (236k) | screen pdf (288k) | software]
Broman KW (2003) Mapping quantitative trait loci in the case of a spike in the phenotype distribution. Genetics 163:1169-1175
[PubMed | pdf (250k)]
Becanovic K, Wallstrom E, Kornek B, Glaser A, Broman KW, Dahlman I, Olofsson P, Holmdahl R, Luthman H, Lassmann H, Olsson T (2003) New loci regulating rat myelin oligodendrocyte glycoprotein-induced experimental autoimmune encephalomyelitis. J Immunol 170:1062-1069
[PubMed | pdf (208k)]


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
[Abstract | pdf (326k) | discussion (519k) | software]
Jun AS, Broman KW, Do DV, Akpek EK, Stark WJ, Gottsch JD (2002) Endothelial dystrophy, iris hypoplasia, congenital cataract, and stromal thinning (EDICT) syndrome maps to chromosome 15q22.1-q25.3. Am J Ophthalmol 134:172-176
[PubMed | pdf (189k)]
Broman KW, Rowe LB, Churchill GA, Paigen K (2002) Crossover interference in the mouse. Genetics 160:1123-1131
[PubMed | pdf (165k)]


Hunter KW, Broman KW, Le Voyer T, Lukes L, Cozma D, Debies MT, Rouse J, Welch DR (2001) Predisposition to efficient mammary tumor metastatic progression is linked to the breast cancer metastasis suppressor gene Brms1. Cancer Research 61:8866-8872
[PubMed | pdf (314k)]
Ravenel JD, Broman KW, Perlman EJ, Niemitz EL, Jayawardena TM, Bell DW, Haber DA, Uejima H, Feinberg AP (2001) Loss of imprinting of Insulin-Like Growth Factor-II (IGF2) gene in distinguishing specific biologic subtypes of Wilms tumor. J Natl Cancer Inst 93:1698-1703
[PubMed | pdf (330k)]
Broman KW (2001) Review of statistical methods for QTL mapping in experimental crosses. Lab Animal 30(7):44-52
Note: The publisher requires that I make the following statement: "The paper can only be downloaded for personal study use and cannot be copied for commercial purposes without the permission of the publisher."
[PubMed | pdf (836k)]
Broman KW (2001) Estimation of allele frequencies with data on sibships. Genet Epidemiol 20:307-315
[PubMed | pdf (107k) | Erratum: Genet Epidemiol 23:465-466, 2002 (pdf 56k)]
Giglio S, Broman KW, Matsumoto N, Calvari V, Gimelli G, Neumann T, Ohashi H, Voullaire L, Larizza D, Giorda R, Weber JL, Ledbetter DH, Zuffardi O (2001) Olfactory receptor-gene clusters, genomic-inversion polymorphisms, and common chromosome rearrangements. Am J Hum Genet 68:874-883
[PubMed | pdf (1494k)]
Boyartchuk VL, Broman KW, Mosher RE, D'Orazio SEF, Starnbach MN, Dietrich WF (2001) Multigenic control of Listeria monocytogenes susceptibility in mice. Nat Genet 27:259-260
[PubMed | pdf (609k) | methods (pdf 113k) | figure A (pdf 13k) | related technical report (pdf 62k)]
Yu A, Zhao C, Fan Y, Jang W, Mungall AJ, Deloukas P, Olsen A, Doggett NA, Ghebranious N, Broman KW, Weber JL (2001) Comparison of human genetic and sequence-based physical maps. Nature 409:951-953
[PubMed | pdf (129k)]
Lichter-Konecki U, Broman KW, Blau EB, Konecki DS (2001) Genetic and physical mapping of the locus for autosomal dominant renal Fanconi syndrome, on chromosome 15q15.3 Am J Hum Genet 68:264-268
[PubMed | pdf (636k)]


