Broman KW, Sen Ś (2009) A Guide to QTL Mapping with R/qtl. Springer, New York Online complements Amazon Springer R/qtl doi

journal articles

in preparation

Lobo AK, Traeger LL, Keller MP, Attie AD, Rey FE, Broman KW (2019) Identification of sample mix-ups and mixtures in microbiome data in Diversity Outbred mice. bioRxiv doi:10.1101/529040 pdf GitHub R/mbmixture software doi


Keller MP, Rabaglia ME, Schueler KL, Stapleton DS, Gatti DM, Vincent M, Mitok KA, Wang Z, Ishimura T, Simonett SP, Emfinger CH, Das R, Beck T, Kendziorski C, Broman KW, Yandell BS, Churchill GA, Attie AD (2019) Gene loci associated with insulin secretion in islets from non-diabetic mice. J Clin Invest 130:4419-4432 PubMed pdf doi

Kemis JH, Linke V, Barrett KL, Boehm FJ, Traeger LL, Keller MP, Rabaglia ME, Schueler KL, Stapleton DS, Gatti DM, Churchill GA, Amador-Noguez D, Russell JD, Yandell BS, Broman KW, Coon JJ, Attie AD, Rey FE (2019) Genetic determinants of gut microbiota composition and bile acid profiles in mice. PLoS Genet 15: e1008073 PubMed pdf doi

Boehm FJ, Chesler EJ, Yandell BS, Broman KW (2019) Testing pleiotropy vs. separate QTL in multiparental populations. G3 9:2317-2324 PubMed pdf GitHub qtl2pleio software doi

Boehm F, Yandell B, Broman KW (2019) qtl2pleio: Testing pleiotropy vs. separate QTL in multiparental populations. J Open Source Software 4(38):1435 pdf qtl2pleio software doi

Broman KW, Gatti DM, Svenson KL, Sen Ś, Churchill GA (2019) Cleaning genotype data from Diversity Outbred mice. G3 9:1571-1579 PubMed pdf supporting info GitHub doi

Broman KW, Gatti DM, Simecek P, Furlotte NA, Prins P, Sen Ś, Yandell BS, Churchill GA (2019) R/qtl2: software for mapping quantitative trait loci with high-dimensional data and multi-parent populations. Genetics 211:495-502 PubMed pdf GitHub R/qtl2 software doi


Palus M, Sohrabi Y, Broman KW, Strnad H, Šíma M, Růžek D, Volkova V, Slapničková M, Vojtíšková J, Mrázková L, Salát J, Lipoldová M (2018) A novel locus on mouse chromosome 7 that influences survival after infection with tick-borne encephalitis virus. BMC Neurosci 19:39 PubMed pdf doi

Keller MP, Gatti DM, Schueler KL, Rabaglia ME, Stapleton DS, Simecek P, Vincent M, Allen S, Broman AT, Bacher R, Kendziorski C, Broman KW, Yandell BS, Churchill GA, Attie AD (2018) Genetic drivers of pancreatic islet function. Genetics 209:335-356 PubMed pdf doi

Broman KW, Woo KH (2018) Data organization in spreadsheets. Am Stat 72:2-10 pdf GitHub doi

Keele GR, Prokop JW, He H, Holl K, Littrell J, Deal A, Francic S, Cui L, Gatti DM, Broman KW, Tschannen M, Tsaih S-W, Zagloul M, Kim Y, Baur B, Fox J, Robinson M, Levy S, Flister MJ, Mott R, Valdar W, Solberg Woods LC (2018) Genetic fine-mapping and identification of candidate genes and variants for adiposity traits in outbred rats. Obesity 26:213-222 PubMed pdf doi


Florek NW, Kamlangdee A, Mutschler JP, Kingstad-Bakke B, Schultz-Darken N, Broman KW, Osorio JE, Friedrich TC (2017) A modified vaccinia Ankara vaccine vector expressing a mosaic H5 hemagglutinin reduces viral shedding in rhesus macaques. PLoS ONE 12:e0181738 PubMed pdf doi

Wang RJ, Gray MM, Parmenter MD, Broman KW, Payseur BA (2017) Recombination rate variation in mice from an isolated island. Mol Ecol 26:457-470 PubMed pdf doi


Keller MP, Paul PK, Rabaglia ME, Stapleton DS, Schueler KL, Broman AT, Ye SI, Leng N, Brandon CJ, Neto EC, Plaisier CL, Simonett SP, Kebede MA, Sheynkman GM, Klein MA, Baliga NS, Smith LM, Broman KW, Yandell BS, Kendziorski C, Attie AD (2016) The transcription factor Nfatc2 regulates β-cell proliferation and genes associated with type 2 diabetes in mouse and human islets. PLoS Genet 12:e1006466 PubMed pdf supporting info doi

Parmenter MD, Gray MM, Hogan CA, Ford IN, Broman KW, Vinyard CJ, Payseur BA (2016) Genetics of skeletal evolution in unusually large mice from Gough Island. Genetics 204:1559-1572 PubMed pdf supporting info doi