Kissebah AH, Sonnenberg GE, Myklebust J, Goldstein M, Broman K, James RG, Marks JA, Krakower GR, Jacob HJ, Weber J, Martin L, Blangero J, Comuzzie AG (2000) Quantitative trait loci on chromosomes 3 and 17 influence phenotypes of the metabolic syndrome. Proc Natl Acad Sci USA 97:14478-14483
[PubMed | pdf (200k)]
Witte JS, Goddard KAB, Conti DV, Elston RC, Lin J, Suarez BK, Broman KW, Burmester JK, Weber JL, Catalona WJ (2000) Genomewide scan for prostate cancer-aggressiveness loci. Am J Hum Genet 67:92-99
[PubMed | pdf (243k)]
Broman KW, Weber JL (2000) Characterization of human crossover interference. Am J Hum Genet 66:1911-1926
[PubMed | pdf (291k) | Expanded version of tables 1-2 | Expanded version of figure 3] (313k) | ps.Z (318k)]
Suarez BK, Lin J, Burmester JK, Broman KW, Weber JL, Banerjee TK, Goddard KAB, Witte JS, Elston RC, Catalona WJ (2000) A genome screen of multiplex prostate cancer sibships. Am J Hum Genet 66:933-944
[PubMed | pdf (291k)]
Brown AS, Feingold E, Broman KW, Sherman SL (2000) Genome-wide variation in recombination in female meiosis: A risk factor for non-disjunction of chromosome 21. Hum Mol Genet 9:515-523
[PubMed | pdf (196k)]


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
[PubMed | pdf (202k) | Supplemental table (pdf 28k) | Errata]
Related editorial by AG Clark [pdf (133k)]
Broman KW, Weber JL (1999) Method for constructing confidently ordered linkage maps. Genet Epidemiol 16:337-343
[PubMed | pdf (51k) | Build your own map]
Neff MW, Broman KW, Mellersh CS, Ray K, Acland GM, Aguirre GD, Ziegle JS, Ostrander EA, Rine J (1999) A second-generation genetic linkage map of the domestic dog, Canis familiaris. Genetics 151:803-820
[PubMed | pdf (262k) | Supplemental data]


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
[PubMed | pdf (534k) | Maps and data | Marker search | Build your own map | Supplemental data]
Broman K, Speed T, Tigges M (1998) Estimation of antigen-responsive T cell frequencies in PBMC from human subjects. Stat Sci 13:4-8
[Abstract | pdf (556k) | Data | R/npem software]


Broman K, Speed T, Tigges M (1996) Estimation of antigen-responsive T cell frequencies in PBMC from human subjects. J Immunol Meth 198:119-132
[PubMed | pdf (740k) | Data | R/npem software]
Dernburg AF, Broman KW, Fung JC, Marshall WF, Philips J, Agard DA, Sedat JW (1996) Perturbation of nuclear architecture by long-distance chromosome interactions. Cell 85:745-759
[PubMed | pdf (11,382k)]


Broman KW (2005) Mapping expression in randomized rodent genomes. Nat Genet 37:209-210
[PubMed | pdf (349k)]
Broman KW, Feingold E (2004) SNPs made routine. Nat Methods 1:104-105
[PubMed | pdf (70k)]


Sieberts SK, Broman KW, Gudbjartsson DF (2004) "Biased towards the null" means reduced power. Am J Hum Genet 75:720-722
(Response to Schork and Greenwood, Am J Hum Genet 74:306-316, 2004)
[PubMed | pdf (60k)]
Broman KW, Caffo BS (2003) Simulation-based P values: Response to North et al. Am J Hum Genet 72:496
(Response to North et al., Am J Hum Genet 71:439-441, 2002)
[PubMed | pdf (93k)]
Ravenel JD, Perlman EJ, Broman KW, Feinberg AP (2002) Response: Re: Loss of imprinting of Insulin-Like Growth Factor-II (IGF2) gene in distinguishing specific biologic subtypes of Wilms tumor. J Natl Cancer Inst 94:1809-1810
(Response to Morison et al., J Natl Cancer Inst 94:1809, 2002)
[pdf (37k)]
Broman KW, Weber JL (1998) Estimation of pairwise relationships in the presence of genotyping errors. Am J Hum Genet 63:1563-1564
[PubMed | pdf (429k) | RelCheck software]