Zigler JS Jr, Hodgkinson CA, Wright M, Klise A, Sundin O, Broman KW, Hejtmancik F, Huang H, Patek B, Sergeev Y, Hose S, Brayton C, Xaiodong J, Vasquez D, Maragakis N, Mori S, Goldman D, Hoke A, Sinha D (2016) A spontaneous missense mutation in branched chain keto acid dehydrogenase kinase in the rat affects both the central and peripheral nervous systems. PLoS ONE 11:e0160447 PubMed pdf supporting info doi

Sloan Z, Arends D, Broman KW, Centeno A, Furlotte N, Nijveen H, Yan L, Zhou X, Williams RW, Prins P (2016) GeneNetwork: framework for web-based genetics. J Open Source Software 1(2):25 pdf doi

De Simone M, Spagnuolo L, Lorè NI, Cigana C, De Fino I, Broman KW, Iraqi FA, Bragonzi A (2016) Mapping genetic determinants of host susceptibility to Pseudomonas aeruginosa lung infection in mice. BMC Genomics 17:351 PubMed pdf doi

Tian J, Keller MP, Broman AT, Kendziorski C, Yandell BS, Attie AD, Broman KW (2016) The dissection of expression quantitative trait locus hotspots. Genetics 202:1563-1574 PubMed pdf supplement data qtlpvl software doi

Gruhn JR, Al-Asmar N, Fasnacht R, Maylor-Hagen H, Peinado V, Rubio C, Broman KW, Hunt PA, Hassold T (2016) Correlations between synaptic initiation and meiotic recombination: A study of humans and mice. Am J Hum Genet 98:102-115 PubMed pdf doi

Kwak I-L, Moore CR, Spalding EP, Broman KW (2016) Mapping quantitative trait loci underlying function-valued traits using functional principal component analysis and multi-trait mapping. G3 6:79-86 PubMed pdf data funqtl software doi


Tian J, Keller MP, Oler AT, Rabaglia ME, Schueler KL, Stapleton DS, Broman AT, Zhao W, Kendziorski C, Yandell BS, Hagenbuch B, Broman KW, Attie AD (2015) Identification of the bile acid transporter Slco1a6 as a candidate gene that broadly affects gene expression in mouse pancreatic islets. Genetics 201:1253-1262 PubMed pdf supplement data doi

Broman KW, Keller MP, Broman AT, Kendziorski C, Yandell BS, Sen Ś, Attie AD (2015) Identification and correction of sample mix-ups in expression genetic data: A case study. G3 5:2177-2186 PubMed pdf data GitHub R/lineup software doi

Gray MM, Parmenter MD, Hogan CA, Ford I, Cuthbert RJ, Ryan PG, Broman KW, Payseur BA (2015) Genetics of rapid and extreme size evolution in island mice. Genetics 201:213-228 PubMed pdf data doi

Whitney KD, Broman KW, Kane NC, Hovick SM, Randell RA, Rieseberg LH (2015) Quantitative trait locus mapping identifies candidate alleles involved in adaptive introgression and range expansion in a wild sunflower. Mol Ecol 24:2194-2211 PubMed pdf supplementary material doi

Broman KW (2015) R/qtlcharts: interactive graphics for quantitative trait locus mapping. Genetics 199:359-361 PubMed pdf GitHub R/qtlcharts software doi


Florek NW, Weinfurter JT, Jegaskanda S, Brewoo JN, Powell TD, Young GR, Das SC, Hatta M, Broman KW, Hungnes O, Dudman SG, Kawaoka Y, Kent SJ, Stinchcomb DT, Osorio JE, Friedrich TC (2014) Modified vaccinia Ankara encoding influenza virus hemagglutinin induces heterosubtypic immunity in macaques. J Virol 88:13418-13428 PubMed pdf (446k) doi

Gatti DM, Svenson KL, Shabalin A, Wu L-Y, Valdar W, Simecek P, Goodwin N, Cheng R, Pomp D, Palmer A, Chesler EJ, Broman KW, Churchill GA (2014) Quantitative trait locus mapping methods for Diversity Outbred mice. G3 4:1623-1633 PubMed pdf (2.5M) Data doi

Street VA, Kujawa SG, Manichaikul A, Broman KW, Kallman JC, Shilling DJ, Iwata AJ, Robinson LC, Robbins CA, Li J, Liberman MC, Tempel BL (2014) Resistance to noise-induced hearing loss in 129S6 and MOLF mice: Identification of independent, overlapping, and interacting chromosomal regions. J Assoc Res Otolaryngol 15:721-738 PubMed pdf doi

Kwak I-Y, Moore CR, Spalding EP, Broman KW (2014) A simple regression-based method to map quantitative trait loci underlying function-valued phenotypes. Genetics 197: 1409-1416 PubMed pdf (1.2M) GitHub Data funqtl software doi

Broman KW (2014) Fourteen years of R/qtl: Just barely sustainable. J Open Res Softw 2(1):e11 PubMed pdf (948k) Source on GitHub doi