Proceedings and book chapters

Broman KW (2012) Applied statistics and exposition (commentary). In: Dudoit S (ed) Selected Works of Terry Speed, Springer, pp 353-355
González-Recio O, López de Maturana E, Vega AT, Engelman CD, Broman KW (2009) Detecting single-nucleotide polymorphism by single-nucleotide polymorphism interactions in rheumatoid arthritis by a two-step approach with machine learning and a Bayesian threshold least absolute shrinkage and selection operator (LASSO) model. BMC Proc 3(Suppl 7):S63
[PubMed | pdf (278k)]
Broman KW, Heath SC (2007) Managing and manipulating genetic data. In: Barnes MR, Gray IC (eds) Bioinformatics for Geneticists, 2nd edition, Wiley, pp. 17-31
[Abstract | pdf (250k) | Wiley | Amazon]
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
[Abstract | pdf (139k)]
Weber JL, Broman KW (2001) Genotyping for human whole-genome scans: Past, present, and future. In: Rao DC, Province MA (eds) Genetic Dissection of Complex Traits. Vol 42: Advances in Genetics. Academic Press, New York, pp 77-96
[PubMed | pdf (3.2M) | Amazon]
Broman KW (1999) Cleaning genotype data. In: Goldin L, Amos CI, Chase GA, Goldstein AM, Jarvik GP, Martinez MM, Suarez BK, Weeks DE, Wijsman EM, MacCluer JE. Genetics Workshop 11: Analysis of genetic and environmental factors in common diseases. Genet Epidemiol 17(Supp 1):S79-S83
[Pubmed | pdf (95k)]
Broman KW, Speed TP (1999) A review of methods for identifying QTLs in experimental crosses. In: Seillier-Moiseiwitsch F (ed) Statistics in Molecular Biology and Genetics. IMS Lecture Notes-Monograph Series, Vol 33, pp 114-142
[Abstract | Amazon | pdf (249k) | ps.gz (74k) | R/qtl software | f2 software]

Technical reports

Broman KW, Keller MP, Broman AT, Kendziorski C, Yandell BS, Sen Ś, Attie AD (2014) Identification and correction of sample mix-ups in expression genetic data: A case study. arXiv:1402.2633
[Abstract | pdf (2.8M)]
Broman KW (2013) Thirteen years of R/qtl: Just barely sustainable. arXiv:1309.1192
[pdf (131k) | source on github]
Broman KW (2011) Haplotype probabilities in advanced intercross populations. Technical report #223, Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison
[Abstract | pdf (157k)]
Broman KW (2010) Genetic map construction with R/qtl. Technical report #214, Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison
[Abstract | pdf (1.5M)]
Manichaikul A, Moon JY, Sen Ś, Yandell BS, Broman KW (2008) A model selection approach for the identification of quantitative trait loci in experimental crosses, allowing epistasis. Technical report #205, Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison
[Abstract | pdf (562k)]
Broman KW (2006) Use of hidden Markov models for QTL mapping. Working paper 125, Department of Biostatistics, Johns Hopkins University, Baltimore, MD
[Abstract | pdf (94k)]
Broman KW (2004) The genomes of recombinant inbred lines: The gory details. Working paper 47, Department of Biostatistics, Johns Hopkins University, Baltimore, MD
[Abstract | pdf (313k) | Published paper (pdf 525k) | Related software]
Blades NJ, Broman KW (2002) Estimating the number of essential genes in a genome by random transposon mutagenesis. Technical Report MS02-20, Department of Biostatistics, Johns Hopkins University, Baltimore, MD
[Abstract | pdf (360k)]
Broman KW, Boyartchuk VL, Dietrich WF (2000) Mapping time-to-death quantitative trait loci in a mouse cross with high survival rates. Technical Report MS00-04, Department of Biostatistics, Johns Hopkins University, Baltimore, MD
[Abstract | pdf (62k)]
Broman K, Speed T, Tigges M (1996) Estimation of antigen-responsive T cell frequencies in PBMC from human subjects. Technical Report #454, Department of Statistics, University of California, Berkeley
[Abstract | pdf (388k) | ps.Z (169k) | Data | R/npem software]
Bowman KO, Shenton LR, Kastenbaum MA, Broman K (1992) Overdispersion: Notes on discrete distributions. Technical Report ORNL/TM-12167, Oak Ridge National Laboratory


Broman KW (1997) Identifying quantitative trait loci in experimental crosses. PhD dissertation, Department of Statistics, University of California, Berkeley
[Abstract | pdf (653k) | ps.Z (297k) | R/qtl software | f2 software]

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Last modified: Tue Feb 11 19:53:15 2014