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. Am J Hum Genet 95:108-112 PubMed pdf (2.0M) doi

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) doi

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 Genet 10:e1004125 PubMed pdf (1.5M) doi


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) doi

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 pdf (1.6M) Data doi

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) Data doi

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) doi

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) doi


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) GitHub doi

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) doi

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) doi

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) doi

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) doi

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 doi

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 doi

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) [xqtl] doi

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) doi

Broman KW (2012) Genotype probabilities at intermediate generations in the construction of recombinant inbred lines. Genetics 190:403-412 PubMed pdf (1.1M) GitHub doi

Broman KW (2012) Haplotype probabilities in advanced intercross populations. G3 2:199-202 PubMed pdf (649k) GitHub doi

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) doi

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) doi

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 doi


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) doi

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 doi

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) doi

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) doi

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) doi

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) doi


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) doi

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) doi

Arends D, Prins P, Jansen RC, Broman KW (2010) R/qtl: High-throughput multiple QTL mapping. Bioinformatics 26:2990-2992 PubMed pdf (181k) R/qtl doi

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) doi

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 doi

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) doi

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) doi

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 doi


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) doi

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) doi

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) doi

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) doi

Dumont BL, Broman KW, Payseur BA (2009) Variation in genomic recombination rates among heterogeneous stock mice. Genetics 182:1345-1349 PubMed pdf (468k) doi

Manichaikul A, Broman KW (2009) Binary trait mapping in experimental crosses with selective genotyping. Genetics 182:863-874 PubMed pdf (576k) doi

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) doi

Sen Ś, Johannes F, Broman KW (2009) Selective genotyping and phenotyping strategies in a complex trait context. Genetics 181:1613-1626 PubMed pdf (469k) doi

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) doi [Erratum: Genetics 184:607, 2010 pdf (89k) doi]


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 doi

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 doi

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) doi

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 doi

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 doi

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) doi

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) doi

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) doi


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) doi

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) doi

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 doi

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) doi

Teuscher F, Broman KW (2007) Haplotype probabilities for multiple-strain recombinant inbred lines. Genetics 175:1267-1274 PubMed pdf (722k) doi

Sen Ś, Satagopan JM, Broman KW, Churchill GA (2007) R/qtlDesign: Inbred line cross experimental design. Mamm Genome 18:87-93 PubMed pdf (138k) R/qtlDesign software doi

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) doi

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) doi


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) Data doi

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) doi

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) doi

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) doi

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) doi

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) doi

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) doi

Grant GR, 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) doi

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) doi

Shrestha S, Strathdee SA, Broman KW, Smith MW (2006) Unknown biological mixtures evaluation using STR analytical quantification. Electrophoresis 27:409-415 PubMed pdf (125k) doi

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) doi

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) doi


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) doi

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) doi

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) doi

Broman KW (2005) The genomes of recombinant inbred lines. Genetics 169:1133-1146 PubMed pdf (525k) R/ricalc doi [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) doi

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) doi

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) doi


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 PubMed pdf (168k) doi

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) doi

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) doi

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 doi

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) doi

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) doi

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) doi

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 doi

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) doi

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) doi


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) doi

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) doi

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) doi

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) R/negenes doi

Broman KW, Wu H, Sen Ś, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889-890 PubMed pdf (236k) R/qtl doi

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) doi


Broman KW, Speed TP (2002) A model selection approach for the identification of quantitative trait loci in experimental crosses. J Roy Stat Soc B 64:641-656 Abstract pdf (326k) doi

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) doi

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) doi

Broman KW (2001) Review of statistical methods for QTL mapping in experimental crosses. Lab Animal 30(7):44-52 PubMed pdf (836k)
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.”

Broman KW (2001) Estimation of allele frequencies with data on sibships. Genet Epidemiol 20:307-315 PubMed pdf (107k) doi [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) doi

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) doi

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) doi

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) doi


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) doi

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) doi

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 doi

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) doi

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) doi


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) doi [Errata]

Broman KW, Weber JL (1999) Method for constructing confidently ordered linkage maps. Genet Epidemiol 16:337-343 PubMed pdf (51k) doi

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) Supplemental data doi

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


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 doi

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 (11M) doi


Broman KW (2005) Mapping expression in randomized rodent genomes. Nat Genet 37:209-210 PubMed pdf (349k) doi

Broman KW, Feingold E (2004) SNPs made routine. Nat Methods 1:104-105 PubMed pdf (70k) doi


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) doi

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) doi

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) doi

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) doi

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 Springer Amazon [Note: The PDFs at Springer are free.]

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) doi

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) 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) doi

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 pdf (249k) Amazon

technical reports

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)

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)

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)

Bowman KO, Shenton LR, Kastenbaum MA, Broman K (1992) Overdispersion: Notes on discrete distributions. Technical Report ORNL/TM-12167, Oak Ridge National Laboratory Abstract pdf (388k)


Broman KW (1997) Identifying quantitative trait loci in experimental crosses. PhD dissertation, Department of Statistics, University of California, Berkeley Abstract pdf (653k)